[{"month":"08","page":"5706 - 5710","acknowledged_ssus":[{"_id":"M-Shop"}],"publication":"Nano Letters","type":"journal_article","date_created":"2018-12-11T11:48:47Z","publist_id":"6808","abstract":[{"text":"Heavy holes confined in quantum dots are predicted to be promising candidates for the realization of spin qubits with long coherence times. Here we focus on such heavy-hole states confined in germanium hut wires. By tuning the growth density of the latter we can realize a T-like structure between two neighboring wires. Such a structure allows the realization of a charge sensor, which is electrostatically and tunnel coupled to a quantum dot, with charge-transfer signals as high as 0.3 e. By integrating the T-like structure into a radiofrequency reflectometry setup, single-shot measurements allowing the extraction of hole tunneling times are performed. The extracted tunneling times of less than 10 μs are attributed to the small effective mass of Ge heavy-hole states and pave the way toward projective spin readout measurements.","lang":"eng"}],"year":"2017","citation":{"ista":"Vukušić L, Kukucka J, Watzinger H, Katsaros G. 2017. Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. Nano Letters. 17(9), 5706–5710.","ama":"Vukušić L, Kukucka J, Watzinger H, Katsaros G. Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. Nano Letters. 2017;17(9):5706-5710. doi:10.1021/acs.nanolett.7b02627","apa":"Vukušić, L., Kukucka, J., Watzinger, H., & Katsaros, G. (2017). Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.7b02627","short":"L. Vukušić, J. Kukucka, H. Watzinger, G. Katsaros, Nano Letters 17 (2017) 5706–5710.","mla":"Vukušić, Lada, et al. “Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry.” Nano Letters, vol. 17, no. 9, American Chemical Society, 2017, pp. 5706–10, doi:10.1021/acs.nanolett.7b02627.","chicago":"Vukušić, Lada, Josip Kukucka, Hannes Watzinger, and Georgios Katsaros. “Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry.” Nano Letters. American Chemical Society, 2017. https://doi.org/10.1021/acs.nanolett.7b02627.","ieee":"L. Vukušić, J. Kukucka, H. Watzinger, and G. Katsaros, “Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry,” Nano Letters, vol. 17, no. 9. American Chemical Society, pp. 5706–5710, 2017."},"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pubrep_id":"865","publication_identifier":{"issn":["1530-6984"]},"publication_status":"published","intvolume":" 17","corr_author":"1","date_published":"2017-08-10T00:00:00Z","_id":"840","file":[{"file_size":2449546,"date_updated":"2020-07-14T12:48:13Z","relation":"main_file","date_created":"2018-12-12T10:12:33Z","file_name":"IST-2017-865-v1+1_acs.nanolett.7b02627.pdf","file_id":"4951","checksum":"761371a0129b2aa442424b9561450ece","content_type":"application/pdf","access_level":"open_access","creator":"system"}],"status":"public","external_id":{"isi":["000411043500078"]},"publisher":"American Chemical Society","article_processing_charge":"No","issue":"9","oa":1,"doi":"10.1021/acs.nanolett.7b02627","scopus_import":"1","has_accepted_license":"1","author":[{"full_name":"Vukusic, Lada","last_name":"Vukusic","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","first_name":"Lada","orcid":"0000-0003-2424-8636"},{"first_name":"Josip","full_name":"Kukucka, Josip","last_name":"Kukucka","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hannes","last_name":"Watzinger","full_name":"Watzinger, Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8342-202X","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","full_name":"Katsaros, Georgios"}],"day":"10","ddc":["539"],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"7977","relation":"popular_science"},{"status":"public","id":"7996","relation":"dissertation_contains"},{"status":"public","id":"69","relation":"dissertation_contains"}]},"department":[{"_id":"GeKa"}],"oa_version":"Published Version","volume":17,"file_date_updated":"2020-07-14T12:48:13Z","title":"Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry","date_updated":"2026-04-08T14:09:47Z","license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"project":[{"call_identifier":"FP7","name":"Towards Spin qubits and Majorana fermions in Germanium self assembled hut-wires","grant_number":"335497","_id":"25517E86-B435-11E9-9278-68D0E5697425"}]},{"ec_funded":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"date_updated":"2025-07-10T12:01:35Z","title":"On the lengths of curves passing through boundary points of a planar convex shape","article_type":"original","oa_version":"Submitted Version","volume":124,"department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"day":"01","author":[{"first_name":"Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy","last_name":"Akopyan"},{"last_name":"Vysotsky","full_name":"Vysotsky, Vladislav","first_name":"Vladislav"}],"scopus_import":"1","doi":"10.4169/amer.math.monthly.124.7.588","issue":"7","oa":1,"article_processing_charge":"No","publisher":"Mathematical Association of America","external_id":{"arxiv":["1605.07997"],"isi":["000413947300002"]},"status":"public","_id":"909","date_published":"2017-01-01T00:00:00Z","arxiv":1,"intvolume":" 124","publication_identifier":{"issn":["0002-9890"]},"publication_status":"published","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","citation":{"ieee":"A. Akopyan and V. Vysotsky, “On the lengths of curves passing through boundary points of a planar convex shape,” The American Mathematical Monthly, vol. 124, no. 7. Mathematical Association of America, pp. 588–596, 2017.","chicago":"Akopyan, Arseniy, and Vladislav Vysotsky. “On the Lengths of Curves Passing through Boundary Points of a Planar Convex Shape.” The American Mathematical Monthly. Mathematical Association of America, 2017. https://doi.org/10.4169/amer.math.monthly.124.7.588.","short":"A. Akopyan, V. Vysotsky, The American Mathematical Monthly 124 (2017) 588–596.","apa":"Akopyan, A., & Vysotsky, V. (2017). On the lengths of curves passing through boundary points of a planar convex shape. The American Mathematical Monthly. Mathematical Association of America. https://doi.org/10.4169/amer.math.monthly.124.7.588","mla":"Akopyan, Arseniy, and Vladislav Vysotsky. “On the Lengths of Curves Passing through Boundary Points of a Planar Convex Shape.” The American Mathematical Monthly, vol. 124, no. 7, Mathematical Association of America, 2017, pp. 588–96, doi:10.4169/amer.math.monthly.124.7.588.","ama":"Akopyan A, Vysotsky V. On the lengths of curves passing through boundary points of a planar convex shape. The American Mathematical Monthly. 2017;124(7):588-596. doi:10.4169/amer.math.monthly.124.7.588","ista":"Akopyan A, Vysotsky V. 2017. On the lengths of curves passing through boundary points of a planar convex shape. The American Mathematical Monthly. 124(7), 588–596."},"year":"2017","publist_id":"6534","abstract":[{"text":"We study the lengths of curves passing through a fixed number of points on the boundary of a convex shape in the plane. We show that, for any convex shape K, there exist four points on the boundary of K such that the length of any curve passing through these points is at least half of the perimeter of K. It is also shown that the same statement does not remain valid with the additional constraint that the points are extreme points of K. Moreover, the factor ½ cannot be achieved with any fixed number of extreme points. We conclude the paper with a few other inequalities related to the perimeter of a convex shape.","lang":"eng"}],"date_created":"2018-12-11T11:49:09Z","publication":"The American Mathematical Monthly","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1605.07997"}],"page":"588 - 596","month":"01"},{"intvolume":" 207","publication_status":"published","pubrep_id":"974","isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2017","quality_controlled":"1","citation":{"chicago":"Novak, Sebastian, and Nicholas H Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.117.300129.","ieee":"S. Novak and N. H. Barton, “When does frequency-independent selection maintain genetic variation?,” Genetics, vol. 207, no. 2. Genetics Society of America, pp. 653–668, 2017.","ista":"Novak S, Barton NH. 2017. When does frequency-independent selection maintain genetic variation? Genetics. 207(2), 653–668.","apa":"Novak, S., & Barton, N. H. (2017). When does frequency-independent selection maintain genetic variation? Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300129","short":"S. Novak, N.H. Barton, Genetics 207 (2017) 653–668.","mla":"Novak, Sebastian, and Nicholas H. Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” Genetics, vol. 207, no. 2, Genetics Society of America, 2017, pp. 653–68, doi:10.1534/genetics.117.300129.","ama":"Novak S, Barton NH. When does frequency-independent selection maintain genetic variation? Genetics. 2017;207(2):653-668. doi:10.1534/genetics.117.300129"},"date_created":"2018-12-11T11:49:09Z","publist_id":"6533","abstract":[{"lang":"eng","text":"Frequency-independent selection is generally considered as a force that acts to reduce the genetic variation in evolving populations, yet rigorous arguments for this idea are scarce. When selection fluctuates in time, it is unclear whether frequency-independent selection may maintain genetic polymorphism without invoking additional mechanisms. We show that constant frequency-independent selection with arbitrary epistasis on a well-mixed haploid population eliminates genetic variation if we assume linkage equilibrium between alleles. To this end, we introduce the notion of frequency-independent selection at the level of alleles, which is sufficient to prove our claim and contains the notion of frequency-independent selection on haploids. When selection and recombination are weak but of the same order, there may be strong linkage disequilibrium; numerical calculations show that stable equilibria are highly unlikely. Using the example of a diallelic two-locus model, we then demonstrate that frequency-independent selection that fluctuates in time can maintain stable polymorphism if linkage disequilibrium changes its sign periodically. We put our findings in the context of results from the existing literature and point out those scenarios in which the possible role of frequency-independent selection in maintaining genetic variation remains unclear.