[{"doi":"10.1109/CVPR.2017.747","publication_identifier":{"isbn":["978-153860457-1"]},"date_created":"2018-12-11T11:49:11Z","year":"2017","has_accepted_license":"1","ddc":["000"],"conference":{"start_date":"2017-07-21","name":"CVPR: Computer Vision and Pattern Recognition","end_date":"2017-07-26","location":"Honolulu, HA, United States"},"corr_author":"1","file":[{"date_created":"2019-01-18T12:49:38Z","content_type":"application/pdf","file_name":"2017_CVPR_Swoboda2.pdf","creator":"dernst","file_id":"5848","access_level":"open_access","relation":"main_file","checksum":"e38a2740daad1ea178465843b5072906","file_size":944332,"date_updated":"2020-07-14T12:48:15Z"}],"quality_controlled":"1","author":[{"first_name":"Paul","last_name":"Swoboda","id":"446560C6-F248-11E8-B48F-1D18A9856A87","full_name":"Swoboda, Paul"},{"full_name":"Rother, Carsten","last_name":"Rother","first_name":"Carsten"},{"full_name":"Abu Alhaija, Carsten","last_name":"Abu Alhaija","first_name":"Carsten"},{"first_name":"Dagmar","last_name":"Kainmueller","full_name":"Kainmueller, Dagmar"},{"full_name":"Savchynskyy, Bogdan","last_name":"Savchynskyy","first_name":"Bogdan"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":2017,"title":"A study of lagrangean decompositions and dual ascent solvers for graph matching","article_processing_charge":"No","page":"7062-7071","external_id":{"isi":["000418371407018"]},"publication_status":"published","abstract":[{"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.","lang":"eng"}],"status":"public","day":"01","ec_funded":1,"citation":{"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","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.","short":"P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, B. Savchynskyy, in:, IEEE, 2017, pp. 7062–7071.","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.","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.","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","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."},"project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"publist_id":"6525","scopus_import":"1","_id":"916","intvolume":" 2017","oa_version":"Submitted Version","type":"conference","date_published":"2017-01-01T00:00:00Z","language":[{"iso":"eng"}],"month":"01","date_updated":"2024-11-04T13:52:34Z","department":[{"_id":"VlKo"}],"publisher":"IEEE","isi":1,"file_date_updated":"2020-07-14T12:48:15Z","oa":1},{"isi":1,"oa":1,"file_date_updated":"2020-07-14T12:48:15Z","language":[{"iso":"eng"}],"month":"07","date_published":"2017-07-01T00:00:00Z","publisher":"IEEE","department":[{"_id":"VlKo"}],"date_updated":"2024-11-04T13:52:34Z","intvolume":" 2017","oa_version":"Submitted Version","type":"conference","publist_id":"6524","_id":"917","scopus_import":"1","citation":{"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.","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","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.","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","short":"P. Swoboda, J. Kuske, B. Savchynskyy, in:, IEEE, 2017, pp. 4950–4960.","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."},"project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"ec_funded":1,"status":"public","day":"01","page":"4950-4960","article_processing_charge":"No","abstract":[{"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.","lang":"eng"}],"external_id":{"isi":["000418371405005"]},"publication_status":"published","title":"A dual ascent framework for Lagrangean decomposition of combinatorial problems","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Paul","last_name":"Swoboda","full_name":"Swoboda, Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kuske","first_name":"Jan","full_name":"Kuske, Jan"},{"full_name":"Savchynskyy, Bogdan","last_name":"Savchynskyy","first_name":"Bogdan"}],"volume":2017,"corr_author":"1","file":[{"creator":"dernst","date_created":"2019-01-18T12:45:55Z","file_name":"2017_CVPR_Swoboda.pdf","content_type":"application/pdf","relation":"main_file","checksum":"72fd291046bd8e5717961bd68f6b6f03","access_level":"open_access","file_size":898652,"date_updated":"2020-07-14T12:48:15Z","file_id":"5847"}],"quality_controlled":"1","has_accepted_license":"1","ddc":["000"],"conference":{"name":"CVPR: Computer Vision and Pattern Recognition","start_date":"2017-07-21","location":"Honolulu, HA, United States","end_date":"2017-07-26"},"year":"2017","date_created":"2018-12-11T11:49:11Z","publication_identifier":{"isbn":["978-153860457-1"]},"doi":"10.1109/CVPR.2017.526"},{"publist_id":"6483","_id":"938","oa_version":"Published Version","type":"dissertation","date_published":"2017-06-02T00:00:00Z","language":[{"iso":"eng"}],"month":"06","date_updated":"2026-04-08T14:20:45Z","department":[{"_id":"JiFr"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-07-14T12:48:15Z","oa":1,"alternative_title":["ISTA Thesis"],"day":"02","pubrep_id":"842","status":"public","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.","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.","short":"M. Adamowski, Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana , Institute of Science and Technology Austria, 2017.","ieee":"M. Adamowski, “Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ,” Institute of Science and Technology Austria, 2017.","ama":"Adamowski M. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . 2017. doi:10.15479/AT:ISTA:th_842","ista":"Adamowski M. 2017. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria."},"related_material":{"record":[{"relation":"part_of_dissertation","id":"1591","status":"public"}]},"author":[{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","first_name":"Maciek","last_name":"Adamowski"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","supervisor":[{"last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"title":"Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ","degree_awarded":"PhD","article_processing_charge":"No","page":"117","publication_status":"published","abstract":[{"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.","lang":"eng"}],"doi":"10.15479/AT:ISTA:th_842","publication_identifier":{"issn":["2663-337X"]},"date_created":"2018-12-11T11:49:18Z","year":"2017","has_accepted_license":"1","ddc":["581","583","580"],"corr_author":"1","file":[{"file_name":"2017_Adamowski-Thesis_Source.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2019-04-05T09:03:20Z","creator":"dernst","file_id":"6215","date_updated":"2020-07-14T12:48:15Z","file_size":46903863,"checksum":"193425764d9aaaed3ac57062a867b315","relation":"source_file","access_level":"closed"},{"date_updated":"2020-07-14T12:48:15Z","file_size":8698888,"relation":"main_file","checksum":"df5ab01be81f821e1b958596a1ec8d21","access_level":"open_access","file_id":"6216","creator":"dernst","content_type":"application/pdf","file_name":"2017_Adamowski-Thesis.pdf","date_created":"2019-04-05T09:03:19Z"}]},{"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"citation":{"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","ista":"Midya B, Konotop V. 2017. Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. 119(3), 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.","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.","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","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."},"day":"18","status":"public","ec_funded":1,"date_updated":"2025-06-04T08:20:23Z","arxiv":1,"publisher":"American Physical Society","department":[{"_id":"MiLe"}],"date_published":"2017-07-18T00:00:00Z","month":"07","language":[{"iso":"eng"}],"oa":1,"isi":1,"scopus_import":"1","_id":"939","publist_id":"6481","type":"journal_article","intvolume":" 119","oa_version":"Submitted Version","main_file_link":[{"url":"https://arxiv.org/abs/1706.04085 ","open_access":"1"}],"quality_controlled":"1","corr_author":"1","publication":"Physical Review Letters","doi":"10.1103/PhysRevLett.119.033905","publication_identifier":{"issn":["0031-9007"]},"issue":"3","article_number":"033905","date_created":"2018-12-11T11:49:18Z","year":"2017","title":"Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons","publication_status":"published","external_id":{"isi":["000405718200012"],"arxiv":["1706.04085 "]},"abstract":[{"lang":"eng","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."}],"article_processing_charge":"No","volume":119,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Midya, Bikashkali","id":"456187FC-F248-11E8-B48F-1D18A9856A87","last_name":"Midya","first_name":"Bikashkali"},{"last_name":"Konotop","first_name":"Vladimir","full_name":"Konotop, Vladimir"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Xuan","last_name":"Le","full_name":"Le, Xuan"},{"first_name":"Duc Hiep","last_name":"Chu","full_name":"Chu, Duc Hiep","id":"3598E630-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lo","first_name":"David","full_name":"Lo, David"},{"first_name":"Claire","last_name":"Le Goues","full_name":"Le Goues, Claire"},{"full_name":"Visser, Willem","first_name":"Willem","last_name":"Visser"}],"title":"JFIX: Semantics-based repair of Java programs via symbolic PathFinder","publication_status":"published","external_id":{"isi":["000462903600038"]},"abstract":[{"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/ ","lang":"eng"}],"article_processing_charge":"No","page":"376 - 379 ","publication":"Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis","doi":"10.1145/3092703.3098225","date_created":"2018-12-11T11:49:19Z","year":"2017","conference":{"location":"Santa Barbara, CA, United States","end_date":"2017-07-14","start_date":"2017-07-10","name":"ISSTA: International Symposium on Software Testing and Analysis"},"ddc":["000"],"main_file_link":[{"url":"https://core.ac.uk/download/pdf/111759662.pdf","open_access":"1"}],"quality_controlled":"1","corr_author":"1","scopus_import":"1","_id":"941","publist_id":"6478","type":"conference","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).","oa_version":"Published Version","date_updated":"2026-06-18T19:51:19Z","department":[{"_id":"ToHe"}],"publisher":"ACM","date_published":"2017-07-10T00:00:00Z","month":"07","language":[{"iso":"eng"}],"oa":1,"isi":1,"status":"public","day":"10","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"citation":{"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.","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","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.","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.","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.","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.","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"}},{"citation":{"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.","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","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.","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","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.","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.","short":"X. Le, D.H. Chu, D. Lo, C. Le Goues, W. Visser, in:, ACM, 2017, pp. 593–604."},"project":[{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","call_identifier":"FWF","name":"Moderne Concurrency Paradigms"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems"}],"status":"public","day":"01","date_published":"2017-09-01T00:00:00Z","language":[{"iso":"eng"}],"month":"09","date_updated":"2025-04-15T06:25:57Z","publisher":"ACM","department":[{"_id":"ToHe"}],"isi":1,"publist_id":"6477","scopus_import":"1","_id":"942","oa_version":"None","type":"conference","conference":{"end_date":"2017-09-08","location":"Paderborn, Germany","name":"FSE: Foundations of Software Engineering","start_date":"2017-09-04"},"quality_controlled":"1","publication_identifier":{"isbn":["978-145035105-8"]},"doi":"10.1145/3106237.3106309","date_created":"2018-12-11T11:49:19Z","year":"2017","title":"S3: Syntax- and semantic-guided repair synthesis via programming by examples","article_processing_charge":"No","page":"593 - 604","publication_status":"published","external_id":{"isi":["000414279300055"]},"abstract":[{"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. ","lang":"eng"}],"author":[{"last_name":"Le","first_name":"Xuan","full_name":"Le, Xuan"},{"last_name":"Chu","first_name":"Duc Hiep","full_name":"Chu, Duc Hiep","id":"3598E630-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","last_name":"Lo","full_name":"Lo, David"},{"full_name":"Le Goues, Claire","first_name":"Claire","last_name":"Le Goues"},{"full_name":"Visser, Willem","first_name":"Willem","last_name":"Visser"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":"F130154"},{"publication":"Science","issue":"6345","doi":"10.1126/science.aam5887","publication_identifier":{"issn":["0036-8075"]},"year":"2017","date_created":"2018-12-11T11:49:20Z","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568706/"}],"quality_controlled":"1","corr_author":"1","pmid":1,"volume":356,"author":[{"full_name":"Zagórski, Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7896-7762","first_name":"Marcin P","last_name":"Zagórski"},{"first_name":"Yoji","last_name":"Tabata","full_name":"Tabata, Yoji"},{"last_name":"Brandenberg","first_name":"Nathalie","full_name":"Brandenberg, Nathalie"},{"last_name":"Lutolf","first_name":"Matthias","full_name":"Lutolf, Matthias"},{"last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"},{"last_name":"Bollenbach","first_name":"Tobias","full_name":"Bollenbach, Tobias"},{"full_name":"Briscoe, James","last_name":"Briscoe","first_name":"James"},{"full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","first_name":"Anna"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Decoding of position in the developing neural tube from antiparallel morphogen gradients","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."