--- _id: '936' abstract: - lang: eng text: Homeostatic replacement of epithelial cells from basal precursors is a multistep process involving progenitor cell specification, radial intercalation and, finally, apical surface emergence. Recent data demonstrate that actin-based pushing under the control of the formin protein Fmn1 drives apical emergence in nascent multiciliated epithelial cells (MCCs), but little else is known about this actin network or the control of Fmn1. Here, we explore the role of the small GTPase RhoA in MCC apical emergence. Disruption of RhoA function reduced the rate of apical surface expansion and decreased the final size of the apical domain. Analysis of cell shapes suggests that RhoA alters the balance of forces exerted on the MCC apical surface. Finally, quantitative time-lapse imaging and fluorescence recovery after photobleaching studies argue that RhoA works in concert with Fmn1 to control assembly of the specialized apical actin network in MCCs. These data provide new molecular insights into epithelial apical surface assembly and could also shed light on mechanisms of apical lumen formation author: - first_name: Jakub full_name: Sedzinski, Jakub last_name: Sedzinski - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Fan full_name: Tu, Fan last_name: Tu - first_name: Maté full_name: Biro, Maté last_name: Biro - first_name: John full_name: Wallingford, John last_name: Wallingford citation: ama: Sedzinski J, Hannezo EB, Tu F, Biro M, Wallingford J. RhoA regulates actin network dynamics during apical surface emergence in multiciliated epithelial cells . Journal of Cell Science. 2017;130(5). doi:10.1242/jcs.202234 apa: Sedzinski, J., Hannezo, E. B., Tu, F., Biro, M., & Wallingford, J. (2017). RhoA regulates actin network dynamics during apical surface emergence in multiciliated epithelial cells . Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.202234 chicago: Sedzinski, Jakub, Edouard B Hannezo, Fan Tu, Maté Biro, and John Wallingford. “RhoA Regulates Actin Network Dynamics during Apical Surface Emergence in Multiciliated Epithelial Cells .” Journal of Cell Science. Company of Biologists, 2017. https://doi.org/10.1242/jcs.202234. ieee: J. Sedzinski, E. B. Hannezo, F. Tu, M. Biro, and J. Wallingford, “RhoA regulates actin network dynamics during apical surface emergence in multiciliated epithelial cells ,” Journal of Cell Science, vol. 130, no. 5. Company of Biologists, 2017. ista: Sedzinski J, Hannezo EB, Tu F, Biro M, Wallingford J. 2017. RhoA regulates actin network dynamics during apical surface emergence in multiciliated epithelial cells . Journal of Cell Science. 130(5). mla: Sedzinski, Jakub, et al. “RhoA Regulates Actin Network Dynamics during Apical Surface Emergence in Multiciliated Epithelial Cells .” Journal of Cell Science, vol. 130, no. 5, Company of Biologists, 2017, doi:10.1242/jcs.202234. short: J. Sedzinski, E.B. Hannezo, F. Tu, M. Biro, J. Wallingford, Journal of Cell Science 130 (2017). date_created: 2018-12-11T11:49:17Z date_published: 2017-01-01T00:00:00Z date_updated: 2021-01-12T08:22:02Z day: '01' doi: 10.1242/jcs.202234 extern: '1' intvolume: ' 130' issue: '5' language: - iso: eng month: '01' oa_version: None publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '6507' quality_controlled: '1' status: public title: 'RhoA regulates actin network dynamics during apical surface emergence in multiciliated epithelial cells ' type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 130 year: '2017' ... --- _id: '937' abstract: - lang: eng text: During epithelial cytokinesis, the remodelling of adhesive cell-cell contacts between the dividing cell and its neighbours has profound implications for the integrity, arrangement and morphogenesis of proliferative tissues. In both vertebrates and invertebrates, this remodelling requires the activity of non-muscle myosin II (MyoII) in the interphasic cells neighbouring the dividing cell. However, the mechanisms that coordinate cytokinesis and MyoII activity in the neighbours are unknown. Here we show that in the Drosophila notum epithelium, each cell division is associated with a mechanosensing and transmission event that controls MyoII dynamics in neighbouring cells. We find that the ring pulling forces promote local junction elongation, which results in local E-cadherin dilution at the ingressing adherens junction. In turn, the reduction in E-cadherin concentration and the contractility of the neighbouring cells promote self-organized actomyosin flows, ultimately leading to accumulation of MyoII at the base of the ingressing junction. Although force transduction has been extensively studied in the context of adherens junction reinforcement to stabilize adhesive cell-cell contacts, we propose an alternative mechanosensing mechanism that coordinates actomyosin dynamics between epithelial cells and sustains the remodelling of the adherens junction in response to mechanical forces. author: - first_name: Diana full_name: Pinheiro, Diana last_name: Pinheiro - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Sophie full_name: Herszterg, Sophie last_name: Herszterg - first_name: Floris full_name: Bosveld, Floris last_name: Bosveld - first_name: Isabelle full_name: Gaugué, Isabelle last_name: Gaugué - first_name: Maria full_name: Balakireva, Maria last_name: Balakireva - first_name: Zhimin full_name: Wang, Zhimin last_name: Wang - first_name: Inês full_name: Cristo, Inês last_name: Cristo - first_name: Stéphane full_name: Rigaud, Stéphane last_name: Rigaud - first_name: Olga full_name: Markova, Olga last_name: Markova - first_name: Yohanns full_name: Bellaïche, Yohanns last_name: Bellaïche citation: ama: Pinheiro D, Hannezo EB, Herszterg S, et al. Transmission of cytokinesis forces via E cadherin dilution and actomyosin flows. Nature. 2017;545(7652):103-107. doi:10.1038/nature22041 apa: Pinheiro, D., Hannezo, E. B., Herszterg, S., Bosveld, F., Gaugué, I., Balakireva, M., … Bellaïche, Y. (2017). Transmission of cytokinesis forces via E cadherin dilution and actomyosin flows. Nature. Nature Publishing Group. https://doi.org/10.1038/nature22041 chicago: Pinheiro, Diana, Edouard B Hannezo, Sophie Herszterg, Floris Bosveld, Isabelle Gaugué, Maria Balakireva, Zhimin Wang, et al. “Transmission of Cytokinesis Forces via E Cadherin Dilution and Actomyosin Flows.” Nature. Nature Publishing Group, 2017. https://doi.org/10.1038/nature22041. ieee: D. Pinheiro et al., “Transmission of cytokinesis forces via E cadherin dilution and actomyosin flows,” Nature, vol. 545, no. 7652. Nature Publishing Group, pp. 103–107, 2017. ista: Pinheiro D, Hannezo EB, Herszterg S, Bosveld F, Gaugué I, Balakireva M, Wang Z, Cristo I, Rigaud S, Markova O, Bellaïche Y. 2017. Transmission of cytokinesis forces via E cadherin dilution and actomyosin flows. Nature. 