[{"external_id":{"isi":["000440484800002"]},"day":"30","date_published":"2018-07-30T00:00:00Z","oa_version":"Published Version","author":[{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Roux","full_name":"Roux, Camille","first_name":"Camille"},{"full_name":"Gagnaire, Pierre","first_name":"Pierre","last_name":"Gagnaire"},{"last_name":"Romiguier","full_name":"Romiguier, Jonathan","first_name":"Jonathan"},{"last_name":"Faivre","full_name":"Faivre, Nicolas","first_name":"Nicolas"},{"first_name":"John","full_name":"Welch, John","last_name":"Welch"},{"last_name":"Bierne","full_name":"Bierne, Nicolas","first_name":"Nicolas"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","doi":"10.7717/peerj.5198","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:44:50Z","volume":2018,"year":"2018","has_accepted_license":"1","oa":1,"title":"The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies","article_processing_charge":"No","date_updated":"2023-10-17T12:25:28Z","_id":"139","abstract":[{"lang":"eng","text":"Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymousmutations computed either fromexome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the jSFS, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e., periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding jSFS, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed."}],"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"language":[{"iso":"eng"}],"publist_id":"7784","publisher":"PeerJ","publication":"PeerJ","scopus_import":"1","file_date_updated":"2020-07-14T12:44:48Z","file":[{"file_id":"5739","creator":"dernst","access_level":"open_access","content_type":"application/pdf","checksum":"7d55ae22598a1c70759cd671600cff53","file_name":"2018_PeerJ_Fraisse.pdf","date_updated":"2020-07-14T12:44:48Z","file_size":1480792,"date_created":"2018-12-18T09:42:11Z","relation":"main_file"}],"quality_controlled":"1","citation":{"mla":"Fraisse, Christelle, et al. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” <i>PeerJ</i>, vol. 2018, no. 7, 30083438, PeerJ, 2018, doi:<a href=\"https://doi.org/10.7717/peerj.5198\">10.7717/peerj.5198</a>.","short":"C. Fraisse, C. Roux, P. Gagnaire, J. Romiguier, N. Faivre, J. Welch, N. Bierne, PeerJ 2018 (2018).","ieee":"C. Fraisse <i>et al.</i>, “The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies,” <i>PeerJ</i>, vol. 2018, no. 7. PeerJ, 2018.","ista":"Fraisse C, Roux C, Gagnaire P, Romiguier J, Faivre N, Welch J, Bierne N. 2018. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018(7), 30083438.","chicago":"Fraisse, Christelle, Camille Roux, Pierre Gagnaire, Jonathan Romiguier, Nicolas Faivre, John Welch, and Nicolas Bierne. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” <i>PeerJ</i>. PeerJ, 2018. <a href=\"https://doi.org/10.7717/peerj.5198\">https://doi.org/10.7717/peerj.5198</a>.","apa":"Fraisse, C., Roux, C., Gagnaire, P., Romiguier, J., Faivre, N., Welch, J., &#38; Bierne, N. (2018). The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. <i>PeerJ</i>. PeerJ. <a href=\"https://doi.org/10.7717/peerj.5198\">https://doi.org/10.7717/peerj.5198</a>","ama":"Fraisse C, Roux C, Gagnaire P, et al. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. <i>PeerJ</i>. 2018;2018(7). doi:<a href=\"https://doi.org/10.7717/peerj.5198\">10.7717/peerj.5198</a>"},"publication_status":"published","intvolume":"      2018","article_number":"30083438","isi":1,"month":"07","issue":"7","ddc":["576"],"type":"journal_article"},{"article_type":"original","publication_status":"published","quality_controlled":"1","citation":{"ieee":"S. Hille, M. Akhmanova, M. Glanc, A. J. Johnson, and J. Friml, “Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation,” <i>International Journal of Molecular Sciences</i>, vol. 19, no. 11. MDPI, 2018.","ista":"Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. 2018. Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. 19(11).","mla":"Hille, Sander, et al. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” <i>International Journal of Molecular Sciences</i>, vol. 19, no. 11, MDPI, 2018, doi:<a href=\"https://doi.org/10.3390/ijms19113566\">10.3390/ijms19113566</a>.","short":"S. Hille, M. Akhmanova, M. Glanc, A.J. Johnson, J. Friml, International Journal of Molecular Sciences 19 (2018).","ama":"Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. <i>International Journal of Molecular Sciences</i>. 2018;19(11). doi:<a href=\"https://doi.org/10.3390/ijms19113566\">10.3390/ijms19113566</a>","chicago":"Hille, Sander, Maria Akhmanova, Matous Glanc, Alexander J Johnson, and Jiří Friml. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” <i>International Journal of Molecular Sciences</i>. MDPI, 2018. <a href=\"https://doi.org/10.3390/ijms19113566\">https://doi.org/10.3390/ijms19113566</a>.","apa":"Hille, S., Akhmanova, M., Glanc, M., Johnson, A. J., &#38; Friml, J. (2018). Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms19113566\">https://doi.org/10.3390/ijms19113566</a>"},"publisher":"MDPI","publication":"International Journal of Molecular Sciences","scopus_import":"1","file_date_updated":"2020-07-14T12:44:50Z","file":[{"date_created":"2018-12-17T16:04:11Z","file_size":2200593,"date_updated":"2020-07-14T12:44:50Z","file_name":"2018_IJMS_Hille.pdf","relation":"main_file","file_id":"5719","checksum":"e4b59c2599b0ca26ebf5b8434bcde94a","content_type":"application/pdf","access_level":"open_access","creator":"dernst"}],"abstract":[{"lang":"eng","text":"The intercellular transport of auxin is driven by PIN-formed (PIN) auxin efflux carriers. PINs are localized at the plasma membrane (PM) and on constitutively recycling endomembrane vesicles. Therefore, PINs can mediate auxin transport either by direct translocation across the PM or by pumping auxin into secretory vesicles (SVs), leading to its secretory release upon fusion with the PM. Which of these two mechanisms dominates is a matter of debate. Here, we addressed the issue with a mathematical modeling approach. We demonstrate that the efficiency of secretory transport depends on SV size, half-life of PINs on the PM, pH, exocytosis frequency and PIN density. 3D structured illumination microscopy (SIM) was used to determine PIN density on the PM. Combining this data with published values of the other parameters, we show that the transport activity of PINs in SVs would have to be at least 1000× greater than on the PM in order to produce a comparable macroscopic auxin transport. If both transport mechanisms operated simultaneously and PINs were equally active on SVs and PM, the contribution of secretion to the total auxin flux would be negligible. In conclusion, while secretory vesicle-mediated transport of auxin is an intriguing and theoretically possible model, it is unlikely to be a major mechanism of auxin transport inplanta."}],"department":[{"_id":"DaSi"},{"_id":"JiFr"}],"publist_id":"8042","language":[{"iso":"eng"}],"ddc":["580"],"type":"journal_article","ec_funded":1,"issue":"11","intvolume":"        19","isi":1,"month":"11","doi":"10.3390/ijms19113566","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:44:09Z","volume":19,"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"first_name":"Sander","full_name":"Hille, Sander","last_name":"Hille"},{"id":"3425EC26-F248-11E8-B48F-1D18A9856A87","last_name":"Akhmanova","first_name":"Maria","full_name":"Akhmanova, Maria","orcid":"0000-0003-1522-3162"},{"last_name":"Glanc","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","first_name":"Matous","full_name":"Glanc, Matous"},{"orcid":"0000-0002-2739-8843","first_name":"Alexander J","full_name":"Johnson, Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Friml, Jirí","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"status":"public","day":"12","date_published":"2018-11-12T00:00:00Z","external_id":{"isi":["000451528500282"]},"date_updated":"2023-09-18T08:09:32Z","_id":"14","article_processing_charge":"No","title":"Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation","oa":1,"publication_identifier":{"eissn":["1422-0067"]},"year":"2018","project":[{"call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF"}],"acknowledgement":"European Research Council (ERC): 742985 to Jiri Friml; M.A. was supported by the Austrian Science Fund (FWF) (M2379-B28); AJ was supported by the Austria Science Fund (FWF): I03630 to Jiri Friml.","has_accepted_license":"1"},{"publication_identifier":{"issn":["03029743"]},"oa":1,"has_accepted_license":"1","project":[{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","call_identifier":"FWF","grant_number":"S11402-N23"}],"year":"2018","related_material":{"record":[{"id":"6894","status":"public","relation":"dissertation_contains"}]},"conference":{"end_date":"2018-07-17","start_date":"2018-07-14","name":"CAV: Computer Aided Verification","location":"Oxford, United Kingdom"},"_id":"140","date_updated":"2023-09-19T09:30:43Z","article_processing_charge":"No","title":"Space-time interpolants","date_published":"2018-07-18T00:00:00Z","day":"18","external_id":{"isi":["000491481600025"]},"volume":10981,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:44:50Z","doi":"10.1007/978-3-319-96145-3_25","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"full_name":"Frehse, Goran","first_name":"Goran","last_name":"Frehse"},{"orcid":"0000-0001-8180-0904","first_name":"Mirco","full_name":"Giacobbe, Mirco","last_name":"Giacobbe","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"}],"status":"public","oa_version":"Published Version","page":"468 - 486","month":"07","isi":1,"pubrep_id":"1010","intvolume":"     10981","type":"conference","ddc":["005"],"scopus_import":"1","file_date_updated":"2020-07-14T12:44:50Z","file":[{"relation":"main_file","date_created":"2018-12-12T10:17:53Z","file_size":563710,"file_name":"IST-2018-1010-v1+1_space-time_interpolants.pdf","date_updated":"2020-07-14T12:44:50Z","content_type":"application/pdf","checksum":"6dca832f575d6b3f0ea9dff56f579142","creator":"system","access_level":"open_access","file_id":"5310"}],"publisher":"Springer","language":[{"iso":"eng"}],"publist_id":"7783","department":[{"_id":"ToHe"}],"abstract":[{"lang":"eng","text":"Reachability analysis is difficult for hybrid automata with affine differential equations, because the reach set needs to be approximated. Promising abstraction techniques usually employ interval methods or template polyhedra. Interval methods account for dense time and guarantee soundness, and there are interval-based tools that overapproximate affine flowpipes. But interval methods impose bounded and rigid shapes, which make refinement expensive and fixpoint detection difficult. Template polyhedra, on the other hand, can be adapted flexibly and can be unbounded, but sound template refinement for unbounded reachability analysis has been implemented only for systems with piecewise constant dynamics. We capitalize on the advantages of both techniques, combining interval arithmetic and template polyhedra, using the former to abstract time and the latter to abstract space. During a CEGAR loop, whenever a spurious error trajectory is found, we compute additional space constraints and split time intervals, and use these space-time interpolants to eliminate the counterexample. Space-time interpolation offers a lazy, flexible framework for increasing precision while guaranteeing soundness, both for error avoidance and fixpoint detection. To the best of out knowledge, this is the first abstraction refinement scheme for the reachability analysis over unbounded and dense time of affine hybrid systems, which is both sound and automatic. We demonstrate the effectiveness of our algorithm with several benchmark examples, which cannot be handled by other tools."