[{"isi":1,"article_processing_charge":"No","file":[{"relation":"main_file","access_level":"open_access","date_created":"2019-02-06T08:49:52Z","file_name":"2018_JournalExperMed_Reversat.pdf","checksum":"687beea1d64c213f4cb9e3c29ec11a14","creator":"dernst","date_updated":"2020-07-14T12:47:09Z","file_id":"5931","file_size":1216437,"content_type":"application/pdf"}],"scopus_import":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.1084/jem.20181934","volume":215,"quality_controlled":"1","citation":{"ista":"Reversat A, Sixt MK. 2018. IgM’s exit route. Journal of Experimental Medicine. 215(12), 2959–2961.","short":"A. Reversat, M.K. Sixt, Journal of Experimental Medicine 215 (2018) 2959–2961.","ieee":"A. Reversat and M. K. Sixt, “IgM’s exit route,” <i>Journal of Experimental Medicine</i>, vol. 215, no. 12. Rockefeller University Press, pp. 2959–2961, 2018.","ama":"Reversat A, Sixt MK. IgM’s exit route. <i>Journal of Experimental Medicine</i>. 2018;215(12):2959-2961. doi:<a href=\"https://doi.org/10.1084/jem.20181934\">10.1084/jem.20181934</a>","apa":"Reversat, A., &#38; Sixt, M. K. (2018). IgM’s exit route. <i>Journal of Experimental Medicine</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1084/jem.20181934\">https://doi.org/10.1084/jem.20181934</a>","mla":"Reversat, Anne, and Michael K. Sixt. “IgM’s Exit Route.” <i>Journal of Experimental Medicine</i>, vol. 215, no. 12, Rockefeller University Press, 2018, pp. 2959–61, doi:<a href=\"https://doi.org/10.1084/jem.20181934\">10.1084/jem.20181934</a>.","chicago":"Reversat, Anne, and Michael K Sixt. “IgM’s Exit Route.” <i>Journal of Experimental Medicine</i>. Rockefeller University Press, 2018. <a href=\"https://doi.org/10.1084/jem.20181934\">https://doi.org/10.1084/jem.20181934</a>."},"page":"2959-2961","status":"public","publication":"Journal of Experimental Medicine","ddc":["570"],"month":"11","date_published":"2018-11-20T00:00:00Z","date_updated":"2026-04-16T09:54:07Z","department":[{"_id":"MiSi"}],"has_accepted_license":"1","issue":"12","type":"journal_article","file_date_updated":"2020-07-14T12:47:09Z","day":"20","date_created":"2018-12-16T22:59:18Z","language":[{"iso":"eng"}],"author":[{"id":"35B76592-F248-11E8-B48F-1D18A9856A87","last_name":"Reversat","first_name":"Anne","full_name":"Reversat, Anne","orcid":"0000-0003-0666-8928"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","publication_identifier":{"issn":["0022-1007"]},"external_id":{"isi":["000451920600002"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"publisher":"Rockefeller University Press","oa":1,"intvolume":"       215","title":"IgM's exit route","publication_status":"published","_id":"5672","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The release of IgM is the first line of an antibody response and precedes the generation of high affinity IgG in germinal centers. Once secreted by freshly activated plasmablasts, IgM is released into the efferent lymph of reactive lymph nodes as early as 3 d after immunization. As pentameric IgM has an enormous size of 1,000 kD, its diffusibility is low, and one might wonder how it can pass through the densely lymphocyte-packed environment of a lymph node parenchyma in order to reach its exit. In this issue of JEM, Thierry et al. show that, in order to reach the blood stream, IgM molecules take a specific micro-anatomical route via lymph node conduits."}],"year":"2018"},{"title":"Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division","_id":"5673","publication_status":"published","oa_version":"Submitted Version","pmid":1,"ec_funded":1,"oa":1,"intvolume":"         4","abstract":[{"text":"Cell polarity, manifested by the localization of proteins to distinct polar plasma membrane domains, is a key prerequisite of multicellular life. In plants, PIN auxin transporters are prominent polarity markers crucial for a plethora of developmental processes. Cell polarity mechanisms in plants are distinct from other eukaryotes and still largely elusive. In particular, how the cell polarities are propagated and maintained following cell division remains unknown. Plant cytokinesis is orchestrated by the cell plate—a transient centrifugally growing endomembrane compartment ultimately forming the cross wall1. Trafficking of polar membrane proteins is typically redirected to the cell plate, and these will consequently have opposite polarity in at least one of the daughter cells2–5. Here, we provide mechanistic insights into post-cytokinetic re-establishment of cell polarity as manifested by the apical, polar localization of PIN2. We show that the apical domain is defined in a cell-intrinsic manner and that re-establishment of PIN2 localization to this domain requires de novo protein secretion and endocytosis, but not basal-to-apical transcytosis. Furthermore, we identify a PINOID-related kinase WAG1, which phosphorylates PIN2 in vitro6 and is transcriptionally upregulated specifically in dividing cells, as a crucial regulator of post-cytokinetic PIN2 polarity re-establishment.","lang":"eng"}],"year":"2018","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30518833"}],"project":[{"call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"publication_identifier":{"issn":["2055-0278"]},"external_id":{"isi":["000454576600017"],"pmid":["30518833"]},"publisher":"Nature Research","date_updated":"2025-04-14T07:45:02Z","department":[{"_id":"JiFr"}],"issue":"12","type":"journal_article","page":"1082-1088","status":"public","publication":"Nature Plants","date_published":"2018-12-03T00:00:00Z","month":"12","language":[{"iso":"eng"}],"date_created":"2018-12-16T22:59:18Z","day":"03","author":[{"first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous"},{"full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","last_name":"Fendrych","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"}],"scopus_import":"1","isi":1,"article_processing_charge":"No","volume":4,"quality_controlled":"1","citation":{"mla":"Glanc, Matous, et al. “Mechanistic Framework for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” <i>Nature Plants</i>, vol. 4, no. 12, Nature Research, 2018, pp. 1082–88, doi:<a href=\"https://doi.org/10.1038/s41477-018-0318-3\">10.1038/s41477-018-0318-3</a>.","ama":"Glanc M, Fendrych M, Friml J. Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. <i>Nature Plants</i>. 2018;4(12):1082-1088. doi:<a href=\"https://doi.org/10.1038/s41477-018-0318-3\">10.1038/s41477-018-0318-3</a>","apa":"Glanc, M., Fendrych, M., &#38; Friml, J. (2018). Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. <i>Nature Plants</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41477-018-0318-3\">https://doi.org/10.1038/s41477-018-0318-3</a>","chicago":"Glanc, Matous, Matyas Fendrych, and Jiří Friml. “Mechanistic Framework for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” <i>Nature Plants</i>. Nature Research, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0318-3\">https://doi.org/10.1038/s41477-018-0318-3</a>.","short":"M. Glanc, M. Fendrych, J. Friml, Nature Plants 4 (2018) 1082–1088.","ista":"Glanc M, Fendrych M, Friml J. 2018. Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. 4(12), 1082–1088.","ieee":"M. Glanc, M. Fendrych, and J. Friml, “Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division,” <i>Nature Plants</i>, vol. 4, no. 12. Nature Research, pp. 1082–1088, 2018."},"doi":"10.1038/s41477-018-0318-3","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publisher":"Rockefeller University Press","external_id":{"isi":["000451960800018"],"pmid":["30228162 "]},"publication_identifier":{"issn":["0021-9525"]},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30228162"}],"abstract":[{"text":"In epithelial tissues, cells tightly connect to each other through cell–cell junctions, but they also present the remarkable capacity of reorganizing themselves without compromising tissue integrity. Upon injury, simple epithelia efficiently resolve small lesions through the action of actin cytoskeleton contractile structures at the wound edge and cellular rearrangements. However, the underlying mechanisms and how they cooperate are still poorly understood. In this study, we combine live imaging and theoretical modeling to reveal a novel and indispensable role for occluding junctions (OJs) in this process. We demonstrate that OJ loss of function leads to defects in wound-closure dynamics: instead of contracting, wounds dramatically increase their area. OJ mutants exhibit phenotypes in cell shape, cellular rearrangements, and mechanical properties as well as in actin cytoskeleton dynamics at the wound edge. We propose that OJs are essential for wound closure by impacting on epithelial mechanics at the tissue level, which in turn is crucial for correct regulation of the cellular events occurring at the wound edge.","lang":"eng"}],"year":"2018","ec_funded":1,"oa":1,"intvolume":"       217","pmid":1,"oa_version":"Submitted Version","title":"Occluding junctions as novel regulators of tissue mechanics during wound repair","publication_status":"published","_id":"5676","doi":"10.1083/jcb.201804048","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":217,"quality_controlled":"1","citation":{"apa":"Carvalho, L., Patricio, P., Ponte, S., Heisenberg, C.-P. J., Almeida, L., Nunes, A. S., … Jacinto, A. (2018). Occluding junctions as novel regulators of tissue mechanics during wound repair. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.201804048\">https://doi.org/10.1083/jcb.201804048</a>","ama":"Carvalho L, Patricio P, Ponte S, et al. Occluding junctions as novel regulators of tissue mechanics during wound repair. <i>Journal of Cell Biology</i>. 2018;217(12):4267-4283. doi:<a href=\"https://doi.org/10.1083/jcb.201804048\">10.1083/jcb.201804048</a>","mla":"Carvalho, Lara, et al. “Occluding Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” <i>Journal of Cell Biology</i>, vol. 217, no. 12, Rockefeller University Press, 2018, pp. 4267–83, doi:<a href=\"https://doi.org/10.1083/jcb.201804048\">10.1083/jcb.201804048</a>.","chicago":"Carvalho, Lara, Pedro Patricio, Susana Ponte, Carl-Philipp J Heisenberg, Luis Almeida, André S. Nunes, Nuno A.M. Araújo, and Antonio Jacinto. “Occluding Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2018. <a href=\"https://doi.org/10.1083/jcb.201804048\">https://doi.org/10.1083/jcb.201804048</a>.","short":"L. Carvalho, P. Patricio, S. Ponte, C.-P.J. Heisenberg, L. Almeida, A.S. Nunes, N.A.M. Araújo, A. Jacinto, Journal of Cell Biology 217 (2018) 4267–4283.","ista":"Carvalho L, Patricio P, Ponte S, Heisenberg C-PJ, Almeida L, Nunes AS, Araújo NAM, Jacinto A. 2018. Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. 217(12), 4267–4283.","ieee":"L. Carvalho <i>et al.</i>, “Occluding junctions as novel regulators of tissue mechanics during wound repair,” <i>Journal of Cell Biology</i>, vol. 217, no. 12. Rockefeller University Press, pp. 4267–4283, 2018."