545(7652), 103–107. mla: Pinheiro, Diana, et al. “Transmission of Cytokinesis Forces via E Cadherin Dilution and Actomyosin Flows.” Nature, vol. 545, no. 7652, Nature Publishing Group, 2017, pp. 103–07, doi:10.1038/nature22041. short: D. Pinheiro, E.B. Hannezo, S. Herszterg, F. Bosveld, I. Gaugué, M. Balakireva, Z. Wang, I. Cristo, S. Rigaud, O. Markova, Y. Bellaïche, Nature 545 (2017) 103–107. date_created: 2018-12-11T11:49:18Z date_published: 2017-05-04T00:00:00Z date_updated: 2021-01-12T08:22:02Z day: '04' doi: 10.1038/nature22041 extern: '1' intvolume: ' 545' issue: '7652' language: - iso: eng month: '05' oa_version: None page: 103 - 107 publication: Nature publication_identifier: issn: - '00280836' publication_status: published publisher: Nature Publishing Group publist_id: '6504' quality_controlled: '1' status: public title: Transmission of cytokinesis forces via E cadherin dilution and actomyosin flows type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 545 year: '2017' ... --- OA_place: publisher _id: '938' abstract: - lang: eng text: The thesis encompasses several topics of plant cell biology which were studied in the model plant Arabidopsis thaliana. Chapter 1 concerns the plant hormone auxin and its polar transport through cells and tissues. The highly controlled, directional transport of auxin is facilitated by plasma membrane-localized transporters. Transporters from the PIN family direct auxin transport due to their polarized localizations at cell membranes. Substantial effort has been put into research on cellular trafficking of PIN proteins, which is thought to underlie their polar distribution. I participated in a forward genetic screen aimed at identifying novel regulators of PIN polarity. The screen yielded several genes which may be involved in PIN polarity regulation or participate in polar auxin transport by other means. Chapter 2 focuses on the endomembrane system, with particular attention to clathrin-mediated endocytosis. The project started with identification of several proteins that interact with clathrin light chains. Among them, I focused on two putative homologues of auxilin, which in non-plant systems is an endocytotic factor known for uncoating clathrin-coated vesicles in the final step of endocytosis. The body of my work consisted of an in-depth characterization of transgenic A. thaliana lines overexpressing these putative auxilins in an inducible manner. Overexpression of these proteins leads to an inhibition of endocytosis, as documented by imaging of cargoes and clathrin-related endocytic machinery. An extension of this work is an investigation into a concept of homeostatic regulation acting between distinct transport processes in the endomembrane system. With auxilin overexpressing lines, where endocytosis is blocked specifically, I made observations on the mutual relationship between two opposite trafficking processes of secretion and endocytosis. In Chapter 3, I analyze cortical microtubule arrays and their relationship to auxin signaling and polarized growth in elongating cells. In plants, microtubules are organized into arrays just below the plasma membrane, and it is thought that their function is to guide membrane-docked cellulose synthase complexes. These, in turn, influence cell wall structure and cell shape by directed deposition of cellulose fibres. In elongating cells, cortical microtubule arrays are able to reorient in relation to long cell axis, and these reorientations have been linked to cell growth and to signaling of growth-regulating factors such as auxin or light. In this chapter, I am addressing the causal relationship between microtubule array reorientation, growth, and auxin signaling. I arrive at a model where array reorientation is not guided by auxin directly, but instead is only controlled by growth, which, in turn, is regulated by auxin. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Maciek full_name: Adamowski, Maciek id: 45F536D2-F248-11E8-B48F-1D18A9856A87 last_name: Adamowski orcid: 0000-0001-6463-5257 citation: ama: Adamowski M. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . 2017. doi: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 chicago: Adamowski, Maciek. “Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana .” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_842. ieee: M. Adamowski, “Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ,” Institute of Science and Technology Austria, 2017. ista: Adamowski M. 2017. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria. 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. corr_author: '1' date_created: 2018-12-11T11:49:18Z date_published: 2017-06-02T00:00:00Z date_updated: 2026-04-08T14:20:45Z day: '02' ddc: - '581' - '583' - '580' degree_awarded: PhD department: - _id: JiFr doi: 10.15479/AT:ISTA:th_842 file: - access_level: closed checksum: 193425764d9aaaed3ac57062a867b315 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-05T09:03:20Z date_updated: 2020-07-14T12:48:15Z file_id: '6215' file_name: 2017_Adamowski-Thesis_Source.docx file_size: 46903863 relation: source_file - access_level: open_access checksum: df5ab01be81f821e1b958596a1ec8d21 content_type: application/pdf creator: dernst date_created: 2019-04-05T09:03:19Z date_updated: 2020-07-14T12:48:15Z file_id: '6216' file_name: 2017_Adamowski-Thesis.pdf file_size: 8698888 relation: main_file file_date_updated: 2020-07-14T12:48:15Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '117' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6483' pubrep_id: '842' related_material: record: - id: '1591' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: 'Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ' type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2017' ... --- _id: '939' 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_number: '033905' article_processing_charge: No arxiv: 1 author: - first_name: Bikashkali full_name: Midya, Bikashkali id: 456187FC-F248-11E8-B48F-1D18A9856A87 last_name: Midya - first_name: Vladimir full_name: Konotop, Vladimir last_name: Konotop 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' 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.' ieee: 'B. Midya and V. Konotop, “Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons,” Physical Review Letters, vol. 119, no. 3. American Physical Society, 2017.' ista: 'Midya B, Konotop V. 2017. Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. 119(3), 033905.' 