}],"publication_status":"published","citation":{"chicago":"Frehse, Goran, Mirco Giacobbe, and Thomas A Henzinger. “Space-Time Interpolants,” 10981:468–86. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_25\">https://doi.org/10.1007/978-3-319-96145-3_25</a>.","apa":"Frehse, G., Giacobbe, M., &#38; Henzinger, T. A. (2018). Space-time interpolants (Vol. 10981, pp. 468–486). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_25\">https://doi.org/10.1007/978-3-319-96145-3_25</a>","ama":"Frehse G, Giacobbe M, Henzinger TA. Space-time interpolants. In: Vol 10981. Springer; 2018:468-486. doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_25\">10.1007/978-3-319-96145-3_25</a>","short":"G. Frehse, M. Giacobbe, T.A. Henzinger, in:, Springer, 2018, pp. 468–486.","mla":"Frehse, Goran, et al. <i>Space-Time Interpolants</i>. Vol. 10981, Springer, 2018, pp. 468–86, doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_25\">10.1007/978-3-319-96145-3_25</a>.","ieee":"G. Frehse, M. Giacobbe, and T. A. Henzinger, “Space-time interpolants,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 468–486.","ista":"Frehse G, Giacobbe M, Henzinger TA. 2018. Space-time interpolants. CAV: Computer Aided Verification, LNCS, vol. 10981, 468–486."},"alternative_title":["LNCS"],"quality_controlled":"1"},{"oa_version":"Published Version","status":"public","author":[{"full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","last_name":"Baykusheva"},{"last_name":"Wörner","full_name":"Wörner, Hans Jakob","first_name":"Hans Jakob"}],"extern":"1","doi":"10.1103/physrevx.8.031060","date_created":"2023-08-10T06:34:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":8,"day":"01","date_published":"2018-07-01T00:00:00Z","article_processing_charge":"No","title":"Chiral discrimination through bielliptical high-harmonic spectroscopy","date_updated":"2023-08-22T07:42:07Z","_id":"14003","year":"2018","oa":1,"publication_identifier":{"eissn":["2160-3308"]},"quality_controlled":"1","citation":{"mla":"Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Chiral Discrimination through Bielliptical High-Harmonic Spectroscopy.” <i>Physical Review X</i>, vol. 8, no. 3, 031060, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/physrevx.8.031060\">10.1103/physrevx.8.031060</a>.","short":"D.R. Baykusheva, H.J. Wörner, Physical Review X 8 (2018).","ieee":"D. R. Baykusheva and H. J. Wörner, “Chiral discrimination through bielliptical high-harmonic spectroscopy,” <i>Physical Review X</i>, vol. 8, no. 3. American Physical Society, 2018.","ista":"Baykusheva DR, Wörner HJ. 2018. Chiral discrimination through bielliptical high-harmonic spectroscopy. Physical Review X. 8(3), 031060.","apa":"Baykusheva, D. R., &#38; Wörner, H. J. (2018). Chiral discrimination through bielliptical high-harmonic spectroscopy. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevx.8.031060\">https://doi.org/10.1103/physrevx.8.031060</a>","chicago":"Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Chiral Discrimination through Bielliptical High-Harmonic Spectroscopy.” <i>Physical Review X</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/physrevx.8.031060\">https://doi.org/10.1103/physrevx.8.031060</a>.","ama":"Baykusheva DR, Wörner HJ. Chiral discrimination through bielliptical high-harmonic spectroscopy. <i>Physical Review X</i>. 2018;8(3). doi:<a href=\"https://doi.org/10.1103/physrevx.8.031060\">10.1103/physrevx.8.031060</a>"},"keyword":["General Physics and Astronomy"],"article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"Molecular chirality plays an essential role in most biochemical processes. The observation and quantification of chirality-sensitive signals, however, remains extremely challenging, especially on ultrafast timescales and in dilute media. Here, we describe the experimental realization of an all-optical and ultrafast scheme for detecting chiral dynamics in molecules. This technique is based on high-harmonic generation by a combination of two-color counterrotating femtosecond laser pulses with polarization states tunable from linear to circular. We demonstrate two different implementations of chiral-sensitive high-harmonic spectroscopy on an ensemble of randomly oriented methyloxirane molecules in the gas phase. Using two elliptically polarized fields, we observe that the ellipticities maximizing the harmonic signal reach up to \r\n4.4\r\n±\r\n0.2\r\n%\r\n (at 17.6 eV). Using two circularly polarized fields, we observe circular dichroisms ranging up to \r\n13\r\n±\r\n6\r\n%\r\n (28.3–33.1 eV). Our theoretical analysis confirms that the observed chiral response originates from subfemtosecond electron dynamics driven by the magnetic component of the driving laser field. This assignment is supported by the experimental observation of a strong intensity dependence of the chiral effects and its agreement with theory. We moreover report and explain a pronounced variation of the signal strength and dichroism with the driving-field ellipticities and harmonic orders. Finally, we demonstrate the sensitivity of the experimental observables to the shape of the electron hole. This technique for chiral discrimination will yield femtosecond temporal resolution when integrated in a pump-probe scheme and subfemtosecond resolution on chiral charge migration in a self-probing scheme."}],"language":[{"iso":"eng"}],"publisher":"American Physical Society","publication":"Physical Review X","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1103/PhysRevX.8.031060"}],"type":"journal_article","intvolume":"         8","article_number":"031060","month":"07","issue":"3"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530"},{"last_name":"Loitzenbauer","first_name":"Veronika","full_name":"Loitzenbauer, Veronika"},{"first_name":"Simin","full_name":"Oraee, Simin","last_name":"Oraee"},{"id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","last_name":"Toman","first_name":"Viktor","full_name":"Toman, Viktor","orcid":"0000-0001-9036-063X"}],"status":"public","oa_version":"Published Version","volume":10982,"date_created":"2018-12-11T11:44:51Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1007/978-3-319-96142-2_13","external_id":{"isi":["000491469700013"]},"date_published":"2018-07-18T00:00:00Z","day":"18","title":"Symbolic algorithms for graphs and Markov decision processes with fairness objectives","article_processing_charge":"No","related_material":{"record":[{"status":"public","id":"10199","relation":"dissertation_contains"}]},"conference":{"end_date":"2018-07-17","start_date":"2018-07-14","name":"CAV: Computer Aided Verification","location":"Oxford, United Kingdom"},"_id":"141","date_updated":"2025-07-14T09:10:15Z","has_accepted_license":"1","year":"2018","project":[{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"Acknowledgements. K. C. and M. H. are partially supported by the Vienna Science and Technology Fund (WWTF) grant ICT15-003. K. C. is partially supported by the Austrian Science Fund (FWF): S11407-N23 (RiSE/SHiNE), and an ERC Start Grant (279307: Graph Games). V. T. is partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie Grant Agreement No. 665385.","oa":1,"citation":{"mla":"Chatterjee, Krishnendu, et al. <i>Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives</i>. Vol. 10982, Springer, 2018, pp. 178–97, doi:<a href=\"https://doi.org/10.1007/978-3-319-96142-2_13\">10.1007/978-3-319-96142-2_13</a>.","short":"K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, S. Oraee, V. Toman, in:, Springer, 2018, pp. 178–197.","ista":"Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. 2018. Symbolic algorithms for graphs and Markov decision processes with fairness objectives. CAV: Computer Aided Verification, LNCS, vol. 10982, 178–197.","ieee":"K. Chatterjee, M. H. Henzinger, V. Loitzenbauer, S. Oraee, and V. Toman, “Symbolic algorithms for graphs and Markov decision processes with fairness objectives,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10982, pp. 178–197.","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Veronika Loitzenbauer, Simin Oraee, and Viktor Toman. “Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives,” 10982:178–97. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-96142-2_13\">https://doi.org/10.1007/978-3-319-96142-2_13</a>.","apa":"Chatterjee, K., Henzinger, M. H., Loitzenbauer, V., Oraee, S., &#38; Toman, V. (2018). Symbolic algorithms for graphs and Markov decision processes with fairness objectives (Vol. 10982, pp. 178–197). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-319-96142-2_13\">https://doi.org/10.1007/978-3-319-96142-2_13</a>","ama":"Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. Symbolic algorithms for graphs and Markov decision processes with fairness objectives. In: Vol 10982. Springer; 2018:178-197. doi:<a href=\"https://doi.org/10.1007/978-3-319-96142-2_13\">10.1007/978-3-319-96142-2_13</a>"},"quality_controlled":"1","alternative_title":["LNCS"],"publication_status":"published","publist_id":"7782","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"abstract":[{"text":"Given a model and a specification, the fundamental model-checking problem asks for algorithmic verification of whether the model satisfies the specification. We consider graphs and Markov decision processes (MDPs), which are fundamental models for reactive systems. One of the very basic specifications that arise in verification of reactive systems is the strong fairness (aka Streett) objective. Given different types of requests and corresponding grants, the objective requires that for each type, if the request event happens infinitely often, then the corresponding grant event must also happen infinitely often. All ω -regular objectives can be expressed as Streett objectives and hence they are canonical in verification. To handle the state-space explosion, symbolic algorithms are required that operate on a succinct implicit representation of the system rather than explicitly accessing the system. While explicit algorithms for graphs and MDPs with Streett objectives have been widely studied, there has been no improvement of the basic symbolic algorithms. The worst-case numbers of symbolic steps required for the basic symbolic algorithms are as follows: quadratic for graphs and cubic for MDPs. In this work we present the first sub-quadratic symbolic algorithm for graphs with Streett objectives, and our algorithm is sub-quadratic even for MDPs. Based on our algorithmic insights we present an implementation of the new symbolic approach and show that it improves the existing approach on several academic benchmark examples.","lang":"eng"}],"file_date_updated":"2020-07-14T12:44:53Z","file":[{"relation":"main_file","date_created":"2018-12-18T08:52:38Z","file_size":675606,"date_updated":"2020-07-14T12:44:53Z","file_name":"2018_LNCS_Chatterjee.pdf","checksum":"1a6ffa4febe8bb8ac28be3adb3eafebc","content_type":"application/pdf","access_level":"open_access","creator":"dernst","file_id":"5737"}],"scopus_import":"1","publisher":"Springer","type":"conference","ddc":["000"],"isi":1,"month":"07","intvolume":"     10982","ec_funded":1,"page":"178-197"},{"date_created":"2023-08-22T14:12:48Z","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","author":[{"first_name":"Vincent","full_name":"Fortuin, Vincent","last_name":"Fortuin"},{"last_name":"Hüser","first_name":"Matthias","full_name":"Hüser, Matthias"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","full_name":"Locatello, Francesco","first_name":"Francesco","orcid":"0000-0002-4850-0683"},{"first_name":"Heiko","full_name":"Strathmann, Heiko","last_name":"Strathmann"},{"last_name":"Rätsch","first_name":"Gunnar","full_name":"Rätsch, Gunnar"}],"status":"public","quality_controlled":"1","extern":"1","citation":{"ista":"Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. 