[{"department":[{"_id":"JaMa"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.jfa.2017.05.003","day":"01","oa_version":"Submitted Version","type":"journal_article","date_updated":"2023-09-22T10:00:18Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","scopus_import":"1","publication_identifier":{"issn":["00221236"]},"page":"1810 - 1869","external_id":{"isi":["000406082300005"]},"date_published":"2017-09-01T00:00:00Z","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."}],"publication_status":"published","_id":"956","oa":1,"title":"Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance","publication":"Journal of Functional Analysis","year":"2017","author":[{"full_name":"Carlen, Eric","first_name":"Eric","last_name":"Carlen"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","first_name":"Jan","last_name":"Maas"}],"quality_controlled":"1","citation":{"mla":"Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for Quantum Markov Semigroups with Detailed Balance.” <i>Journal of Functional Analysis</i>, vol. 273, no. 5, Academic Press, 2017, pp. 1810–69, doi:<a href=\"https://doi.org/10.1016/j.jfa.2017.05.003\">10.1016/j.jfa.2017.05.003</a>.","apa":"Carlen, E., &#38; Maas, J. (2017). Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. <i>Journal of Functional Analysis</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jfa.2017.05.003\">https://doi.org/10.1016/j.jfa.2017.05.003</a>","ieee":"E. Carlen and J. Maas, “Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance,” <i>Journal of Functional Analysis</i>, vol. 273, no. 5. Academic Press, pp. 1810–1869, 2017.","ama":"Carlen E, Maas J. Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. <i>Journal of Functional Analysis</i>. 2017;273(5):1810-1869. doi:<a href=\"https://doi.org/10.1016/j.jfa.2017.05.003\">10.1016/j.jfa.2017.05.003</a>","short":"E. Carlen, J. Maas, Journal of Functional Analysis 273 (2017) 1810–1869.","chicago":"Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for Quantum Markov Semigroups with Detailed Balance.” <i>Journal of Functional Analysis</i>. Academic Press, 2017. <a href=\"https://doi.org/10.1016/j.jfa.2017.05.003\">https://doi.org/10.1016/j.jfa.2017.05.003</a>.","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."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1609.01254"}],"status":"public","month":"09","date_created":"2018-12-11T11:49:24Z","isi":1,"publist_id":"6452","intvolume":"       273","publisher":"Academic Press","volume":273,"issue":"5"},{"department":[{"_id":"HaJa"}],"doi":"10.1007/978-1-4939-6940-1_5","language":[{"iso":"eng"}],"oa_version":"None","series_title":"Synthetic Protein Switches","date_updated":"2021-01-12T08:22:13Z","type":"book_chapter","day":"15","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","alternative_title":["Methods in Molecular Biology"],"scopus_import":1,"publication_identifier":{"issn":["10643745"]},"date_published":"2017-03-15T00:00:00Z","page":"71 - 87","project":[{"name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","grant_number":"RGY0084/2012","_id":"255BFFFA-B435-11E9-9278-68D0E5697425"}],"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","publication":"Synthetic Protein Switches","title":"Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors","_id":"957","year":"2017","citation":{"ieee":"B. Clifton <i>et al.</i>, “Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors,” in <i>Synthetic Protein Switches</i>, 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. <i>Synthetic Protein Switches</i>. Vol 1596. Synthetic Protein Switches. Springer; 2017:71-87. doi:<a href=\"https://doi.org/10.1007/978-1-4939-6940-1_5\">10.1007/978-1-4939-6940-1_5</a>","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.","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 <i>Synthetic Protein Switches</i>, edited by Viktor Stein, 1596:71–87. Synthetic Protein Switches. Springer, 2017. <a href=\"https://doi.org/10.1007/978-1-4939-6940-1_5\">https://doi.org/10.1007/978-1-4939-6940-1_5</a>.","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.","apa":"Clifton, B., Whitfield, J., Sanchez-Romero, I., Herde, M., Henneberger, C., Janovjak, H. L., &#38; Jackson, C. (2017). Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In V. Stein (Ed.), <i>Synthetic Protein Switches</i> (Vol. 1596, pp. 71–87). Springer. <a href=\"https://doi.org/10.1007/978-1-4939-6940-1_5\">https://doi.org/10.1007/978-1-4939-6940-1_5</a>","mla":"Clifton, Ben, et al. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” <i>Synthetic Protein Switches</i>, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 71–87, doi:<a href=\"https://doi.org/10.1007/978-1-4939-6940-1_5\">10.1007/978-1-4939-6940-1_5</a>."},"author":[{"last_name":"Clifton","first_name":"Ben","full_name":"Clifton, Ben"},{"last_name":"Whitfield","first_name":"Jason","full_name":"Whitfield, Jason"},{"last_name":"Sanchez Romero","first_name":"Inmaculada","full_name":"Sanchez Romero, Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Herde, Michel","first_name":"Michel","last_name":"Herde"},{"full_name":"Henneberger, Christian","last_name":"Henneberger","first_name":"Christian"},{"last_name":"Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315"},{"full_name":"Jackson, Colin","last_name":"Jackson","first_name":"Colin"}],"quality_controlled":"1","month":"03","date_created":"2018-12-11T11:49:24Z","status":"public","intvolume":"      1596","publist_id":"6451","editor":[{"last_name":"Stein","first_name":"Viktor","full_name":"Stein, Viktor"}],"publisher":"Springer","volume":1596},{"day":"01","date_updated":"2023-02-23T14:01:26Z","type":"journal_article","oa_version":"Preprint","article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","doi":"10.1016/j.endm.2017.06.025","language":[{"iso":"eng"}],"page":"93-99","date_published":"2017-08-01T00:00:00Z","external_id":{"arxiv":["1609.08136"]},"arxiv":1,"publication_identifier":{"issn":["1571-0653"]},"scopus_import":"1","year":"2017","quality_controlled":"1","author":[{"first_name":"Afonso S.","last_name":"Bandeira","full_name":"Bandeira, Afonso S."