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.' short: B. Midya, V. Konotop, Physical Review Letters 119 (2017). corr_author: '1' date_created: 2018-12-11T11:49:18Z date_published: 2017-07-18T00:00:00Z date_updated: 2025-06-04T08:20:23Z day: '18' department: - _id: MiLe doi: 10.1103/PhysRevLett.119.033905 ec_funded: 1 external_id: arxiv: - '1706.04085 ' isi: - '000405718200012' intvolume: ' 119' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: 'https://arxiv.org/abs/1706.04085 ' month: '07' oa: 1 oa_version: Submitted Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physical Review Letters publication_identifier: issn: - 0031-9007 publication_status: published publisher: American Physical Society publist_id: '6481' quality_controlled: '1' scopus_import: '1' status: public title: 'Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2017' ... --- _id: '94' abstract: - lang: eng text: We introduce a method for breaking Lorentz reciprocity based upon the noncommutation of frequency conversion and delay. The method requires no magnetic materials or resonant physics, allowing for the design of scalable and broadband nonreciprocal circuits. With this approach, two types of gyrators - universal building blocks for linear, nonreciprocal circuits - are constructed. Using one of these gyrators, we create a circulator with >15 dB of isolation across the 5-9 GHz band. Our designs may be readily extended to any platform with suitable frequency conversion elements, including semiconducting devices for telecommunication or an on-chip superconducting implementation for quantum information processing. article_number: '147703' arxiv: 1 author: - first_name: Eric full_name: Rosenthal, Eric last_name: Rosenthal - first_name: Benjamin full_name: Chapman, Benjamin last_name: Chapman - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 - first_name: Joseph full_name: Kerckhoff, Joseph last_name: Kerckhoff - first_name: Konrad full_name: Lehnert, Konrad last_name: Lehnert citation: ama: Rosenthal E, Chapman B, Higginbotham AP, Kerckhoff J, Lehnert K. Breaking Lorentz reciprocity with frequency conversion and delay. APS Physics, Physical Review Letters. 2017;119(14). doi:10.1103/PhysRevLett.119.147703 apa: Rosenthal, E., Chapman, B., Higginbotham, A. P., Kerckhoff, J., & Lehnert, K. (2017). Breaking Lorentz reciprocity with frequency conversion and delay. APS Physics, Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.119.147703 chicago: Rosenthal, Eric, Benjamin Chapman, Andrew P Higginbotham, Joseph Kerckhoff, and Konrad Lehnert. “Breaking Lorentz Reciprocity with Frequency Conversion and Delay.” APS Physics, Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.119.147703. ieee: E. Rosenthal, B. Chapman, A. P. Higginbotham, J. Kerckhoff, and K. Lehnert, “Breaking Lorentz reciprocity with frequency conversion and delay,” APS Physics, Physical Review Letters, vol. 119, no. 14. American Physical Society, 2017. ista: Rosenthal E, Chapman B, Higginbotham AP, Kerckhoff J, Lehnert K. 2017. Breaking Lorentz reciprocity with frequency conversion and delay. APS Physics, Physical Review Letters. 119(14), 147703. mla: Rosenthal, Eric, et al. “Breaking Lorentz Reciprocity with Frequency Conversion and Delay.” APS Physics, Physical Review Letters, vol. 119, no. 14, 147703, American Physical Society, 2017, doi:10.1103/PhysRevLett.119.147703. short: E. Rosenthal, B. Chapman, A.P. Higginbotham, J. Kerckhoff, K. Lehnert, APS Physics, Physical Review Letters 119 (2017). date_created: 2018-12-11T11:44:35Z date_published: 2017-10-06T00:00:00Z date_updated: 2021-01-12T08:22:04Z day: '06' doi: 10.1103/PhysRevLett.119.147703 extern: '1' external_id: arxiv: - '1705.09548' intvolume: ' 119' issue: '14' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.09548 month: '10' oa: 1 oa_version: Submitted Version publication: APS Physics, Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '7960' quality_controlled: '1' status: public title: Breaking Lorentz reciprocity with frequency conversion and delay type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2017' ... --- _id: '941' abstract: - lang: eng text: 'Recently there has been a proliferation of automated program repair (APR) techniques, targeting various programming languages. Such techniques can be generally classified into two families: syntactic- and semantics-based. Semantics-based APR, on which we focus, typically uses symbolic execution to infer semantic constraints and then program synthesis to construct repairs conforming to them. While syntactic-based APR techniques have been shown successful on bugs in real-world programs written in both C and Java, semantics-based APR techniques mostly target C programs. This leaves empirical comparisons of the APR families not fully explored, and developers without a Java-based semantics APR technique. We present JFix, a semantics-based APR framework that targets Java, and an associated Eclipse plugin. JFix is implemented atop Symbolic PathFinder, a well-known symbolic execution engine for Java programs. It extends one particular APR technique (Angelix), and is designed to be sufficiently generic to support a variety of such techniques. We demonstrate that semantics-based APR can indeed efficiently and effectively repair a variety of classes of bugs in large real-world Java programs. This supports our claim that the framework can both support developers seeking semantics-based repair of bugs in Java programs, as well as enable larger scale empirical studies comparing syntactic- and semantics-based APR targeting Java. The demonstration of our tool is available via the project website at: https://xuanbachle.github.io/semanticsrepair/ ' acknowledgement: We thank Vu Le (Microsoft Research, Redmond), and anonymous reviewers for their comments. Duc-Hiep Chu was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award). article_processing_charge: No author: - first_name: Xuan full_name: Le, Xuan last_name: Le - first_name: Duc Hiep full_name: Chu, Duc Hiep id: 3598E630-F248-11E8-B48F-1D18A9856A87 last_name: Chu - first_name: David full_name: Lo, David last_name: Lo - first_name: Claire full_name: Le Goues, Claire last_name: Le Goues - first_name: Willem full_name: Visser, Willem last_name: Visser citation: 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' 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' 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.' 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.' 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.' 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.' 