2018. SOM-VAE: Interpretable discrete representation learning on time series. International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","ieee":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, and G. Rätsch, “SOM-VAE: Interpretable discrete representation learning on time series,” in <i>International Conference on Learning Representations</i>, New Orleans, LA, United States, 2018.","short":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, G. Rätsch, in:, International Conference on Learning Representations, 2018.","mla":"Fortuin, Vincent, et al. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” <i>International Conference on Learning Representations</i>, 2018.","ama":"Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. SOM-VAE: Interpretable discrete representation learning on time series. In: <i>International Conference on Learning Representations</i>. ; 2018.","apa":"Fortuin, V., Hüser, M., Locatello, F., Strathmann, H., &#38; Rätsch, G. (2018). SOM-VAE: Interpretable discrete representation learning on time series. In <i>International Conference on Learning Representations</i>. New Orleans, LA, United States.","chicago":"Fortuin, Vincent, Matthias Hüser, Francesco Locatello, Heiko Strathmann, and Gunnar Rätsch. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” In <i>International Conference on Learning Representations</i>, 2018."},"day":"06","date_published":"2018-06-06T00:00:00Z","publication":"International Conference on Learning Representations","abstract":[{"lang":"eng","text":"High-dimensional time series are common in many domains. Since human\r\ncognition is not optimized to work well in high-dimensional spaces, these areas\r\ncould benefit from interpretable low-dimensional representations. However, most\r\nrepresentation learning algorithms for time series data are difficult to\r\ninterpret. This is due to non-intuitive mappings from data features to salient\r\nproperties of the representation and non-smoothness over time. To address this\r\nproblem, we propose a new representation learning framework building on ideas\r\nfrom interpretable discrete dimensionality reduction and deep generative\r\nmodeling. This framework allows us to learn discrete representations of time\r\nseries, which give rise to smooth and interpretable embeddings with superior\r\nclustering performance. We introduce a new way to overcome the\r\nnon-differentiability in discrete representation learning and present a\r\ngradient-based version of the traditional self-organizing map algorithm that is\r\nmore performant than the original. Furthermore, to allow for a probabilistic\r\ninterpretation of our method, we integrate a Markov model in the representation\r\nspace. This model uncovers the temporal transition structure, improves\r\nclustering performance even further and provides additional explanatory\r\ninsights as well as a natural representation of uncertainty. We evaluate our\r\nmodel in terms of clustering performance and interpretability on static\r\n(Fashion-)MNIST data, a time series of linearly interpolated (Fashion-)MNIST\r\nimages, a chaotic Lorenz attractor system with two macro states, as well as on\r\na challenging real world medical time series application on the eICU data set.\r\nOur learned representations compare favorably with competitor methods and\r\nfacilitate downstream tasks on the real world data."}],"external_id":{"arxiv":["1806.02199"]},"department":[{"_id":"FrLo"}],"language":[{"iso":"eng"}],"date_updated":"2023-09-13T06:35:12Z","_id":"14198","type":"conference","conference":{"start_date":"2019-05-06","end_date":"2019-05-09","location":"New Orleans, LA, United States","name":"ICLR: International Conference on Learning Representations"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.02199"}],"arxiv":1,"title":"SOM-VAE: Interpretable discrete representation learning on time series","article_processing_charge":"No","oa":1,"year":"2018","month":"06"},{"conference":{"location":"Oxford, United Kingdom","name":"CAV: Computer Aided Verification","end_date":"2018-07-17","start_date":"2018-07-14"},"_id":"142","date_updated":"2023-09-15T12:12:08Z","title":"Reachable set over-approximation for nonlinear systems using piecewise barrier tubes","article_processing_charge":"No","oa":1,"has_accepted_license":"1","year":"2018","project":[{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211"}],"acknowledgement":"Austrian Science Fund FWF: S11402-N23, S11405-N23, Z211-N32","volume":10981,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:44:51Z","doi":"10.1007/978-3-319-96145-3_24","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","author":[{"orcid":"0000-0002-3066-6941","first_name":"Hui","full_name":"Kong, Hui","last_name":"Kong","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ezio","full_name":"Bartocci, Ezio","last_name":"Bartocci"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A"}],"oa_version":"Published Version","date_published":"2018-07-18T00:00:00Z","day":"18","external_id":{"isi":["000491481600024"]},"type":"conference","ddc":["000"],"page":"449 - 467","month":"07","isi":1,"intvolume":"     10981","publication_status":"published","citation":{"mla":"Kong, Hui, et al. <i>Reachable Set Over-Approximation for Nonlinear Systems Using Piecewise Barrier Tubes</i>. Vol. 10981, Springer, 2018, pp. 449–67, doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_24\">10.1007/978-3-319-96145-3_24</a>.","short":"H. Kong, E. Bartocci, T.A. Henzinger, in:, Springer, 2018, pp. 449–467.","ieee":"H. Kong, E. Bartocci, and T. A. Henzinger, “Reachable set over-approximation for nonlinear systems using piecewise barrier tubes,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 449–467.","ista":"Kong H, Bartocci E, Henzinger TA. 2018. Reachable set over-approximation for nonlinear systems using piecewise barrier tubes. CAV: Computer Aided Verification, LNCS, vol. 10981, 449–467.","apa":"Kong, H., Bartocci, E., &#38; Henzinger, T. A. (2018). Reachable set over-approximation for nonlinear systems using piecewise barrier tubes (Vol. 10981, pp. 449–467). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_24\">https://doi.org/10.1007/978-3-319-96145-3_24</a>","chicago":"Kong, Hui, Ezio Bartocci, and Thomas A Henzinger. “Reachable Set Over-Approximation for Nonlinear Systems Using Piecewise Barrier Tubes,” 10981:449–67. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_24\">https://doi.org/10.1007/978-3-319-96145-3_24</a>.","ama":"Kong H, Bartocci E, Henzinger TA. Reachable set over-approximation for nonlinear systems using piecewise barrier tubes. In: Vol 10981. Springer; 2018:449-467. doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_24\">10.1007/978-3-319-96145-3_24</a>"},"alternative_title":["LNCS"],"quality_controlled":"1","file_date_updated":"2020-07-14T12:44:53Z","file":[{"creator":"dernst","access_level":"open_access","content_type":"application/pdf","checksum":"fd95e8026deacef3dc752a733bb9355f","file_id":"5718","relation":"main_file","file_name":"2018_LNCS_Kong.pdf","date_updated":"2020-07-14T12:44:53Z","file_size":5591566,"date_created":"2018-12-17T15:57:06Z"}],"scopus_import":"1","publisher":"Springer","department":[{"_id":"ToHe"}],"publist_id":"7781","language":[{"iso":"eng"}],"abstract":[{"text":"We address the problem of analyzing the reachable set of a polynomial nonlinear continuous system by over-approximating the flowpipe of its dynamics. The common approach to tackle this problem is to perform a numerical integration over a given time horizon based on Taylor expansion and interval arithmetic. However, this method results to be very conservative when there is a large difference in speed between trajectories as time progresses. In this paper, we propose to use combinations of barrier functions, which we call piecewise barrier tube (PBT), to over-approximate flowpipe. The basic idea of PBT is that for each segment of a flowpipe, a coarse box which is big enough to contain the segment is constructed using sampled simulation and then in the box we compute by linear programming a set of barrier functions (called barrier tube or BT for short) which work together to form a tube surrounding the flowpipe. The benefit of using PBT is that (1) BT is independent of time and hence can avoid being stretched and deformed by time; and (2) a small number of BTs can form a tight over-approximation for the flowpipe, which means that the computation required to decide whether the BTs intersect the unsafe set can be reduced significantly. We implemented a prototype called PBTS in C++. Experiments on some benchmark systems show that our approach is effective.","lang":"eng"}]},{"day":"15","date_published":"2018-04-15T00:00:00Z","external_id":{"arxiv":["1708.01733"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-08-22T14:15:20Z","volume":84,"oa_version":"Preprint","status":"public","author":[{"orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"full_name":"Khanna, Rajiv","first_name":"Rajiv","last_name":"Khanna"},{"first_name":"Joydeep","full_name":"Ghosh, Joydeep","last_name":"Ghosh"},{"full_name":"Rätsch, Gunnar","first_name":"Gunnar","last_name":"Rätsch"}],"extern":"1","oa":1,"year":"2018","date_updated":"2023-09-13T07:52:40Z","_id":"14201","conference":{"start_date":"2018-04-09","end_date":"2018-04-11","name":"AISTATS: Conference on Artificial Intelligence and Statistics","location":"Playa Blanca, Lanzarote"},"title":"Boosting variational inference: An optimization perspective","article_processing_charge":"No","publisher":"ML Research Press","scopus_import":"1","publication":"Proceedings of the 21st International Conference on Artificial Intelligence and Statistics","abstract":[{"lang":"eng","text":"Variational inference is a popular technique to approximate a possibly\r\nintractable Bayesian posterior with a more tractable one. Recently, boosting\r\nvariational inference has been proposed as a new paradigm to approximate the\r\nposterior by a mixture of densities by greedily adding components to the\r\nmixture. However, as is the case with many other variational inference\r\nalgorithms, its theoretical properties have not been studied. In the present\r\nwork, we study the convergence properties of this approach from a modern\r\noptimization viewpoint by establishing connections to the classic Frank-Wolfe\r\nalgorithm. Our analyses yields novel theoretical insights regarding the\r\nsufficient conditions for convergence, explicit rates, and algorithmic\r\nsimplifications. Since a lot of focus in previous works for variational\r\ninference has been on tractability, our work is especially important as a much\r\nneeded attempt to bridge the gap between probabilistic models and their\r\ncorresponding theoretical properties."