\r\n"}],"type":"journal_article","publication":"Genetics","page":"653 - 668","month":"10","project":[{"grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7"}],"ec_funded":1,"title":"When does frequency-independent selection maintain genetic variation?","date_updated":"2025-04-15T08:22:21Z","file_date_updated":"2020-07-14T12:48:15Z","oa_version":"Submitted Version","volume":207,"department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"author":[{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","last_name":"Novak","orcid":"0000-0002-2519-824X","first_name":"Sebastian"},{"full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"}],"day":"01","ddc":["576"],"doi":"10.1534/genetics.117.300129","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","oa":1,"issue":"2","publisher":"Genetics Society of America","status":"public","file":[{"file_size":494268,"date_created":"2018-12-12T10:17:12Z","relation":"main_file","date_updated":"2020-07-14T12:48:15Z","file_name":"IST-2018-974-v1+1_manuscript.pdf","file_id":"5264","checksum":"f7c32dabf52e6d9e709d9203761e39fd","content_type":"application/pdf","access_level":"open_access","creator":"system"}],"external_id":{"isi":["000412232600019"]},"_id":"910","date_published":"2017-10-01T00:00:00Z","corr_author":"1"},{"oa":1,"article_processing_charge":"No","publisher":"BMVA Press","external_id":{"arxiv":["1705.04258"]},"status":"public","file":[{"creator":"dernst","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2017_BMVC_Royer.pdf","date_updated":"2020-08-10T07:14:33Z","date_created":"2020-08-10T07:14:33Z","relation":"main_file","file_id":"8224","file_size":1625363}],"_id":"911","date_published":"2017-09-01T00:00:00Z","corr_author":"1","arxiv":1,"project":[{"grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7"}],"ec_funded":1,"title":"Probabilistic image colorization","date_updated":"2026-04-08T07:26:44Z","file_date_updated":"2020-08-10T07:14:33Z","oa_version":"Published Version","department":[{"_id":"ChLa"}],"related_material":{"record":[{"status":"public","id":"8390","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"ddc":["000"],"day":"01","author":[{"orcid":"0000-0002-8407-0705","first_name":"Amélie","full_name":"Royer, Amélie","last_name":"Royer","id":"3811D890-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","full_name":"Kolesnikov, Alexander","last_name":"Kolesnikov"},{"last_name":"Lampert","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph"}],"has_accepted_license":"1","scopus_import":"1","doi":"10.5244/c.31.85","citation":{"ista":"Royer A, Kolesnikov A, Lampert C. 2017. Probabilistic image colorization. BMVC: British Machine Vision Conference, 85.1-85.12.","mla":"Royer, Amélie, et al. Probabilistic Image Colorization. BMVA Press, 2017, p. 85.1-85.12, doi:10.5244/c.31.85.","short":"A. Royer, A. Kolesnikov, C. Lampert, in:, BMVA Press, 2017, p. 85.1-85.12.","apa":"Royer, A., Kolesnikov, A., & Lampert, C. (2017). Probabilistic image colorization (p. 85.1-85.12). Presented at the BMVC: British Machine Vision Conference, London, United Kingdom: BMVA Press. https://doi.org/10.5244/c.31.85","ama":"Royer A, Kolesnikov A, Lampert C. Probabilistic image colorization. In: BMVA Press; 2017:85.1-85.12. doi:10.5244/c.31.85","chicago":"Royer, Amélie, Alexander Kolesnikov, and Christoph Lampert. “Probabilistic Image Colorization,” 85.1-85.12. BMVA Press, 2017. https://doi.org/10.5244/c.31.85.","ieee":"A. Royer, A. Kolesnikov, and C. Lampert, “Probabilistic image colorization,” presented at the BMVC: British Machine Vision Conference, London, United Kingdom, 2017, p. 85.1-85.12."},"year":"2017","quality_controlled":"1","abstract":[{"lang":"eng","text":"We develop a probabilistic technique for colorizing grayscale natural images. In light of the intrinsic uncertainty of this task, the proposed probabilistic framework has numerous desirable properties. In particular, our model is able to produce multiple plausible and vivid colorizations for a given grayscale image and is one of the first colorization models to provide a proper stochastic sampling scheme. Moreover, our training procedure is supported by a rigorous theoretical framework that does not require any ad hoc heuristics and allows for efficient modeling and learning of the joint pixel color distribution.We demonstrate strong quantitative and qualitative experimental results on the CIFAR-10 dataset and the challenging ILSVRC 2012 dataset."}],"publist_id":"6532","date_created":"2018-12-11T11:49:09Z","type":"conference","page":"85.1-85.12","conference":{"end_date":"2017-09-07","location":"London, United Kingdom","name":"BMVC: British Machine Vision Conference","start_date":"2017-09-04"},"month":"09","publication_identifier":{"eisbn":["190172560X"]},"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"department":[{"_id":"VlKo"}],"language":[{"iso":"eng"}],"author":[{"first_name":"Paul","last_name":"Swoboda","full_name":"Swoboda, Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Andres, Bjoern","last_name":"Andres","first_name":"Bjoern"}],"day":"01","ddc":["000"],"scopus_import":"1","doi":"10.1109/CVPR.2017.530","has_accepted_license":"1","project":[{"call_identifier":"FP7","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"ec_funded":1,"title":"A message passing algorithm for the minimum cost multicut problem","date_updated":"2024-11-04T13:52:34Z","file_date_updated":"2020-07-14T12:48:15Z","oa_version":"Submitted Version","volume":2017,"_id":"915","date_published":"2017-07-01T00:00:00Z","corr_author":"1","article_processing_charge":"No","oa":1,"publisher":"IEEE","external_id":{"isi":["000418371405009"]},"file":[{"content_type":"application/pdf","access_level":"open_access","creator":"dernst","checksum":"7e51dacefa693574581a32da3eff63dc","file_id":"5849","date_updated":"2020-07-14T12:48:15Z","date_created":"2019-01-18T12:52:46Z","relation":"main_file","file_name":"Swoboda_A_Message_Passing_CVPR_2017_paper.pdf","file_size":883264}],"status":"public","isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 2017","publication_status":"published","publication_identifier":{"isbn":["978-153860457-1"]},"conference":{"location":"Honolulu, HA, United States","name":"CVPR: Computer Vision and Pattern Recognition","end_date":"2017-07-26","start_date":"2017-07-21"},"month":"07","quality_controlled":"1","citation":{"ieee":"P. Swoboda and B. Andres, “A message passing algorithm for the minimum cost multicut problem,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 4990–4999.","chicago":"Swoboda, Paul, and Bjoern Andres. “A Message Passing Algorithm for the Minimum Cost Multicut Problem,” 2017:4990–99. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.530.","ama":"Swoboda P, Andres B. A message passing algorithm for the minimum cost multicut problem. In: Vol 2017. IEEE; 2017:4990-4999. doi:10.1109/CVPR.2017.530","short":"P. Swoboda, B. Andres, in:, IEEE, 2017, pp. 4990–4999.","apa":"Swoboda, P., & Andres, B. (2017). A message passing algorithm for the minimum cost multicut problem (Vol. 2017, pp. 4990–4999). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.530","mla":"Swoboda, Paul, and Bjoern Andres. A Message Passing Algorithm for the Minimum Cost Multicut Problem. Vol. 2017, IEEE, 2017, pp. 4990–99, doi:10.1109/CVPR.2017.530.","ista":"Swoboda P, Andres B. 2017. A message passing algorithm for the minimum cost multicut problem. CVPR: Computer Vision and Pattern Recognition vol. 2017, 4990–4999."},"year":"2017","date_created":"2018-12-11T11:49:11Z","abstract":[{"text":"We propose a dual decomposition and linear program relaxation of the NP-hard minimum cost multicut problem. Unlike other polyhedral relaxations of the multicut polytope, it is amenable to efficient optimization by message passing. Like other polyhedral relaxations, it can be tightened efficiently by cutting planes. We define an algorithm that alternates between message passing and efficient separation of cycle- and odd-wheel inequalities. This algorithm is more efficient than state-of-the-art algorithms based on linear programming, including algorithms written in the framework of leading commercial software, as we show in experiments with large instances of the problem from applications in computer vision, biomedical image analysis and data mining.","lang":"eng"}],"publist_id":"6526","type":"conference","page":"4990-4999"},{"external_id":{"isi":["000418371407018"]},"status":"public","file":[{"access_level":"open_access","content_type":"application/pdf","creator":"dernst","checksum":"e38a2740daad1ea178465843b5072906","file_id":"5848","relation":"main_file","date_updated":"2020-07-14T12:48:15Z","date_created":"2019-01-18T12:49:38Z","file_name":"2017_CVPR_Swoboda2.pdf","file_size":944332}],"oa":1,"article_processing_charge":"No","publisher":"IEEE","corr_author":"1","_id":"916","date_published":"2017-01-01T00:00:00Z","file_date_updated":"2020-07-14T12:48:15Z","oa_version":"Submitted Version","volume":2017,"ec_funded":1,"project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"}],"title":"A study of lagrangean decompositions and dual ascent solvers for graph matching","date_updated":"2024-11-04T13:52:34Z","day":"01","ddc":["000"],"author":[{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda","full_name":"Swoboda, Paul","first_name":"Paul"},{"first_name":"Carsten","last_name":"Rother","full_name":"Rother, Carsten"},{"first_name":"Carsten","last_name":"Abu Alhaija","full_name":"Abu Alhaija, Carsten"},{"first_name":"Dagmar","full_name":"Kainmueller, Dagmar","last_name":"Kainmueller"},{"first_name":"Bogdan","last_name":"Savchynskyy","full_name":"Savchynskyy, Bogdan"}],"has_accepted_license":"1","doi":"10.1109/CVPR.2017.747","scopus_import":"1","department":[{"_id":"VlKo"}],"language":[{"iso":"eng"}],"type":"conference","page":"7062-7071","quality_controlled":"1","citation":{"ista":"Swoboda P, Rother C, Abu Alhaija C, Kainmueller D, Savchynskyy B. 2017. A study of lagrangean decompositions and dual ascent solvers for graph matching. CVPR: Computer Vision and Pattern Recognition vol. 2017, 7062–7071.","ama":"Swoboda P, Rother C, Abu Alhaija C, Kainmueller D, Savchynskyy B. A study of lagrangean decompositions and dual ascent solvers for graph matching. In: Vol 2017. IEEE; 2017:7062-7071. doi:10.1109/CVPR.2017.747","apa":"Swoboda, P., Rother, C., Abu Alhaija, C., Kainmueller, D., & Savchynskyy, B. (2017). A study of lagrangean decompositions and dual ascent solvers for graph matching (Vol. 2017, pp. 7062–7071). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.747","short":"P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, B. Savchynskyy, in:, IEEE, 2017, pp. 7062–7071.","mla":"Swoboda, Paul, et al. A Study of Lagrangean Decompositions and Dual Ascent Solvers for Graph Matching. Vol. 2017, IEEE, 2017, pp. 7062–71, doi:10.1109/CVPR.2017.747.","chicago":"Swoboda, Paul, Carsten Rother, Carsten Abu Alhaija, Dagmar Kainmueller, and Bogdan Savchynskyy. “A Study of Lagrangean Decompositions and Dual Ascent Solvers for Graph Matching,” 2017:7062–71. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.747.","ieee":"P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, and B. Savchynskyy, “A study of lagrangean decompositions and dual ascent solvers for graph matching,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 7062–7071."},"year":"2017","publist_id":"6525","abstract":[{"lang":"eng","text":"We study the quadratic assignment problem, in computer vision also known as graph matching. Two leading solvers for this problem optimize the Lagrange decomposition duals with sub-gradient and dual ascent (also known as message passing) updates. We explore this direction further and propose several additional Lagrangean relaxations of the graph matching problem along with corresponding algorithms, which are all based on a common dual ascent framework. Our extensive empirical evaluation gives several theoretical insights and suggests a new state-of-the-art anytime solver for the considered problem. Our improvement over state-of-the-art is particularly visible on a new dataset with large-scale sparse problem instances containing more than 500 graph nodes each."}],"date_created":"2018-12-11T11:49:11Z","month":"01","conference":{"name":"CVPR: Computer Vision and Pattern Recognition","location":"Honolulu, HA, United States","end_date":"2017-07-26","start_date":"2017-07-21"},"publication_status":"published","publication_identifier":{"isbn":["978-153860457-1"]},"intvolume":" 2017","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"publication_identifier":{"isbn":["978-153860457-1"]},"publication_status":"published","intvolume":" 2017","month":"07","conference":{"end_date":"2017-07-26","name":"CVPR: Computer Vision and Pattern Recognition","location":"Honolulu, HA, United States","start_date":"2017-07-21"},"type":"conference","page":"4950-4960","citation":{"chicago":"Swoboda, Paul, Jan Kuske, and Bogdan Savchynskyy. “A Dual Ascent Framework for Lagrangean Decomposition of Combinatorial Problems,” 2017:4950–60. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.526.","ieee":"P. Swoboda, J. Kuske, and B. Savchynskyy, “A dual ascent framework for Lagrangean decomposition of combinatorial problems,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 4950–4960.","ista":"Swoboda P, Kuske J, Savchynskyy B. 2017. A dual ascent framework for Lagrangean decomposition of combinatorial problems. CVPR: Computer Vision and Pattern Recognition vol. 2017, 4950–4960.","ama":"Swoboda P, Kuske J, Savchynskyy B. A dual ascent framework for Lagrangean decomposition of combinatorial problems. In: Vol 2017. IEEE; 2017:4950-4960. doi:10.1109/CVPR.2017.526","apa":"Swoboda, P., Kuske, J., & Savchynskyy, B. (2017). A dual ascent framework for Lagrangean decomposition of combinatorial problems (Vol. 2017, pp. 4950–4960). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.526","short":"P. Swoboda, J. Kuske, B. Savchynskyy, in:, IEEE, 2017, pp. 4950–4960.","mla":"Swoboda, Paul, et al. A Dual Ascent Framework for Lagrangean Decomposition of Combinatorial Problems. Vol. 2017, IEEE, 2017, pp. 4950–60, doi:10.1109/CVPR.2017.526."},"year":"2017","quality_controlled":"1","date_created":"2018-12-11T11:49:11Z","abstract":[{"lang":"eng","text":"We propose a general dual ascent framework for Lagrangean decomposition of combinatorial problems. Although methods of this type have shown their efficiency for a number of problems, so far there was no general algorithm applicable to multiple problem types. In this work, we propose such a general algorithm. It depends on several parameters, which can be used to optimize its performance in each particular setting. We demonstrate efficacy of our method on graph matching and multicut problems, where it outperforms state-of-the-art solvers including those based on subgradient optimization and off-the-shelf linear programming solvers."}],"publist_id":"6524","author":[{"first_name":"Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda","full_name":"Swoboda, Paul"},{"full_name":"Kuske, Jan","last_name":"Kuske","first_name":"Jan"},{"full_name":"Savchynskyy, Bogdan","last_name":"Savchynskyy","first_name":"Bogdan"}],"day":"01","ddc":["000"],"scopus_import":"1","doi":"10.1109/CVPR.2017.526","has_accepted_license":"1","department":[{"_id":"VlKo"}],"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:48:15Z","volume":2017,"oa_version":"Submitted Version","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"}],"ec_funded":1,"date_updated":"2024-11-04T13:52:34Z","title":"A dual ascent framework for Lagrangean decomposition of combinatorial problems","corr_author":"1","_id":"917","date_published":"2017-07-01T00:00:00Z","status":"public","file":[{"file_size":898652,"file_name":"2017_CVPR_Swoboda.pdf","relation":"main_file","date_created":"2019-01-18T12:45:55Z","date_updated":"2020-07-14T12:48:15Z","file_id":"5847","checksum":"72fd291046bd8e5717961bd68f6b6f03","creator":"dernst","access_level":"open_access","content_type":"application/pdf"}],"external_id":{"isi":["000418371405005"]},"article_processing_charge":"No","oa":1,"publisher":"IEEE"},{"corr_author":"1","date_published":"2017-06-02T00:00:00Z","_id":"938","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","creator":"dernst","checksum":"193425764d9aaaed3ac57062a867b315","relation":"source_file","date_updated":"2020-07-14T12:48:15Z","date_created":"2019-04-05T09:03:20Z","file_name":"2017_Adamowski-Thesis_Source.docx","file_id":"6215","file_size":46903863},{"checksum":"df5ab01be81f821e1b958596a1ec8d21","access_level":"open_access","content_type":"application/pdf","creator":"dernst","file_size":8698888,"relation":"main_file","date_created":"2019-04-05T09:03:19Z","date_updated":"2020-07-14T12:48:15Z","file_name":"2017_Adamowski-Thesis.pdf","file_id":"6216"}],"status":"public","publisher":"Institute of Science and Technology Austria","oa":1,"article_processing_charge":"No","has_accepted_license":"1","doi":"10.15479/AT:ISTA:th_842","day":"02","ddc":["581","583","580"],"author":[{"orcid":"0000-0001-6463-5257","first_name":"Maciek","last_name":"Adamowski","full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"related_material":{"record":[{"id":"1591","status":"public","relation":"part_of_dissertation"}]},"oa_version":"Published Version","file_date_updated":"2020-07-14T12:48:15Z","title":"Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ","date_updated":"2026-04-08T14:20:45Z","month":"06","OA_place":"publisher","page":"117","degree_awarded":"PhD","type":"dissertation","abstract":[{"lang":"eng","text":"The thesis encompasses several topics of plant cell biology which were studied in the model plant Arabidopsis thaliana. Chapter 1 concerns the plant hormone auxin and its polar transport through cells and tissues. The highly controlled, directional transport of auxin is facilitated by plasma membrane-localized transporters. Transporters from the PIN family direct auxin transport due to their polarized localizations at cell membranes. Substantial effort has been put into research on cellular trafficking of PIN proteins, which is thought to underlie their polar distribution. I participated in a forward genetic screen aimed at identifying novel regulators of PIN polarity. The screen yielded several genes which may be involved in PIN polarity regulation or participate in polar auxin transport by other means. Chapter 2 focuses on the endomembrane system, with particular attention to clathrin-mediated endocytosis. The project started with identification of several proteins that interact with clathrin light chains. Among them, I focused on two putative homologues of auxilin, which in non-plant systems is an endocytotic factor known for uncoating clathrin-coated vesicles in the final step of endocytosis. The body of my work consisted of an in-depth characterization of transgenic A. thaliana lines overexpressing these putative auxilins in an inducible manner. Overexpression of these proteins leads to an inhibition of endocytosis, as documented by imaging of cargoes and clathrin-related endocytic machinery. An extension of this work is an investigation into a concept of homeostatic regulation acting between distinct transport processes in the endomembrane system. With auxilin overexpressing lines, where endocytosis is blocked specifically, I made observations on the mutual relationship between two opposite trafficking processes of secretion and endocytosis. In Chapter 3, I analyze cortical microtubule arrays and their relationship to auxin signaling and polarized growth in elongating cells. In plants, microtubules are organized into arrays just below the plasma membrane, and it is thought that their function is to guide membrane-docked cellulose synthase complexes. These, in turn, influence cell wall structure and cell shape by directed deposition of cellulose fibres. In elongating cells, cortical microtubule arrays are able to reorient in relation to long cell axis, and these reorientations have been linked to cell growth and to signaling of growth-regulating factors such as auxin or light. In this chapter, I am addressing the causal relationship between microtubule array reorientation, growth, and auxin signaling. I arrive at a model where array reorientation is not guided by auxin directly, but instead is only controlled by growth, which, in turn, is regulated by auxin."}],"publist_id":"6483","date_created":"2018-12-11T11:49:18Z","year":"2017","citation":{"chicago":"Adamowski, Maciek. “Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana .” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_842.","ieee":"M. Adamowski, “Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ,” Institute of Science and Technology Austria, 2017.","ista":"Adamowski M. 2017. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria.","ama":"Adamowski M. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . 2017. doi:10.15479/AT:ISTA:th_842","short":"M. Adamowski, Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana , Institute of Science and Technology Austria, 2017.","apa":"Adamowski, M. (2017). Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_842","mla":"Adamowski, Maciek. Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana . Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_842."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","pubrep_id":"842","supervisor":[{"full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří"}],"publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"]},{"scopus_import":"1","doi":"10.1103/PhysRevLett.119.033905","author":[{"id":"456187FC-F248-11E8-B48F-1D18A9856A87","last_name":"Midya","full_name":"Midya, Bikashkali","first_name":"Bikashkali"},{"first_name":"Vladimir","last_name":"Konotop","full_name":"Konotop, Vladimir"}],"day":"18","language":[{"iso":"eng"}],"department":[{"_id":"MiLe"}],"oa_version":"Submitted Version","volume":119,"article_number":"033905","date_updated":"2025-06-04T08:20:23Z","title":"Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons","ec_funded":1,"project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"arxiv":1,"corr_author":"1","date_published":"2017-07-18T00:00:00Z","_id":"939","external_id":{"isi":["000405718200012"],"arxiv":["1706.04085 "]},"status":"public","publisher":"American Physical Society","article_processing_charge":"No","oa":1,"issue":"3","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publication_identifier":{"issn":["0031-9007"]},"intvolume":" 119","month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.04085 "}],"type":"journal_article","publication":"Physical Review Letters","date_created":"2018-12-11T11:49:18Z","abstract":[{"text":"We reveal the existence of continuous families of guided single-mode solitons in planar waveguides with weakly nonlinear active core and absorbing boundaries. Stable propagation of TE and TM-polarized solitons is accompanied by attenuation of all other modes, i.e., the waveguide features properties of conservative and dissipative systems. If the linear spectrum of the waveguide possesses exceptional points, which occurs in the case of TM polarization, an originally focusing (defocusing) material nonlinearity may become effectively defocusing (focusing). This occurs due to the geometric phase of the carried eigenmode when the surface impedance encircles the exceptional point. In its turn, the change of the effective nonlinearity ensures the existence of dark (bright) solitons in spite of focusing (defocusing) Kerr nonlinearity of the core. The existence of an exceptional point can also result in anomalous enhancement of the effective nonlinearity. In terms of practical applications, the nonlinearity of the reported waveguide can be manipulated by controlling the properties of the absorbing cladding.","lang":"eng"}],"publist_id":"6481","quality_controlled":"1","citation":{"chicago":"Midya, Bikashkali, and Vladimir Konotop. “Waveguides with Absorbing Boundaries: Nonlinearity Controlled by an Exceptional Point and Solitons.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.119.033905.","ieee":"B. Midya and V. Konotop, “Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons,” Physical Review Letters, vol. 119, no. 3. American Physical Society, 2017.","ista":"Midya B, Konotop V. 2017. Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. 119(3), 033905.","apa":"Midya, B., & Konotop, V. (2017). Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.119.033905","short":"B. Midya, V. Konotop, Physical Review Letters 119 (2017).","mla":"Midya, Bikashkali, and Vladimir Konotop. “Waveguides with Absorbing Boundaries: Nonlinearity Controlled by an Exceptional Point and Solitons.” Physical Review Letters, vol. 119, no. 3, 033905, American Physical Society, 2017, doi:10.1103/PhysRevLett.119.033905.","ama":"Midya B, Konotop V. Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. 2017;119(3). doi:10.1103/PhysRevLett.119.033905"},"year":"2017"},{"quality_controlled":"1","citation":{"ieee":"X. Le, D. H. Chu, D. Lo, C. Le Goues, and W. Visser, “JFIX: Semantics-based repair of Java programs via symbolic PathFinder,” in Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, Santa Barbara, CA, United States, 2017, pp. 376–379.","chicago":"Le, Xuan, Duc Hiep Chu, David Lo, Claire Le Goues, and Willem Visser. “JFIX: Semantics-Based Repair of Java Programs via Symbolic PathFinder.” In Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, 376–79. ACM, 2017. https://doi.org/10.1145/3092703.3098225.","ama":"Le X, Chu DH, Lo D, Le Goues C, Visser W. JFIX: Semantics-based repair of Java programs via symbolic PathFinder. In: Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis. ACM; 2017:376-379. doi:10.1145/3092703.3098225","mla":"Le, Xuan, et al. “JFIX: Semantics-Based Repair of Java Programs via Symbolic PathFinder.” Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, ACM, 2017, pp. 376–79, doi:10.1145/3092703.3098225.","apa":"Le, X., Chu, D. H., Lo, D., Le Goues, C., & Visser, W. (2017). JFIX: Semantics-based repair of Java programs via symbolic PathFinder. In Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis (pp. 376–379). Santa Barbara, CA, United States: ACM. https://doi.org/10.1145/3092703.3098225","short":"X. Le, D.H. Chu, D. Lo, C. Le Goues, W. Visser, in:, Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, ACM, 2017, pp. 376–379.","ista":"Le X, Chu DH, Lo D, Le Goues C, Visser W. 2017. JFIX: Semantics-based repair of Java programs via symbolic PathFinder. Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis. ISSTA: International Symposium on Software Testing and Analysis, 376–379."},"year":"2017","date_created":"2018-12-11T11:49:19Z","abstract":[{"lang":"eng","text":"Recently there has been a proliferation of automated program repair (APR) techniques, targeting various programming languages. Such techniques can be generally classified into two families: syntactic- and semantics-based. Semantics-based APR, on which we focus, typically uses symbolic execution to infer semantic constraints and then program synthesis to construct repairs conforming to them. While syntactic-based APR techniques have been shown successful on bugs in real-world programs written in both C and Java, semantics-based APR techniques mostly target C programs. This leaves empirical comparisons of the APR families not fully explored, and developers without a Java-based semantics APR technique. We present JFix, a semantics-based APR framework that targets Java, and an associated Eclipse plugin. JFix is implemented atop Symbolic PathFinder, a well-known symbolic execution engine for Java programs. It extends one particular APR technique (Angelix), and is designed to be sufficiently generic to support a variety of such techniques. We demonstrate that semantics-based APR can indeed efficiently and effectively repair a variety of classes of bugs in large real-world Java programs. This supports our claim that the framework can both support developers seeking semantics-based repair of bugs in Java programs, as well as enable larger scale empirical studies comparing syntactic- and semantics-based APR targeting Java. The demonstration of our tool is available via the project website at: https://xuanbachle.github.io/semanticsrepair/ "}],"publist_id":"6478","publication":"Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis","type":"conference","page":"376 - 379 ","main_file_link":[{"open_access":"1","url":"https://core.ac.uk/download/pdf/111759662.pdf"}],"conference":{"end_date":"2017-07-14","name":"ISSTA: International Symposium on Software Testing and Analysis","location":"Santa Barbara, CA, United States","start_date":"2017-07-10"},"month":"07","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"acknowledgement":"We thank Vu Le (Microsoft Research, Redmond), and anonymous reviewers for their comments. Duc-Hiep Chu was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award).","article_processing_charge":"No","oa":1,"publisher":"ACM","external_id":{"isi":["000462903600038"]},"status":"public","_id":"941","date_published":"2017-07-10T00:00:00Z","corr_author":"1","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"title":"JFIX: Semantics-based repair of Java programs via symbolic PathFinder","date_updated":"2026-06-18T19:51:19Z","oa_version":"Published Version","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"author":[{"first_name":"Xuan","full_name":"Le, Xuan","last_name":"Le"},{"first_name":"Duc Hiep","full_name":"Chu, Duc Hiep","last_name":"Chu","id":"3598E630-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","full_name":"Lo, David","last_name":"Lo"},{"full_name":"Le Goues, Claire","last_name":"Le Goues","first_name":"Claire"},{"first_name":"Willem","full_name":"Visser, Willem","last_name":"Visser"}],"day":"10","ddc":["000"],"doi":"10.1145/3092703.3098225","scopus_import":"1"},{"oa_version":"None","volume":"F130154","date_updated":"2025-04-15T06:25:57Z","title":"S3: Syntax- and semantic-guided repair synthesis via programming by examples","project":[{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"},{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"doi":"10.1145/3106237.3106309","scopus_import":"1","author":[{"full_name":"Le, Xuan","last_name":"Le","first_name":"Xuan"},{"full_name":"Chu, Duc Hiep","last_name":"Chu","id":"3598E630-F248-11E8-B48F-1D18A9856A87","first_name":"Duc Hiep"},{"first_name":"David","full_name":"Lo, David","last_name":"Lo"},{"last_name":"Le Goues","full_name":"Le Goues, Claire","first_name":"Claire"},{"first_name":"Willem","last_name":"Visser","full_name":"Visser, Willem"}],"day":"01","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"external_id":{"isi":["000414279300055"]},"status":"public","publisher":"ACM","article_processing_charge":"No","date_published":"2017-09-01T00:00:00Z","_id":"942","publication_identifier":{"isbn":["978-145035105-8"]},"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"page":"593 - 604","type":"conference","date_created":"2018-12-11T11:49:19Z","abstract":[{"lang":"eng","text":"A notable class of techniques for automatic program repair is known as semantics-based. Such techniques, e.g., Angelix, infer semantic specifications via symbolic execution, and then use program synthesis to construct new code that satisfies those inferred specifications. However, the obtained specifications are naturally incomplete, leaving the synthesis engine with a difficult task of synthesizing a general solution from a sparse space of many possible solutions that are consistent with the provided specifications but that do not necessarily generalize. We present S3, a new repair synthesis engine that leverages programming-by-examples methodology to synthesize high-quality bug repairs. The novelty in S3 that allows it to tackle the sparse search space to create more general repairs is three-fold: (1) A systematic way to customize and constrain the syntactic search space via a domain-specific language, (2) An efficient enumeration-based search strategy over the constrained search space, and (3) A number of ranking features based on measures of the syntactic and semantic distances between candidate solutions and the original buggy program. We compare S3’s repair effectiveness with state-of-the-art synthesis engines Angelix, Enumerative, and CVC4. S3 can successfully and correctly fix at least three times more bugs than the best baseline on datasets of 52 bugs in small programs, and 100 bugs in real-world large programs. "}],"publist_id":"6477","year":"2017","quality_controlled":"1","citation":{"chicago":"Le, Xuan, Duc Hiep Chu, David Lo, Claire Le Goues, and Willem Visser. “S3: Syntax- and Semantic-Guided Repair Synthesis via Programming by Examples,” F130154:593–604. ACM, 2017. https://doi.org/10.1145/3106237.3106309.","ieee":"X. Le, D. H. Chu, D. Lo, C. Le Goues, and W. Visser, “S3: Syntax- and semantic-guided repair synthesis via programming by examples,” presented at the FSE: Foundations of Software Engineering, Paderborn, Germany, 2017, vol. F130154, pp. 593–604.","ista":"Le X, Chu DH, Lo D, Le Goues C, Visser W. 2017. S3: Syntax- and semantic-guided repair synthesis via programming by examples. FSE: Foundations of Software Engineering vol. F130154, 593–604.","apa":"Le, X., Chu, D. H., Lo, D., Le Goues, C., & Visser, W. (2017). S3: Syntax- and semantic-guided repair synthesis via programming by examples (Vol. F130154, pp. 593–604). Presented at the FSE: Foundations of Software Engineering, Paderborn, Germany: ACM. https://doi.org/10.1145/3106237.3106309","mla":"Le, Xuan, et al. S3: Syntax- and Semantic-Guided Repair Synthesis via Programming by Examples. Vol. F130154, ACM, 2017, pp. 593–604, doi:10.1145/3106237.3106309.","short":"X. Le, D.H. Chu, D. Lo, C. Le Goues, W. Visser, in:, ACM, 2017, pp. 593–604.","ama":"Le X, Chu DH, Lo D, Le Goues C, Visser W. S3: Syntax- and semantic-guided repair synthesis via programming by examples. In: Vol F130154. ACM; 2017:593-604. doi:10.1145/3106237.3106309"},"month":"09","conference":{"end_date":"2017-09-08","name":"FSE: Foundations of Software Engineering","location":"Paderborn, Germany","start_date":"2017-09-04"}},{"language":[{"iso":"eng"}],"department":[{"_id":"AnKi"},{"_id":"GaTk"}],"scopus_import":"1","doi":"10.1126/science.aam5887","day":"30","author":[{"orcid":"0000-0001-7896-7762","first_name":"Marcin P","last_name":"Zagórski","full_name":"Zagórski, Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yoji","last_name":"Tabata","full_name":"Tabata, Yoji"},{"first_name":"Nathalie","full_name":"Brandenberg, Nathalie","last_name":"Brandenberg"},{"full_name":"Lutolf, Matthias","last_name":"Lutolf","first_name":"Matthias"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455"},{"full_name":"Bollenbach, Tobias","last_name":"Bollenbach","first_name":"Tobias"},{"last_name":"Briscoe","full_name":"Briscoe, James","first_name":"James"},{"first_name":"Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna","last_name":"Kicheva"}],"date_updated":"2025-07-10T12:01:45Z","title":"Decoding of position in the developing neural tube from antiparallel morphogen gradients","ec_funded":1,"project":[{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish","_id":"2524F500-B435-11E9-9278-68D0E5697425","grant_number":"201439","call_identifier":"FP7"}],"volume":356,"oa_version":"Submitted Version","date_published":"2017-06-30T00:00:00Z","_id":"943","corr_author":"1","publisher":"American Association for the Advancement of Science","issue":"6345","oa":1,"article_processing_charge":"No","pmid":1,"status":"public","external_id":{"pmid":["28663499"],"isi":["000404351500036"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"intvolume":" 356","publication_identifier":{"issn":["0036-8075"]},"publication_status":"published","month":"06","publist_id":"6474","abstract":[{"lang":"eng","text":"Like many developing tissues, the vertebrate neural tube is patterned by antiparallel morphogen gradients. To understand how these inputs are interpreted, we measured morphogen signaling and target gene expression in mouse embryos and chick ex vivo assays. From these data, we derived and validated a characteristic decoding map that relates morphogen input to the positional identity of neural progenitors. Analysis of the observed responses indicates that the underlying interpretation strategy minimizes patterning errors in response to the joint input of noisy opposing gradients. We reverse-engineered a transcriptional network that provides a mechanistic basis for the observed cell fate decisions and accounts for the precision and dynamics of pattern formation. Together, our data link opposing gradient dynamics in a growing tissue to precise pattern formation."}],"date_created":"2018-12-11T11:49:20Z","year":"2017","citation":{"ista":"Zagórski MP, Tabata Y, Brandenberg N, Lutolf M, Tkačik G, Bollenbach T, Briscoe J, Kicheva A. 2017. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. 356(6345), 1379–1383.","ama":"Zagórski MP, Tabata Y, Brandenberg N, et al. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. 2017;356(6345):1379-1383. doi:10.1126/science.aam5887","apa":"Zagórski, M. P., Tabata, Y., Brandenberg, N., Lutolf, M., Tkačik, G., Bollenbach, T., … Kicheva, A. (2017). Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aam5887","short":"M.P. Zagórski, Y. Tabata, N. Brandenberg, M. Lutolf, G. Tkačik, T. Bollenbach, J. Briscoe, A. Kicheva, Science 356 (2017) 1379–1383.","mla":"Zagórski, Marcin P., et al. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” Science, vol. 356, no. 6345, American Association for the Advancement of Science, 2017, pp. 1379–83, doi:10.1126/science.aam5887.","chicago":"Zagórski, Marcin P, Yoji Tabata, Nathalie Brandenberg, Matthias Lutolf, Gašper Tkačik, Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aam5887.","ieee":"M. P. Zagórski et al., “Decoding of position in the developing neural tube from antiparallel morphogen gradients,” Science, vol. 356, no. 6345. American Association for the Advancement of Science, pp. 1379–1383, 2017."},"quality_controlled":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568706/","open_access":"1"}],"page":"1379 - 1383","type":"journal_article","publication":"Science"},{"citation":{"chicago":"Beattie, Robert J, Maria P Postiglione, Laura Burnett, Susanne Laukoter, Carmen Streicher, Florian Pauler, Guanxi Xiao, et al. “Mosaic Analysis with Double Markers Reveals Distinct Sequential Functions of Lgl1 in Neural Stem Cells.” Neuron. Cell Press, 2017. https://doi.org/10.1016/j.neuron.2017.04.012.","ieee":"R. J. Beattie et al., “Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells,” Neuron, vol. 94, no. 3. Cell Press, p. 517–533.e3, 2017.","ista":"Beattie RJ, Postiglione MP, Burnett L, Laukoter S, Streicher C, Pauler F, Xiao G, Klezovitch O, Vasioukhin V, Ghashghaei T, Hippenmeyer S. 2017. Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. Neuron. 94(3), 517–533.e3.","mla":"Beattie, Robert J., et al. “Mosaic Analysis with Double Markers Reveals Distinct Sequential Functions of Lgl1 in Neural Stem Cells.” Neuron, vol. 94, no. 3, Cell Press, 2017, p. 517–533.e3, doi:10.1016/j.neuron.2017.04.012.","short":"R.J. Beattie, M.P. Postiglione, L. Burnett, S. Laukoter, C. Streicher, F. Pauler, G. Xiao, O. Klezovitch, V. Vasioukhin, T. Ghashghaei, S. Hippenmeyer, Neuron 94 (2017) 517–533.e3.","apa":"Beattie, R. J., Postiglione, M. P., Burnett, L., Laukoter, S., Streicher, C., Pauler, F., … Hippenmeyer, S. (2017). Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. Neuron. Cell Press. https://doi.org/10.1016/j.neuron.2017.04.012","ama":"Beattie RJ, Postiglione MP, Burnett L, et al. Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. Neuron. 2017;94(3):517-533.e3. doi:10.1016/j.neuron.2017.04.012"},"year":"2017","quality_controlled":"1","date_created":"2018-12-11T11:49:20Z","publist_id":"6473","abstract":[{"lang":"eng","text":"The concerted production of neurons and glia by neural stem cells (NSCs) is essential for neural circuit assembly. In the developing cerebral cortex, radial glia progenitors (RGPs) generate nearly all neocortical neurons and certain glia lineages. RGP proliferation behavior shows a high degree of non-stochasticity, thus a deterministic characteristic of neuron and glia production. However, the cellular and molecular mechanisms controlling RGP behavior and proliferation dynamics in neurogenesis and glia generation remain unknown. By using mosaic analysis with double markers (MADM)-based genetic paradigms enabling the sparse and global knockout with unprecedented single-cell resolution, we identified Lgl1 as a critical regulatory component. We uncover Lgl1-dependent tissue-wide community effects required for embryonic cortical neurogenesis and novel cell-autonomous Lgl1 functions controlling RGP-mediated glia genesis and postnatal NSC behavior. These results suggest that NSC-mediated neuron and glia production is tightly regulated through the concerted interplay of sequential Lgl1-dependent global and cell intrinsic mechanisms."