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. conference: end_date: 2017-07-14 location: Santa Barbara, CA, United States name: 'ISSTA: International Symposium on Software Testing and Analysis' start_date: 2017-07-10 corr_author: '1' date_created: 2018-12-11T11:49:19Z date_published: 2017-07-10T00:00:00Z date_updated: 2026-06-18T19:51:19Z day: '10' ddc: - '000' department: - _id: ToHe doi: 10.1145/3092703.3098225 external_id: isi: - '000462903600038' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://core.ac.uk/download/pdf/111759662.pdf month: '07' oa: 1 oa_version: Published Version page: '376 - 379 ' project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: Formal methods for the design and analysis of complex systems publication: Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis publication_status: published publisher: ACM publist_id: '6478' quality_controlled: '1' scopus_import: '1' status: public title: 'JFIX: Semantics-based repair of Java programs via symbolic PathFinder' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '942' abstract: - lang: eng text: 'A notable class of techniques for automatic program repair is known as semantics-based. Such techniques, e.g., Angelix, infer semantic specifications via symbolic execution, and then use program synthesis to construct new code that satisfies those inferred specifications. However, the obtained specifications are naturally incomplete, leaving the synthesis engine with a difficult task of synthesizing a general solution from a sparse space of many possible solutions that are consistent with the provided specifications but that do not necessarily generalize. We present S3, a new repair synthesis engine that leverages programming-by-examples methodology to synthesize high-quality bug repairs. The novelty in S3 that allows it to tackle the sparse search space to create more general repairs is three-fold: (1) A systematic way to customize and constrain the syntactic search space via a domain-specific language, (2) An efficient enumeration-based search strategy over the constrained search space, and (3) A number of ranking features based on measures of the syntactic and semantic distances between candidate solutions and the original buggy program. We compare S3’s repair effectiveness with state-of-the-art synthesis engines Angelix, Enumerative, and CVC4. S3 can successfully and correctly fix at least three times more bugs than the best baseline on datasets of 52 bugs in small programs, and 100 bugs in real-world large programs. ' article_processing_charge: No author: - first_name: Xuan full_name: Le, Xuan last_name: Le - first_name: Duc Hiep full_name: Chu, Duc Hiep id: 3598E630-F248-11E8-B48F-1D18A9856A87 last_name: Chu - first_name: David full_name: Lo, David last_name: Lo - first_name: Claire full_name: Le Goues, Claire last_name: Le Goues - first_name: Willem full_name: Visser, Willem last_name: Visser citation: 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' 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.' ieee: 'X. Le, D. H. Chu, D. Lo, C. Le Goues, and W. Visser, “S3: Syntax- and semantic-guided repair synthesis via programming by examples,” presented at the FSE: Foundations of Software Engineering, Paderborn, Germany, 2017, vol. F130154, pp. 593–604.' ista: 'Le X, Chu DH, Lo D, Le Goues C, Visser W. 2017. S3: Syntax- and semantic-guided repair synthesis via programming by examples. FSE: Foundations of Software Engineering vol. F130154, 593–604.' mla: 'Le, Xuan, et al. S3: Syntax- and Semantic-Guided Repair Synthesis via Programming by Examples. Vol. F130154, ACM, 2017, pp. 593–604, doi:10.1145/3106237.3106309.' short: X. Le, D.H. Chu, D. Lo, C. Le Goues, W. Visser, in:, ACM, 2017, pp. 593–604. conference: end_date: 2017-09-08 location: Paderborn, Germany name: 'FSE: Foundations of Software Engineering' start_date: 2017-09-04 date_created: 2018-12-11T11:49:19Z date_published: 2017-09-01T00:00:00Z date_updated: 2025-04-15T06:25:57Z day: '01' department: - _id: ToHe doi: 10.1145/3106237.3106309 external_id: isi: - '000414279300055' isi: 1 language: - iso: eng month: '09' oa_version: None page: 593 - 604 project: - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: Formal methods for the design and analysis of complex systems publication_identifier: isbn: - 978-145035105-8 publication_status: published publisher: ACM publist_id: '6477' quality_controlled: '1' scopus_import: '1' status: public title: 'S3: Syntax- and semantic-guided repair synthesis via programming by examples' type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: F130154 year: '2017' ... --- _id: '943' 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. article_processing_charge: No author: - first_name: Marcin P full_name: Zagórski, Marcin P id: 343DA0DC-F248-11E8-B48F-1D18A9856A87 last_name: Zagórski orcid: 0000-0001-7896-7762 - first_name: Yoji full_name: Tabata, Yoji last_name: Tabata - first_name: Nathalie full_name: Brandenberg, Nathalie last_name: Brandenberg - first_name: Matthias full_name: Lutolf, Matthias last_name: Lutolf - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Tobias full_name: Bollenbach, Tobias last_name: Bollenbach - first_name: James full_name: Briscoe, James last_name: Briscoe - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 citation: ama: Zagórski MP, Tabata Y, Brandenberg N, et al. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. 2017;356(6345):1379-1383. doi:10.1126/science.aam5887 apa: Zagórski, M. P., Tabata, Y., Brandenberg, N., Lutolf, M., Tkačik, G., Bollenbach, T., … Kicheva, A. (2017). Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aam5887 chicago: Zagórski, Marcin P, Yoji Tabata, Nathalie Brandenberg, Matthias Lutolf, Gašper Tkačik, Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aam5887. ieee: M. P. Zagórski et al., “Decoding of position in the developing neural tube from antiparallel morphogen gradients,” Science, vol. 356, no. 6345. American Association for the Advancement of Science, pp. 1379–1383, 2017. 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. 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. short: M.P. Zagórski, Y. Tabata, N. Brandenberg, M. Lutolf, G. Tkačik, T. Bollenbach, J. Briscoe, A. Kicheva, Science 356 (2017) 1379–1383. corr_author: '1' date_created: 2018-12-11T11:49:20Z date_published: 2017-06-30T00:00:00Z date_updated: 2025-07-10T12:01:45Z day: '30' department: - _id: AnKi - _id: GaTk doi: 10.1126/science.aam5887 ec_funded: 1 external_id: isi: - '000404351500036' pmid: - '28663499' intvolume: ' 356' isi: 1 issue: '6345' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568706/ month: '06' oa: 1 oa_version: Submitted Version page: 1379 - 1383 pmid: 1 project: - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation - _id: B6FC0238-B512-11E9-945C-1524E6697425 call_identifier: H2020 grant_number: '680037' name: Coordination of Patterning And Growth In the Spinal Cord - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 2524F500-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '201439' name: Developing High-Throughput Bioassays for Human Cancers in Zebrafish publication: Science publication_identifier: issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science publist_id: '6474' quality_controlled: '1' scopus_import: '1' status: public title: Decoding of position in the developing neural tube from antiparallel morphogen gradients type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 356 year: '2017' ... --- _id: '944' 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. acknowledged_ssus: - _id: Bio - _id: PreCl article_processing_charge: No author: - first_name: Robert J full_name: Beattie, Robert J id: 2E26DF60-F248-11E8-B48F-1D18A9856A87 