}],"department":[{"_id":"FrLo"}],"language":[{"iso":"eng"}],"publication_status":"published","quality_controlled":"1","alternative_title":["PMLR"],"citation":{"short":"F. Locatello, R. Khanna, J. Ghosh, G. Rätsch, in:, Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, ML Research Press, 2018, pp. 464–472.","mla":"Locatello, Francesco, et al. “Boosting Variational Inference: An Optimization Perspective.” <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i>, vol. 84, ML Research Press, 2018, pp. 464–72.","ista":"Locatello F, Khanna R, Ghosh J, Rätsch G. 2018. Boosting variational inference: An optimization perspective. Proceedings of the 21st International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics, PMLR, vol. 84, 464–472.","ieee":"F. Locatello, R. Khanna, J. Ghosh, and G. Rätsch, “Boosting variational inference: An optimization perspective,” in <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i>, Playa Blanca, Lanzarote, 2018, vol. 84, pp. 464–472.","apa":"Locatello, F., Khanna, R., Ghosh, J., &#38; Rätsch, G. (2018). Boosting variational inference: An optimization perspective. In <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i> (Vol. 84, pp. 464–472). Playa Blanca, Lanzarote: ML Research Press.","chicago":"Locatello, Francesco, Rajiv Khanna, Joydeep Ghosh, and Gunnar Rätsch. “Boosting Variational Inference: An Optimization Perspective.” In <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i>, 84:464–72. ML Research Press, 2018.","ama":"Locatello F, Khanna R, Ghosh J, Rätsch G. Boosting variational inference: An optimization perspective. In: <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i>. Vol 84. ML Research Press; 2018:464-472."},"page":"464-472","intvolume":"        84","month":"04","type":"conference","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.01733"}],"arxiv":1},{"main_file_link":[{"url":"https://arxiv.org/abs/1806.02185","open_access":"1"}],"arxiv":1,"type":"conference","intvolume":"        31","month":"06","quality_controlled":"1","citation":{"ama":"Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. Boosting black box variational inference. In: <i>Advances in Neural Information Processing Systems</i>. Vol 31. Neural Information Processing Systems Foundation; 2018.","chicago":"Locatello, Francesco, Gideon Dresdner, Rajiv Khanna, Isabel Valera, and Gunnar Rätsch. “Boosting Black Box Variational Inference.” In <i>Advances in Neural Information Processing Systems</i>, Vol. 31. Neural Information Processing Systems Foundation, 2018.","apa":"Locatello, F., Dresdner, G., Khanna, R., Valera, I., &#38; Rätsch, G. (2018). Boosting black box variational inference. In <i>Advances in Neural Information Processing Systems</i> (Vol. 31). Montreal, Canada: Neural Information Processing Systems Foundation.","ieee":"F. Locatello, G. Dresdner, R. Khanna, I. Valera, and G. Rätsch, “Boosting black box variational inference,” in <i>Advances in Neural Information Processing Systems</i>, Montreal, Canada, 2018, vol. 31.","ista":"Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. 2018. Boosting black box variational inference. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 31.","short":"F. Locatello, G. Dresdner, R. Khanna, I. Valera, G. Rätsch, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2018.","mla":"Locatello, Francesco, et al. “Boosting Black Box Variational Inference.” <i>Advances in Neural Information Processing Systems</i>, vol. 31, Neural Information Processing Systems Foundation, 2018."},"publication_status":"published","abstract":[{"lang":"eng","text":"Approximating a probability density in a tractable manner is a central task\r\nin Bayesian statistics. Variational Inference (VI) is a popular technique that\r\nachieves tractability by choosing a relatively simple variational family.\r\nBorrowing ideas from the classic boosting framework, recent approaches attempt\r\nto \\emph{boost} VI by replacing the selection of a single density with a\r\ngreedily constructed mixture of densities. In order to guarantee convergence,\r\nprevious works impose stringent assumptions that require significant effort for\r\npractitioners. Specifically, they require a custom implementation of the greedy\r\nstep (called the LMO) for every probabilistic model with respect to an\r\nunnatural variational family of truncated distributions. Our work fixes these\r\nissues with novel theoretical and algorithmic insights. On the theoretical\r\nside, we show that boosting VI satisfies a relaxed smoothness assumption which\r\nis sufficient for the convergence of the functional Frank-Wolfe (FW) algorithm.\r\nFurthermore, we rephrase the LMO problem and propose to maximize the Residual\r\nELBO (RELBO) which replaces the standard ELBO optimization in VI. These\r\ntheoretical enhancements allow for black box implementation of the boosting\r\nsubroutine. Finally, we present a stopping criterion drawn from the duality gap\r\nin the classic FW analyses and exhaustive experiments to illustrate the\r\nusefulness of our theoretical and algorithmic contributions."}],"department":[{"_id":"FrLo"}],"language":[{"iso":"eng"}],"publisher":"Neural Information Processing Systems Foundation","publication":"Advances in Neural Information Processing Systems","scopus_import":"1","title":"Boosting black box variational inference","article_processing_charge":"No","date_updated":"2023-09-13T07:38:24Z","_id":"14202","conference":{"name":"NeurIPS: Neural Information Processing Systems","location":"Montreal, Canada","end_date":"2018-12-08","start_date":"2018-12-03"},"year":"2018","oa":1,"publication_identifier":{"eissn":["1049-5258"],"isbn":["9781510884472"]},"oa_version":"Preprint","author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"full_name":"Dresdner, Gideon","first_name":"Gideon","last_name":"Dresdner"},{"first_name":"Rajiv","full_name":"Khanna, Rajiv","last_name":"Khanna"},{"last_name":"Valera","first_name":"Isabel","full_name":"Valera, Isabel"},{"last_name":"Rätsch","first_name":"Gunnar","full_name":"Rätsch, Gunnar"}],"status":"public","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-08-22T14:15:40Z","volume":31,"external_id":{"arxiv":["1806.02185"]},"day":"06","date_published":"2018-06-06T00:00:00Z"},{"arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.08544"}],"type":"conference","intvolume":"        80","month":"07","page":"5727-5736","citation":{"short":"A. Yurtsever, O. Fercoq, F. Locatello, V. Cevher, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 5727–5736.","mla":"Yurtsever, Alp, et al. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” <i>Proceedings of the 35th International Conference on Machine Learning</i>, vol. 80, ML Research Press, 2018, pp. 5727–36.","ieee":"A. Yurtsever, O. Fercoq, F. Locatello, and V. Cevher, “A conditional gradient framework for composite convex minimization with applications to semidefinite programming,” in <i>Proceedings of the 35th International Conference on Machine Learning</i>, Stockholm, Sweden, 2018, vol. 80, pp. 5727–5736.","ista":"Yurtsever A, Fercoq O, Locatello F, Cevher V. 2018. A conditional gradient framework for composite convex minimization with applications to semidefinite programming. Proceedings of the 35th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 80, 5727–5736.","apa":"Yurtsever, A., Fercoq, O., Locatello, F., &#38; Cevher, V. (2018). A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In <i>Proceedings of the 35th International Conference on Machine Learning</i> (Vol. 80, pp. 5727–5736). Stockholm, Sweden: ML Research Press.","chicago":"Yurtsever, Alp, Olivier Fercoq, Francesco Locatello, and Volkan Cevher. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” In <i>Proceedings of the 35th International Conference on Machine Learning</i>, 80:5727–36. ML Research Press, 2018.","ama":"Yurtsever A, Fercoq O, Locatello F, Cevher V. A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In: <i>Proceedings of the 35th International Conference on Machine Learning</i>. Vol 80. ML Research Press; 2018:5727-5736."},"alternative_title":["PMLR"],"quality_controlled":"1","publication_status":"published","abstract":[{"text":"We propose a conditional gradient framework for a composite convex minimization template with broad applications. Our approach combines smoothing and homotopy techniques under the CGM framework, and provably achieves the optimal O(1/k−−√) convergence rate. We demonstrate that the same rate holds if the linear subproblems are solved approximately with additive or multiplicative error. In contrast with the relevant work, we are able to characterize the convergence when the non-smooth term is an indicator function. Specific applications of our framework include the non-smooth minimization, semidefinite programming, and minimization with linear inclusion constraints over a compact domain. Numerical evidence demonstrates the benefits of our framework.","lang":"eng"}],"department":[{"_id":"FrLo"}],"language":[{"iso":"eng"}],"publisher":"ML Research Press","publication":"Proceedings of the 35th International Conference on Machine Learning","article_processing_charge":"No","title":"A conditional gradient framework for composite convex minimization with applications to semidefinite programming","_id":"14203","date_updated":"2023-09-13T08:13:39Z","conference":{"name":"ICML: International Conference on Machine Learning","location":"Stockholm, Sweden","end_date":"2018-07-15","start_date":"2018-07-10"},"year":"2018","oa":1,"oa_version":"Preprint","extern":"1","author":[{"full_name":"Yurtsever, Alp","first_name":"Alp","last_name":"Yurtsever"},{"full_name":"Fercoq, Olivier","first_name":"Olivier","last_name":"Fercoq"},{"first_name":"Francesco","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello"},{"last_name":"Cevher","first_name":"Volkan","full_name":"Cevher, Volkan"}],"status":"public","volume":80,"date_created":"2023-08-22T14:16:01Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1804.08544"]},"day":"15","date_published":"2018-07-15T00:00:00Z"},{"publication_status":"published","quality_controlled":"1","alternative_title":["PMLR"],"citation":{"mla":"Locatello, Francesco, et al. “On Matching Pursuit and Coordinate Descent.” <i>Proceedings of the 35th International Conference on Machine Learning</i>, vol. 80, ML Research Press, 2018, pp. 3198–207.","short":"F. Locatello, A. Raj, S.P. Karimireddy, G. Rätsch, B. Schölkopf, S.U. Stich, M. Jaggi, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 3198–3207.","ista":"Locatello F, Raj A, Karimireddy SP, Rätsch G, Schölkopf B, Stich SU, Jaggi M. 2018. On matching pursuit and coordinate descent. Proceedings of the 35th International Conference on Machine Learning. , PMLR, vol. 80, 3198–3207.","ieee":"F. Locatello <i>et al.