},"article_processing_charge":"No","isi":1,"scopus_import":"1","author":[{"last_name":"Carvalho","first_name":"Lara","full_name":"Carvalho, Lara"},{"full_name":"Patricio, Pedro","first_name":"Pedro","last_name":"Patricio"},{"first_name":"Susana","last_name":"Ponte","full_name":"Ponte, Susana"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"},{"last_name":"Almeida","first_name":"Luis","full_name":"Almeida, Luis"},{"first_name":"André S.","last_name":"Nunes","full_name":"Nunes, André S."},{"last_name":"Araújo","first_name":"Nuno A.M.","full_name":"Araújo, Nuno A.M."},{"full_name":"Jacinto, Antonio","first_name":"Antonio","last_name":"Jacinto"}],"date_created":"2018-12-16T22:59:19Z","day":"01","language":[{"iso":"eng"}],"publication":"Journal of Cell Biology","date_published":"2018-12-01T00:00:00Z","month":"12","page":"4267-4283","status":"public","department":[{"_id":"CaHe"}],"issue":"12","type":"journal_article","date_updated":"2025-07-10T11:52:53Z"},{"article_type":"original","day":"01","language":[{"iso":"eng"}],"date_created":"2018-12-16T22:59:19Z","author":[{"first_name":"Albert","last_name":"Benveniste","full_name":"Benveniste, Albert"},{"full_name":"Nickovic, Dejan","last_name":"Nickovic","first_name":"Dejan"},{"full_name":"Caillaud, Benoît","first_name":"Benoît","last_name":"Caillaud"},{"last_name":"Passerone","first_name":"Roberto","full_name":"Passerone, Roberto"},{"full_name":"Raclet, Jean Baptiste","first_name":"Jean Baptiste","last_name":"Raclet"},{"full_name":"Reinkemeier, Philipp","first_name":"Philipp","last_name":"Reinkemeier"},{"last_name":"Sangiovanni-Vincentelli","first_name":"Alberto","full_name":"Sangiovanni-Vincentelli, Alberto"},{"full_name":"Damm, Werner","first_name":"Werner","last_name":"Damm"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"full_name":"Larsen, Kim G.","last_name":"Larsen","first_name":"Kim G."}],"status":"public","page":"124-400","date_published":"2018-05-01T00:00:00Z","month":"05","publication":"Foundations and Trends in Electronic Design Automation","date_updated":"2023-10-17T11:53:09Z","issue":"2-3","type":"journal_article","department":[{"_id":"ToHe"}],"doi":"10.1561/1000000053","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","citation":{"ista":"Benveniste A, Nickovic D, Caillaud B, Passerone R, Raclet JB, Reinkemeier P, Sangiovanni-Vincentelli A, Damm W, Henzinger TA, Larsen KG. 2018. Contracts for system design. Foundations and Trends in Electronic Design Automation. 12(2–3), 124–400.","short":"A. Benveniste, D. Nickovic, B. Caillaud, R. Passerone, J.B. Raclet, P. Reinkemeier, A. Sangiovanni-Vincentelli, W. Damm, T.A. Henzinger, K.G. Larsen, Foundations and Trends in Electronic Design Automation 12 (2018) 124–400.","ieee":"A. Benveniste <i>et al.</i>, “Contracts for system design,” <i>Foundations and Trends in Electronic Design Automation</i>, vol. 12, no. 2–3. Now Publishers, pp. 124–400, 2018.","ama":"Benveniste A, Nickovic D, Caillaud B, et al. Contracts for system design. <i>Foundations and Trends in Electronic Design Automation</i>. 2018;12(2-3):124-400. doi:<a href=\"https://doi.org/10.1561/1000000053\">10.1561/1000000053</a>","apa":"Benveniste, A., Nickovic, D., Caillaud, B., Passerone, R., Raclet, J. B., Reinkemeier, P., … Larsen, K. G. (2018). Contracts for system design. <i>Foundations and Trends in Electronic Design Automation</i>. Now Publishers. <a href=\"https://doi.org/10.1561/1000000053\">https://doi.org/10.1561/1000000053</a>","mla":"Benveniste, Albert, et al. “Contracts for System Design.” <i>Foundations and Trends in Electronic Design Automation</i>, vol. 12, no. 2–3, Now Publishers, 2018, pp. 124–400, doi:<a href=\"https://doi.org/10.1561/1000000053\">10.1561/1000000053</a>.","chicago":"Benveniste, Albert, Dejan Nickovic, Benoît Caillaud, Roberto Passerone, Jean Baptiste Raclet, Philipp Reinkemeier, Alberto Sangiovanni-Vincentelli, Werner Damm, Thomas A Henzinger, and Kim G. Larsen. “Contracts for System Design.” <i>Foundations and Trends in Electronic Design Automation</i>. Now Publishers, 2018. <a href=\"https://doi.org/10.1561/1000000053\">https://doi.org/10.1561/1000000053</a>."},"volume":12,"article_processing_charge":"No","scopus_import":"1","year":"2018","abstract":[{"lang":"eng","text":"Recently, contract-based design has been proposed as an “orthogonal” approach that complements system design methodologies proposed so far to cope with the complexity of system design. Contract-based design provides a rigorous scaffolding for verification, analysis, abstraction/refinement, and even synthesis. A number of results have been obtained in this domain but a unified treatment of the topic that can help put contract-based design in perspective was missing. This monograph intends to provide such a treatment where contracts are precisely defined and characterized so that they can be used in design methodologies with no ambiguity. In particular, this monograph identifies the essence of complex system design using contracts through a mathematical “meta-theory”, where all the properties of the methodology are derived from a very abstract and generic notion of contract. We show that the meta-theory provides deep and illuminating links with existing contract and interface theories, as well as guidelines for designing new theories. Our study encompasses contracts for both software and systems, with emphasis on the latter. We illustrate the use of contracts with two examples: requirement engineering for a parking garage management, and the development of contracts for timing and scheduling in the context of the Autosar methodology in use in the automotive sector."}],"main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-00757488/"}],"intvolume":"        12","oa":1,"_id":"5677","publication_status":"published","title":"Contracts for system design","oa_version":"Submitted Version","publisher":"Now Publishers","publication_identifier":{"issn":["1551-3939"]}},{"publisher":"Springer","publication_identifier":{"isbn":["9783030027674"],"issn":["0302-9743"]},"external_id":{"arxiv":["1806.06683"],"isi":["000916310900011"]},"alternative_title":["LNCS"],"project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"year":"2018","abstract":[{"lang":"eng","text":"We study the almost-sure termination problem for probabilistic programs. First, we show that supermartingales with lower bounds on conditional absolute difference provide a sound approach for the almost-sure termination problem. Moreover, using this approach we can obtain explicit optimal bounds on tail probabilities of non-termination within a given number of steps. Second, we present a new approach based on Central Limit Theorem for the almost-sure termination problem, and show that this approach can establish almost-sure termination of programs which none of the existing approaches can handle. Finally, we discuss algorithmic approaches for the two above methods that lead to automated analysis techniques for almost-sure termination of probabilistic programs."}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1806.06683"}],"conference":{"start_date":"2018-12-02","end_date":"2018-12-06","name":"16th Asian Symposium on Programming Languages and Systems, APLAS","location":"Wellington, New Zealand"},"arxiv":1,"intvolume":"     11275","oa":1,"_id":"5679","title":"New approaches for almost-sure termination of probabilistic programs","oa_version":"Preprint","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.1007/978-3-030-02768-1_11","quality_controlled":"1","citation":{"ieee":"M. Huang, H. Fu, and K. Chatterjee, “New approaches for almost-sure termination of probabilistic programs,” presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS, Wellington, New Zealand, 2018, vol. 11275, pp. 181–201.","short":"M. Huang, H. Fu, K. Chatterjee, in:, S. Ryu (Ed.), Springer, 2018, pp. 181–201.","ista":"Huang M, Fu H, Chatterjee K. 2018. New approaches for almost-sure termination of probabilistic programs. 16th Asian Symposium on Programming Languages and Systems, APLAS, LNCS, vol. 11275, 181–201.","chicago":"Huang, Mingzhang, Hongfei Fu, and Krishnendu Chatterjee. “New Approaches for Almost-Sure Termination of Probabilistic Programs.” edited by Sukyoung Ryu, 11275:181–201. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-030-02768-1_11\">https://doi.org/10.1007/978-3-030-02768-1_11</a>.","mla":"Huang, Mingzhang, et al. <i>New Approaches for Almost-Sure Termination of Probabilistic Programs</i>. Edited by Sukyoung Ryu, vol. 11275, Springer, 2018, pp. 181–201, doi:<a href=\"https://doi.org/10.1007/978-3-030-02768-1_11\">10.1007/978-3-030-02768-1_11</a>.","ama":"Huang M, Fu H, Chatterjee K. New approaches for almost-sure termination of probabilistic programs. In: Ryu S, ed. Vol 11275. Springer; 2018:181-201. doi:<a href=\"https://doi.org/10.1007/978-3-030-02768-1_11\">10.1007/978-3-030-02768-1_11</a>","apa":"Huang, M., Fu, H., &#38; Chatterjee, K. (2018). New approaches for almost-sure termination of probabilistic programs. In S. Ryu (Ed.) (Vol. 11275, pp. 181–201). Presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS, Wellington, New Zealand: Springer. <a href=\"https://doi.org/10.1007/978-3-030-02768-1_11\">https://doi.org/10.1007/978-3-030-02768-1_11</a>"},"volume":11275,"isi":1,"article_processing_charge":"No","editor":[{"full_name":"Ryu, Sukyoung","last_name":"Ryu","first_name":"Sukyoung"}],"scopus_import":"1","date_created":"2018-12-16T22:59:20Z","language":[{"iso":"eng"}],"day":"01","author":[{"last_name":"Huang","first_name":"Mingzhang","full_name":"Huang, Mingzhang"},{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"status":"public","page":"181-201","month":"12","date_published":"2018-12-01T00:00:00Z","date_updated":"2026-04-16T09:54:21Z","type":"conference","department":[{"_id":"KrCh"}]},{"citation":{"short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M.A. Nowak, Communications Biology 1 (2018).","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. 2018. Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. 1(1), 71.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. A. Nowak, “Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory,” <i>Communications Biology</i>, vol. 1, no. 1. Springer Nature, 2018.","mla":"Pavlogiannis, Andreas, et al. “Construction of Arbitrarily Strong Amplifiers of Natural Selection Using Evolutionary Graph Theory.” <i>Communications Biology</i>, vol. 1, no. 1, 71, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s42003-018-0078-7\">10.1038/s42003-018-0078-7</a>.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. A. (2018). Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-018-0078-7\">https://doi.org/10.1038/s42003-018-0078-7</a>","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. <i>Communications Biology</i>. 