last_name: Beattie orcid: 0000-0002-8483-8753 - first_name: Maria P full_name: Postiglione, Maria P id: 2C67902A-F248-11E8-B48F-1D18A9856A87 last_name: Postiglione - first_name: Laura full_name: Burnett, Laura id: 3B717F68-F248-11E8-B48F-1D18A9856A87 last_name: Burnett orcid: 0000-0002-8937-410X - first_name: Susanne full_name: Laukoter, Susanne id: 2D6B7A9A-F248-11E8-B48F-1D18A9856A87 last_name: Laukoter orcid: 0000-0002-7903-3010 - first_name: Carmen full_name: Streicher, Carmen id: 36BCB99C-F248-11E8-B48F-1D18A9856A87 last_name: Streicher - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Guanxi full_name: Xiao, Guanxi last_name: Xiao - first_name: Olga full_name: Klezovitch, Olga last_name: Klezovitch - first_name: Valeri full_name: Vasioukhin, Valeri last_name: Vasioukhin - first_name: Troy full_name: Ghashghaei, Troy last_name: Ghashghaei - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: 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 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. ieee: R. J. Beattie et al., “Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells,” Neuron, vol. 94, no. 3. Cell Press, p. 517–533.e3, 2017. ista: Beattie RJ, Postiglione MP, Burnett L, Laukoter S, Streicher C, Pauler F, Xiao G, Klezovitch O, Vasioukhin V, Ghashghaei T, Hippenmeyer S. 2017. Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. Neuron. 94(3), 517–533.e3. mla: Beattie, Robert J., et al. “Mosaic Analysis with Double Markers Reveals Distinct Sequential Functions of Lgl1 in Neural Stem Cells.” Neuron, vol. 94, no. 3, Cell Press, 2017, p. 517–533.e3, doi:10.1016/j.neuron.2017.04.012. short: R.J. Beattie, M.P. Postiglione, L. Burnett, S. Laukoter, C. Streicher, F. Pauler, G. Xiao, O. Klezovitch, V. Vasioukhin, T. Ghashghaei, S. Hippenmeyer, Neuron 94 (2017) 517–533.e3. corr_author: '1' date_created: 2018-12-11T11:49:20Z date_published: 2017-05-03T00:00:00Z date_updated: 2026-04-16T09:57:27Z day: '03' department: - _id: SiHi - _id: MaJö doi: 10.1016/j.neuron.2017.04.012 ec_funded: 1 external_id: isi: - '000400466700011' intvolume: ' 94' isi: 1 issue: '3' language: - iso: eng month: '05' oa_version: None page: 517 - 533.e3 project: - _id: 25D61E48-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618444' name: Molecular Mechanisms of Cerebral Cortex Development - _id: 25D7962E-B435-11E9-9278-68D0E5697425 grant_number: RGP0053/2014 name: Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Cell Press publist_id: '6473' quality_controlled: '1' scopus_import: '1' status: public title: Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 94 year: '2017' ... --- _id: '9445' 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_number: e30674 article_processing_charge: No article_type: original author: - first_name: David B full_name: Lyons, David B last_name: Lyons - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 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 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. ieee: D. B. Lyons and D. Zilberman, “DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes,” eLife, vol. 6. eLife Sciences Publications, 2017. ista: Lyons DB, Zilberman D. 2017. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 6, e30674. 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. short: D.B. Lyons, D. Zilberman, ELife 6 (2017). date_created: 2021-06-02T14:28:58Z date_published: 2017-11-15T00:00:00Z date_updated: 2021-12-14T07:54:36Z day: '15' ddc: - '570' department: - _id: DaZi doi: 10.7554/elife.30674 extern: '1' external_id: pmid: - '29140247' file: - access_level: open_access checksum: 4cfcdd67511ae4aed3d993550e46e146 content_type: application/pdf creator: cziletti date_created: 2021-06-02T14:33:36Z date_updated: 2021-06-02T14:33:36Z file_id: '9446' file_name: 2017_eLife_Lyons.pdf file_size: 1603102 relation: main_file success: 1 file_date_updated: 2021-06-02T14:33:36Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: eissn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 6 year: '2017' ... --- _id: '945' abstract: - lang: eng text: While chromosome-wide dosage compensation of the X chromosome has been found in many species, studies in ZW clades have indicated that compensation of the Z is more localized and/or incomplete. In the ZW Lepidoptera, some species show complete compensation of the Z chromosome, while others lack full equalization, but what drives these inconsistencies is unclear. Here, we compare patterns of male and female gene expression on the Z chromosome of two closely related butterfly species, Papilio xuthus and Papilio machaon, and in multiple tissues of two moths species, Plodia interpunctella and Bombyx mori, which were previously found to differ in the extent to which they equalize Z-linked gene expression between the sexes. We find that, while some species and tissues seem to have incomplete dosage compensation, this is in fact due to the accumulation of male-biased genes and the depletion of female-biased genes on the Z chromosome. Once this is accounted for, the Z chromosome is fully compensated in all four species, through the up-regulation of Z expression in females and in some cases additional down-regulation in males. We further find that both sex-biased genes and Z-linked genes have increased rates of expression divergence in this clade, and that this can lead to fast shifts in patterns of gene expression even between closely related species. Taken together, these results show that the uneven distribution of sex-biased genes on sex chromosomes can confound conclusions about dosage compensation and that Z chromosome-wide dosage compensation is not only possible but ubiquitous among Lepidoptera. article_processing_charge: Yes (in subscription journal) author: - first_name: Ann K full_name: Huylmans, Ann K id: 4C0A3874-F248-11E8-B48F-1D18A9856A87 last_name: Huylmans orcid: 0000-0001-8871-4961 - first_name: Ariana full_name: Macon, Ariana id: 2A0848E2-F248-11E8-B48F-1D18A9856A87 last_name: Macon - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: 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 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. ieee: A. K. Huylmans, A. Macon, and B. Vicoso, “Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome,” Molecular Biology and Evolution, vol. 34, no. 10. Oxford University Press, pp. 2637–2649, 2017. ista: Huylmans AK, Macon A, Vicoso B. 2017. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. 34(10), 2637–2649. mla: Huylmans, Ann K., et al. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” Molecular Biology and Evolution, vol. 34, no. 10, Oxford University Press, 2017, pp. 2637–49, doi:10.1093/molbev/msx190. short: A.K. Huylmans, A. Macon, B. Vicoso, Molecular Biology and Evolution 34 (2017) 2637–2649. date_created: 2018-12-11T11:49:20Z date_published: 2017-07-06T00:00:00Z date_updated: 2026-04-16T09:58:19Z day: '06' ddc: - '570' - '576' department: - _id: BeVi doi: 10.1093/molbev/msx190 external_id: isi: - '000411814800016' file: - access_level: open_access checksum: 009fd68043211d645ceb9d1de28274f2 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:23Z date_updated: 2020-07-14T12:48:15Z file_id: '4810' file_name: IST-2017-848-v1+1_2017_Vicoso_GlobalDosage.pdf file_size: 462863 relation: main_file file_date_updated: 2020-07-14T12:48:15Z has_accepted_license: '1' intvolume: ' 34' isi: 1 issue: '10' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 2637 - 2649 project: - _id: 250ED89C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28842-B22 name: Sex chromosome evolution under male- and female- heterogamety publication: Molecular Biology and Evolution publication_identifier: issn: - 0737-4038 publication_status: published publisher: Oxford University Press publist_id: '6472' pubrep_id: '848' quality_controlled: '1' scopus_import: '1' status: public title: Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 34 year: '2017' ... --- _id: '946' abstract: - lang: eng text: Roots navigate through soil integrating environmental signals to orient their growth. The Arabidopsis root is a widely used model for developmental, physiological and cell biological studies. Live imaging greatly aids these efforts, but the horizontal sample position and continuous root tip displacement present significant difficulties. Here, we develop a confocal microscope setup for vertical sample mounting and integrated directional illumination. We present TipTracker – a custom software for automatic tracking of diverse moving objects usable on various microscope setups. Combined, this enables observation of root tips growing along the natural gravity vector over prolonged periods of time, as well as the ability to induce rapid gravity or light stimulation. We also track migrating cells in the developing zebrafish embryo, demonstrating the utility of this system in the acquisition of high-resolution data sets of dynamic samples. We provide detailed descriptions of the tools enabling the easy implementation on other microscopes. acknowledged_ssus: - _id: M-Shop - _id: Bio 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" article_number: e26792 article_processing_charge: Yes author: - first_name: Daniel full_name: Von Wangenheim, Daniel id: 49E91952-F248-11E8-B48F-1D18A9856A87 last_name: Von Wangenheim orcid: 0000-0002-6862-1247 - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Matyas full_name: Fendrych, Matyas id: 43905548-F248-11E8-B48F-1D18A9856A87 last_name: Fendrych orcid: 0000-0002-9767-8699 - first_name: Vanessa full_name: Barone, Vanessa id: 419EECCC-F248-11E8-B48F-1D18A9856A87 last_name: Barone orcid: 0000-0003-2676-3367 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: 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 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 chicago: Wangenheim, Daniel von, Robert Hauschild, Matyas Fendrych, Vanessa Barone, Eva Benková, and Jiří Friml. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.26792. ieee: D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, and J. Friml, “Live tracking of moving samples in confocal microscopy for vertically grown roots,” eLife, vol. 6. eLife Sciences Publications, 2017. ista: von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. 2017. Live tracking of moving samples in confocal microscopy for vertically grown roots. eLife. 6, e26792. mla: von Wangenheim, Daniel, et al. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” ELife, vol. 6, e26792, eLife Sciences Publications, 2017, doi:10.7554/eLife.26792. short: D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, J. Friml, ELife 6 (2017). date_created: 2018-12-11T11:49:21Z date_published: 2017-06-19T00:00:00Z date_updated: 2025-04-15T06:37:26Z day: '19' ddc: - '570' department: - _id: JiFr - _id: Bio - _id: CaHe - _id: EvBe doi: 10.7554/eLife.26792 ec_funded: 1 external_id: isi: - '000404728300001' file: - access_level: open_access checksum: 9af3398cb0d81f99d79016a616df22e9 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:57Z date_updated: 2020-07-14T12:48:15Z file_id: '5315' file_name: IST-2017-847-v1+1_elife-26792-v2.pdf file_size: 19581847 relation: main_file file_date_updated: 2020-07-14T12:48:15Z has_accepted_license: '1' intvolume: ' 6' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 2572ED28-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02128 name: Molecular basis of root growth inhibition by auxin - _id: 2542D156-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I 1774-B16 name: Hormone cross-talk drives nutrient dependent plant development - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: eLife publication_status: published publisher: eLife Sciences Publications publist_id: '6471' pubrep_id: '847' quality_controlled: '1' related_material: record: - id: '5566' relation: popular_science status: public scopus_import: '1' status: public title: Live tracking of moving samples in confocal microscopy for vertically grown roots tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 6 year: '2017' ... --- _id: '950' 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" alternative_title: - LIPIcs article_number: '17' arxiv: 1 author: - first_name: Guy full_name: Avni, Guy id: 463C8BC2-F248-11E8-B48F-1D18A9856A87 last_name: Avni orcid: 0000-0001-5588-8287 - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Ventsislav K full_name: Chonev, Ventsislav K id: 36CBE2E6-F248-11E8-B48F-1D18A9856A87 last_name: Chonev citation: 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' 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' 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. 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.' ista: 'Avni G, Henzinger TA, Chonev VK. 2017. Infinite-duration bidding games. CONCUR: Concurrency Theory, LIPIcs, vol. 85, 17.' 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. short: G. Avni, T.A. Henzinger, V.K. Chonev, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-09-07 location: Berlin, Germany name: 'CONCUR: Concurrency Theory' start_date: 2017-09-05 date_created: 2018-12-11T11:49:22Z date_published: 2017-09-01T00:00:00Z date_updated: 2025-07-10T11:53:48Z day: '01' ddc: - '000' department: - _id: ToHe - _id: KrCh doi: 10.4230/LIPIcs.CONCUR.2017.21 external_id: arxiv: - '1705.01433' file: - access_level: open_access checksum: 6d5cccf755207b91ccbef95d8275b013 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:00Z date_updated: 2020-07-14T12:48:16Z file_id: '5318' file_name: IST-2017-844-v1+1_concur-cr.pdf file_size: 335170 relation: main_file file_date_updated: 2020-07-14T12:48:16Z has_accepted_license: '1' intvolume: ' 85' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: Formal methods for the design and analysis of complex systems publication_identifier: issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '6466' pubrep_id: '844' quality_controlled: '1' related_material: record: - id: '6752' relation: later_version status: public scopus_import: 1 status: public title: Infinite-duration bidding games tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 85 year: '2017' ... --- _id: '9506' abstract: - lang: eng text: Methylation in the bodies of active genes is common in animals and vascular plants. Evolutionary patterns indicate homeostatic functions for this type of methylation. article_number: '87' article_processing_charge: No author: - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: 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 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 chicago: Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation in Plants and Animals.” Genome Biology. Springer Nature, 2017. https://doi.org/10.1186/s13059-017-1230-2. ieee: D. Zilberman, “An evolutionary case for functional gene body methylation in plants and animals,” Genome Biology, vol. 18, no. 1. Springer Nature, 2017. ista: Zilberman D. 2017. An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. 18(1), 87. 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. short: D. Zilberman, Genome Biology 18 (2017). date_created: 2021-06-07T12:27:39Z date_published: 2017-05-09T00:00:00Z date_updated: 2021-12-14T07:55:02Z day: '09' ddc: - '570' department: - _id: DaZi doi: 10.1186/s13059-017-1230-2 extern: '1' external_id: pmid: - '28486944' file: - access_level: open_access checksum: 5a455ad914e7d225b1baa4ab07fd925e content_type: application/pdf creator: asandaue date_created: 2021-06-07T12:31:36Z date_updated: 2021-06-07T12:31:36Z file_id: '9507' file_name: 2017_GenomeBiology_Zilberman.pdf file_size: 278183 relation: main_file success: 1 file_date_updated: 2021-06-07T12:31:36Z has_accepted_license: '1' intvolume: ' 18' issue: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 publication: Genome Biology publication_identifier: eissn: - 1465-6906 issn: - 1474-760X publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: An evolutionary case for functional gene body methylation in plants and animals tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 18 year: '2017' ... --- _id: '952' 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. article_processing_charge: No author: - first_name: Michael full_name: Turelli, Michael last_name: Turelli - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: 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' 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' 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.' 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.' 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.' 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.' short: M. Turelli, N.H. Barton, Theoretical Population Biology 115 (2017) 45–60. date_created: 2018-12-11T11:49:22Z date_published: 2017-06-01T00:00:00Z date_updated: 2025-07-10T12:01:49Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1016/j.tpb.2017.03.003 external_id: pmid: - '28411063' file: - access_level: open_access checksum: 9aeff86fa7de69f7a15cf4fc60d57d01 content_type: application/pdf creator: dernst date_created: 2019-04-17T06:39:45Z date_updated: 2020-07-14T12:48:16Z file_id: '6327' file_name: 2017_TheoreticalPopulationBio_Turelli.pdf file_size: 2073856 relation: main_file file_date_updated: 2020-07-14T12:48:16Z has_accepted_license: '1' intvolume: ' 115' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '06' oa: 1 oa_version: Submitted Version page: 45 - 60 pmid: 1 publication: Theoretical Population Biology publication_identifier: issn: - 0040-5809 publication_status: published publisher: Elsevier publist_id: '6463' pubrep_id: '972' quality_controlled: '1' scopus_import: '1' status: public title: 'Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti' tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 115 year: '2017' ... --- _id: '954' 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. article_number: e25192 article_processing_charge: Yes author: - first_name: Mato full_name: Lagator, Mato id: 345D25EC-F248-11E8-B48F-1D18A9856A87 last_name: Lagator - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: 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 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. 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. 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. 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. short: M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017). date_created: 2018-12-11T11:49:23Z date_published: 2017-05-18T00:00:00Z date_updated: 2025-07-10T12:01:50Z day: '18' ddc: - '576' department: - _id: CaGu - _id: NiBa - _id: JoBo doi: 10.7554/eLife.25192 ec_funded: 1 external_id: isi: - '000404024800001' file: - access_level: open_access checksum: 59cdd4400fb41280122d414fea971546 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:49Z date_updated: 2020-07-14T12:48:16Z file_id: '5306' file_name: IST-2017-841-v1+1_elife-25192-v2.pdf file_size: 2441529 relation: main_file - access_level: open_access checksum: b69024880558b858eb8c5d47a92b6377 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:50Z date_updated: 2020-07-14T12:48:16Z file_id: '5307' file_name: IST-2017-841-v1+2_elife-25192-figures-v2.pdf file_size: 3752660 relation: main_file file_date_updated: 2020-07-14T12:48:16Z has_accepted_license: '1' intvolume: ' 6' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 2578D616-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '648440' name: Selective Barriers to Horizontal Gene Transfer publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications publist_id: '6460' pubrep_id: '841' quality_controlled: '1' scopus_import: '1' status: public title: On the mechanistic nature of epistasis in a canonical cis-regulatory element tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2017' ... --- _id: '955' 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_number: '216' article_processing_charge: Yes (in subscription journal) author: - first_name: Tamar full_name: Friedlander, Tamar id: 36A5845C-F248-11E8-B48F-1D18A9856A87 last_name: Friedlander - first_name: Roshan full_name: Prizak, Roshan id: 4456104E-F248-11E8-B48F-1D18A9856A87 last_name: Prizak - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: 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 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 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. 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. 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. 