</i>, “On matching pursuit and coordinate descent,” in <i>Proceedings of the 35th International Conference on Machine Learning</i>, 2018, vol. 80, pp. 3198–3207.","chicago":"Locatello, Francesco, Anant Raj, Sai Praneeth Karimireddy, Gunnar Rätsch, Bernhard Schölkopf, Sebastian U. Stich, and Martin Jaggi. “On Matching Pursuit and Coordinate Descent.” In <i>Proceedings of the 35th International Conference on Machine Learning</i>, 80:3198–3207. ML Research Press, 2018.","apa":"Locatello, F., Raj, A., Karimireddy, S. P., Rätsch, G., Schölkopf, B., Stich, S. U., &#38; Jaggi, M. (2018). On matching pursuit and coordinate descent. In <i>Proceedings of the 35th International Conference on Machine Learning</i> (Vol. 80, pp. 3198–3207). ML Research Press.","ama":"Locatello F, Raj A, Karimireddy SP, et al. On matching pursuit and coordinate descent. In: <i>Proceedings of the 35th International Conference on Machine Learning</i>. Vol 80. ML Research Press; 2018:3198-3207."},"publisher":"ML Research Press","scopus_import":"1","publication":"Proceedings of the 35th International Conference on Machine Learning","abstract":[{"lang":"eng","text":"Two popular examples of first-order optimization methods over linear spaces are coordinate descent and matching pursuit algorithms, with their randomized variants. While the former targets the optimization by moving along coordinates, the latter considers a generalized notion of directions. Exploiting the connection between the two algorithms, we present a unified analysis of both, providing affine invariant sublinear O(1/t) rates on smooth objectives and linear convergence on strongly convex objectives. As a byproduct of our affine invariant analysis of matching pursuit, our rates for steepest coordinate descent are the tightest known. Furthermore, we show the first accelerated convergence rate O(1/t2) for matching pursuit and steepest coordinate descent on convex objectives."}],"language":[{"iso":"eng"}],"department":[{"_id":"FrLo"}],"type":"conference","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.09539"}],"arxiv":1,"page":"3198-3207","intvolume":"        80","month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-08-22T14:16:25Z","volume":80,"oa_version":"Preprint","author":[{"last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","first_name":"Francesco","full_name":"Locatello, Francesco"},{"full_name":"Raj, Anant","first_name":"Anant","last_name":"Raj"},{"last_name":"Karimireddy","full_name":"Karimireddy, Sai Praneeth","first_name":"Sai Praneeth"},{"full_name":"Rätsch, Gunnar","first_name":"Gunnar","last_name":"Rätsch"},{"first_name":"Bernhard","full_name":"Schölkopf, Bernhard","last_name":"Schölkopf"},{"last_name":"Stich","full_name":"Stich, Sebastian U.","first_name":"Sebastian U."},{"first_name":"Martin","full_name":"Jaggi, Martin","last_name":"Jaggi"}],"status":"public","extern":"1","day":"01","date_published":"2018-07-01T00:00:00Z","external_id":{"arxiv":["1803.09539"]},"date_updated":"2023-09-13T08:19:05Z","_id":"14204","article_processing_charge":"No","title":"On matching pursuit and coordinate descent","oa":1,"year":"2018"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-08-22T14:25:34Z","publication_status":"published","oa_version":"Preprint","status":"public","quality_controlled":"1","author":[{"full_name":"Locatello, Francesco","first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello"},{"first_name":"Damien","full_name":"Vincent, Damien","last_name":"Vincent"},{"last_name":"Tolstikhin","first_name":"Ilya","full_name":"Tolstikhin, Ilya"},{"last_name":"Ratsch","full_name":"Ratsch, Gunnar","first_name":"Gunnar"},{"last_name":"Gelly","full_name":"Gelly, Sylvain","first_name":"Sylvain"},{"first_name":"Bernhard","full_name":"Scholkopf, Bernhard","last_name":"Scholkopf"}],"extern":"1","citation":{"ieee":"F. Locatello, D. Vincent, I. Tolstikhin, G. Ratsch, S. Gelly, and B. Scholkopf, “Clustering meets implicit generative models,” in <i>6th International Conference on Learning Representations</i>, Vancouver, Canada, 2018.","ista":"Locatello F, Vincent D, Tolstikhin I, Ratsch G, Gelly S, Scholkopf B. 2018. Clustering meets implicit generative models. 6th International Conference on Learning Representations. International Conference on Machine Learning.","mla":"Locatello, Francesco, et al. “Clustering Meets Implicit Generative Models.” <i>6th International Conference on Learning Representations</i>, 2018.","short":"F. Locatello, D. Vincent, I. Tolstikhin, G. Ratsch, S. Gelly, B. Scholkopf, in:, 6th International Conference on Learning Representations, 2018.","ama":"Locatello F, Vincent D, Tolstikhin I, Ratsch G, Gelly S, Scholkopf B. Clustering meets implicit generative models. In: <i>6th International Conference on Learning Representations</i>. ; 2018.","apa":"Locatello, F., Vincent, D., Tolstikhin, I., Ratsch, G., Gelly, S., &#38; Scholkopf, B. (2018). Clustering meets implicit generative models. In <i>6th International Conference on Learning Representations</i>. Vancouver, Canada.","chicago":"Locatello, Francesco, Damien Vincent, Ilya Tolstikhin, Gunnar Ratsch, Sylvain Gelly, and Bernhard Scholkopf. “Clustering Meets Implicit Generative Models.” In <i>6th International Conference on Learning Representations</i>, 2018."},"day":"01","date_published":"2018-05-01T00:00:00Z","scopus_import":"1","publication":"6th International Conference on Learning Representations","abstract":[{"lang":"eng","text":"Clustering is a cornerstone of unsupervised learning which can be thought as disentangling multiple generative mechanisms underlying the data. In this paper we introduce an algorithmic framework to train mixtures of implicit generative models which we particularize for variational autoencoders. Relying on an additional set of discriminators, we propose a competitive procedure in which the models only need to approximate the portion of the data distribution from which they can produce realistic samples. As a byproduct, each model is simpler to train, and a clustering interpretation arises naturally from the partitioning of the training points among the models. We empirically show that our approach splits the training distribution in a reasonable way and increases the quality of the generated samples."}],"external_id":{"arxiv":["1804.11130"]},"department":[{"_id":"FrLo"}],"language":[{"iso":"eng"}],"date_updated":"2023-09-13T09:08:24Z","_id":"14224","type":"conference","conference":{"end_date":"2018-05-03","start_date":"2018-04-30","name":"International Conference on Machine Learning","location":"Vancouver, Canada"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.11130"}],"arxiv":1,"article_processing_charge":"No","title":"Clustering meets implicit generative models","oa":1,"year":"2018","month":"05"},{"oa_version":"Published Version","status":"public","author":[{"full_name":"Bräuning, Bastian","first_name":"Bastian","last_name":"Bräuning"},{"first_name":"Eva","full_name":"Bertosin, Eva","last_name":"Bertosin"},{"full_name":"Praetorius, Florian M","first_name":"Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","last_name":"Praetorius"},{"first_name":"Christian","full_name":"Ihling, Christian","last_name":"Ihling"},{"full_name":"Schatt, Alexandra","first_name":"Alexandra","last_name":"Schatt"},{"last_name":"Adler","full_name":"Adler, Agnes","first_name":"Agnes"},{"last_name":"Richter","first_name":"Klaus","full_name":"Richter, Klaus"},{"first_name":"Andrea","full_name":"Sinz, Andrea","last_name":"Sinz"},{"first_name":"Hendrik","full_name":"Dietz, Hendrik","last_name":"Dietz"},{"last_name":"Groll","full_name":"Groll, Michael","first_name":"Michael"}],"extern":"1","doi":"10.1038/s41467-018-04139-2","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-09-06T12:07:33Z","volume":9,"external_id":{"pmid":["29728606"]},"day":"04","date_published":"2018-05-04T00:00:00Z","article_processing_charge":"No","title":"Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB","date_updated":"2023-11-07T11:46:12Z","_id":"14284","year":"2018","oa":1,"publication_identifier":{"issn":["2041-1723"]},"quality_controlled":"1","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"citation":{"apa":"Bräuning, B., Bertosin, E., Praetorius, F. M., Ihling, C., Schatt, A., Adler, A., … Groll, M. (2018). Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-018-04139-2\">https://doi.org/10.1038/s41467-018-04139-2</a>","chicago":"Bräuning, Bastian, Eva Bertosin, Florian M Praetorius, Christian Ihling, Alexandra Schatt, Agnes Adler, Klaus Richter, Andrea Sinz, Hendrik Dietz, and Michael Groll. “Structure and Mechanism of the Two-Component α-Helical Pore-Forming Toxin YaxAB.” <i>Nature Communications</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41467-018-04139-2\">https://doi.org/10.1038/s41467-018-04139-2</a>.","ama":"Bräuning B, Bertosin E, Praetorius FM, et al. Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB. <i>Nature Communications</i>. 2018;9. doi:<a href=\"https://doi.org/10.1038/s41467-018-04139-2\">10.1038/s41467-018-04139-2</a>","short":"B. Bräuning, E. Bertosin, F.M. Praetorius, C. Ihling, A. Schatt, A. Adler, K. Richter, A. Sinz, H. Dietz, M. Groll, Nature Communications 9 (2018).","mla":"Bräuning, Bastian, et al. “Structure and Mechanism of the Two-Component α-Helical Pore-Forming Toxin YaxAB.” <i>Nature Communications</i>, vol. 9, 1806, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-018-04139-2\">10.1038/s41467-018-04139-2</a>.","ieee":"B. Bräuning <i>et al.</i>, “Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB,” <i>Nature Communications</i>, vol. 9. Springer Nature, 2018.","ista":"Bräuning B, Bertosin E, Praetorius FM, Ihling C, Schatt A, Adler A, Richter K, Sinz A, Dietz H, Groll M. 2018. Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB. Nature Communications. 9, 1806."