}],"publication":"Neuron","type":"journal_article","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"page":"517 - 533.e3","month":"05","intvolume":" 94","publication_status":"published","publication_identifier":{"issn":["0896-6273"]},"isi":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","issue":"3","publisher":"Cell Press","external_id":{"isi":["000400466700011"]},"status":"public","_id":"944","date_published":"2017-05-03T00:00:00Z","corr_author":"1","ec_funded":1,"project":[{"name":"Molecular Mechanisms of Cerebral Cortex Development","grant_number":"618444","_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"RGP0053/2014","_id":"25D7962E-B435-11E9-9278-68D0E5697425","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level"}],"title":"Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells","date_updated":"2026-04-16T09:57:27Z","oa_version":"None","volume":94,"department":[{"_id":"SiHi"},{"_id":"MaJö"}],"language":[{"iso":"eng"}],"author":[{"full_name":"Beattie, Robert J","last_name":"Beattie","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J","orcid":"0000-0002-8483-8753"},{"id":"2C67902A-F248-11E8-B48F-1D18A9856A87","last_name":"Postiglione","full_name":"Postiglione, Maria P","first_name":"Maria P"},{"orcid":"0000-0002-8937-410X","first_name":"Laura","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","last_name":"Burnett","full_name":"Burnett, Laura"},{"first_name":"Susanne","orcid":"0000-0002-7903-3010","full_name":"Laukoter, Susanne","last_name":"Laukoter","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen","last_name":"Streicher","first_name":"Carmen"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","full_name":"Pauler, Florian","first_name":"Florian","orcid":"0000-0002-7462-0048"},{"first_name":"Guanxi","last_name":"Xiao","full_name":"Xiao, Guanxi"},{"first_name":"Olga","full_name":"Klezovitch, Olga","last_name":"Klezovitch"},{"full_name":"Vasioukhin, Valeri","last_name":"Vasioukhin","first_name":"Valeri"},{"full_name":"Ghashghaei, Troy","last_name":"Ghashghaei","first_name":"Troy"},{"orcid":"0000-0003-2279-1061","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"}],"day":"03","scopus_import":"1","doi":"10.1016/j.neuron.2017.04.012"},{"department":[{"_id":"DaZi"}],"language":[{"iso":"eng"}],"author":[{"full_name":"Lyons, David B","last_name":"Lyons","first_name":"David B"},{"orcid":"0000-0002-0123-8649","first_name":"Daniel","last_name":"Zilberman","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"day":"15","ddc":["570"],"scopus_import":"1","doi":"10.7554/elife.30674","has_accepted_license":"1","title":"DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes","date_updated":"2021-12-14T07:54:36Z","article_type":"original","extern":"1","file_date_updated":"2021-06-02T14:33:36Z","volume":6,"oa_version":"Published Version","article_number":"e30674","_id":"9445","date_published":"2017-11-15T00:00:00Z","article_processing_charge":"No","oa":1,"publisher":"eLife Sciences Publications","file":[{"file_id":"9446","file_name":"2017_eLife_Lyons.pdf","relation":"main_file","date_updated":"2021-06-02T14:33:36Z","date_created":"2021-06-02T14:33:36Z","file_size":1603102,"success":1,"creator":"cziletti","access_level":"open_access","content_type":"application/pdf","checksum":"4cfcdd67511ae4aed3d993550e46e146"}],"external_id":{"pmid":["29140247"]},"status":"public","pmid":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 6","publication_identifier":{"eissn":["2050-084X"]},"publication_status":"published","month":"11","year":"2017","quality_controlled":"1","citation":{"chicago":"Lyons, David B, and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/elife.30674.","ieee":"D. B. Lyons and D. Zilberman, “DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes,” eLife, vol. 6. eLife Sciences Publications, 2017.","ista":"Lyons DB, Zilberman D. 2017. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 6, e30674.","ama":"Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 2017;6. doi:10.7554/elife.30674","short":"D.B. Lyons, D. Zilberman, ELife 6 (2017).","apa":"Lyons, D. B., & Zilberman, D. (2017). DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.30674","mla":"Lyons, David B., and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife, vol. 6, e30674, eLife Sciences Publications, 2017, doi:10.7554/elife.30674."},"date_created":"2021-06-02T14:28:58Z","abstract":[{"lang":"eng","text":"Cytosine methylation regulates essential genome functions across eukaryotes, but the fundamental question of whether nucleosomal or naked DNA is the preferred substrate of plant and animal methyltransferases remains unresolved. Here, we show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome, suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases in vivo. Furthermore, we show that simultaneous mutation of DDM1 and linker histone H1 in Arabidopsis reproduces the strong linker-specific methylation patterns of species that diverged from flowering plants and animals over a billion years ago. Our results indicate that in the absence of remodeling, nucleosomes are strong barriers to DNA methyltransferases. Linker-specific methylation can evolve simply by breaking the connection between nucleosome remodeling and DNA methylation."}],"type":"journal_article","publication":"eLife"},{"ddc":["570","576"],"day":"06","author":[{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans","full_name":"Huylmans, Ann K","first_name":"Ann K","orcid":"0000-0001-8871-4961"},{"first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","full_name":"Macon, Ariana"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz","first_name":"Beatriz","orcid":"0000-0002-4579-8306"}],"has_accepted_license":"1","doi":"10.1093/molbev/msx190","scopus_import":"1","department":[{"_id":"BeVi"}],"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:48:15Z","oa_version":"Published Version","volume":34,"project":[{"call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety","_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22"}],"date_updated":"2026-04-16T09:58:19Z","title":"Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome","_id":"945","date_published":"2017-07-06T00:00:00Z","external_id":{"isi":["000411814800016"]},"file":[{"checksum":"009fd68043211d645ceb9d1de28274f2","creator":"system","access_level":"open_access","content_type":"application/pdf","file_size":462863,"file_name":"IST-2017-848-v1+1_2017_Vicoso_GlobalDosage.pdf","relation":"main_file","date_created":"2018-12-12T10:10:23Z","date_updated":"2020-07-14T12:48:15Z","file_id":"4810"}],"status":"public","issue":"10","oa":1,"article_processing_charge":"Yes (in subscription journal)","publisher":"Oxford University Press","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"isi":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","pubrep_id":"848","publication_status":"published","publication_identifier":{"issn":["0737-4038"]},"intvolume":" 34","month":"07","publication":"Molecular Biology and Evolution","type":"journal_article","page":"2637 - 2649","citation":{"chicago":"Huylmans, Ann K, Ariana Macon, and Beatriz Vicoso. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” Molecular Biology and Evolution. Oxford University Press, 2017. https://doi.org/10.1093/molbev/msx190.","ieee":"A. K. Huylmans, A. Macon, and B. Vicoso, “Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome,” Molecular Biology and Evolution, vol. 34, no. 10. Oxford University Press, pp. 2637–2649, 2017.","ista":"Huylmans AK, Macon A, Vicoso B. 2017. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. 34(10), 2637–2649.","mla":"Huylmans, Ann K., et al. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” Molecular Biology and Evolution, vol. 34, no. 10, Oxford University Press, 2017, pp. 2637–49, doi:10.1093/molbev/msx190.","short":"A.K. Huylmans, A. Macon, B. Vicoso, Molecular Biology and Evolution 34 (2017) 2637–2649.","apa":"Huylmans, A. K., Macon, A., & Vicoso, B. (2017). Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msx190","ama":"Huylmans AK, Macon A, Vicoso B. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. 2017;34(10):2637-2649. doi:10.1093/molbev/msx190"},"year":"2017","quality_controlled":"1","publist_id":"6472","abstract":[{"lang":"eng","text":"While chromosome-wide dosage compensation of the X chromosome has been found in many species, studies in ZW clades have indicated that compensation of the Z is more localized and/or incomplete. In the ZW Lepidoptera, some species show complete compensation of the Z chromosome, while others lack full equalization, but what drives these inconsistencies is unclear. Here, we compare patterns of male and female gene expression on the Z chromosome of two closely related butterfly species, Papilio xuthus and Papilio machaon, and in multiple tissues of two moths species, Plodia interpunctella and Bombyx mori, which were previously found to differ in the extent to which they equalize Z-linked gene expression between the sexes. We find that, while some species and tissues seem to have incomplete dosage compensation, this is in fact due to the accumulation of male-biased genes and the depletion of female-biased genes on the Z chromosome. Once this is accounted for, the Z chromosome is fully compensated in all four species, through the up-regulation of Z expression in females and in some cases additional down-regulation in males. We further find that both sex-biased genes and Z-linked genes have increased rates of expression divergence in this clade, and that this can lead to fast shifts in patterns of gene expression even between closely related species. Taken together, these results show that the uneven distribution of sex-biased genes on sex chromosomes can confound conclusions about dosage compensation and that Z chromosome-wide dosage compensation is not only possible but ubiquitous among Lepidoptera."