}],"publication_status":"published","external_id":{"pmid":["28663499"],"isi":["000404351500036"]},"page":"1379 - 1383","article_processing_charge":"No","status":"public","day":"30","ec_funded":1,"project":[{"grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF"},{"grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"201439","_id":"2524F500-B435-11E9-9278-68D0E5697425","name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish","call_identifier":"FP7"}],"citation":{"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.","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","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","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.","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.","short":"M.P. Zagórski, Y. Tabata, N. Brandenberg, M. Lutolf, G. Tkačik, T. Bollenbach, J. Briscoe, A. Kicheva, Science 356 (2017) 1379–1383."},"_id":"943","scopus_import":"1","publist_id":"6474","type":"journal_article","oa_version":"Submitted Version","intvolume":" 356","publisher":"American Association for the Advancement of Science","department":[{"_id":"AnKi"},{"_id":"GaTk"}],"date_updated":"2025-07-10T12:01:45Z","language":[{"iso":"eng"}],"month":"06","date_published":"2017-06-30T00:00:00Z","oa":1,"isi":1},{"oa_version":"None","intvolume":" 94","type":"journal_article","publist_id":"6473","scopus_import":"1","_id":"944","isi":1,"date_published":"2017-05-03T00:00:00Z","month":"05","language":[{"iso":"eng"}],"date_updated":"2026-04-16T09:57:27Z","department":[{"_id":"SiHi"},{"_id":"MaJö"}],"publisher":"Cell Press","ec_funded":1,"status":"public","day":"03","citation":{"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","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.","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.","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.","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.","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.","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"},"project":[{"call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development","_id":"25D61E48-B435-11E9-9278-68D0E5697425","grant_number":"618444"},{"name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","grant_number":"RGP0053/2014","_id":"25D7962E-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Beattie, Robert J","orcid":"0000-0002-8483-8753","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J","last_name":"Beattie"},{"id":"2C67902A-F248-11E8-B48F-1D18A9856A87","full_name":"Postiglione, Maria P","first_name":"Maria P","last_name":"Postiglione"},{"full_name":"Burnett, Laura","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8937-410X","first_name":"Laura","last_name":"Burnett"},{"first_name":"Susanne","last_name":"Laukoter","full_name":"Laukoter, Susanne","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7903-3010"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen","first_name":"Carmen","last_name":"Streicher"},{"first_name":"Florian","last_name":"Pauler","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048"},{"full_name":"Xiao, Guanxi","first_name":"Guanxi","last_name":"Xiao"},{"full_name":"Klezovitch, Olga","first_name":"Olga","last_name":"Klezovitch"},{"full_name":"Vasioukhin, Valeri","last_name":"Vasioukhin","first_name":"Valeri"},{"first_name":"Troy","last_name":"Ghashghaei","full_name":"Ghashghaei, Troy"},{"first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","volume":94,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"article_processing_charge":"No","page":"517 - 533.e3","external_id":{"isi":["000400466700011"]},"publication_status":"published","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."}],"title":"Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells","date_created":"2018-12-11T11:49:20Z","year":"2017","doi":"10.1016/j.neuron.2017.04.012","publication_identifier":{"issn":["0896-6273"]},"issue":"3","publication":"Neuron","corr_author":"1","quality_controlled":"1"},{"scopus_import":"1","_id":"9445","type":"journal_article","intvolume":" 6","oa_version":"Published Version","article_type":"original","date_updated":"2021-12-14T07:54:36Z","department":[{"_id":"DaZi"}],"publisher":"eLife Sciences Publications","date_published":"2017-11-15T00:00:00Z","month":"11","language":[{"iso":"eng"}],"file_date_updated":"2021-06-02T14:33:36Z","oa":1,"day":"15","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"ama":"Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 2017;6. doi:10.7554/elife.30674","ista":"Lyons DB, Zilberman D. 2017. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 6, e30674.","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.","short":"D.B. Lyons, D. Zilberman, ELife 6 (2017).","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.","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","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."},"pmid":1,"volume":6,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"first_name":"David B","last_name":"Lyons","full_name":"Lyons, David B"},{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel"}],"extern":"1","title":"DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes","external_id":{"pmid":["29140247"]},"publication_status":"published","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."}],"article_processing_charge":"No","license":"https://creativecommons.org/licenses/by/4.0/","publication":"eLife","publication_identifier":{"eissn":["2050-084X"]},"doi":"10.7554/elife.30674","article_number":"e30674","date_created":"2021-06-02T14:28:58Z","year":"2017","ddc":["570"],"has_accepted_license":"1","quality_controlled":"1","file":[{"checksum":"4cfcdd67511ae4aed3d993550e46e146","relation":"main_file","access_level":"open_access","date_updated":"2021-06-02T14:33:36Z","file_size":1603102,"file_id":"9446","creator":"cziletti","success":1,"date_created":"2021-06-02T14:33:36Z","file_name":"2017_eLife_Lyons.pdf","content_type":"application/pdf"}]},{"oa":1,"file_date_updated":"2020-07-14T12:48:15Z","isi":1,"department":[{"_id":"BeVi"}],"publisher":"Oxford University Press","date_updated":"2026-04-16T09:58:19Z","month":"07","language":[{"iso":"eng"}],"date_published":"2017-07-06T00:00:00Z","type":"journal_article","intvolume":" 34","oa_version":"Published Version","_id":"945","scopus_import":"1","publist_id":"6472","project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22","call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety"}],"citation":{"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","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.","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.","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.","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"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"848","day":"06","abstract":[{"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.","lang":"eng"}],"publication_status":"published","external_id":{"isi":["000411814800016"]},"page":"2637 - 2649","article_processing_charge":"Yes (in subscription journal)","title":"Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome","volume":34,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961","full_name":"Huylmans, Ann K","first_name":"Ann K","last_name":"Huylmans"},{"last_name":"Macon","first_name":"Ariana","full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"file":[{"file_id":"4810","date_updated":"2020-07-14T12:48:15Z","file_size":462863,"relation":"main_file","checksum":"009fd68043211d645ceb9d1de28274f2","access_level":"open_access","file_name":"IST-2017-848-v1+1_2017_Vicoso_GlobalDosage.