},"article_type":"original","publication_status":"published","abstract":[{"text":"Pore-forming toxins (PFT) are virulence factors that transform from soluble to membrane-bound states. The Yersinia YaxAB system represents a family of binary α-PFTs with orthologues in human, insect, and plant pathogens, with unknown structures. YaxAB was shown to be cytotoxic and likely involved in pathogenesis, though the molecular basis for its two-component lytic mechanism remains elusive. Here, we present crystal structures of YaxA and YaxB, together with a cryo-electron microscopy map of the YaxAB complex. Our structures reveal a pore predominantly composed of decamers of YaxA–YaxB heterodimers. Both subunits bear membrane-active moieties, but only YaxA is capable of binding to membranes by itself. YaxB can subsequently be recruited to membrane-associated YaxA and induced to present its lytic transmembrane helices. Pore formation can progress by further oligomerization of YaxA–YaxB dimers. Our results allow for a comparison between pore assemblies belonging to the wider ClyA-like family of α-PFTs, highlighting diverse pore architectures.","lang":"eng"}],"language":[{"iso":"eng"}],"publisher":"Springer Nature","publication":"Nature Communications","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-018-04139-2"}],"type":"journal_article","intvolume":"         9","article_number":"1806","month":"05"},{"month":"07","isi":1,"ec_funded":1,"page":"185 - 194","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.10985"}],"type":"conference","publist_id":"7780","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"abstract":[{"text":"Vector Addition Systems with States (VASS) provide a well-known and fundamental model for the analysis of concurrent processes, parameterized systems, and are also used as abstract models of programs in resource bound analysis. In this paper we study the problem of obtaining asymptotic bounds on the termination time of a given VASS. In particular, we focus on the practically important case of obtaining polynomial bounds on termination time. Our main contributions are as follows: First, we present a polynomial-time algorithm for deciding whether a given VASS has a linear asymptotic complexity. We also show that if the complexity of a VASS is not linear, it is at least quadratic. Second, we classify VASS according to quantitative properties of their cycles. We show that certain singularities in these properties are the key reason for non-polynomial asymptotic complexity of VASS. In absence of singularities, we show that the asymptotic complexity is always polynomial and of the form Θ(nk), for some integer k d, where d is the dimension of the VASS. We present a polynomial-time algorithm computing the optimal k. For general VASS, the same algorithm, which is based on a complete technique for the construction of ranking functions in VASS, produces a valid lower bound, i.e., a k such that the termination complexity is (nk). Our results are based on new insights into the geometry of VASS dynamics, which hold the potential for further applicability to VASS analysis.","lang":"eng"}],"scopus_import":"1","publisher":"IEEE","citation":{"ama":"Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. Efficient algorithms for asymptotic bounds on termination time in VASS. In: Vol F138033. IEEE; 2018:185-194. doi:<a href=\"https://doi.org/10.1145/3209108.3209191\">10.1145/3209108.3209191</a>","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Antonín Kučera, Petr Novotný, Dominik Velan, and Florian Zuleger. “Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS,” F138033:185–94. IEEE, 2018. <a href=\"https://doi.org/10.1145/3209108.3209191\">https://doi.org/10.1145/3209108.3209191</a>.","apa":"Brázdil, T., Chatterjee, K., Kučera, A., Novotný, P., Velan, D., &#38; Zuleger, F. (2018). Efficient algorithms for asymptotic bounds on termination time in VASS (Vol. F138033, pp. 185–194). Presented at the LICS: Logic in Computer Science, Oxford, United Kingdom: IEEE. <a href=\"https://doi.org/10.1145/3209108.3209191\">https://doi.org/10.1145/3209108.3209191</a>","ista":"Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. 2018. Efficient algorithms for asymptotic bounds on termination time in VASS. LICS: Logic in Computer Science, ACM/IEEE Symposium on Logic in Computer Science, vol. F138033, 185–194.","ieee":"T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, and F. Zuleger, “Efficient algorithms for asymptotic bounds on termination time in VASS,” presented at the LICS: Logic in Computer Science, Oxford, United Kingdom, 2018, vol. F138033, pp. 185–194.","mla":"Brázdil, Tomáš, et al. <i>Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS</i>. Vol. F138033, IEEE, 2018, pp. 185–94, doi:<a href=\"https://doi.org/10.1145/3209108.3209191\">10.1145/3209108.3209191</a>.","short":"T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, F. Zuleger, in:, IEEE, 2018, pp. 185–194."},"quality_controlled":"1","alternative_title":["ACM/IEEE Symposium on Logic in Computer Science"],"publication_status":"published","year":"2018","project":[{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"}],"publication_identifier":{"isbn":["978-1-4503-5583-4"]},"oa":1,"article_processing_charge":"No","title":"Efficient algorithms for asymptotic bounds on termination time in VASS","conference":{"location":"Oxford, United Kingdom","name":"LICS: Logic in Computer Science","end_date":"2018-07-12","start_date":"2018-07-09"},"_id":"143","date_updated":"2025-06-02T08:53:48Z","external_id":{"isi":["000545262800020"]},"date_published":"2018-07-09T00:00:00Z","day":"09","author":[{"last_name":"Brázdil","first_name":"Tomáš","full_name":"Brázdil, Tomáš"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"first_name":"Antonín","full_name":"Kučera, Antonín","last_name":"Kučera"},{"last_name":"Novotny","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotny, Petr","first_name":"Petr"},{"first_name":"Dominik","full_name":"Velan, Dominik","last_name":"Velan"},{"last_name":"Zuleger","first_name":"Florian","full_name":"Zuleger, Florian"}],"status":"public","oa_version":"Preprint","volume":"F138033","date_created":"2018-12-11T11:44:51Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1145/3209108.3209191"},{"title":"Genetically encoding the spatial arrangement of DNA and proteins in self-assembling nanostructures","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://mediatum.ub.tum.de/1398662"}],"type":"dissertation","_id":"14306","date_updated":"2023-11-07T11:43:38Z","month":"01","year":"2018","degree_awarded":"PhD","oa":1,"citation":{"short":"F.M. Praetorius, Genetically Encoding the Spatial Arrangement of DNA and Proteins in Self-Assembling Nanostructures, Technische Universität München, 2018.","mla":"Praetorius, Florian M. <i>Genetically Encoding the Spatial Arrangement of DNA and Proteins in Self-Assembling Nanostructures</i>. Technische Universität München, 2018.","ieee":"F. M. Praetorius, “Genetically encoding the spatial arrangement of DNA and proteins in self-assembling nanostructures,” Technische Universität München, 2018.","ista":"Praetorius FM. 2018. Genetically encoding the spatial arrangement of DNA and proteins in self-assembling nanostructures. Technische Universität München.","chicago":"Praetorius, Florian M. “Genetically Encoding the Spatial Arrangement of DNA and Proteins in Self-Assembling Nanostructures.” Technische Universität München, 2018.","apa":"Praetorius, F. M. (2018). <i>Genetically encoding the spatial arrangement of DNA and proteins in self-assembling nanostructures</i>. Technische Universität München.","ama":"Praetorius FM. Genetically encoding the spatial arrangement of DNA and proteins in self-assembling nanostructures. 2018."},"extern":"1","status":"public","author":[{"id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","last_name":"Praetorius","full_name":"Praetorius, Florian M","first_name":"Florian M"}],"oa_version":"Published Version","supervisor":[{"full_name":"Dietz, Hendrik","first_name":"Hendrik","last_name":"Dietz"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-09-06T13:11:22Z","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Function and activity of biomolecules often depend on their spatial arrangement. The method introduced here allows genetically encoding the spatial arrangement of proteins and DNA. The approach relies on staple proteins that fold double-stranded DNA into user-defined shapes. This thesis describes the development of staple proteins based on the DNA recognition of TAL effectors and presents experimentally derived rules for designing a variety of self-assembling nanoscale shapes featuring structural motifs such as curvature, vertices, corners, and multilayer helix packing. "}],"date_published":"2018-01-16T00:00:00Z","day":"16","publisher":"Technische Universität München"},{"language":[{"iso":"eng"}],"department":[{"_id":"FrLo"}],"external_id":{"arxiv":["1804.11130"]},"abstract":[{"lang":"eng","text":"A common assumption in causal modeling posits that the data is generated by a\r\nset of independent mechanisms, and algorithms should aim to recover this\r\nstructure. Standard unsupervised learning, however, is often concerned with\r\ntraining a single model to capture the overall distribution or aspects thereof.\r\nInspired by clustering approaches, we consider mixtures of implicit generative\r\nmodels that ``disentangle'' the independent generative mechanisms underlying\r\nthe data. Relying on an additional set of discriminators, we propose a\r\ncompetitive training procedure in which the models only need to capture the\r\nportion of the data distribution from which they can produce realistic samples.\r\nAs a by-product, each model is simpler and faster to train. We empirically show\r\nthat our approach splits the training distribution in a sensible way and\r\nincreases the quality of the generated samples."}],"publication":"arXiv","date_published":"2018-04-30T00:00:00Z","day":"30","citation":{"ista":"Locatello F, Vincent D, Tolstikhin I, Rätsch G, Gelly S, Schölkopf B. Competitive training of mixtures of independent deep generative models. arXiv, 1804.11130.","ieee":"F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, and B. Schölkopf, “Competitive training of mixtures of independent deep generative models,” <i>arXiv</i>. .","mla":"Locatello, Francesco, et al. “Competitive Training of Mixtures of Independent Deep Generative Models.” <i>ArXiv</i>, 1804.11130, doi:<a href=\"https://doi.org/10.48550/arXiv.1804.11130\">10.48550/arXiv.1804.11130</a>.","short":"F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, B. Schölkopf, ArXiv (n.d.).","ama":"Locatello F, Vincent D, Tolstikhin I, Rätsch G, Gelly S, Schölkopf B. Competitive training of mixtures of independent deep generative models. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.1804.11130\">10.48550/arXiv.1804.11130</a>","apa":"Locatello, F., Vincent, D., Tolstikhin, I., Rätsch, G., Gelly, S., &#38; Schölkopf, B. (n.d.). Competitive training of mixtures of independent deep generative models. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.1804.11130\">https://doi.org/10.48550/arXiv.1804.11130</a>","chicago":"Locatello, Francesco, Damien Vincent, Ilya Tolstikhin, Gunnar Rätsch, Sylvain Gelly, and Bernhard Schölkopf. “Competitive Training of Mixtures of Independent Deep Generative Models.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.1804.11130\">https://doi.org/10.48550/arXiv.1804.11130</a>."