}],"date_created":"2018-12-11T11:49:20Z"},{"isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pubrep_id":"847","publication_status":"published","intvolume":" 6","month":"06","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"type":"journal_article","publication":"eLife","date_created":"2018-12-11T11:49:21Z","publist_id":"6471","abstract":[{"lang":"eng","text":"Roots navigate through soil integrating environmental signals to orient their growth. The Arabidopsis root is a widely used model for developmental, physiological and cell biological studies. Live imaging greatly aids these efforts, but the horizontal sample position and continuous root tip displacement present significant difficulties. Here, we develop a confocal microscope setup for vertical sample mounting and integrated directional illumination. We present TipTracker – a custom software for automatic tracking of diverse moving objects usable on various microscope setups. Combined, this enables observation of root tips growing along the natural gravity vector over prolonged periods of time, as well as the ability to induce rapid gravity or light stimulation. We also track migrating cells in the developing zebrafish embryo, demonstrating the utility of this system in the acquisition of high-resolution data sets of dynamic samples. We provide detailed descriptions of the tools enabling the easy implementation on other microscopes."}],"quality_controlled":"1","citation":{"chicago":"Wangenheim, Daniel von, Robert Hauschild, Matyas Fendrych, Vanessa Barone, Eva Benková, and Jiří Friml. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.26792.","ieee":"D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, and J. Friml, “Live tracking of moving samples in confocal microscopy for vertically grown roots,” eLife, vol. 6. eLife Sciences Publications, 2017.","ista":"von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. 2017. Live tracking of moving samples in confocal microscopy for vertically grown roots. eLife. 6, e26792.","mla":"von Wangenheim, Daniel, et al. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” ELife, vol. 6, e26792, eLife Sciences Publications, 2017, doi:10.7554/eLife.26792.","short":"D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, J. Friml, ELife 6 (2017).","apa":"von Wangenheim, D., Hauschild, R., Fendrych, M., Barone, V., Benková, E., & Friml, J. (2017). Live tracking of moving samples in confocal microscopy for vertically grown roots. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.26792","ama":"von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. Live tracking of moving samples in confocal microscopy for vertically grown roots. eLife. 2017;6. doi:10.7554/eLife.26792"},"year":"2017","scopus_import":"1","doi":"10.7554/eLife.26792","has_accepted_license":"1","author":[{"id":"49E91952-F248-11E8-B48F-1D18A9856A87","full_name":"Von Wangenheim, Daniel","last_name":"Von Wangenheim","first_name":"Daniel","orcid":"0000-0002-6862-1247"},{"first_name":"Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matyas","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","last_name":"Fendrych","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barone","full_name":"Barone, Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","orcid":"0000-0003-2676-3367"},{"last_name":"Benková","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí","orcid":"0000-0002-8302-7596"}],"ddc":["570"],"day":"19","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"popular_science","id":"5566","status":"public"}]},"department":[{"_id":"JiFr"},{"_id":"Bio"},{"_id":"CaHe"},{"_id":"EvBe"}],"volume":6,"oa_version":"Published Version","article_number":"e26792","file_date_updated":"2020-07-14T12:48:15Z","date_updated":"2025-04-15T06:37:26Z","title":"Live tracking of moving samples in confocal microscopy for vertically grown roots","ec_funded":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"name":"Molecular basis of root growth inhibition by auxin","_id":"2572ED28-B435-11E9-9278-68D0E5697425","grant_number":"M02128","call_identifier":"FWF"},{"_id":"2542D156-B435-11E9-9278-68D0E5697425","grant_number":"I 1774-B16","name":"Hormone cross-talk drives nutrient dependent plant development","call_identifier":"FWF"},{"name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7"}],"date_published":"2017-06-19T00:00:00Z","_id":"946","external_id":{"isi":["000404728300001"]},"file":[{"checksum":"9af3398cb0d81f99d79016a616df22e9","creator":"system","access_level":"open_access","content_type":"application/pdf","file_size":19581847,"file_id":"5315","file_name":"IST-2017-847-v1+1_elife-26792-v2.pdf","relation":"main_file","date_created":"2018-12-12T10:17:57Z","date_updated":"2020-07-14T12:48:15Z"}],"status":"public","publisher":"eLife Sciences Publications","article_processing_charge":"Yes","acknowledgement":"Funding: Marie Curie Actions (FP7/2007-2013 no 291734) to Daniel von Wangenheim; Austrian Science Fund (M 2128-B21) to Matyáš Fendrych; Austrian Science Fund (FWF01_I1774S) to Eva Benková; European Research Council (FP7/2007-2013 no 282300) to Jiří Friml. \r\nThe authors are grateful to the Miba Machine Shop at IST Austria for their contribution to the microscope setup and to Yvonne Kemper for reading, understanding and correcting the manuscript.\r\n#BioimagingFacility","oa":1},{"month":"09","conference":{"start_date":"2017-09-05","location":"Berlin, Germany","name":"CONCUR: Concurrency Theory","end_date":"2017-09-07"},"type":"conference","quality_controlled":"1","citation":{"short":"G. Avni, T.A. Henzinger, V.K. Chonev, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Avni, Guy, et al. Infinite-Duration Bidding Games. Vol. 85, 17, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.CONCUR.2017.21.","apa":"Avni, G., Henzinger, T. A., & Chonev, V. K. (2017). Infinite-duration bidding games (Vol. 85). Presented at the CONCUR: Concurrency Theory, Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2017.21","ama":"Avni G, Henzinger TA, Chonev VK. Infinite-duration bidding games. In: Vol 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.CONCUR.2017.21","ista":"Avni G, Henzinger TA, Chonev VK. 2017. Infinite-duration bidding games. CONCUR: Concurrency Theory, LIPIcs, vol. 85, 17.","ieee":"G. Avni, T. A. Henzinger, and V. K. Chonev, “Infinite-duration bidding games,” presented at the CONCUR: Concurrency Theory, Berlin, Germany, 2017, vol. 85.","chicago":"Avni, Guy, Thomas A Henzinger, and Ventsislav K Chonev. “Infinite-Duration Bidding Games,” Vol. 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.CONCUR.2017.21."},"year":"2017","date_created":"2018-12-11T11:49:22Z","publist_id":"6466","abstract":[{"text":"Two-player games on graphs are widely studied in formal methods as they model the interaction between a system and its environment. The game is played by moving a token throughout a graph to produce an infinite path. There are several common modes to determine how the players move the token through the graph; e.g., in turn-based games the players alternate turns in moving the token. We study the bidding mode of moving the token, which, to the best of our knowledge, has never been studied in infinite-duration games. Both players have separate budgets, which sum up to $1$. In each turn, a bidding takes place. Both players submit bids simultaneously, and a bid is legal if it does not exceed the available budget. The winner of the bidding pays his bid to the other player and moves the token. For reachability objectives, repeated bidding games have been studied and are called Richman games. There, a central question is the existence and computation of threshold budgets; namely, a value t\\in [0,1] such that if\\PO's budget exceeds $t$, he can win the game, and if\\PT's budget exceeds 1-t, he can win the game. We focus on parity games and mean-payoff games. We show the existence of threshold budgets in these games, and reduce the problem of finding them to Richman games. We also determine the strategy-complexity of an optimal strategy. Our most interesting result shows that memoryless strategies suffice for mean-payoff bidding games. \r\n","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pubrep_id":"844","publication_status":"published","publication_identifier":{"issn":["1868-8969"]},"alternative_title":["LIPIcs"],"intvolume":" 85","arxiv":1,"_id":"950","date_published":"2017-09-01T00:00:00Z","external_id":{"arxiv":["1705.01433"]},"file":[{"file_size":335170,"file_id":"5318","file_name":"IST-2017-844-v1+1_concur-cr.pdf","date_created":"2018-12-12T10:18:00Z","relation":"main_file","date_updated":"2020-07-14T12:48:16Z","checksum":"6d5cccf755207b91ccbef95d8275b013","creator":"system","access_level":"open_access","content_type":"application/pdf"}],"status":"public","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"full_name":"Avni, Guy","last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy","orcid":"0000-0001-5588-8287"},{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"last_name":"Chonev","full_name":"Chonev, Ventsislav K","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Ventsislav K"}],"day":"01","ddc":["000"],"scopus_import":1,"doi":"10.4230/LIPIcs.CONCUR.2017.21","has_accepted_license":"1","related_material":{"record":[{"status":"public","id":"6752","relation":"later_version"}]},"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:48:16Z","oa_version":"Published Version","volume":85,"article_number":"17","project":[{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF"}],"title":"Infinite-duration bidding games","date_updated":"2025-07-10T11:53:48Z"},{"_id":"9506","date_published":"2017-05-09T00:00:00Z","status":"public","file":[{"file_name":"2017_GenomeBiology_Zilberman.pdf","date_created":"2021-06-07T12:31:36Z","date_updated":"2021-06-07T12:31:36Z","relation":"main_file","file_id":"9507","file_size":278183,"creator":"asandaue","content_type":"application/pdf","access_level":"open_access","success":1,"checksum":"5a455ad914e7d225b1baa4ab07fd925e"}],"external_id":{"pmid":["28486944"]},"pmid":1,"article_processing_charge":"No","issue":"1","oa":1,"publisher":"Springer Nature","author":[{"full_name":"Zilberman, Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","orcid":"0000-0002-0123-8649"}],"day":"09","ddc":["570"],"scopus_import":"1","doi":"10.1186/s13059-017-1230-2","has_accepted_license":"1","department":[{"_id":"DaZi"}],"language":[{"iso":"eng"}],"file_date_updated":"2021-06-07T12:31:36Z","extern":"1","oa_version":"Published Version","volume":18,"article_number":"87","title":"An evolutionary case for functional gene body methylation in plants and animals","date_updated":"2021-12-14T07:55:02Z","month":"05","publication":"Genome Biology","type":"journal_article","quality_controlled":"1","year":"2017","citation":{"ista":"Zilberman D. 2017. An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. 18(1), 87.","ama":"Zilberman D. An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. 