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:10:23Z","creator":"system"}],"quality_controlled":"1","ddc":["570","576"],"has_accepted_license":"1","year":"2017","date_created":"2018-12-11T11:49:20Z","publication":"Molecular Biology and Evolution","issue":"10","doi":"10.1093/molbev/msx190","publication_identifier":{"issn":["0737-4038"]}},{"ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"pubrep_id":"847","status":"public","day":"19","citation":{"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.","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.","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","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.","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.","short":"D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, J. Friml, ELife 6 (2017)."},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"_id":"2572ED28-B435-11E9-9278-68D0E5697425","grant_number":"M02128","call_identifier":"FWF","name":"Molecular basis of root growth inhibition by auxin"},{"name":"Hormone cross-talk drives nutrient dependent plant development","call_identifier":"FWF","grant_number":"I 1774-B16","_id":"2542D156-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"oa_version":"Published Version","intvolume":" 6","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","type":"journal_article","publist_id":"6471","_id":"946","scopus_import":"1","isi":1,"oa":1,"file_date_updated":"2020-07-14T12:48:15Z","language":[{"iso":"eng"}],"month":"06","date_published":"2017-06-19T00:00:00Z","department":[{"_id":"JiFr"},{"_id":"Bio"},{"_id":"CaHe"},{"_id":"EvBe"}],"publisher":"eLife Sciences Publications","date_updated":"2025-04-15T06:37:26Z","year":"2017","date_created":"2018-12-11T11:49:21Z","article_number":"e26792","doi":"10.7554/eLife.26792","publication":"eLife","file":[{"date_updated":"2020-07-14T12:48:15Z","file_size":19581847,"access_level":"open_access","relation":"main_file","checksum":"9af3398cb0d81f99d79016a616df22e9","file_id":"5315","creator":"system","file_name":"IST-2017-847-v1+1_elife-26792-v2.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:17:57Z"}],"quality_controlled":"1","has_accepted_license":"1","ddc":["570"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Von Wangenheim, Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247","last_name":"Von Wangenheim","first_name":"Daniel"},{"first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fendrych","first_name":"Matyas","full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699"},{"id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa","last_name":"Barone","first_name":"Vanessa"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva"},{"last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"volume":6,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"related_material":{"record":[{"status":"public","relation":"popular_science","id":"5566"}]},"article_processing_charge":"Yes","abstract":[{"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.","lang":"eng"}],"external_id":{"isi":["000404728300001"]},"publication_status":"published","title":"Live tracking of moving samples in confocal microscopy for vertically grown roots"},{"status":"public","pubrep_id":"844","day":"01","alternative_title":["LIPIcs"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"citation":{"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.","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","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.","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.","short":"G. Avni, T.A. Henzinger, V.K. Chonev, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","ista":"Avni G, Henzinger TA, Chonev VK. 2017. Infinite-duration bidding games. CONCUR: Concurrency Theory, LIPIcs, vol. 85, 17.","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"},"_id":"950","scopus_import":1,"publist_id":"6466","type":"conference","oa_version":"Published Version","intvolume":" 85","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"arxiv":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_updated":"2025-07-10T11:53:48Z","month":"09","language":[{"iso":"eng"}],"date_published":"2017-09-01T00:00:00Z","oa":1,"file_date_updated":"2020-07-14T12:48:16Z","publication_identifier":{"issn":["1868-8969"]},"doi":"10.4230/LIPIcs.CONCUR.2017.21","article_number":"17","year":"2017","date_created":"2018-12-11T11:49:22Z","ddc":["000"],"conference":{"name":"CONCUR: Concurrency Theory","start_date":"2017-09-05","end_date":"2017-09-07","location":"Berlin, Germany"},"has_accepted_license":"1","quality_controlled":"1","file":[{"creator":"system","date_created":"2018-12-12T10:18:00Z","content_type":"application/pdf","file_name":"IST-2017-844-v1+1_concur-cr.pdf","access_level":"open_access","checksum":"6d5cccf755207b91ccbef95d8275b013","relation":"main_file","date_updated":"2020-07-14T12:48:16Z","file_size":335170,"file_id":"5318"}],"related_material":{"record":[{"status":"public","id":"6752","relation":"later_version"}]},"volume":85,"author":[{"full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","first_name":"Guy","last_name":"Avni"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Chonev, Ventsislav K","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Ventsislav K","last_name":"Chonev"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Infinite-duration bidding games","abstract":[{"lang":"eng","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"}],"external_id":{"arxiv":["1705.01433"]},"publication_status":"published"},{"_id":"9506","scopus_import":"1","oa_version":"Published Version","intvolume":" 18","type":"journal_article","month":"05","language":[{"iso":"eng"}],"date_published":"2017-05-09T00:00:00Z","department":[{"_id":"DaZi"}],"publisher":"Springer Nature","date_updated":"2021-12-14T07:55:02Z","oa":1,"file_date_updated":"2021-06-07T12:31:36Z","day":"09","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"short":"D. Zilberman, Genome Biology 18 (2017).","ieee":"D. Zilberman, “An evolutionary case for functional gene body methylation in plants and animals,” Genome Biology, vol. 18, no. 1. Springer Nature, 2017.","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","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.","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."