},"extern":"1","author":[{"first_name":"Francesco","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello"},{"last_name":"Vincent","first_name":"Damien","full_name":"Vincent, Damien"},{"first_name":"Ilya","full_name":"Tolstikhin, Ilya","last_name":"Tolstikhin"},{"full_name":"Rätsch, Gunnar","first_name":"Gunnar","last_name":"Rätsch"},{"full_name":"Gelly, Sylvain","first_name":"Sylvain","last_name":"Gelly"},{"full_name":"Schölkopf, Bernhard","first_name":"Bernhard","last_name":"Schölkopf"}],"status":"public","oa_version":"Preprint","publication_status":"submitted","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-09-13T12:20:49Z","doi":"10.48550/arXiv.1804.11130","month":"04","article_number":"1804.11130","year":"2018","oa":1,"article_processing_charge":"No","title":"Competitive training of mixtures of independent deep generative models","arxiv":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1804.11130","open_access":"1"}],"_id":"14327","type":"preprint","date_updated":"2023-09-13T12:23:03Z"},{"article_processing_charge":"No","title":"A theory of register monitors","conference":{"end_date":"2018-07-12","start_date":"2018-07-09","name":"LICS: Logic in Computer Science","location":"Oxford, UK"},"date_updated":"2023-09-08T11:49:13Z","_id":"144","type":"conference","isi":1,"month":"07","year":"2018","page":"394 - 403","quality_controlled":"1","author":[{"first_name":"Thomas","full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"last_name":"Saraç","full_name":"Saraç, Ege","first_name":"Ege"}],"status":"public","alternative_title":["ACM/IEEE Symposium on Logic in Computer Science"],"citation":{"ista":"Ferrere T, Henzinger TA, Saraç E. 2018. A theory of register monitors. LICS: Logic in Computer Science, ACM/IEEE Symposium on Logic in Computer Science, vol. Part F138033, 394–403.","ieee":"T. Ferrere, T. A. Henzinger, and E. Saraç, “A theory of register monitors,” presented at the LICS: Logic in Computer Science, Oxford, UK, 2018, vol. Part F138033, pp. 394–403.","short":"T. Ferrere, T.A. Henzinger, E. Saraç, in:, IEEE, 2018, pp. 394–403.","mla":"Ferrere, Thomas, et al. <i>A Theory of Register Monitors</i>. Vol. Part F138033, IEEE, 2018, pp. 394–403, doi:<a href=\"https://doi.org/10.1145/3209108.3209194\">10.1145/3209108.3209194</a>.","ama":"Ferrere T, Henzinger TA, Saraç E. A theory of register monitors. In: Vol Part F138033. IEEE; 2018:394-403. doi:<a href=\"https://doi.org/10.1145/3209108.3209194\">10.1145/3209108.3209194</a>","apa":"Ferrere, T., Henzinger, T. A., &#38; Saraç, E. (2018). A theory of register monitors (Vol. Part F138033, pp. 394–403). Presented at the LICS: Logic in Computer Science, Oxford, UK: IEEE. <a href=\"https://doi.org/10.1145/3209108.3209194\">https://doi.org/10.1145/3209108.3209194</a>","chicago":"Ferrere, Thomas, Thomas A Henzinger, and Ege Saraç. “A Theory of Register Monitors,” Part F138033:394–403. IEEE, 2018. <a href=\"https://doi.org/10.1145/3209108.3209194\">https://doi.org/10.1145/3209108.3209194</a>."},"oa_version":"None","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:44:52Z","publication_status":"published","volume":"Part F138033","doi":"10.1145/3209108.3209194","external_id":{"isi":["000545262800041"]},"language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"publist_id":"7779","abstract":[{"lang":"eng","text":"The task of a monitor is to watch, at run-time, the execution of a reactive system, and signal the occurrence of a safety violation in the observed sequence of events. While finite-state monitors have been studied extensively, in practice, monitoring software also makes use of unbounded memory. We define a model of automata equipped with integer-valued registers which can execute only a bounded number of instructions between consecutive events, and thus can form the theoretical basis for the study of infinite-state monitors. We classify these register monitors according to the number k of available registers, and the type of register instructions. In stark contrast to the theory of computability for register machines, we prove that for every k 1, monitors with k + 1 counters (with instruction set 〈+1, =〉) are strictly more expressive than monitors with k counters. We also show that adder monitors (with instruction set 〈1, +, =〉) are strictly more expressive than counter monitors, but are complete for monitoring all computable safety -languages for k = 6. Real-time monitors are further required to signal the occurrence of a safety violation as soon as it occurs. The expressiveness hierarchy for counter monitors carries over to real-time monitors. We then show that 2 adders cannot simulate 3 counters in real-time. Finally, we show that real-time adder monitors with inequalities are as expressive as real-time Turing machines."}],"date_published":"2018-07-09T00:00:00Z","scopus_import":"1","day":"09","publisher":"IEEE"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","author":[{"last_name":"Truckenbrodt","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","full_name":"Truckenbrodt, Sven M","first_name":"Sven M"},{"last_name":"Viplav","full_name":"Viplav, Abhiyan","first_name":"Abhiyan"},{"last_name":"Jähne","full_name":"Jähne, Sebsatian","first_name":"Sebsatian"},{"last_name":"Vogts","full_name":"Vogts, Angela","first_name":"Angela"},{"last_name":"Denker","first_name":"Annette","full_name":"Denker, Annette"},{"last_name":"Wildhagen","full_name":"Wildhagen, Hanna","first_name":"Hanna"},{"full_name":"Fornasiero, Eugenio","first_name":"Eugenio","last_name":"Fornasiero"},{"first_name":"Silvio","full_name":"Rizzoli, Silvio","last_name":"Rizzoli"}],"oa_version":"Published Version","date_created":"2018-12-11T11:44:52Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":37,"doi":"10.15252/embj.201798044","pmid":1,"external_id":{"pmid":["29950309"],"isi":["000440416900005"]},"date_published":"2018-08-01T00:00:00Z","day":"01","title":"Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission","article_processing_charge":"No","date_updated":"2023-09-13T09:02:48Z","_id":"145","has_accepted_license":"1","acknowledgement":"We thank Reinhard Jahn for providing a plasmid for YFP-SNAP25. We thank Erwin Neher for help with the development of the mathematical model of the synaptic vesicle life cycle. We thank Martin Meschkat, Andreas Höbartner, Annedore Punge, and Peer Hoopmann for help with the experiments. We thank Burkhard Rammner for providing the illustrations of synaptic vesicle and protein dynamics. We thank Manuel Maidorn, Martin Helm, and Katharina N. Richter for critically reading the manuscript. S.T. was supported by an Excellence Stipend of the Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences (GGNB). E.F.F. is a recipient of long-term fellowships from the European Molecular Biology Organization (ALTF_797-2012) and from the Human Frontier Science Program (HFSP_LT000830/2013). The work was supported by grants to S.O.R. from the European Research Council (ERC-2013-CoG NeuroMolAnatomy) and from the Deutsche Forschungsgemeinschaft (Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, SFB1190/P09, SFB889/A05, and SFB1286/A03, and DFG RI 1967 7/1). The nanoSIMS instrument was funded by the German Federal Ministry of Education and Research (03F0626A).","year":"2018","publication_identifier":{"issn":["0261-4189"]},"oa":1,"quality_controlled":"1","citation":{"mla":"Truckenbrodt, Sven M., et al. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” <i>The EMBO Journal</i>, vol. 37, no. 15, e98044, Wiley, 2018, doi:<a href=\"https://doi.org/10.15252/embj.201798044\">10.15252/embj.201798044</a>.","short":"S.M. Truckenbrodt, A. Viplav, S. Jähne, A. Vogts, A. Denker, H. Wildhagen, E. Fornasiero, S. Rizzoli, The EMBO Journal 37 (2018).","ieee":"S. M. Truckenbrodt <i>et al.</i>, “Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission,” <i>The EMBO Journal</i>, vol. 37, no. 15. Wiley, 2018.","ista":"Truckenbrodt SM, Viplav A, Jähne S, Vogts A, Denker A, Wildhagen H, Fornasiero E, Rizzoli S. 2018. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. 37(15), e98044.","apa":"Truckenbrodt, S. M., Viplav, A., Jähne, S., Vogts, A., Denker, A., Wildhagen, H., … Rizzoli, S. (2018). Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. <i>The EMBO Journal</i>. Wiley. <a href=\"https://doi.org/10.15252/embj.201798044\">https://doi.org/10.15252/embj.201798044</a>","chicago":"Truckenbrodt, Sven M, Abhiyan Viplav, Sebsatian Jähne, Angela Vogts, Annette Denker, Hanna Wildhagen, Eugenio Fornasiero, and Silvio Rizzoli. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” <i>The EMBO Journal</i>. Wiley, 2018. <a href=\"https://doi.org/10.15252/embj.201798044\">https://doi.org/10.15252/embj.201798044</a>.","ama":"Truckenbrodt SM, Viplav A, Jähne S, et al. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. <i>The EMBO Journal</i>. 2018;37(15). doi:<a href=\"https://doi.org/10.15252/embj.201798044\">10.15252/embj.201798044</a>"},"publication_status":"published","article_type":"original","department":[{"_id":"JoDa"}],"language":[{"iso":"eng"}],"publist_id":"7778","abstract":[{"text":"Aged proteins can become hazardous to cellular function, by accumulating molecular damage. This implies that cells should preferentially rely on newly produced ones. We tested this hypothesis in cultured hippocampal neurons, focusing on synaptic transmission. We found that newly synthesized vesicle proteins were incorporated in the actively recycling pool of vesicles responsible for all neurotransmitter release during physiological activity. We observed this for the calcium sensor Synaptotagmin 1, for the neurotransmitter transporter VGAT, and for the fusion protein VAMP2 (Synaptobrevin 2). Metabolic labeling of proteins and visualization by secondary ion mass spectrometry enabled us to query the entire protein makeup of the actively recycling vesicles, which we found to be younger than that of non-recycling vesicles. The young vesicle proteins remained in use for up to ~ 24 h, during which they participated in recycling a few hundred times. They were afterward reluctant to release and were degraded after an additional ~ 24–48 h. We suggest that the recycling pool of synaptic vesicles relies on newly synthesized proteins, while the inactive reserve pool contains older proteins.","lang":"eng"}],"publication":"The EMBO Journal","file_date_updated":"2020-07-14T12:44:56Z","file":[{"content_type":"application/pdf","checksum":"a540feb6c9af6aefc78de531461a8835","creator":"dernst","access_level":"open_access","file_id":"5710","relation":"main_file","date_created":"2018-12-17T14:17:29Z","file_size":2846470,"file_name":"2018_EMBO_Truckenbrodt.pdf","date_updated":"2020-07-14T12:44:56Z"}],"scopus_import":"1","publisher":"Wiley","ddc":["570"],"type":"journal_article","isi":1,"month":"08","intvolume":"        37","article_number":"e98044","issue":"15"},{"intvolume":"         4","isi":1,"month":"07","page":"596 - 604","issue":"8","ddc":["580"],"type":"journal_article","abstract":[{"lang":"eng","text":"The root cap protects the stem cell niche of angiosperm roots from damage. In Arabidopsis, lateral root cap (LRC) cells covering the meristematic zone are regularly lost through programmed cell death, while the outermost layer of the root cap covering the tip is repeatedly sloughed. Efficient coordination with stem cells producing new layers is needed to maintain a constant size of the cap. We present a signalling pair, the peptide IDA-LIKE1 (IDL1) and its receptor HAESA-LIKE2 (HSL2), mediating such communication. Live imaging over several days characterized this process from initial fractures in LRC cell files to full separation of a layer. Enhanced expression of IDL1 in the separating root cap layers resulted in increased frequency of sloughing, balanced with generation of new layers in a HSL2-dependent manner. Transcriptome analyses linked IDL1-HSL2 signalling to the transcription factors BEARSKIN1/2 and genes associated with programmed cell death. Mutations in either IDL1 or HSL2 slowed down cell division, maturation and separation. Thus, IDL1-HSL2 signalling potentiates dynamic regulation of the homeostatic balance between stem cell division and sloughing activity."