2018;1(1). doi:<a href=\"https://doi.org/10.1038/s42003-018-0078-7\">10.1038/s42003-018-0078-7</a>","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin A. Nowak. “Construction of Arbitrarily Strong Amplifiers of Natural Selection Using Evolutionary Graph Theory.” <i>Communications Biology</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s42003-018-0078-7\">https://doi.org/10.1038/s42003-018-0078-7</a>."},"quality_controlled":"1","volume":1,"doi":"10.1038/s42003-018-0078-7","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","file":[{"file_id":"5752","file_size":1804194,"content_type":"application/pdf","creator":"dernst","checksum":"a9db825fa3b64a51ff3de035ec973b3e","date_updated":"2020-07-14T12:47:10Z","file_name":"2018_CommBiology_Pavlogiannis.pdf","access_level":"open_access","date_created":"2018-12-18T13:37:04Z","relation":"main_file"}],"article_processing_charge":"No","isi":1,"author":[{"last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"},{"full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Nowak, Martin A.","first_name":"Martin A.","last_name":"Nowak"}],"day":"14","date_created":"2018-12-18T13:22:58Z","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:10Z","related_material":{"record":[{"relation":"popular_science","id":"5559","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7196"}]},"type":"journal_article","issue":"1","has_accepted_license":"1","department":[{"_id":"KrCh"}],"date_updated":"2026-04-08T07:24:11Z","date_published":"2018-06-14T00:00:00Z","month":"06","ddc":["004","519","576"],"publication":"Communications Biology","status":"public","article_number":"71","publisher":"Springer Nature","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7"},{"grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"isi":["000461126500071"]},"publication_identifier":{"issn":["2399-3642"]},"license":"https://creativecommons.org/licenses/by/4.0/","pubrep_id":"1045","year":"2018","abstract":[{"text":"Because of the intrinsic randomness of the evolutionary process, a mutant with a fitness advantage has some chance to be selected but no certainty. Any experiment that searches for advantageous mutants will lose many of them due to random drift. It is therefore of great interest to find population structures that improve the odds of advantageous mutants. Such structures are called amplifiers of natural selection: they increase the probability that advantageous mutants are selected. Arbitrarily strong amplifiers guarantee the selection of advantageous mutants, even for very small fitness advantage. Despite intensive research over the past decade, arbitrarily strong amplifiers have remained rare. Here we show how to construct a large variety of them. Our amplifiers are so simple that they could be useful in biotechnology, when optimizing biological molecules, or as a diagnostic tool, when searching for faster dividing cells or viruses. They could also occur in natural population structures.","lang":"eng"}],"oa_version":"Published Version","_id":"5751","publication_status":"published","title":"Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory","intvolume":"         1","oa":1,"ec_funded":1},{"citation":{"ista":"Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>.","short":"C. Fraisse, (2018).","ieee":"C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.’” Institute of Science and Technology Austria, 2018.","mla":"Fraisse, Christelle. <i>Supplementary Files for “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.”</i> Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>.","apa":"Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:/5757\">https://doi.org/10.15479/at:ista:/5757</a>","ama":"Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” 2018. doi:<a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>","chicago":"Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/at:ista:/5757\">https://doi.org/10.15479/at:ista:/5757</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:/5757","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"contributor":[{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"first_name":"Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","file":[{"file_name":"FileS1.zip","relation":"main_file","date_created":"2018-12-19T14:19:52Z","access_level":"open_access","file_size":369837892,"content_type":"application/zip","file_id":"5758","date_updated":"2020-07-14T12:47:11Z","checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd","creator":"cfraisse"},{"file_id":"5759","file_size":84856909,"content_type":"application/zip","creator":"cfraisse","checksum":"3592e467b4d8206650860b612d6e12f3","date_updated":"2020-07-14T12:47:11Z","file_name":"FileS2.zip","relation":"main_file","date_created":"2018-12-19T14:19:49Z","access_level":"open_access"},{"file_name":"FileS3.txt","relation":"main_file","access_level":"open_access","date_created":"2018-12-19T14:19:49Z","file_size":881133,"content_type":"text/plain","file_id":"5760","date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","checksum":"c37ac5d5437c457338afc128c1240655"},{"access_level":"open_access","date_created":"2018-12-19T14:19:49Z","relation":"main_file","file_name":"FileS4.txt","creator":"cfraisse","checksum":"943dfd14da61817441e33e3e3cb8cdb9","date_updated":"2020-07-14T12:47:11Z","file_id":"5761","file_size":883742,"content_type":"text/plain"},{"file_name":"FileS5.txt","relation":"main_file","date_created":"2018-12-19T14:19:49Z","access_level":"open_access","content_type":"text/plain","file_size":2495437,"file_id":"5762","date_updated":"2020-07-14T12:47:11Z","checksum":"1c669b6c4690ec1bbca3e2da9f566d17","creator":"cfraisse"},{"file_name":"FileS6.txt","relation":"main_file","date_created":"2018-12-19T14:19:50Z","access_level":"open_access","file_size":15913457,"content_type":"text/plain","file_id":"5763","date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","checksum":"f40f661b987ca6fb6b47f650cbbb04e6"},{"file_id":"5764","file_size":2584120,"content_type":"text/plain","checksum":"25f41e5b8a075669c6c88d4c6713bf6f","creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","file_name":"FileS7.txt","access_level":"open_access","date_created":"2018-12-19T14:19:50Z","relation":"main_file"},{"file_id":"5765","content_type":"text/plain","file_size":2446059,"checksum":"f6c0bd3e63e14ddf5445bd69b43a9152","creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","file_name":"FileS8.txt","relation":"main_file","access_level":"open_access","date_created":"2018-12-19T14:19:50Z"},{"relation":"main_file","access_level":"open_access","date_created":"2018-12-19T14:19:50Z","file_name":"FileS9.txt","creator":"cfraisse","checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae","date_updated":"2020-07-14T12:47:11Z","file_id":"5766","content_type":"text/plain","file_size":100737}],"author":[{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"}],"file_date_updated":"2020-07-14T12:47:11Z","day":"19","date_created":"2018-12-19T14:22:35Z","related_material":{"record":[{"id":"6089","status":"public","relation":"research_paper"}]},"keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"],"abstract":[{"lang":"eng","text":"File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total # of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites, excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the Eyre-Walker and Keightley method on binned data and using all variants."}],"year":"2018","has_accepted_license":"1","oa_version":"Published Version","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"type":"research_data","title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","date_updated":"2025-04-15T08:18:38Z","_id":"5757","ec_funded":1,"oa":1,"ddc":["576"],"date_published":"2018-12-19T00:00:00Z","month":"12","status":"public"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/science.aao0980"}],"abstract":[{"text":"Cuprate superconductors have long been thought of as having strong electronic correlations but negligible spin-orbit coupling. Using spin- and angle-resolved photoemission spectroscopy, we discovered that one of the most studied cuprate superconductors, Bi2212, has a nontrivial spin texture with a spin-momentum locking that circles the Brillouin zone center and a spin-layer locking that allows states of opposite spin to be localized in different parts of the unit cell. Our findings pose challenges for the vast majority of models of cuprates, such as the Hubbard model and its variants, where spin-orbit interaction has been mostly neglected, and open the intriguing question of how the high-temperature superconducting state emerges in the presence of this nontrivial spin texture. ","lang":"eng"}],"year":"2018","oa_version":"Published Version","title":"Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor","publication_status":"published","_id":"5767","oa":1,"intvolume":"       362","publisher":"American Association for the Advancement of Science","external_id":{"isi":["000452994400048"]},"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"author":[{"full_name":"Gotlieb, Kenneth","first_name":"Kenneth","last_name":"Gotlieb"},{"first_name":"Chiu-Yun","last_name":"Lin","full_name":"Lin, Chiu-Yun"},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"},{"full_name":"Zhang, Wentao","last_name":"Zhang","first_name":"Wentao"},{"full_name":"Smallwood, Christopher L.","first_name":"Christopher L.","last_name":"Smallwood"},{"full_name":"Jozwiak, Christopher","last_name":"Jozwiak","first_name":"Christopher"},{"full_name":"Eisaki, Hiroshi","last_name":"Eisaki","first_name":"Hiroshi"},{"full_name":"Hussain, Zahid","last_name":"Hussain","first_name":"Zahid"},{"full_name":"Vishwanath, Ashvin","first_name":"Ashvin","last_name":"Vishwanath"},{"full_name":"Lanzara, Alessandra","last_name":"Lanzara","first_name":"Alessandra"}],"date_created":"2018-12-19T14:53:50Z","language":[{"iso":"eng"}],"day":"14","article_type":"original","acknowledgement":" M.S. was supported by the Gordon and Betty Moore Foundation s EPiQS Initiative through grant GBMF4307","department":[{"_id":"MaSe"}],"issue":"6420","type":"journal_article","date_updated":"2026-06-18T18:55:21Z","publication":"Science","ddc":["530"],"month":"12","date_published":"2018-12-14T00:00:00Z","page":"1271-1275","status":"public","volume":362,"quality_controlled":"1","citation":{"ista":"Gotlieb K, Lin C-Y, Serbyn M, Zhang W, Smallwood CL, Jozwiak C, Eisaki H, Hussain Z, Vishwanath A, Lanzara A. 2018. Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. 362(6420), 1271–1275.","short":"K. Gotlieb, C.-Y. Lin, M. Serbyn, W. Zhang, C.L. Smallwood, C. Jozwiak, H. Eisaki, Z. Hussain, A. Vishwanath, A. Lanzara, Science 362 (2018) 1271–1275.","ieee":"K. Gotlieb <i>et al.</i>, “Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor,” <i>Science</i>, vol. 362, no. 6420. American Association for the Advancement of Science, pp. 1271–1275, 2018.","ama":"Gotlieb K, Lin C-Y, Serbyn M, et al. Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. <i>Science</i>. 2018;362(6420):1271-1275. doi:<a href=\"https://doi.org/10.1126/science.aao0980\">10.1126/science.aao0980</a>","apa":"Gotlieb, K., Lin, C.-Y., Serbyn, M., Zhang, W., Smallwood, C. L., Jozwiak, C., … Lanzara, A. (2018). Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aao0980\">https://doi.org/10.1126/science.aao0980</a>","mla":"Gotlieb, Kenneth, et al. “Revealing Hidden Spin-Momentum Locking in a High-Temperature Cuprate Superconductor.” <i>Science</i>, vol. 362, no. 6420, American Association for the Advancement of Science, 2018, pp. 1271–75, doi:<a href=\"https://doi.org/10.1126/science.aao0980\">10.1126/science.aao0980</a>.","chicago":"Gotlieb, Kenneth, Chiu-Yun Lin, Maksym Serbyn, Wentao Zhang, Christopher L. Smallwood, Christopher Jozwiak, Hiroshi Eisaki, Zahid Hussain, Ashvin Vishwanath, and Alessandra Lanzara. “Revealing Hidden Spin-Momentum Locking in a High-Temperature Cuprate Superconductor.” <i>Science</i>. American Association for the Advancement of Science, 2018. <a href=\"https://doi.org/10.1126/science.aao0980\">https://doi.org/10.1126/science.aao0980</a>."},"doi":"10.1126/science.aao0980","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","article_processing_charge":"No","isi":1},{"publisher":"National Academy of Sciences","external_id":{"isi":["000452866000022"],"pmid":["30478053"]},"publication_identifier":{"issn":["0027-8424"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30478053","open_access":"1"}],"abstract":[{"text":"Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as a truncated sphere in the immature virion. Proteolytic cleavage of Gag induces dramatic structural rearrangements; a subset of cleaved CA subsequently assembles into the mature core, whose architecture varies among retroviruses. Murine leukemia virus (MLV) is the prototypical γ-retrovirus and serves as the basis of retroviral vectors, but the structure of the MLV CA layer is unknown. Here we have combined X-ray crystallography with cryoelectron tomography to determine the structures of immature and mature MLV CA layers within authentic viral particles. This reveals the structural changes associated with maturation, and, by comparison with HIV-1, uncovers conserved and variable features. In contrast to HIV-1, most MLV CA is used for assembly of the mature core, which adopts variable, multilayered morphologies and does not form a closed structure. Unlike in HIV-1, there is similarity between protein–protein interfaces in the immature MLV CA layer and those in the mature CA layer, and structural maturation of MLV could be achieved through domain rotations that largely maintain hexameric interactions. Nevertheless, the dramatic architectural change on maturation indicates that extensive disassembly and reassembly are required for mature core growth. The core morphology suggests that wrapping of the genome in CA sheets may be sufficient to protect the MLV ribonucleoprotein during cell entry.","lang":"eng"}],"year":"2018","oa_version":"Submitted Version","title":"Structure and architecture of immature and mature murine leukemia virus capsids","publication_status":"published","_id":"5770","oa":1,"intvolume":"       115","pmid":1,"volume":115,"citation":{"ista":"Qu K, Glass B, Doležal M, Schur FK, Murciano B, Rein A, Rumlová M, Ruml T, Kräusslich H-G, Briggs JAG. 2018. Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences of the United States of America. 115(50), E11751–E11760.","short":"K. Qu, B. Glass, M. Doležal, F.K. Schur, B. Murciano, A. Rein, M. Rumlová, T. Ruml, H.-G. Kräusslich, J.A.G. Briggs, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) E11751–E11760.","ieee":"K. Qu <i>et al.</i>, “Structure and architecture of immature and mature murine leukemia virus capsids,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 50. National Academy of Sciences, pp. E11751–E11760, 2018.","apa":"Qu, K., Glass, B., Doležal, M., Schur, F. K., Murciano, B., Rein, A., … Briggs, J. A. G. (2018). Structure and architecture of immature and mature murine leukemia virus capsids. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1811580115\">https://doi.org/10.1073/pnas.1811580115</a>","ama":"Qu K, Glass B, Doležal M, et al. Structure and architecture of immature and mature murine leukemia virus capsids. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2018;115(50):E11751-E11760. doi:<a href=\"https://doi.org/10.1073/pnas.1811580115\">10.1073/pnas.1811580115</a>","mla":"Qu, Kun, et al. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 50, National Academy of Sciences, 2018, pp. E11751–60, doi:<a href=\"https://doi.org/10.1073/pnas.1811580115\">10.1073/pnas.1811580115</a>.","chicago":"Qu, Kun, Bärbel Glass, Michal Doležal, Florian KM Schur, Brice Murciano, Alan Rein, Michaela Rumlová, Tomáš Ruml, Hans-Georg Kräusslich, and John A. G. Briggs. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1811580115\">https://doi.org/10.1073/pnas.1811580115</a>."},"quality_controlled":"1","doi":"10.1073/pnas.1811580115","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","article_processing_charge":"No","isi":1,"author":[{"full_name":"Qu, Kun","first_name":"Kun","last_name":"Qu"},{"last_name":"Glass","first_name":"Bärbel","full_name":"Glass, Bärbel"},{"first_name":"Michal","last_name":"Doležal","full_name":"Doležal, Michal"},{"full_name":"Schur, Florian","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian"},{"full_name":"Murciano, Brice","first_name":"Brice","last_name":"Murciano"},{"full_name":"Rein, Alan","first_name":"Alan","last_name":"Rein"},{"full_name":"Rumlová, Michaela","last_name":"Rumlová","first_name":"Michaela"},{"full_name":"Ruml, Tomáš","first_name":"Tomáš","last_name":"Ruml"},{"last_name":"Kräusslich","first_name":"Hans-Georg","full_name":"Kräusslich, Hans-Georg"},{"last_name":"Briggs","first_name":"John A. G.","full_name":"Briggs, John A. G."}],"language":[{"iso":"eng"}],"date_created":"2018-12-20T21:09:37Z","day":"11","department":[{"_id":"FlSc"}],"issue":"50","type":"journal_article","date_updated":"2025-06-03T11:56:09Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","date_published":"2018-12-11T00:00:00Z","month":"12","page":"E11751-E11760","status":"public"},{"publisher":"National Academy of Sciences","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication_identifier":{"issn":["0027-8424"]},"external_id":{"isi":["000452866000068"]},"abstract":[{"lang":"eng","text":"Bioluminescence is found across the entire tree of life, conferring a spectacular set of visually oriented functions from attracting mates to scaring off predators. Half a dozen different luciferins, molecules that emit light when enzymatically oxidized, are known. However, just one biochemical pathway for luciferin biosynthesis has been described in full, which is found only in bacteria. Here, we report identification of the fungal luciferase and three other key enzymes that together form the biosynthetic cycle of the fungal luciferin from caffeic acid, a simple and widespread metabolite. Introduction of the identified genes into the genome of the yeast Pichia pastoris along with caffeic acid biosynthesis genes resulted in a strain that is autoluminescent in standard media. We analyzed evolution of the enzymes of the luciferin biosynthesis cycle and found that fungal bioluminescence emerged through a series of events that included two independent gene duplications. The retention of the duplicated enzymes of the luciferin pathway in nonluminescent fungi shows that the gene duplication was followed by functional sequence divergence of enzymes of at least one gene in the biosynthetic pathway and suggests that the evolution of fungal bioluminescence proceeded through several closely related stepping stone nonluminescent biochemical reactions with adaptive roles. The availability of a complete eukaryotic luciferin biosynthesis pathway provides several applications in biomedicine and bioengineering."}],"year":"2018","title":"Genetically encodable bioluminescent system from fungi","_id":"5780","publication_status":"published","oa_version":"Published Version","oa":1,"intvolume":"       115","volume":115,"citation":{"ieee":"A. A. Kotlobay <i>et al.</i>, “Genetically encodable bioluminescent system from fungi,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 50. National Academy of Sciences, pp. 12728–12732, 2018.","short":"A.A. Kotlobay, K. Sarkisyan, Y.A. Mokrushina, M. Marcet-Houben, E.O. Serebrovskaya, N.M. Markina, L. Gonzalez Somermeyer, A.Y. Gorokhovatsky, A. Vvedensky, K.V. Purtov, V.N. Petushkov, N.S. Rodionova, T.V. Chepurnyh, L. Fakhranurova, E.B. Guglya, R. Ziganshin, A.S. Tsarkova, Z.M. Kaskova, V. Shender, M. Abakumov, T.O. Abakumova, I.S. Povolotskaya, F.M. Eroshkin, A.G. Zaraisky, A.S. Mishin, S.V. Dolgov, T.Y. Mitiouchkina, E.P. Kopantzev, H.E. Waldenmaier, A.G. Oliveira, Y. Oba, E. Barsova, E.A. Bogdanova, T. Gabaldón, C.V. Stevani, S. Lukyanov, I.V. Smirnov, J.I. Gitelson, F. Kondrashov, I.V. Yampolsky, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) 12728–12732.","ista":"Kotlobay AA, Sarkisyan K, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO, Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov VN, Rodionova NS, Chepurnyh TV, Fakhranurova L, Guglya EB, Ziganshin R, Tsarkova AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldón T, Stevani CV, Lukyanov S, Smirnov IV, Gitelson JI, Kondrashov F, Yampolsky IV. 2018. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 115(50), 12728–12732.","chicago":"Kotlobay, Alexey A., Karen Sarkisyan, Yuliana A. Mokrushina, Marina Marcet-Houben, Ekaterina O. Serebrovskaya, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, et al. “Genetically Encodable Bioluminescent System from Fungi.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1803615115\">https://doi.org/10.1073/pnas.1803615115</a>.","mla":"Kotlobay, Alexey A., et al. “Genetically Encodable Bioluminescent System from Fungi.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 50, National Academy of Sciences, 2018, pp. 12728–32, doi:<a href=\"https://doi.org/10.1073/pnas.1803615115\">10.1073/pnas.1803615115</a>.","ama":"Kotlobay AA, Sarkisyan K, Mokrushina YA, et al. Genetically encodable bioluminescent system from fungi. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2018;115(50):12728-12732. doi:<a href=\"https://doi.org/10.1073/pnas.1803615115\">10.1073/pnas.1803615115</a>","apa":"Kotlobay, A. A., Sarkisyan, K., Mokrushina, Y. A., Marcet-Houben, M., Serebrovskaya, E. O., Markina, N. M., … Yampolsky, I. V. (2018). Genetically encodable bioluminescent system from fungi. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1803615115\">https://doi.org/10.1073/pnas.1803615115</a>"},"quality_controlled":"1","doi":"10.1073/pnas.1803615115","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","isi":1,"article_processing_charge":"No","file":[{"file_name":"2018_PNAS_Kotlobay.pdf","date_created":"2019-02-05T15:21:40Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":1271988,"file_id":"5926","date_updated":"2020-07-14T12:47:11Z","checksum":"46b2c12185eb2ddb598f4c7b4bd267bf","creator":"dernst"}],"file_date_updated":"2020-07-14T12:47:11Z","day":"11","date_created":"2018-12-23T22:59:18Z","language":[{"iso":"eng"}],"author":[{"last_name":"Kotlobay","first_name":"Alexey A.","full_name":"Kotlobay, Alexey A."},{"last_name":"Sarkisyan","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","full_name":"Sarkisyan, Karen","orcid":"0000-0002-5375-6341"},{"full_name":"Mokrushina, Yuliana A.","first_name":"Yuliana A.","last_name":"Mokrushina"},{"first_name":"Marina","last_name":"Marcet-Houben","full_name":"Marcet-Houben, Marina"},{"first_name":"Ekaterina O.","last_name":"Serebrovskaya","full_name":"Serebrovskaya, Ekaterina O."},{"last_name":"Markina","first_name":"Nadezhda M.","full_name":"Markina, Nadezhda M."},{"first_name":"Louisa","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","last_name":"Gonzalez Somermeyer","orcid":"0000-0001-9139-5383","full_name":"Gonzalez Somermeyer, Louisa"},{"full_name":"Gorokhovatsky, Andrey Y.","first_name":"Andrey Y.","last_name":"Gorokhovatsky"},{"last_name":"Vvedensky","first_name":"Andrey","full_name":"Vvedensky, Andrey"},{"full_name":"Purtov, Konstantin V.","first_name":"Konstantin V.","last_name":"Purtov"},{"full_name":"Petushkov, Valentin N.","last_name":"Petushkov","first_name":"Valentin N."},{"full_name":"Rodionova, Natalja S.","first_name":"Natalja S.","last_name":"Rodionova"},{"last_name":"Chepurnyh","first_name":"Tatiana V.","full_name":"Chepurnyh, Tatiana V."},{"last_name":"Fakhranurova","first_name":"Liliia","full_name":"Fakhranurova, Liliia"},{"full_name":"Guglya, Elena B.","last_name":"Guglya","first_name":"Elena B."},{"full_name":"Ziganshin, Rustam","first_name":"Rustam","last_name":"Ziganshin"},{"last_name":"Tsarkova","first_name":"Aleksandra S.","full_name":"Tsarkova, Aleksandra S."},{"last_name":"Kaskova","first_name":"Zinaida M.","full_name":"Kaskova, Zinaida M."},{"full_name":"Shender, Victoria","last_name":"Shender","first_name":"Victoria"},{"first_name":"Maxim","last_name":"Abakumov","full_name":"Abakumov, Maxim"},{"full_name":"Abakumova, Tatiana O.","first_name":"Tatiana O.","last_name":"Abakumova"},{"full_name":"Povolotskaya, Inna S.","first_name":"Inna S.","last_name":"Povolotskaya"},{"last_name":"Eroshkin","first_name":"Fedor M.","full_name":"Eroshkin, Fedor M."},{"full_name":"Zaraisky, Andrey G.","first_name":"Andrey G.","last_name":"Zaraisky"},{"last_name":"Mishin","first_name":"Alexander S.","full_name":"Mishin, Alexander S."},{"first_name":"Sergey V.","last_name":"Dolgov","full_name":"Dolgov, Sergey V."},{"full_name":"Mitiouchkina, Tatiana Y.","last_name":"Mitiouchkina","first_name":"Tatiana Y."},{"last_name":"Kopantzev","first_name":"Eugene P.","full_name":"Kopantzev, Eugene P."},{"last_name":"Waldenmaier","first_name":"Hans E.","full_name":"Waldenmaier, Hans E."},{"full_name":"Oliveira, Anderson G.","first_name":"Anderson G.","last_name":"Oliveira"},{"full_name":"Oba, Yuichi","last_name":"Oba","first_name":"Yuichi"},{"last_name":"Barsova","first_name":"Ekaterina","full_name":"Barsova, Ekaterina"},{"full_name":"Bogdanova, Ekaterina A.","first_name":"Ekaterina A.","last_name":"Bogdanova"},{"last_name":"Gabaldón","first_name":"Toni","full_name":"Gabaldón, Toni"},{"full_name":"Stevani, Cassius V.","last_name":"Stevani","first_name":"Cassius V."},{"last_name":"Lukyanov","first_name":"Sergey","full_name":"Lukyanov, Sergey"},{"full_name":"Smirnov, Ivan V.","first_name":"Ivan V.","last_name":"Smirnov"},{"full_name":"Gitelson, Josef I.","last_name":"Gitelson","first_name":"Josef I."},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"first_name":"Ilia V.","last_name":"Yampolsky","full_name":"Yampolsky, Ilia V."}],"date_updated":"2025-07-10T11:52:58Z","department":[{"_id":"FyKo"}],"has_accepted_license":"1","type":"journal_article","issue":"50","page":"12728-12732","status":"public","publication":"Proceedings of the National Academy of Sciences of the United States of America","date_published":"2018-12-11T00:00:00Z","ddc":["580"],"month":"12"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1111/dgd.12570","volume":60,"citation":{"ieee":"E. B. Hannezo and B. D. Simons, “Statistical theory of branching morphogenesis,” <i>Development Growth and Differentiation</i>, vol. 60, no. 9. Wiley, pp. 512–521, 2018.","ista":"Hannezo EB, Simons BD. 2018. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 60(9), 512–521.","short":"E.B. Hannezo, B.D. Simons, Development Growth and Differentiation 60 (2018) 512–521.","chicago":"Hannezo, Edouard B, and Benjamin D. Simons. “Statistical Theory of Branching Morphogenesis.” <i>Development Growth and Differentiation</i>. Wiley, 2018. <a href=\"https://doi.org/10.1111/dgd.12570\">https://doi.org/10.1111/dgd.12570</a>.","mla":"Hannezo, Edouard B., and Benjamin D. Simons. “Statistical Theory of Branching Morphogenesis.” <i>Development Growth and Differentiation</i>, vol. 60, no. 9, Wiley, 2018, pp. 512–21, doi:<a href=\"https://doi.org/10.1111/dgd.12570\">10.1111/dgd.12570</a>.","apa":"Hannezo, E. B., &#38; Simons, B. D. (2018). Statistical theory of branching morphogenesis. <i>Development Growth and Differentiation</i>. Wiley. <a href=\"https://doi.org/10.1111/dgd.12570\">https://doi.org/10.1111/dgd.12570</a>","ama":"Hannezo EB, Simons BD. Statistical theory of branching morphogenesis. <i>Development Growth and Differentiation</i>. 2018;60(9):512-521. doi:<a href=\"https://doi.org/10.1111/dgd.12570\">10.1111/dgd.12570</a>"},"quality_controlled":"1","article_processing_charge":"No","file":[{"file_size":1313606,"content_type":"application/pdf","file_id":"5933","date_updated":"2020-07-14T12:47:11Z","creator":"dernst","checksum":"a6d30b0785db902c734a84fecb2eadd9","file_name":"2018_DevGrowh_Hannezo.pdf","access_level":"open_access","date_created":"2019-02-06T10:40:46Z","relation":"main_file"}],"isi":1,"scopus_import":"1","author":[{"first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"full_name":"Simons, Benjamin D.","last_name":"Simons","first_name":"Benjamin D."}],"file_date_updated":"2020-07-14T12:47:11Z","language":[{"iso":"eng"}],"day":"09","date_created":"2018-12-30T22:59:14Z","publication":"Development Growth and Differentiation","ddc":["570"],"month":"12","date_published":"2018-12-09T00:00:00Z","page":"512-521","status":"public","department":[{"_id":"EdHa"}],"has_accepted_license":"1","type":"journal_article","issue":"9","date_updated":"2025-07-10T11:52:59Z","publisher":"Wiley","external_id":{"isi":["000453555100002"]},"publication_identifier":{"issn":["0012-1592"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"text":"Branching  morphogenesis  remains  a  subject  of  abiding  interest.  Although  much  is  \r\nknown about the gene regulatory programs and signaling pathways that operate at \r\nthe cellular scale, it has remained unclear how the macroscopic features of branched \r\norgans,  including  their  size,  network  topology  and  spatial  patterning,  are  encoded.  \r\nLately, it has been proposed that, these features can be explained quantitatively in \r\nseveral organs within a single unifying framework. Based on large-\r\nscale organ recon\r\n-\r\nstructions  and  cell  lineage  tracing,  it  has  been  argued  that  morphogenesis  follows  \r\nfrom the collective dynamics of sublineage- \r\nrestricted self- \r\nrenewing progenitor cells, \r\nlocalized at ductal tips, that act cooperatively to drive a serial process of ductal elon\r\n-\r\ngation and stochastic tip bifurcation. By correlating differentiation or cell cycle exit \r\nwith proximity to maturing ducts, this dynamic results in the specification of a com-\r\nplex  network  of  defined  density  and  statistical  organization.  These  results  suggest  \r\nthat, for several mammalian tissues, branched epithelial structures develop as a self- \r\norganized  process,  reliant  upon  a  strikingly  simple,  but  generic,  set  of  local  rules,  \r\nwithout  recourse  to  a  rigid  and  deterministic  sequence  of  genetically  programmed  \r\nevents. Here, we review the basis of these findings and discuss their implications.","lang":"eng"}],"year":"2018","oa":1,"intvolume":"        60","oa_version":"Published Version","title":"Statistical theory of branching morphogenesis","_id":"5787"},{"scopus_import":"1","isi":1,"article_processing_charge":"No","volume":11316,"citation":{"chicago":"Avni, Guy, Thomas A Henzinger, and Rasmus Ibsen-Jensen. “Infinite-Duration Poorman-Bidding Games,” 11316:21–36. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-030-04612-5_2\">https://doi.org/10.1007/978-3-030-04612-5_2</a>.","apa":"Avni, G., Henzinger, T. A., &#38; Ibsen-Jensen, R. (2018). Infinite-duration poorman-bidding games (Vol. 11316, pp. 21–36). Presented at the 14th International Conference on Web and Internet Economics, WINE, Oxford, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-030-04612-5_2\">https://doi.org/10.1007/978-3-030-04612-5_2</a>","ama":"Avni G, Henzinger TA, Ibsen-Jensen R. Infinite-duration poorman-bidding games. In: Vol 11316. Springer; 2018:21-36. doi:<a href=\"https://doi.org/10.1007/978-3-030-04612-5_2\">10.1007/978-3-030-04612-5_2</a>","mla":"Avni, Guy, et al. <i>Infinite-Duration Poorman-Bidding Games</i>. Vol. 11316, Springer, 2018, pp. 21–36, doi:<a href=\"https://doi.org/10.1007/978-3-030-04612-5_2\">10.1007/978-3-030-04612-5_2</a>.","ieee":"G. Avni, T. A. Henzinger, and R. Ibsen-Jensen, “Infinite-duration poorman-bidding games,” presented at the 14th International Conference on Web and Internet Economics, WINE, Oxford, UK, 2018, vol. 11316, pp. 21–36.","ista":"Avni G, Henzinger TA, Ibsen-Jensen R. 2018. Infinite-duration poorman-bidding games. 14th International Conference on Web and Internet Economics, WINE, LNCS, vol. 11316, 21–36.","short":"G. Avni, T.A. Henzinger, R. Ibsen-Jensen, in:, Springer, 2018, pp. 21–36."