},"pmid":1,"extern":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"first_name":"Daniel","last_name":"Zilberman","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"}],"volume":18,"title":"An evolutionary case for functional gene body methylation in plants and animals","article_processing_charge":"No","abstract":[{"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.","lang":"eng"}],"publication_status":"published","external_id":{"pmid":["28486944"]},"issue":"1","publication_identifier":{"issn":["1474-760X"],"eissn":["1465-6906"]},"doi":"10.1186/s13059-017-1230-2","publication":"Genome Biology","year":"2017","date_created":"2021-06-07T12:27:39Z","article_number":"87","has_accepted_license":"1","ddc":["570"],"file":[{"file_size":278183,"date_updated":"2021-06-07T12:31:36Z","access_level":"open_access","checksum":"5a455ad914e7d225b1baa4ab07fd925e","relation":"main_file","file_id":"9507","success":1,"creator":"asandaue","content_type":"application/pdf","file_name":"2017_GenomeBiology_Zilberman.pdf","date_created":"2021-06-07T12:31:36Z"}],"quality_controlled":"1"},{"quality_controlled":"1","file":[{"file_id":"6327","date_updated":"2020-07-14T12:48:16Z","file_size":2073856,"relation":"main_file","checksum":"9aeff86fa7de69f7a15cf4fc60d57d01","access_level":"open_access","file_name":"2017_TheoreticalPopulationBio_Turelli.pdf","content_type":"application/pdf","date_created":"2019-04-17T06:39:45Z","creator":"dernst"}],"has_accepted_license":"1","ddc":["576"],"date_created":"2018-12-11T11:49:22Z","year":"2017","doi":"10.1016/j.tpb.2017.03.003","publication_identifier":{"issn":["0040-5809"]},"publication":"Theoretical Population Biology","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","article_processing_charge":"No","page":"45 - 60","external_id":{"pmid":["28411063"]},"publication_status":"published","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."}],"title":"Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Michael","last_name":"Turelli","full_name":"Turelli, Michael"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H"}],"volume":115,"pmid":1,"citation":{"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.","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.","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","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.","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","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.","short":"M. Turelli, N.H. Barton, Theoretical Population Biology 115 (2017) 45–60."},"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"day":"01","status":"public","pubrep_id":"972","file_date_updated":"2020-07-14T12:48:16Z","oa":1,"date_published":"2017-06-01T00:00:00Z","month":"06","language":[{"iso":"eng"}],"date_updated":"2025-07-10T12:01:49Z","publisher":"Elsevier","department":[{"_id":"NiBa"}],"intvolume":" 115","oa_version":"Submitted Version","type":"journal_article","publist_id":"6463","scopus_import":"1","_id":"952"},{"volume":6,"author":[{"full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","first_name":"Mato"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","first_name":"Tiago","last_name":"Paixao"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"last_name":"Bollback","first_name":"Jonathan P","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","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."}],"publication_status":"published","external_id":{"isi":["000404024800001"]},"article_processing_charge":"Yes","title":"On the mechanistic nature of epistasis in a canonical cis-regulatory element","article_number":"e25192","year":"2017","date_created":"2018-12-11T11:49:23Z","publication":"eLife","publication_identifier":{"issn":["2050-084X"]},"doi":"10.7554/eLife.25192","quality_controlled":"1","file":[{"date_created":"2018-12-12T10:17:49Z","content_type":"application/pdf","file_name":"IST-2017-841-v1+1_elife-25192-v2.pdf","creator":"system","file_id":"5306","relation":"main_file","checksum":"59cdd4400fb41280122d414fea971546","access_level":"open_access","file_size":2441529,"date_updated":"2020-07-14T12:48:16Z"},{"content_type":"application/pdf","file_name":"IST-2017-841-v1+2_elife-25192-figures-v2.pdf","date_created":"2018-12-12T10:17:50Z","creator":"system","file_id":"5307","file_size":3752660,"date_updated":"2020-07-14T12:48:16Z","checksum":"b69024880558b858eb8c5d47a92b6377","relation":"main_file","access_level":"open_access"}],"ddc":["576"],"has_accepted_license":"1","type":"journal_article","intvolume":" 6","oa_version":"Published Version","_id":"954","scopus_import":"1","publist_id":"6460","oa":1,"file_date_updated":"2020-07-14T12:48:16Z","isi":1,"department":[{"_id":"CaGu"},{"_id":"NiBa"},{"_id":"JoBo"}],"publisher":"eLife Sciences Publications","date_updated":"2025-07-10T12:01:50Z","month":"05","language":[{"iso":"eng"}],"date_published":"2017-05-18T00:00:00Z","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"841","day":"18","project":[{"call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020"}],"citation":{"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.","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","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.","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","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.","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.","short":"M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017)."}},{"quality_controlled":"1","file":[{"date_created":"2018-12-12T10:14:14Z","content_type":"application/pdf","file_name":"IST-2017-864-v1+1_s41467-017-00238-8.pdf","creator":"system","file_id":"5064","relation":"main_file","checksum":"29a1b5db458048d3bd5c67e0e2a56818","access_level":"open_access","file_size":998157,"date_updated":"2020-07-14T12:48:16Z"},{"file_id":"5065","access_level":"open_access","relation":"main_file","checksum":"7b78401e52a576cf3e6bbf8d0abadc17","file_size":9715993,"date_updated":"2020-07-14T12:48:16Z","date_created":"2018-12-12T10:14:15Z","file_name":"IST-2017-864-v1+2_41467_2017_238_MOESM1_ESM.pdf","content_type":"application/pdf","creator":"system"}],"corr_author":"1","ddc":["539","576"],"has_accepted_license":"1","article_number":"216","date_created":"2018-12-11T11:49:23Z","year":"2017","publication":"Nature Communications","publication_identifier":{"issn":["2041-1723"]},"doi":"10.1038/s41467-017-00238-8","issue":"1","publication_status":"published","external_id":{"isi":["000407198800005"]},"abstract":[{"lang":"eng","text":"Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge. We show that specialization of new network components is usually slow, but can be drastically accelerated in the presence of regulatory crosstalk and mutations that promote promiscuous interactions between network components."}],"article_processing_charge":"Yes (in subscription journal)","title":"Evolution of new regulatory functions on biophysically realistic fitness landscapes","volume":8,"author":[{"full_name":"Friedlander, Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","last_name":"Friedlander","first_name":"Tamar"},{"first_name":"Roshan","last_name":"Prizak","id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"},{"last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6071"}]},"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"},{"grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF"}],"citation":{"mla":"Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications, vol. 8, no. 1, 216, Nature Publishing Group, 2017, doi:10.1038/s41467-017-00238-8.","chicago":"Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00238-8.","apa":"Friedlander, T., Prizak, R., Barton, N. H., & Tkačik, G. (2017). Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00238-8","ista":"Friedlander T, Prizak R, Barton NH, Tkačik G. 2017. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 8(1), 216.","ama":"Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-00238-8","ieee":"T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new regulatory functions on biophysically realistic fitness landscapes,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.","short":"T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications 8 (2017)."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"pubrep_id":"864","day":"09","status":"public","file_date_updated":"2020-07-14T12:48:16Z","oa":1,"isi":1,"date_updated":"2026-04-08T13:54:24Z","publisher":"Nature Publishing Group","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"date_published":"2017-08-09T00:00:00Z","month":"08","language":[{"iso":"eng"}],"type":"journal_article","intvolume":" 8","oa_version":"Published Version","scopus_import":"1","_id":"955","publist_id":"6459"},{"volume":273,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Carlen","first_name":"Eric","full_name":"Carlen, Eric"},{"orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Maas, Jan","first_name":"Jan","last_name":"Maas"}],"publication_status":"published","external_id":{"arxiv":["1609.01254"],"isi":["000406082300005"]},"abstract":[{"text":"We study a class of ergodic quantum Markov semigroups on finite-dimensional unital C⁎-algebras. These semigroups have a unique stationary state σ, and we are concerned with those that satisfy a quantum detailed balance condition with respect to σ. We show that the evolution on the set of states that is given by such a quantum Markov semigroup is gradient flow for the relative entropy with respect to σ in a particular Riemannian metric on the set of states. This metric is a non-commutative analog of the 2-Wasserstein metric, and in several interesting cases we are able to show, in analogy with work of Otto on gradient flows with respect to the classical 2-Wasserstein metric, that the relative entropy is strictly and uniformly convex with respect to the Riemannian metric introduced here. As a consequence, we obtain a number of new inequalities for the decay of relative entropy for ergodic quantum Markov semigroups with detailed balance.","lang":"eng"}],"article_processing_charge":"No","page":"1810 - 1869","title":"Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance","date_created":"2018-12-11T11:49:24Z","year":"2017","publication":"Journal of Functional Analysis","doi":"10.1016/j.jfa.2017.05.003","publication_identifier":{"issn":["0022-1236"]},"issue":"5","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1609.01254","open_access":"1"}],"type":"journal_article","oa_version":"Submitted Version","intvolume":" 273","scopus_import":"1","_id":"956","publist_id":"6452","oa":1,"isi":1,"date_updated":"2025-06-04T08:14:53Z","department":[{"_id":"JaMa"}],"publisher":"Academic Press","arxiv":1,"date_published":"2017-09-01T00:00:00Z","language":[{"iso":"eng"}],"month":"09","status":"public","day":"01","citation":{"apa":"Carlen, E., & Maas, J. (2017). Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. Journal of Functional Analysis. Academic Press. https://doi.org/10.1016/j.jfa.2017.05.003","chicago":"Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for Quantum Markov Semigroups with Detailed Balance.” Journal of Functional Analysis. Academic Press, 2017. https://doi.org/10.1016/j.jfa.2017.05.003.","mla":"Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for Quantum Markov Semigroups with Detailed Balance.” Journal of Functional Analysis, vol. 273, no. 5, Academic Press, 2017, pp. 1810–69, doi:10.1016/j.jfa.2017.05.003.","ieee":"E. Carlen and J. Maas, “Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance,” Journal of Functional Analysis, vol. 273, no. 5. Academic Press, pp. 1810–1869, 2017.","short":"E. Carlen, J. Maas, Journal of Functional Analysis 273 (2017) 1810–1869.","ista":"Carlen E, Maas J. 2017. Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. Journal of Functional Analysis. 273(5), 1810–1869.","ama":"Carlen E, Maas J. Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. Journal of Functional Analysis. 2017;273(5):1810-1869. doi:10.1016/j.jfa.2017.05.003"}},{"_id":"957","scopus_import":"1","publist_id":"6451","type":"book_chapter","intvolume":" 1596","oa_version":"None","department":[{"_id":"HaJa"}],"publisher":"Springer","date_updated":"2025-07-10T12:01:52Z","language":[{"iso":"eng"}],"month":"03","date_published":"2017-03-15T00:00:00Z","day":"15","status":"public","series_title":"Synthetic Protein Switches","alternative_title":["Methods in Molecular Biology"],"project":[{"_id":"255BFFFA-B435-11E9-9278-68D0E5697425","grant_number":"RGY0084/2012","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors"}],"citation":{"chicago":"Clifton, Ben, Jason Whitfield, Inmaculada Sanchez-Romero, Michel Herde, Christian Henneberger, Harald L Janovjak, and Colin Jackson. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” In Synthetic Protein Switches, edited by Viktor Stein, 1596:71–87. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_5.","apa":"Clifton, B., Whitfield, J., Sanchez-Romero, I., Herde, M., Henneberger, C., Janovjak, H. L., & Jackson, C. (2017). Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 71–87). Springer. https://doi.org/10.1007/978-1-4939-6940-1_5","mla":"Clifton, Ben, et al. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 71–87, doi:10.1007/978-1-4939-6940-1_5.","short":"B. Clifton, J. Whitfield, I. Sanchez-Romero, M. Herde, C. Henneberger, H.L. Janovjak, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 71–87.","ieee":"B. Clifton et al., “Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors,” in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 71–87.","ama":"Clifton B, Whitfield J, Sanchez-Romero I, et al. Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic Protein Switches. Springer; 2017:71-87. doi:10.1007/978-1-4939-6940-1_5","ista":"Clifton B, Whitfield J, Sanchez-Romero I, Herde M, Henneberger C, Janovjak HL, Jackson C. 2017.Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 71–87."