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. short: T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications 8 (2017). corr_author: '1' date_created: 2018-12-11T11:49:23Z date_published: 2017-08-09T00:00:00Z date_updated: 2026-04-08T13:54:24Z day: '09' ddc: - '539' - '576' department: - _id: GaTk - _id: NiBa doi: 10.1038/s41467-017-00238-8 ec_funded: 1 external_id: isi: - '000407198800005' file: - access_level: open_access checksum: 29a1b5db458048d3bd5c67e0e2a56818 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:14Z date_updated: 2020-07-14T12:48:16Z file_id: '5064' file_name: IST-2017-864-v1+1_s41467-017-00238-8.pdf file_size: 998157 relation: main_file - access_level: open_access checksum: 7b78401e52a576cf3e6bbf8d0abadc17 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:15Z date_updated: 2020-07-14T12:48:16Z file_id: '5065' file_name: IST-2017-864-v1+2_41467_2017_238_MOESM1_ESM.pdf file_size: 9715993 relation: main_file file_date_updated: 2020-07-14T12:48:16Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Nature Publishing Group publist_id: '6459' pubrep_id: '864' quality_controlled: '1' related_material: record: - id: '6071' relation: dissertation_contains status: public scopus_import: '1' status: public title: Evolution of new regulatory functions on biophysically realistic fitness landscapes tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2017' ... --- _id: '956' abstract: - lang: eng 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. article_processing_charge: No arxiv: 1 author: - first_name: Eric full_name: Carlen, Eric last_name: Carlen - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 citation: 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 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. 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. 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. 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. short: E. Carlen, J. Maas, Journal of Functional Analysis 273 (2017) 1810–1869. date_created: 2018-12-11T11:49:24Z date_published: 2017-09-01T00:00:00Z date_updated: 2025-06-04T08:14:53Z day: '01' department: - _id: JaMa doi: 10.1016/j.jfa.2017.05.003 external_id: arxiv: - '1609.01254' isi: - '000406082300005' intvolume: ' 273' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1609.01254 month: '09' oa: 1 oa_version: Submitted Version page: 1810 - 1869 publication: Journal of Functional Analysis publication_identifier: issn: - 0022-1236 publication_status: published publisher: Academic Press publist_id: '6452' quality_controlled: '1' scopus_import: '1' status: public title: Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 273 year: '2017' ... --- _id: '957' abstract: - lang: eng 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. alternative_title: - Methods in Molecular Biology article_processing_charge: No author: - first_name: Ben full_name: Clifton, Ben last_name: Clifton - first_name: Jason full_name: Whitfield, Jason last_name: Whitfield - first_name: Inmaculada full_name: Sanchez Romero, Inmaculada id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87 last_name: Sanchez Romero - first_name: Michel full_name: Herde, Michel last_name: Herde - first_name: Christian full_name: Henneberger, Christian last_name: Henneberger - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Colin full_name: Jackson, Colin last_name: Jackson citation: 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' 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 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. 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. 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.' 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. date_created: 2018-12-11T11:49:24Z date_published: 2017-03-15T00:00:00Z date_updated: 2025-07-10T12:01:52Z day: '15' department: - _id: HaJa doi: 10.1007/978-1-4939-6940-1_5 editor: - first_name: Viktor full_name: Stein, Viktor last_name: Stein intvolume: ' 1596' language: - iso: eng month: '03' oa_version: None page: 71 - 87 project: - _id: 255BFFFA-B435-11E9-9278-68D0E5697425 grant_number: RGY0084/2012 name: In situ real-time imaging of neurotransmitter signaling using designer optical sensors publication: Synthetic Protein Switches publication_identifier: issn: - 1064-3745 publication_status: published publisher: Springer publist_id: '6451' quality_controlled: '1' scopus_import: '1' series_title: Synthetic Protein Switches status: public title: Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1596 year: '2017' ... --- _id: '9574' abstract: - lang: eng text: 'Consider the sum X(ξ)=∑ni=1aiξi, where a=(ai)ni=1 is a sequence of non-zero reals and ξ=(ξi)ni=1 is a sequence of i.i.d. Rademacher random variables (that is, Pr[ξi=1]=Pr[ξi=−1]=1/2). The classical Littlewood-Offord problem asks for the best possible upper bound on the concentration probabilities Pr[X=x]. In this paper we study a resilience version of the Littlewood-Offord problem: how many of the ξi is an adversary typically allowed to change without being able to force concentration on a particular value? We solve this problem asymptotically, and present a few interesting open problems.' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Afonso S. full_name: Bandeira, Afonso S. last_name: Bandeira - first_name: Asaf full_name: Ferber, Asaf last_name: Ferber - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 citation: ama: Bandeira AS, Ferber A, Kwan MA. Resilience for the Littlewood-Offord problem. Electronic Notes in Discrete Mathematics. 2017;61:93-99. doi:10.1016/j.endm.2017.06.025 apa: Bandeira, A. S., Ferber, A., & Kwan, M. A. (2017). Resilience for the Littlewood-Offord problem. Electronic Notes in Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2017.06.025 chicago: Bandeira, Afonso S., Asaf Ferber, and Matthew Alan Kwan. “Resilience for the Littlewood-Offord Problem.” Electronic Notes in Discrete Mathematics. Elsevier, 2017. https://doi.org/10.1016/j.endm.2017.06.025. ieee: A. S. Bandeira, A. Ferber, and M. A. Kwan, “Resilience for the Littlewood-Offord problem,” Electronic Notes in Discrete Mathematics, vol. 61. Elsevier, pp. 93–99, 2017. ista: Bandeira AS, Ferber A, Kwan MA. 2017. Resilience for the Littlewood-Offord problem. Electronic Notes in Discrete Mathematics. 61, 93–99. mla: Bandeira, Afonso S., et al. “Resilience for the Littlewood-Offord Problem.” Electronic Notes in Discrete Mathematics, vol. 61, Elsevier, 2017, pp. 93–99, doi:10.1016/j.endm.2017.06.025. short: A.S. Bandeira, A. Ferber, M.A. Kwan, Electronic Notes in Discrete Mathematics 61 (2017) 93–99. date_created: 2021-06-21T06:31:10Z date_published: 2017-08-01T00:00:00Z date_updated: 2023-02-23T14:01:26Z day: '01' doi: 10.1016/j.endm.2017.06.025 extern: '1' external_id: arxiv: - '1609.08136' intvolume: ' 61' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1609.08136 month: '08' oa: 1 oa_version: Preprint page: 93-99 publication: Electronic Notes in Discrete Mathematics publication_identifier: issn: - 1571-0653 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Resilience for the Littlewood-Offord problem type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 61 year: '2017' ...