},"quality_controlled":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.1007/978-3-030-04612-5_2","date_updated":"2026-04-16T09:54:39Z","department":[{"_id":"ToHe"}],"type":"conference","page":"21-36","status":"public","month":"11","date_published":"2018-11-21T00:00:00Z","day":"21","date_created":"2018-12-30T22:59:14Z","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen"}],"project":[{"name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"},{"call_identifier":"FWF","grant_number":"M02369","_id":"264B3912-B435-11E9-9278-68D0E5697425","name":"Formal Methods meets Algorithmic Game Theory"}],"publication_identifier":{"issn":["0302-9743"],"isbn":["9783030046118"]},"alternative_title":["LNCS"],"external_id":{"arxiv":["1804.04372"],"isi":["000865933000002"]},"publisher":"Springer","title":"Infinite-duration poorman-bidding games","_id":"5788","oa_version":"Preprint","oa":1,"intvolume":"     11316","conference":{"start_date":"2018-12-15","end_date":"2018-12-17","name":"14th International Conference on Web and Internet Economics, WINE","location":"Oxford, UK"},"arxiv":1,"abstract":[{"text":"In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the winner or payoff of the game. Such games are central in formal verification since they model the interaction between a non-terminating system and its environment. We study bidding games in which the players bid for the right to move the token. Two bidding rules have been defined. In Richman bidding, in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Poorman bidding is similar except that the winner of the bidding pays the “bank” rather than the other player. While poorman reachability games have been studied before, we present, for the first time, results on infinite-duration poorman games. A central quantity in these games is the ratio between the two players’ initial budgets. The questions we study concern a necessary and sufficient ratio with which a player can achieve a goal. For reachability objectives, such threshold ratios are known to exist for both bidding rules. We show that the properties of poorman reachability games extend to complex qualitative objectives such as parity, similarly to the Richman case. Our most interesting results concern quantitative poorman games, namely poorman mean-payoff games, where we construct optimal strategies depending on the initial ratio, by showing a connection with random-turn based games. The connection in itself is interesting, because it does not hold for reachability poorman games. We also solve the complexity problems that arise in poorman bidding games.","lang":"eng"}],"year":"2018","main_file_link":[{"url":"https://arxiv.org/abs/1804.04372","open_access":"1"}]},{"publisher":"Springer","alternative_title":["LNCS"],"external_id":{"arxiv":["1808.07608"],"isi":["000672802500016"]},"publication_identifier":{"isbn":["9783030044138"]},"arxiv":1,"conference":{"end_date":"2018-09-28","name":"GD: Graph Drawing and Network Visualization","location":"Barcelona, Spain","start_date":"2018-09-26"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.07608"}],"abstract":[{"lang":"eng","text":"Due to data compression or low resolution, nearby vertices and edges of a graph drawing may be bundled to a common node or arc. We model such a “compromised” drawing by a piecewise linear map φ:G → ℝ. We wish to perturb φ by an arbitrarily small ε>0 into a proper drawing (in which the vertices are distinct points, any two edges intersect in finitely many points, and no three edges have a common interior point) that minimizes the number of crossings. An ε-perturbation, for every ε>0, is given by a piecewise linear map (Formula Presented), where with ||·|| is the uniform norm (i.e., sup norm). We present a polynomial-time solution for this optimization problem when G is a cycle and the map φ has no spurs (i.e., no two adjacent edges are mapped to overlapping arcs). We also show that the problem becomes NP-complete (i) when G is an arbitrary graph and φ has no spurs, and (ii) when φ may have spurs and G is a cycle or a union of disjoint paths."}],"year":"2018","oa_version":"Preprint","title":"Crossing minimization in perturbed drawings","publication_status":"published","_id":"5791","oa":1,"volume":"11282 ","citation":{"short":"R. Fulek, C.D. Tóth, in:, Springer, 2018, pp. 229–241.","ista":"Fulek R, Tóth CD. 2018. Crossing minimization in perturbed drawings. GD: Graph Drawing and Network Visualization, LNCS, vol. 11282, 229–241.","ieee":"R. Fulek and C. D. Tóth, “Crossing minimization in perturbed drawings,” presented at the GD: Graph Drawing and Network Visualization, Barcelona, Spain, 2018, vol. 11282, pp. 229–241.","mla":"Fulek, Radoslav, and Csaba D. Tóth. <i>Crossing Minimization in Perturbed Drawings</i>. Vol. 11282, Springer, 2018, pp. 229–41, doi:<a href=\"https://doi.org/10.1007/978-3-030-04414-5_16\">10.1007/978-3-030-04414-5_16</a>.","apa":"Fulek, R., &#38; Tóth, C. D. (2018). Crossing minimization in perturbed drawings (Vol. 11282, pp. 229–241). Presented at the GD: Graph Drawing and Network Visualization, Barcelona, Spain: Springer. <a href=\"https://doi.org/10.1007/978-3-030-04414-5_16\">https://doi.org/10.1007/978-3-030-04414-5_16</a>","ama":"Fulek R, Tóth CD. Crossing minimization in perturbed drawings. In: Vol 11282. Springer; 2018:229-241. doi:<a href=\"https://doi.org/10.1007/978-3-030-04414-5_16\">10.1007/978-3-030-04414-5_16</a>","chicago":"Fulek, Radoslav, and Csaba D. Tóth. “Crossing Minimization in Perturbed Drawings,” 11282:229–41. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-030-04414-5_16\">https://doi.org/10.1007/978-3-030-04414-5_16</a>."},"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-030-04414-5_16","scopus_import":"1","article_processing_charge":"No","isi":1,"author":[{"first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav"},{"full_name":"Tóth, Csaba D.","last_name":"Tóth","first_name":"Csaba D."}],"date_created":"2018-12-30T22:59:15Z","day":"18","language":[{"iso":"eng"}],"department":[{"_id":"UlWa"}],"type":"conference","date_updated":"2025-07-10T11:53:00Z","month":"12","date_published":"2018-12-18T00:00:00Z","page":"229-241","status":"public"},{"volume":121,"citation":{"chicago":"Yakaboylu, Enderalp, Mikhail Shkolnikov, and Mikhail Lemeshko. “Quantum Groups as Hidden Symmetries of Quantum Impurities.” <i>Physical Review Letters</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevLett.121.255302\">https://doi.org/10.1103/PhysRevLett.121.255302</a>.","mla":"Yakaboylu, Enderalp, et al. “Quantum Groups as Hidden Symmetries of Quantum Impurities.” <i>Physical Review Letters</i>, vol. 121, no. 25, 255302, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.121.255302\">10.1103/PhysRevLett.121.255302</a>.","apa":"Yakaboylu, E., Shkolnikov, M., &#38; Lemeshko, M. (2018). Quantum groups as hidden symmetries of quantum impurities. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.121.255302\">https://doi.org/10.1103/PhysRevLett.121.255302</a>","ama":"Yakaboylu E, Shkolnikov M, Lemeshko M. Quantum groups as hidden symmetries of quantum impurities. <i>Physical Review Letters</i>. 2018;121(25). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.121.255302\">10.1103/PhysRevLett.121.255302</a>","ieee":"E. Yakaboylu, M. Shkolnikov, and M. Lemeshko, “Quantum groups as hidden symmetries of quantum impurities,” <i>Physical Review Letters</i>, vol. 121, no. 25. American Physical Society, 2018.","short":"E. Yakaboylu, M. Shkolnikov, M. Lemeshko, Physical Review Letters 121 (2018).","ista":"Yakaboylu E, Shkolnikov M, Lemeshko M. 2018. Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. 121(25), 255302."},"quality_controlled":"1","doi":"10.1103/PhysRevLett.121.255302","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","article_processing_charge":"No","isi":1,"author":[{"first_name":"Enderalp","last_name":"Yakaboylu","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5973-0874","full_name":"Yakaboylu, Enderalp"},{"last_name":"Shkolnikov","id":"35084A62-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Shkolnikov, Mikhail","orcid":"0000-0002-4310-178X"},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko"}],"date_created":"2019-01-06T22:59:12Z","language":[{"iso":"eng"}],"day":"17","article_type":"original","department":[{"_id":"MiLe"}],"type":"journal_article","issue":"25","date_updated":"2025-04-15T06:50:24Z","publication":"Physical Review Letters","month":"12","date_published":"2018-12-17T00:00:00Z","status":"public","article_number":"255302","publisher":"American Physical Society","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"},{"call_identifier":"FWF","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000454178600009"],"arxiv":["1809.00222"]},"publication_identifier":{"issn":["00319007"]},"arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.00222"}],"abstract":[{"lang":"eng","text":"We present an approach to interacting quantum many-body systems based on the notion of quantum groups, also known as q-deformed Lie algebras. In particular, we show that, if the symmetry of a free quantum particle corresponds to a Lie group G, in the presence of a many-body environment this particle can be described by a deformed group, Gq. Crucially, the single deformation parameter, q, contains all the information about the many-particle interactions in the system. We exemplify our approach by considering a quantum rotor interacting with a bath of bosons, and demonstrate that extracting the value of q from closed-form solutions in the perturbative regime allows one to predict the behavior of the system for arbitrary values of the impurity-bath coupling strength, in good agreement with nonperturbative calculations. Furthermore, the value of the deformation parameter allows one to predict at which coupling strengths rotor-bath interactions result in a formation of a stable quasiparticle. The approach based on quantum groups does not only allow for a drastic simplification of impurity problems, but also provides valuable insights into hidden symmetries of interacting many-particle systems."}],"year":"2018","oa_version":"Preprint","title":"Quantum groups as hidden symmetries of quantum impurities","publication_status":"published","_id":"5794","oa":1,"ec_funded":1,"intvolume":"       121"},{"file_date_updated":"2020-07-14T12:47:13Z","date_created":"2019-01-20T22:59:18Z","language":[{"iso":"eng"}],"day":"12","author":[{"id":"43BE2298-F248-11E8-B48F-1D18A9856A87","last_name":"Corominas-Murtra","first_name":"Bernat","full_name":"Corominas-Murtra, Bernat","orcid":"0000-0001-9806-5643"},{"full_name":"Fibla, Martí Sànchez","last_name":"Fibla","first_name":"Martí Sànchez"},{"last_name":"Valverde","first_name":"Sergi","full_name":"Valverde, Sergi"},{"first_name":"Ricard","last_name":"Solé","full_name":"Solé, Ricard"}],"article_type":"original","acknowledgement":"This work was supported by the James McDonnell Foundation (B.C-M., S.V. and R.S.)","date_updated":"2023-10-18T06:41:12Z","has_accepted_license":"1","department":[{"_id":"EdHa"}],"type":"journal_article","issue":"12","status":"public","publication":"Royal Society Open Science","month":"12","date_published":"2018-12-12T00:00:00Z","ddc":["570"],"volume":5,"quality_controlled":"1","citation":{"ieee":"B. Corominas-Murtra, M. S. Fibla, S. Valverde, and R. Solé, “Chromatic transitions in the emergence of syntax networks,” <i>Royal Society Open Science</i>, vol. 5, no. 12. The Royal Society, 2018.","short":"B. Corominas-Murtra, M.S. Fibla, S. Valverde, R. Solé, Royal Society Open Science 5 (2018).","ista":"Corominas-Murtra B, Fibla MS, Valverde S, Solé R. 2018. Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. 