2017;18(1). doi:10.1186/s13059-017-1230-2","short":"D. Zilberman, Genome Biology 18 (2017).","apa":"Zilberman, D. (2017). An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-017-1230-2","mla":"Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation in Plants and Animals.” Genome Biology, vol. 18, no. 1, 87, Springer Nature, 2017, doi:10.1186/s13059-017-1230-2.","chicago":"Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation in Plants and Animals.” Genome Biology. Springer Nature, 2017. https://doi.org/10.1186/s13059-017-1230-2.","ieee":"D. Zilberman, “An evolutionary case for functional gene body methylation in plants and animals,” Genome Biology, vol. 18, no. 1. Springer Nature, 2017."},"date_created":"2021-06-07T12:27:39Z","abstract":[{"lang":"eng","text":"Methylation in the bodies of active genes is common in animals and vascular plants. Evolutionary patterns indicate homeostatic functions for this type of methylation."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"eissn":["1465-6906"],"issn":["1474-760X"]},"publication_status":"published","intvolume":" 18"},{"month":"06","quality_controlled":"1","citation":{"ieee":"M. Turelli and N. H. Barton, “Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti,” Theoretical Population Biology, vol. 115. Elsevier, pp. 45–60, 2017.","chicago":"Turelli, Michael, and Nicholas H Barton. “Deploying Dengue-Suppressing Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” Theoretical Population Biology. Elsevier, 2017. https://doi.org/10.1016/j.tpb.2017.03.003.","short":"M. Turelli, N.H. Barton, Theoretical Population Biology 115 (2017) 45–60.","apa":"Turelli, M., & Barton, N. H. (2017). Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2017.03.003","mla":"Turelli, Michael, and Nicholas H. Barton. “Deploying Dengue-Suppressing Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” Theoretical Population Biology, vol. 115, Elsevier, 2017, pp. 45–60, doi:10.1016/j.tpb.2017.03.003.","ama":"Turelli M, Barton NH. Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. 2017;115:45-60. doi:10.1016/j.tpb.2017.03.003","ista":"Turelli M, Barton NH. 2017. Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. 115, 45–60."},"year":"2017","date_created":"2018-12-11T11:49:22Z","publist_id":"6463","abstract":[{"lang":"eng","text":"A novel strategy for controlling the spread of arboviral diseases such as dengue, Zika and chikungunya is to transform mosquito populations with virus-suppressing Wolbachia. In general, Wolbachia transinfected into mosquitoes induce fitness costs through lower viability or fecundity. These maternally inherited bacteria also produce a frequency-dependent advantage for infected females by inducing cytoplasmic incompatibility (CI), which kills the embryos produced by uninfected females mated to infected males. These competing effects, a frequency-dependent advantage and frequency-independent costs, produce bistable Wolbachia frequency dynamics. Above a threshold frequency, denoted pˆ, CI drives fitness-decreasing Wolbachia transinfections through local populations; but below pˆ, infection frequencies tend to decline to zero. If pˆ is not too high, CI also drives spatial spread once infections become established over sufficiently large areas. We illustrate how simple models provide testable predictions concerning the spatial and temporal dynamics of Wolbachia introductions, focusing on rate of spatial spread, the shape of spreading waves, and the conditions for initiating spread from local introductions. First, we consider the robustness of diffusion-based predictions to incorporating two important features of wMel-Aedes aegypti biology that may be inconsistent with the diffusion approximations, namely fast local dynamics induced by complete CI (i.e., all embryos produced from incompatible crosses die) and long-tailed, non-Gaussian dispersal. With complete CI, our numerical analyses show that long-tailed dispersal changes wave-width predictions only slightly; but it can significantly reduce wave speed relative to the diffusion prediction; it also allows smaller local introductions to initiate spatial spread. Second, we use approximations for pˆ and dispersal distances to predict the outcome of 2013 releases of wMel-infected Aedes aegypti in Cairns, Australia, Third, we describe new data from Ae. aegypti populations near Cairns, Australia that demonstrate long-distance dispersal and provide an approximate lower bound on pˆ for wMel in northeastern Australia. Finally, we apply our analyses to produce operational guidelines for efficient transformation of vector populations over large areas. We demonstrate that even very slow spatial spread, on the order of 10-20 m/month (as predicted), can produce area-wide population transformation within a few years following initial releases covering about 20-30% of the target area."}],"publication":"Theoretical Population Biology","type":"journal_article","page":"45 - 60","pubrep_id":"972","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 115","publication_status":"published","publication_identifier":{"issn":["0040-5809"]},"_id":"952","date_published":"2017-06-01T00:00:00Z","article_processing_charge":"No","oa":1,"publisher":"Elsevier","external_id":{"pmid":["28411063"]},"file":[{"file_size":2073856,"file_id":"6327","relation":"main_file","date_updated":"2020-07-14T12:48:16Z","date_created":"2019-04-17T06:39:45Z","file_name":"2017_TheoreticalPopulationBio_Turelli.pdf","checksum":"9aeff86fa7de69f7a15cf4fc60d57d01","access_level":"open_access","content_type":"application/pdf","creator":"dernst"}],"status":"public","pmid":1,"department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"author":[{"full_name":"Turelli, Michael","last_name":"Turelli","first_name":"Michael"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"}],"day":"01","ddc":["576"],"scopus_import":"1","doi":"10.1016/j.tpb.2017.03.003","has_accepted_license":"1","date_updated":"2025-07-10T12:01:49Z","title":"Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2020-07-14T12:48:16Z","volume":115,"oa_version":"Submitted Version"},{"project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","call_identifier":"FP7"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"call_identifier":"H2020","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer"}],"ec_funded":1,"date_updated":"2025-07-10T12:01:50Z","title":"On the mechanistic nature of epistasis in a canonical cis-regulatory element","file_date_updated":"2020-07-14T12:48:16Z","article_number":"e25192","oa_version":"Published Version","volume":6,"department":[{"_id":"CaGu"},{"_id":"NiBa"},{"_id":"JoBo"}],"language":[{"iso":"eng"}],"ddc":["576"],"day":"18","author":[{"first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","full_name":"Lagator, Mato"},{"orcid":"0000-0003-2361-3953","first_name":"Tiago","full_name":"Paixao, Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"},{"first_name":"Jonathan P","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","doi":"10.7554/eLife.25192","scopus_import":"1","oa":1,"article_processing_charge":"Yes","publisher":"eLife Sciences Publications","external_id":{"isi":["000404024800001"]},"file":[{"checksum":"59cdd4400fb41280122d414fea971546","creator":"system","access_level":"open_access","content_type":"application/pdf","file_size":2441529,"file_id":"5306","file_name":"IST-2017-841-v1+1_elife-25192-v2.pdf","relation":"main_file","date_created":"2018-12-12T10:17:49Z","date_updated":"2020-07-14T12:48:16Z"},{"file_id":"5307","file_name":"IST-2017-841-v1+2_elife-25192-figures-v2.pdf","relation":"main_file","date_created":"2018-12-12T10:17:50Z","date_updated":"2020-07-14T12:48:16Z","file_size":3752660,"creator":"system","content_type":"application/pdf","access_level":"open_access","checksum":"b69024880558b858eb8c5d47a92b6377"}],"status":"public","_id":"954","date_published":"2017-05-18T00:00:00Z","intvolume":" 6","publication_identifier":{"issn":["2050-084X"]},"publication_status":"published","pubrep_id":"841","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","citation":{"ista":"Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. 2017. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 6, e25192.","apa":"Lagator, M., Paixao, T., Barton, N. H., Bollback, J. P., & Guet, C. C. (2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25192","short":"M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017).","mla":"Lagator, Mato, et al. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife, vol. 6, e25192, eLife Sciences Publications, 2017, doi:10.7554/eLife.25192.","ama":"Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 2017;6. doi:10.7554/eLife.25192","chicago":"Lagator, Mato, Tiago Paixao, Nicholas H Barton, Jonathan P Bollback, and Calin C Guet. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25192.","ieee":"M. Lagator, T. Paixao, N. H. Barton, J. P. Bollback, and C. C. Guet, “On the mechanistic nature of epistasis in a canonical cis-regulatory element,” eLife, vol. 6. eLife Sciences Publications, 2017."},"year":"2017","abstract":[{"text":"Understanding the relation between genotype and phenotype remains a major challenge. The difficulty of predicting individual mutation effects, and particularly the interactions between them, has prevented the development of a comprehensive theory that links genotypic changes to their phenotypic effects. We show that a general thermodynamic framework for gene regulation, based on a biophysical understanding of protein-DNA binding, accurately predicts the sign of epistasis in a canonical cis-regulatory element consisting of overlapping RNA polymerase and repressor binding sites. Sign and magnitude of individual mutation effects are sufficient to predict the sign of epistasis and its environmental dependence. Thus, the thermodynamic model offers the correct null prediction for epistasis between mutations across DNA-binding sites. Our results indicate that a predictive theory for the effects of cis-regulatory mutations is possible from first principles, as long as the essential molecular mechanisms and the constraints these impose on a biological system are accounted for.","lang":"eng"}],"publist_id":"6460","date_created":"2018-12-11T11:49:23Z","type":"journal_article","publication":"eLife","month":"05"}]