},"volume":1596,"editor":[{"full_name":"Stein, Viktor","last_name":"Stein","first_name":"Viktor"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Clifton, Ben","last_name":"Clifton","first_name":"Ben"},{"first_name":"Jason","last_name":"Whitfield","full_name":"Whitfield, Jason"},{"first_name":"Inmaculada","last_name":"Sanchez Romero","full_name":"Sanchez Romero, Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michel","last_name":"Herde","full_name":"Herde, Michel"},{"first_name":"Christian","last_name":"Henneberger","full_name":"Henneberger, Christian"},{"last_name":"Janovjak","first_name":"Harald L","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315"},{"full_name":"Jackson, Colin","last_name":"Jackson","first_name":"Colin"}],"title":"Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors","abstract":[{"text":"Small molecule biosensors based on Forster resonance energy transfer (FRET) enable small molecule signaling to be monitored with high spatial and temporal resolution in complex cellular environments. FRET sensors can be constructed by fusing a pair of fluorescent proteins to a suitable recognition domain, such as a member of the solute-binding protein (SBP) superfamily. However, naturally occurring SBPs may be unsuitable for incorporation into FRET sensors due to their low thermostability, which may preclude imaging under physiological conditions, or because the positions of their N- and C-termini may be suboptimal for fusion of fluorescent proteins, which may limit the dynamic range of the resulting sensors. Here, we show how these problems can be overcome using ancestral protein reconstruction and circular permutation. Ancestral protein reconstruction, used as a protein engineering strategy, leverages phylogenetic information to improve the thermostability of proteins, while circular permutation enables the termini of an SBP to be repositioned to maximize the dynamic range of the resulting FRET sensor. We also provide a protocol for cloning the engineered SBPs into FRET sensor constructs using Golden Gate assembly and discuss considerations for in situ characterization of the FRET sensors.","lang":"eng"}],"publication_status":"published","page":"71 - 87","article_processing_charge":"No","publication":"Synthetic Protein Switches","doi":"10.1007/978-1-4939-6940-1_5","publication_identifier":{"issn":["1064-3745"]},"year":"2017","date_created":"2018-12-11T11:49:24Z","quality_controlled":"1"},{"date_created":"2018-12-11T11:49:24Z","year":"2017","publication_identifier":{"issn":["1064-3745"]},"doi":"10.1007/978-1-4939-6940-1_6","publication":"Synthetic Protein Switches","quality_controlled":"1","author":[{"full_name":"Mitchell, Joshua","first_name":"Joshua","last_name":"Mitchell"},{"full_name":"Zhang, William","last_name":"Zhang","first_name":"William"},{"first_name":"Michel","last_name":"Herde","full_name":"Herde, Michel"},{"full_name":"Henneberger, Christian","first_name":"Christian","last_name":"Henneberger"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","last_name":"Janovjak","first_name":"Harald L"},{"first_name":"Megan","last_name":"O'Mara","full_name":"O'Mara, Megan"},{"full_name":"Jackson, Colin","last_name":"Jackson","first_name":"Colin"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","editor":[{"last_name":"Stein","first_name":"Viktor","full_name":"Stein, Viktor"}],"volume":1596,"article_processing_charge":"No","page":"89 - 99","publication_status":"published","abstract":[{"text":"Biosensors that exploit Forster resonance energy transfer (FRET) can be used to visualize biological and physiological processes and are capable of providing detailed information in both spatial and temporal dimensions. In a FRET-based biosensor, substrate binding is associated with a change in the relative positions of two fluorophores, leading to a change in FRET efficiency that may be observed in the fluorescence spectrum. As a result, their design requires a ligand-binding protein that exhibits a conformational change upon binding. However, not all ligand-binding proteins produce responsive sensors upon conjugation to fluorescent proteins or dyes, and identifying the optimum locations for the fluorophores often involves labor-intensive iterative design or high-throughput screening. Combining the genetic fusion of a fluorescent protein to the ligand-binding protein with site-specific covalent attachment of a fluorescent dye can allow fine control over the positions of the two fluorophores, allowing the construction of very sensitive sensors. This relies upon the accurate prediction of the locations of the two fluorophores in bound and unbound states. In this chapter, we describe a method for computational identification of dye-attachment sites that allows the use of cysteine modification to attach synthetic dyes that can be paired with a fluorescent protein for the purposes of creating FRET sensors.","lang":"eng"}],"title":"Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment","alternative_title":["Methods in Molecular Biology"],"series_title":"Synthetic Protein Switches","status":"public","day":"15","citation":{"ieee":"J. Mitchell et al., “Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment,” in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 89–99.","short":"J. Mitchell, W. Zhang, M. Herde, C. Henneberger, H.L. Janovjak, M. O’Mara, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 89–99.","ista":"Mitchell J, Zhang W, Herde M, Henneberger C, Janovjak HL, O’Mara M, Jackson C. 2017.Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 89–99.","ama":"Mitchell J, Zhang W, Herde M, et al. Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic Protein Switches. Springer; 2017:89-99. doi:10.1007/978-1-4939-6940-1_6","apa":"Mitchell, J., Zhang, W., Herde, M., Henneberger, C., Janovjak, H. L., O’Mara, M., & Jackson, C. (2017). Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 89–99). Springer. https://doi.org/10.1007/978-1-4939-6940-1_6","chicago":"Mitchell, Joshua, William Zhang, Michel Herde, Christian Henneberger, Harald L Janovjak, Megan O’Mara, and Colin Jackson. “Method for Developing Optical Sensors Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.” In Synthetic Protein Switches, edited by Viktor Stein, 1596:89–99. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_6.","mla":"Mitchell, Joshua, et al. “Method for Developing Optical Sensors Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.” Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 89–99, doi:10.1007/978-1-4939-6940-1_6."},"intvolume":" 1596","oa_version":"None","type":"book_chapter","publist_id":"6450","scopus_import":"1","_id":"958","date_published":"2017-05-15T00:00:00Z","language":[{"iso":"eng"}],"month":"05","date_updated":"2025-07-10T12:01:54Z","department":[{"_id":"HaJa"}],"publisher":"Springer"},{"abstract":[{"text":"Cell-cell contact formation constitutes the first step in the emergence of multicellularity in evolution, thereby allowing the differentiation of specialized cell types. In metazoan development, cell-cell contact formation is thought to influence cell fate specification, and cell fate specification has been implicated in cell-cell contact formation. However, remarkably little is yet known about whether and how the interaction and feedback between cell-cell contact formation and cell fate specification affect development. Here we identify a positive feedback loop between cell-cell contact duration, morphogen signaling and mesendoderm cell fate specification during zebrafish gastrulation. We show that long lasting cell-cell contacts enhance the competence of prechordal plate (ppl) progenitor cells to respond to Nodal