5(12), 181286.","chicago":"Corominas-Murtra, Bernat, Martí Sànchez Fibla, Sergi Valverde, and Ricard Solé. “Chromatic Transitions in the Emergence of Syntax Networks.” <i>Royal Society Open Science</i>. The Royal Society, 2018. <a href=\"https://doi.org/10.1098/rsos.181286\">https://doi.org/10.1098/rsos.181286</a>.","mla":"Corominas-Murtra, Bernat, et al. “Chromatic Transitions in the Emergence of Syntax Networks.” <i>Royal Society Open Science</i>, vol. 5, no. 12, 181286, The Royal Society, 2018, doi:<a href=\"https://doi.org/10.1098/rsos.181286\">10.1098/rsos.181286</a>.","apa":"Corominas-Murtra, B., Fibla, M. S., Valverde, S., &#38; Solé, R. (2018). Chromatic transitions in the emergence of syntax networks. <i>Royal Society Open Science</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsos.181286\">https://doi.org/10.1098/rsos.181286</a>","ama":"Corominas-Murtra B, Fibla MS, Valverde S, Solé R. Chromatic transitions in the emergence of syntax networks. <i>Royal Society Open Science</i>. 2018;5(12). doi:<a href=\"https://doi.org/10.1098/rsos.181286\">10.1098/rsos.181286</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1098/rsos.181286","scopus_import":"1","isi":1,"article_processing_charge":"No","file":[{"file_size":646732,"content_type":"application/pdf","file_id":"5924","date_updated":"2020-07-14T12:47:13Z","creator":"dernst","checksum":"9664d4417f6b792242e31eea77ce9501","file_name":"2018_RoyalSocOS_Corominas.pdf","relation":"main_file","date_created":"2019-02-05T14:38:09Z","access_level":"open_access"}],"abstract":[{"lang":"eng","text":"The emergence of syntax during childhood is a remarkable example of how complex correlations unfold in nonlinear ways through development. In particular, rapid transitions seem to occur as children reach the age of two, which seems to separate a two-word, tree-like network of syntactic relations among words from the scale-free graphs associated with the adult, complex grammar. Here, we explore the evolution of syntax networks through language acquisition using the chromatic number, which captures the transition and provides a natural link to standard theories on syntactic structures. The data analysis is compared to a null model of network growth dynamics which is shown to display non-trivial and sensible differences. At a more general level, we observe that the chromatic classes define independent regions of the graph, and thus, can be interpreted as the footprints of incompatibility relations, somewhat as opposed to modularity considerations."}],"year":"2018","title":"Chromatic transitions in the emergence of syntax networks","publication_status":"published","_id":"5859","oa_version":"Published Version","pmid":1,"oa":1,"intvolume":"         5","article_number":"181286","publisher":"The Royal Society","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"issn":["2054-5703"]},"external_id":{"isi":["000456566500027"],"pmid":["30662738"]}},{"intvolume":"         7","oa":1,"oa_version":"Published Version","_id":"5861","publication_status":"published","title":"The cell sets the tone","year":"2018","abstract":[{"lang":"eng","text":"In zebrafish larvae, it is the cell type that determines how the cell responds to a chemokine signal."}],"external_id":{"isi":["000434375000001"]},"publication_identifier":{"issn":["2050-084X"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"eLife Sciences Publications","article_number":"e37888","date_published":"2018-06-06T00:00:00Z","month":"06","ddc":["570"],"publication":"eLife","status":"public","type":"journal_article","has_accepted_license":"1","department":[{"_id":"MiSi"}],"date_updated":"2025-07-10T11:53:05Z","article_type":"original","corr_author":"1","author":[{"last_name":"Alanko","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","first_name":"Jonna H","full_name":"Alanko, Jonna H","orcid":"0000-0002-7698-3061"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"language":[{"iso":"eng"}],"date_created":"2019-01-20T22:59:19Z","day":"06","file_date_updated":"2020-07-14T12:47:13Z","file":[{"file_name":"2018_eLife_Alanko.pdf","access_level":"open_access","date_created":"2019-02-13T10:52:11Z","relation":"main_file","content_type":"application/pdf","file_size":358141,"file_id":"5973","date_updated":"2020-07-14T12:47:13Z","creator":"dernst","checksum":"f1c7ec2a809408d763c4b529a98f9a3b"}],"article_processing_charge":"No","isi":1,"scopus_import":"1","doi":"10.7554/eLife.37888","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","citation":{"ama":"Alanko JH, Sixt MK. The cell sets the tone. <i>eLife</i>. 2018;7. doi:<a href=\"https://doi.org/10.7554/eLife.37888\">10.7554/eLife.37888</a>","apa":"Alanko, J. H., &#38; Sixt, M. K. (2018). The cell sets the tone. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.37888\">https://doi.org/10.7554/eLife.37888</a>","mla":"Alanko, Jonna H., and Michael K. Sixt. “The Cell Sets the Tone.” <i>ELife</i>, vol. 7, e37888, eLife Sciences Publications, 2018, doi:<a href=\"https://doi.org/10.7554/eLife.37888\">10.7554/eLife.37888</a>.","chicago":"Alanko, Jonna H, and Michael K Sixt. “The Cell Sets the Tone.” <i>ELife</i>. eLife Sciences Publications, 2018. <a href=\"https://doi.org/10.7554/eLife.37888\">https://doi.org/10.7554/eLife.37888</a>.","short":"J.H. Alanko, M.K. Sixt, ELife 7 (2018).","ista":"Alanko JH, Sixt MK. 2018. The cell sets the tone. eLife. 7, e37888.","ieee":"J. H. Alanko and M. K. Sixt, “The cell sets the tone,” <i>eLife</i>, vol. 7. eLife Sciences Publications, 2018."},"volume":7},{"type":"journal_article","issue":"8","has_accepted_license":"1","department":[{"_id":"GaNo"}],"date_updated":"2023-09-11T14:04:41Z","month":"08","date_published":"2018-08-07T00:00:00Z","ddc":["570"],"publication":"Experimental & Molecular Medicine","status":"public","author":[{"full_name":"Tarlungeanu, Dora-Clara","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","last_name":"Tarlungeanu","first_name":"Dora-Clara"},{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino"}],"date_created":"2019-01-27T22:59:11Z","day":"07","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:13Z","scopus_import":"1","file":[{"file_name":"2018_EMM_Tarlungeanu.pdf","relation":"main_file","date_created":"2019-01-28T15:18:02Z","access_level":"open_access","file_size":1237482,"content_type":"application/pdf","file_id":"5893","date_updated":"2020-07-14T12:47:13Z","creator":"dernst","checksum":"4498301c8c53097c9a1a8ef990936eb5"}],"article_processing_charge":"No","isi":1,"citation":{"ista":"Tarlungeanu D-C, Novarino G. 2018. Genomics in neurodevelopmental disorders: an avenue to personalized medicine. Experimental &#38; Molecular Medicine. 50(8), 100.","short":"D.-C. Tarlungeanu, G. Novarino, Experimental &#38; Molecular Medicine 50 (2018).","ieee":"D.-C. Tarlungeanu and G. Novarino, “Genomics in neurodevelopmental disorders: an avenue to personalized medicine,” <i>Experimental &#38; Molecular Medicine</i>, vol. 50, no. 8. Springer Nature, 2018.","apa":"Tarlungeanu, D.-C., &#38; Novarino, G. (2018). Genomics in neurodevelopmental disorders: an avenue to personalized medicine. <i>Experimental &#38; Molecular Medicine</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s12276-018-0129-7\">https://doi.org/10.1038/s12276-018-0129-7</a>","ama":"Tarlungeanu D-C, Novarino G. Genomics in neurodevelopmental disorders: an avenue to personalized medicine. <i>Experimental &#38; Molecular Medicine</i>. 2018;50(8). doi:<a href=\"https://doi.org/10.1038/s12276-018-0129-7\">10.1038/s12276-018-0129-7</a>","mla":"Tarlungeanu, Dora-Clara, and Gaia Novarino. “Genomics in Neurodevelopmental Disorders: An Avenue to Personalized Medicine.” <i>Experimental &#38; Molecular Medicine</i>, vol. 50, no. 8, 100, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s12276-018-0129-7\">10.1038/s12276-018-0129-7</a>.","chicago":"Tarlungeanu, Dora-Clara, and Gaia Novarino. “Genomics in Neurodevelopmental Disorders: An Avenue to Personalized Medicine.” <i>Experimental &#38; Molecular Medicine</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s12276-018-0129-7\">https://doi.org/10.1038/s12276-018-0129-7</a>."},"quality_controlled":"1","volume":50,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1038/s12276-018-0129-7","oa_version":"Published Version","publication_status":"published","_id":"5888","title":"Genomics in neurodevelopmental disorders: an avenue to personalized medicine","intvolume":"        50","oa":1,"pmid":1,"year":"2018","abstract":[{"lang":"eng","text":"Despite the remarkable number of scientific breakthroughs of the last 100 years, the treatment of neurodevelopmental\r\ndisorders (e.g., autism spectrum disorder, intellectual disability) remains a great challenge. Recent advancements in\r\ngenomics, such as whole-exome or whole-genome sequencing, have enabled scientists to identify numerous\r\nmutations underlying neurodevelopmental disorders. Given the few hundred risk genes that have been discovered,\r\nthe etiological variability and the heterogeneous clinical presentation, the need for genotype — along with phenotype-\r\nbased diagnosis of individual patients has become a requisite. In this review we look at recent advancements in\r\ngenomic analysis and their translation into clinical practice."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"pmid":["30089840"],"isi":["000441266700006"]},"publication_identifier":{"issn":["2092-6413"]},"article_number":"100","publisher":"Springer Nature"},{"scopus_import":1,"editor":[{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"full_name":"Clarke, Edmund M.","first_name":"Edmund M.","last_name":"Clarke"},{"full_name":"Veith, Helmut","last_name":"Veith","first_name":"Helmut"},{"full_name":"Bloem, Roderick","first_name":"Roderick","last_name":"Bloem"}],"publication_identifier":{"isbn":["978-3-319-10574-1"]},"quality_controlled":"1","citation":{"chicago":"Bloem, Roderick, Krishnendu Chatterjee, and Barbara Jobstmann. “Graph Games and Reactive Synthesis.” In <i>Handbook of Model Checking</i>, edited by Thomas A Henzinger, Edmund M. Clarke, Helmut Veith, and Roderick Bloem, 1st ed., 921–62. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-10575-8_27\">https://doi.org/10.1007/978-3-319-10575-8_27</a>.","ama":"Bloem R, Chatterjee K, Jobstmann B. Graph games and reactive synthesis. In: Henzinger TA, Clarke EM, Veith H, Bloem R, eds. <i>Handbook of Model Checking</i>. 