}],"publist_id":"7777","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"publisher":"Nature Publishing Group","file":[{"relation":"main_file","file_size":226829,"date_created":"2019-11-18T16:24:07Z","file_name":"2018_NaturePlants_Shi.pdf","date_updated":"2020-07-14T12:44:56Z","content_type":"application/pdf","checksum":"da33101c76ee1b2dc5ab28fd2ccba9d0","creator":"dernst","access_level":"open_access","file_id":"7043"}],"file_date_updated":"2020-07-14T12:44:56Z","publication":"Nature Plants","scopus_import":"1","quality_controlled":"1","citation":{"apa":"Shi, C. L., von Wangenheim, D., Herrmann, U., Wildhagen, M., Kulik, I., Kopf, A., … Aalen, R. B. (2018). The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. <i>Nature Plants</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41477-018-0212-z\">https://doi.org/10.1038/s41477-018-0212-z</a>","chicago":"Shi, Chun Lin, Daniel von Wangenheim, Ullrich Herrmann, Mari Wildhagen, Ivan Kulik, Andreas Kopf, Takashi Ishida, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” <i>Nature Plants</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0212-z\">https://doi.org/10.1038/s41477-018-0212-z</a>.","ama":"Shi CL, von Wangenheim D, Herrmann U, et al. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. <i>Nature Plants</i>. 2018;4(8):596-604. doi:<a href=\"https://doi.org/10.1038/s41477-018-0212-z\">10.1038/s41477-018-0212-z</a>","mla":"Shi, Chun Lin, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” <i>Nature Plants</i>, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 596–604, doi:<a href=\"https://doi.org/10.1038/s41477-018-0212-z\">10.1038/s41477-018-0212-z</a>.","short":"C.L. Shi, D. von Wangenheim, U. Herrmann, M. Wildhagen, I. Kulik, A. Kopf, T. Ishida, V. Olsson, M.K. Anker, M. Albert, M.A. Butenko, G. Felix, S. Sawa, M. Claassen, J. Friml, R.B. Aalen, Nature Plants 4 (2018) 596–604.","ieee":"C. L. Shi <i>et al.</i>, “The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling,” <i>Nature Plants</i>, vol. 4, no. 8. Nature Publishing Group, pp. 596–604, 2018.","ista":"Shi CL, von Wangenheim D, Herrmann U, Wildhagen M, Kulik I, Kopf A, Ishida T, Olsson V, Anker MK, Albert M, Butenko MA, Felix G, Sawa S, Claassen M, Friml J, Aalen RB. 2018. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. 4(8), 596–604."},"article_type":"original","publication_status":"published","year":"2018","has_accepted_license":"1","oa":1,"title":"The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling","article_processing_charge":"No","date_updated":"2023-09-19T10:08:45Z","_id":"146","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-process-in-root-development-discovered/"}]},"external_id":{"isi":["000443861300016"],"pmid":["30061750"]},"day":"30","date_published":"2018-07-30T00:00:00Z","oa_version":"Submitted Version","status":"public","author":[{"full_name":"Shi, Chun Lin","first_name":"Chun Lin","last_name":"Shi"},{"first_name":"Daniel","full_name":"Von Wangenheim, Daniel","orcid":"0000-0002-6862-1247","id":"49E91952-F248-11E8-B48F-1D18A9856A87","last_name":"Von Wangenheim"},{"first_name":"Ullrich","full_name":"Herrmann, Ullrich","last_name":"Herrmann"},{"last_name":"Wildhagen","first_name":"Mari","full_name":"Wildhagen, Mari"},{"first_name":"Ivan","full_name":"Kulik, Ivan","last_name":"Kulik","id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB"},{"last_name":"Kopf","first_name":"Andreas","full_name":"Kopf, Andreas"},{"last_name":"Ishida","full_name":"Ishida, Takashi","first_name":"Takashi"},{"last_name":"Olsson","first_name":"Vilde","full_name":"Olsson, Vilde"},{"full_name":"Anker, Mari Kristine","first_name":"Mari Kristine","last_name":"Anker"},{"last_name":"Albert","full_name":"Albert, Markus","first_name":"Markus"},{"first_name":"Melinka A","full_name":"Butenko, Melinka A","last_name":"Butenko"},{"first_name":"Georg","full_name":"Felix, Georg","last_name":"Felix"},{"full_name":"Sawa, Shinichiro","first_name":"Shinichiro","last_name":"Sawa"},{"first_name":"Manfred","full_name":"Claassen, Manfred","last_name":"Claassen"},{"first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"last_name":"Aalen","full_name":"Aalen, Reidunn B","first_name":"Reidunn B"}],"pmid":1,"doi":"10.1038/s41477-018-0212-z","date_created":"2018-12-11T11:44:52Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":4},{"type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1105/tpc.18.00127"}],"issue":"10","ec_funded":1,"page":"2553 - 2572","isi":1,"month":"11","intvolume":"        30","publication_status":"published","article_type":"original","citation":{"apa":"Kania, U., Nodzyński, T., Lu, Q., Hicks, G. R., Nerinckx, W., Mishev, K., … Friml, J. (2018). The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. <i>The Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1105/tpc.18.00127\">https://doi.org/10.1105/tpc.18.00127</a>","chicago":"Kania, Urszula, Tomasz Nodzyński, Qing Lu, Glenn R Hicks, Wim Nerinckx, Kiril Mishev, Francois Peurois, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” <i>The Plant Cell</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1105/tpc.18.00127\">https://doi.org/10.1105/tpc.18.00127</a>.","ama":"Kania U, Nodzyński T, Lu Q, et al. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. <i>The Plant Cell</i>. 2018;30(10):2553-2572. doi:<a href=\"https://doi.org/10.1105/tpc.18.00127\">10.1105/tpc.18.00127</a>","mla":"Kania, Urszula, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” <i>The Plant Cell</i>, vol. 30, no. 10, Oxford University Press, 2018, pp. 2553–72, doi:<a href=\"https://doi.org/10.1105/tpc.18.00127\">10.1105/tpc.18.00127</a>.","short":"U. Kania, T. Nodzyński, Q. Lu, G.R. Hicks, W. Nerinckx, K. Mishev, F. Peurois, J. Cherfils, R.R.M. De, P. Grones, S. Robert, E. Russinova, J. Friml, The Plant Cell 30 (2018) 2553–2572.","ieee":"U. Kania <i>et al.</i>, “The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes,” <i>The Plant Cell</i>, vol. 30, no. 10. Oxford University Press, pp. 2553–2572, 2018.","ista":"Kania U, Nodzyński T, Lu Q, Hicks GR, Nerinckx W, Mishev K, Peurois F, Cherfils J, De RRM, Grones P, Robert S, Russinova E, Friml J. 2018. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. 30(10), 2553–2572."},"quality_controlled":"1","publication":"The Plant Cell","scopus_import":"1","publisher":"Oxford University Press","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"publist_id":"7776","abstract":[{"lang":"eng","text":"The trafficking of subcellular cargos in eukaryotic cells crucially depends on vesicle budding, a process mediated by ARF-GEFs (ADP-ribosylation factor guanine nucleotide exchange factors). In plants, ARF-GEFs play essential roles in endocytosis, vacuolar trafficking, recycling, secretion, and polar trafficking. Moreover, they are important for plant development, mainly through controlling the polar subcellular localization of PIN-FORMED (PIN) transporters of the plant hormone auxin. Here, using a chemical genetics screen in Arabidopsis thaliana, we identified Endosidin 4 (ES4), an inhibitor of eukaryotic ARF-GEFs. ES4 acts similarly to and synergistically with the established ARF-GEF inhibitor Brefeldin A and has broad effects on intracellular trafficking, including endocytosis, exocytosis, and vacuolar targeting. Additionally, Arabidopsis and yeast (Sacharomyces cerevisiae) mutants defective in ARF-GEF show altered sensitivity to ES4. ES4 interferes with the activation-based membrane association of the ARF1 GTPases, but not of their mutant variants that are activated independently of ARF-GEF activity. Biochemical approaches and docking simulations confirmed that ES4 specifically targets the SEC7 domain-containing ARF-GEFs. These observations collectively identify ES4 as a chemical tool enabling the study of ARF-GEF-mediated processes, including ARF-GEF-mediated plant development."}],"_id":"147","date_updated":"2025-05-07T11:12:30Z","title":"The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes","article_processing_charge":"No","publication_identifier":{"issn":["1040-4651"]},"oa":1,"acknowledgement":"We thank Gerd Jürgens, Sandra Richter, and Sheng Yang He for providing antibodies; Maciek Adamowski, Fernando Aniento, Sebastian Bednarek, Nico Callewaert, Matyás Fendrych, Elena Feraru, and Mugurel I. Feraru for helpful suggestions; Siamsa Doyle for critical reading of the manuscript and helpful comments and suggestions; and Stephanie Smith and Martine De Cock for help in editing and language corrections. We acknowledge the core facility Cellular Imaging of CEITEC supported by the Czech-BioImaging large RI project (LM2015062 funded by MEYS CR) for their support with obtaining scientific data presented in this article. Plant Sciences Core Facility of CEITEC Masaryk University is gratefully acknowledged for obtaining part of the scientific data presented in this article. We acknowledge support from the Fondation pour la Recherche Médicale and from the Institut National du Cancer (J.C.). The research leading to these results was funded by the European Research Council under the European Union's 7th Framework Program (FP7/2007-2013)/ERC grant agreement numbers 282300 and 742985 and the Czech Science Foundation GAČR (GA18-26981S; J.F.); Ministry of Education, Youth, and Sports/MEYS of the Czech Republic under the Project CEITEC 2020 (LQ1601; T.N.); the China Science Council for a predoctoral fellowship (Q.L.); a joint research project within the framework of cooperation between the Research Foundation-Flanders and the Bulgarian Academy of Sciences (VS.025.13N; K.M. and E.R.); Vetenskapsrådet and Vinnova (Verket för Innovationssystem; S.R.), Knut och Alice Wallenbergs Stiftelse via “Shapesystem” Grant 2012.0050 (S.R.), Kempe stiftelserna (P.G.), Tryggers CTS410 (P.G.).","year":"2018","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300"},{"call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"volume":30,"date_created":"2018-12-11T11:44:52Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1105/tpc.18.00127","pmid":1,"status":"public","author":[{"first_name":"Urszula","full_name":"Kania, Urszula","last_name":"Kania","id":"4AE5C486-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nodzyński, Tomasz","first_name":"Tomasz","last_name":"Nodzyński"},{"full_name":"Lu, Qing","first_name":"Qing","last_name":"Lu"},{"full_name":"Hicks, Glenn R","first_name":"Glenn R","last_name":"Hicks"},{"full_name":"Nerinckx, Wim","first_name":"Wim","last_name":"Nerinckx"},{"full_name":"Mishev, Kiril","first_name":"Kiril","last_name":"Mishev"},{"last_name":"Peurois","first_name":"Francois","full_name":"Peurois, Francois"},{"full_name":"Cherfils, Jacqueline","first_name":"Jacqueline","last_name":"Cherfils"},{"last_name":"De","first_name":"Rycke Riet Maria","full_name":"De, Rycke Riet Maria"},{"last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter","first_name":"Peter"},{"last_name":"Robert","first_name":"Stéphanie","full_name":"Robert, Stéphanie"},{"first_name":"Eugenia","full_name":"Russinova, Eugenia","last_name":"Russinova"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"}],"oa_version":"Published Version","date_published":"2018-11-12T00:00:00Z","day":"12","external_id":{"pmid":["30018156"],"isi":["000450000500023"]}}]