signaling, required for proper ppl cell fate specification. We further show that Nodal signalling romotes ppl cell-cell contact duration, thereby generating an effective positive feedback loop between ppl cell-cell contact duration and cell fate specification. Finally, by using a combination of theoretical modeling and experimentation, we show that this feedback loop determines whether anterior axial mesendoderm cells become ppl progenitors or, instead, turn into endoderm progenitors. Our findings reveal that the gene regulatory networks leading to cell fate diversification within the developing embryo are controlled by the interdependent activities of cell-cell signaling and contact formation.","lang":"eng"}],"publication_status":"published","page":"109","article_processing_charge":"No","degree_awarded":"PhD","title":"Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation","supervisor":[{"first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"OA_place":"publisher","author":[{"id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa","first_name":"Vanessa","last_name":"Barone"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"record":[{"relation":"part_of_dissertation","id":"735","status":"public"},{"status":"public","id":"1100","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"1537"},{"status":"public","relation":"part_of_dissertation","id":"3246"},{"status":"public","relation":"part_of_dissertation","id":"2926"},{"status":"public","relation":"part_of_dissertation","id":"676"},{"status":"public","relation":"part_of_dissertation","id":"1912"}]},"file":[{"creator":"dernst","date_created":"2019-04-05T08:36:52Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"2017_Barone_thesis_final.docx","access_level":"closed","checksum":"242f88c87f2cf267bf05049fa26a687b","relation":"source_file","date_updated":"2020-07-14T12:48:16Z","file_size":14497822,"file_id":"6205"},{"file_id":"6206","access_level":"open_access","checksum":"ba5b0613ed8bade73a409acdd880fb8a","relation":"main_file","file_size":14995941,"date_updated":"2020-07-14T12:48:16Z","date_created":"2019-04-05T08:36:52Z","file_name":"2017_Barone_thesis_.pdf","content_type":"application/pdf","creator":"dernst"}],"corr_author":"1","ddc":["570","590"],"has_accepted_license":"1","year":"2017","date_created":"2018-12-11T11:49:25Z","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:th_825","oa":1,"file_date_updated":"2020-07-14T12:48:16Z","department":[{"_id":"CaHe"}],"publisher":"Institute of Science and Technology Austria","date_updated":"2026-06-18T18:12:40Z","month":"03","language":[{"iso":"eng"}],"date_published":"2017-03-01T00:00:00Z","acknowledgement":"Many people accompanied me during this trip: I would not have reached my destination nor \r\nenjoyed the travelling without them. First of all, thanks to CP. Thanks for making me part of \r\nyour team, always full of diverse, interesting and incredibly competent people and thanks for \r\nall the good science I witnessed and participated in. It has been a \r\nblast, an incredibly \r\nexciting one! Thanks to JLo, for teaching me how to master my pipettes and showing me \r\nthat science is a lot of fun. Many, many thanks to Gabby for teaching me basically everything \r\nabout zebrafish and being always there to advice, sugge\r\nst, support...and play fussball! \r\nThank you to Julien, for the critical eye on things, Pedro, for all the invaluable feedback and \r\nthe amazing kicker matches, and Keisuke, for showing me the light, and to the three of them \r\ntogether for all the good laughs we\r\nhad. My start in Vienna would have been a lot more \r\ndifficult without you guys. Also it would not have been possible without Elena and Inês: \r\nthanks for helping setting up this lab and for the dinners in Gugging. Thanks to Martin, for \r\nhelping me understand \r\nthe physics behind biology. Thanks to Philipp, for the interest and \r\nadvice, and to Michael, for the Viennise take on things. Thanks to Julia, for putting up with \r\nbeing our technician and becoming a friend in the process. And now to the newest members \r\nof th\r\ne lab. Thanks to Daniel for the enthusiasm and the neverending energy and for all your \r\nhelp over the years: thank you! To Jana, for showing me that one doesn’t give up, no matter \r\nwhat. To Shayan, for being such a motivated student. To Matt, for helping out\r\nwith coding \r\nand for finding punk solutions to data analysis problems. Thanks to all the members of the \r\nlab, Verena, Hitoshi, Silvia, Conny, Karla, Nicoletta, Zoltan, Peng, Benoit, Roland, Yuuta and \r\nFeyza, for the wonderful atmosphere in the lab. Many than\r\nks to Koni and Deborah: doing \r\nexperiments would have been much more difficult without your help. Special thanks to Katjia \r\nfor setting up an amazing imaging facility and for building the best team, Robert, Nasser, \r\nAnna and Doreen: thank you for putting up w\r\nith all the late sortings and for helping with all \r\nthe technical problems. Thanks to Eva, Verena and Matthias for keeping the fish happy. Big \r\nthanks to Harald Janovjak for being a present and helpful committee member over the years \r\nand to Patrick Lemaire f\r\nor the helpful insight and extremely interesting discussion we had \r\nabout the project. Also, this journey would not have been the same without all the friends \r\nthat I met in Dresden and then in Vienna: Daniele, Claire, Kuba, Steffi, Harold, Dejan, Irene, \r\nFab\r\nienne, Hande, Tiago, Marianne, Jon, Srdjan, Branca, Uli, Murat, Alex, Conny, Christoph, \r\nCaro, Simone, Barbara, Felipe, Dama, Jose, Hubert and many others that filled my days with \r\nfun and support. A special thank to my family, always close even if they are \r\nkilometers away. \r\nGrazie ai miei fratelli, Nunzio e William, e alla mia mamma, per essermi sempre vicini pur \r\nvivendo a chilometri di distanza. And, last but not least, thanks to Moritz, for putting up with \r\nthe crazy life of a scientist, the living apart for\r\nso long, never knowing when things are going \r\nto happen. Thanks for being a great partner and my number one fan!","type":"dissertation","oa_version":"Published Version","_id":"961","publist_id":"6444","citation":{"mla":"Barone, Vanessa. Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_825.","apa":"Barone, V. (2017). Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_825","chicago":"Barone, Vanessa. “Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_825.","ama":"Barone V. Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. 2017. doi:10.15479/AT:ISTA:th_825","ista":"Barone V. 2017. Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. Institute of Science and Technology Austria.","short":"V. Barone, Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation, Institute of Science and Technology Austria, 2017.","ieee":"V. Barone, “Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation,” Institute of Science and Technology Austria, 2017."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"825","day":"01","alternative_title":["ISTA Thesis"]}]