1st ed. Springer; 2018:921-962. doi:<a href=\"https://doi.org/10.1007/978-3-319-10575-8_27\">10.1007/978-3-319-10575-8_27</a>","apa":"Bloem, R., Chatterjee, K., &#38; Jobstmann, B. (2018). Graph games and reactive synthesis. In T. A. Henzinger, E. M. Clarke, H. Veith, &#38; R. Bloem (Eds.), <i>Handbook of Model Checking</i> (1st ed., pp. 921–962). Springer. <a href=\"https://doi.org/10.1007/978-3-319-10575-8_27\">https://doi.org/10.1007/978-3-319-10575-8_27</a>","mla":"Bloem, Roderick, et al. “Graph Games and Reactive Synthesis.” <i>Handbook of Model Checking</i>, edited by Thomas A Henzinger et al., 1st ed., Springer, 2018, pp. 921–62, doi:<a href=\"https://doi.org/10.1007/978-3-319-10575-8_27\">10.1007/978-3-319-10575-8_27</a>.","ieee":"R. Bloem, K. Chatterjee, and B. Jobstmann, “Graph games and reactive synthesis,” in <i>Handbook of Model Checking</i>, 1st ed., T. A. Henzinger, E. M. Clarke, H. Veith, and R. Bloem, Eds. Springer, 2018, pp. 921–962.","short":"R. Bloem, K. Chatterjee, B. Jobstmann, in:, T.A. Henzinger, E.M. Clarke, H. Veith, R. Bloem (Eds.), Handbook of Model Checking, 1st ed., Springer, 2018, pp. 921–962.","ista":"Bloem R, Chatterjee K, Jobstmann B. 2018.Graph games and reactive synthesis. In: Handbook of Model Checking. , 921–962."},"publist_id":"7995","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-319-10575-8_27","publisher":"Springer","type":"book_chapter","oa_version":"None","department":[{"_id":"KrCh"}],"publication_status":"published","_id":"59","date_updated":"2021-01-12T08:05:10Z","title":"Graph games and reactive synthesis","date_published":"2018-05-19T00:00:00Z","month":"05","publication":"Handbook of Model Checking","status":"public","page":"921 - 962","author":[{"full_name":"Bloem, Roderick","last_name":"Bloem","first_name":"Roderick"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Jobstmann, Barbara","first_name":"Barbara","last_name":"Jobstmann"}],"date_created":"2018-12-11T11:44:24Z","day":"19","language":[{"iso":"eng"}],"year":"2018","abstract":[{"lang":"eng","text":"Graph-based games are an important tool in computer science. They have applications in synthesis, verification, refinement, and far beyond. We review graphbased games with objectives on infinite plays. We give definitions and algorithms to solve the games and to give a winning strategy. The objectives we consider are mostly Boolean, but we also look at quantitative graph-based games and their objectives. Synthesis aims to turn temporal logic specifications into correct reactive systems. We explain the reduction of synthesis to graph-based games (or equivalently tree automata) using synthesis of LTL specifications as an example. We treat the classical approach that uses determinization of parity automata and more modern approaches."}],"edition":"1"},{"oa":1,"title":"Keynote: The first-order logic of signals","publication_status":"published","_id":"5959","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Formalizing properties of systems with continuous dynamics is a challenging task. In this paper, we propose a formal framework for specifying and monitoring rich temporal properties of real-valued signals. We introduce signal first-order logic (SFO) as a specification language that combines first-order logic with linear-real arithmetic and unary function symbols interpreted as piecewise-linear signals. We first show that while the satisfiability problem for SFO is undecidable, its membership and monitoring problems are decidable. We develop an offline monitoring procedure for SFO that has polynomial complexity in the size of the input trace and the specification, for a fixed number of quantifiers and function symbols. We show that the algorithm has computation time linear in the size of the input trace for the important fragment of bounded-response specifications interpreted over input traces with finite variability. We can use our results to extend signal temporal logic with first-order quantifiers over time and value parameters, while preserving its efficient monitoring. We finally demonstrate the practical appeal of our logic through a case study in the micro-electronics domain."}],"year":"2018","conference":{"start_date":"2018-09-30","location":"Turin, Italy","name":"EMSOFT: Embedded Software","end_date":"2018-10-05"},"publication_identifier":{"isbn":["9781538655603"]},"external_id":{"isi":["000492828500005"]},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems"}],"publisher":"IEEE","page":"1-10","status":"public","publication":"2018 International Conference on Embedded Software","date_published":"2018-09-30T00:00:00Z","month":"09","ddc":["000"],"date_updated":"2025-07-10T11:53:06Z","has_accepted_license":"1","department":[{"_id":"ToHe"}],"type":"conference","file_date_updated":"2020-07-14T12:47:13Z","date_created":"2019-02-13T09:19:28Z","language":[{"iso":"eng"}],"day":"30","author":[{"full_name":"Bakhirkin, Alexey","first_name":"Alexey","last_name":"Bakhirkin"},{"orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere"},{"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":"Nickovicl, Deian","last_name":"Nickovicl","first_name":"Deian"}],"isi":1,"article_processing_charge":"No","file":[{"content_type":"application/pdf","file_size":338006,"file_id":"7839","date_updated":"2020-07-14T12:47:13Z","creator":"dernst","checksum":"234a33ad9055b3458fcdda6af251b33a","file_name":"2018_EMSOFT_Bakhirkin.pdf","access_level":"open_access","date_created":"2020-05-14T16:01:29Z","relation":"main_file"}],"scopus_import":"1","doi":"10.1109/emsoft.2018.8537203","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","citation":{"ama":"Bakhirkin A, Ferrere T, Henzinger TA, Nickovicl D. Keynote: The first-order logic of signals. In: <i>2018 International Conference on Embedded Software</i>. IEEE; 2018:1-10. doi:<a href=\"https://doi.org/10.1109/emsoft.2018.8537203\">10.1109/emsoft.2018.8537203</a>","apa":"Bakhirkin, A., Ferrere, T., Henzinger, T. A., &#38; Nickovicl, D. (2018). Keynote: The first-order logic of signals. In <i>2018 International Conference on Embedded Software</i> (pp. 1–10). Turin, Italy: IEEE. <a href=\"https://doi.org/10.1109/emsoft.2018.8537203\">https://doi.org/10.1109/emsoft.2018.8537203</a>","mla":"Bakhirkin, Alexey, et al. “Keynote: The First-Order Logic of Signals.” <i>2018 International Conference on Embedded Software</i>, IEEE, 2018, pp. 1–10, doi:<a href=\"https://doi.org/10.1109/emsoft.2018.8537203\">10.1109/emsoft.2018.8537203</a>.","chicago":"Bakhirkin, Alexey, Thomas Ferrere, Thomas A Henzinger, and Deian Nickovicl. “Keynote: The First-Order Logic of Signals.” In <i>2018 International Conference on Embedded Software</i>, 1–10. IEEE, 2018. <a href=\"https://doi.org/10.1109/emsoft.2018.8537203\">https://doi.org/10.1109/emsoft.2018.8537203</a>.","short":"A. Bakhirkin, T. Ferrere, T.A. Henzinger, D. Nickovicl, in:, 2018 International Conference on Embedded Software, IEEE, 2018, pp. 1–10.","ista":"Bakhirkin A, Ferrere T, Henzinger TA, Nickovicl D. 2018. Keynote: The first-order logic of signals. 2018 International Conference on Embedded Software. EMSOFT: Embedded Software, 1–10.","ieee":"A. Bakhirkin, T. Ferrere, T. A. Henzinger, and D. Nickovicl, “Keynote: The first-order logic of signals,” in <i>2018 International Conference on Embedded Software</i>, Turin, Italy, 2018, pp. 1–10."}},{"arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.01341"}],"year":"2018","abstract":[{"lang":"eng","text":"In this paper we present a reliable method to verify the existence of loops along the uncertain trajectory of a robot, based on proprioceptive measurements only, within a bounded-error context. The loop closure detection is one of the key points in simultaneous localization and mapping (SLAM) methods, especially in homogeneous environments with difficult scenes recognitions. The proposed approach is generic and could be coupled with conventional SLAM algorithms to reliably reduce their computing burden, thus improving the localization and mapping processes in the most challenging environments such as unexplored underwater extents. To prove that a robot performed a loop whatever the uncertainties in its evolution, we employ the notion of topological degree that originates in the field of differential topology. We show that a verification tool based on the topological degree is an optimal method for proving robot loops. This is demonstrated both on datasets from real missions involving autonomous underwater vehicles and by a mathematical discussion."}],"oa_version":"Preprint","_id":"5960","publication_status":"published","title":"Proving the existence of loops in robot trajectories","intvolume":"        37","oa":1,"publisher":"SAGE Publications","external_id":{"isi":["000456881100004"],"arxiv":["1712.01341"]},"publication_identifier":{"eissn":["1741-3176"],"issn":["0278-3649"]},"author":[{"last_name":"Rohou","first_name":"Simon","full_name":"Rohou, Simon"},{"id":"473294AE-F248-11E8-B48F-1D18A9856A87","last_name":"Franek","first_name":"Peter","full_name":"Franek, Peter","orcid":"0000-0001-8878-8397"},{"full_name":"Aubry, Clément","first_name":"Clément","last_name":"Aubry"},{"full_name":"Jaulin, Luc","first_name":"Luc","last_name":"Jaulin"}],"day":"24","date_created":"2019-02-13T09:36:20Z","language":[{"iso":"eng"}],"type":"journal_article","issue":"12","department":[{"_id":"UlWa"}],"date_updated":"2023-09-19T10:41:59Z","date_published":"2018-10-24T00:00:00Z","month":"10","publication":"The International Journal of Robotics Research","status":"public","page":"1500-1516","quality_controlled":"1","citation":{"short":"S. Rohou, P. Franek, C. Aubry, L. Jaulin, The International Journal of Robotics Research 37 (2018) 1500–1516.","ista":"Rohou S, Franek P, Aubry C, Jaulin L. 2018. Proving the existence of loops in robot trajectories. The International Journal of Robotics Research. 37(12), 1500–1516.","ieee":"S. Rohou, P. Franek, C. Aubry, and L. Jaulin, “Proving the existence of loops in robot trajectories,” <i>The International Journal of Robotics Research</i>, vol. 37, no. 12. SAGE Publications, pp. 1500–1516, 2018.","apa":"Rohou, S., Franek, P., Aubry, C., &#38; Jaulin, L. (2018). Proving the existence of loops in robot trajectories. <i>The International Journal of Robotics Research</i>. SAGE Publications. <a href=\"https://doi.org/10.1177/0278364918808367\">https://doi.org/10.1177/0278364918808367</a>","ama":"Rohou S, Franek P, Aubry C, Jaulin L. Proving the existence of loops in robot trajectories. <i>The International Journal of Robotics Research</i>. 2018;37(12):1500-1516. doi:<a href=\"https://doi.org/10.1177/0278364918808367\">10.1177/0278364918808367</a>","mla":"Rohou, Simon, et al. “Proving the Existence of Loops in Robot Trajectories.” <i>The International Journal of Robotics Research</i>, vol. 37, no. 12, SAGE Publications, 2018, pp. 1500–16, doi:<a href=\"https://doi.org/10.1177/0278364918808367\">10.1177/0278364918808367</a>.","chicago":"Rohou, Simon, Peter Franek, Clément Aubry, and Luc Jaulin. “Proving the Existence of Loops in Robot Trajectories.” <i>The International Journal of Robotics Research</i>. SAGE Publications, 2018. <a href=\"https://doi.org/10.1177/0278364918808367\">https://doi.org/10.1177/0278364918808367</a>."},"volume":37,"doi":"10.1177/0278364918808367","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","article_processing_charge":"No","isi":1}]