},{"first_name":"Asaf","last_name":"Ferber","full_name":"Ferber, Asaf"},{"orcid":"0000-0002-4003-7567","full_name":"Kwan, Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","first_name":"Matthew Alan","last_name":"Kwan"}],"extern":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1609.08136"}],"citation":{"apa":"Bandeira, A. S., Ferber, A., &#38; Kwan, M. A. (2017). Resilience for the Littlewood-Offord problem. <i>Electronic Notes in Discrete Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.endm.2017.06.025\">https://doi.org/10.1016/j.endm.2017.06.025</a>","mla":"Bandeira, Afonso S., et al. “Resilience for the Littlewood-Offord Problem.” <i>Electronic Notes in Discrete Mathematics</i>, vol. 61, Elsevier, 2017, pp. 93–99, doi:<a href=\"https://doi.org/10.1016/j.endm.2017.06.025\">10.1016/j.endm.2017.06.025</a>.","ista":"Bandeira AS, Ferber A, Kwan MA. 2017. Resilience for the Littlewood-Offord problem. Electronic Notes in Discrete Mathematics. 61, 93–99.","short":"A.S. Bandeira, A. Ferber, M.A. Kwan, Electronic Notes in Discrete Mathematics 61 (2017) 93–99.","chicago":"Bandeira, Afonso S., Asaf Ferber, and Matthew Alan Kwan. “Resilience for the Littlewood-Offord Problem.” <i>Electronic Notes in Discrete Mathematics</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.endm.2017.06.025\">https://doi.org/10.1016/j.endm.2017.06.025</a>.","ama":"Bandeira AS, Ferber A, Kwan MA. Resilience for the Littlewood-Offord problem. <i>Electronic Notes in Discrete Mathematics</i>. 2017;61:93-99. doi:<a href=\"https://doi.org/10.1016/j.endm.2017.06.025\">10.1016/j.endm.2017.06.025</a>","ieee":"A. S. Bandeira, A. Ferber, and M. A. Kwan, “Resilience for the Littlewood-Offord problem,” <i>Electronic Notes in Discrete Mathematics</i>, vol. 61. Elsevier, pp. 93–99, 2017."},"publication_status":"published","abstract":[{"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.","lang":"eng"}],"oa":1,"_id":"9574","title":"Resilience for the Littlewood-Offord problem","publication":"Electronic Notes in Discrete Mathematics","article_type":"original","publisher":"Elsevier","volume":61,"status":"public","date_created":"2021-06-21T06:31:10Z","month":"08","intvolume":"        61"},{"scopus_import":1,"publication_identifier":{"issn":["10643745"]},"alternative_title":["Methods in Molecular Biology"],"page":"89 - 99","date_published":"2017-05-15T00:00:00Z","department":[{"_id":"HaJa"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-1-4939-6940-1_6","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","day":"15","oa_version":"None","type":"book_chapter","date_updated":"2021-01-12T08:22:13Z","series_title":"Synthetic Protein Switches","publist_id":"6450","intvolume":"      1596","status":"public","month":"05","date_created":"2018-12-11T11:49:24Z","volume":1596,"editor":[{"full_name":"Stein, Viktor","last_name":"Stein","first_name":"Viktor"}],"publisher":"Springer","_id":"958","publication":"Synthetic Protein Switches","title":"Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment","abstract":[{"lang":"eng","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."}],"publication_status":"published","author":[{"full_name":"Mitchell, Joshua","last_name":"Mitchell","first_name":"Joshua"},{"first_name":"William","last_name":"Zhang","full_name":"Zhang, William"},{"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","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Megan","last_name":"O'Mara","full_name":"O'Mara, Megan"},{"last_name":"Jackson","first_name":"Colin","full_name":"Jackson, Colin"}],"quality_controlled":"1","citation":{"ieee":"J. Mitchell <i>et al.</i>, “Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment,” in <i>Synthetic Protein Switches</i>, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 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. <i>Synthetic Protein Switches</i>. Vol 1596. Synthetic Protein Switches. Springer; 2017:89-99. doi:<a href=\"https://doi.org/10.1007/978-1-4939-6940-1_6\">10.1007/978-1-4939-6940-1_6</a>","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.","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 <i>Synthetic Protein Switches</i>, edited by Viktor Stein, 1596:89–99. Synthetic Protein Switches. Springer, 2017. <a href=\"https://doi.org/10.1007/978-1-4939-6940-1_6\">https://doi.org/10.1007/978-1-4939-6940-1_6</a>.","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.","mla":"Mitchell, Joshua, et al. “Method for Developing Optical Sensors Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.” <i>Synthetic Protein Switches</i>, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 89–99, doi:<a href=\"https://doi.org/10.1007/978-1-4939-6940-1_6\">10.1007/978-1-4939-6940-1_6</a>.","apa":"Mitchell, J., Zhang, W., Herde, M., Henneberger, C., Janovjak, H. L., O’Mara, M., &#38; 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.), <i>Synthetic Protein Switches</i> (Vol. 1596, pp. 89–99). Springer. <a href=\"https://doi.org/10.1007/978-1-4939-6940-1_6\">https://doi.org/10.1007/978-1-4939-6940-1_6</a>"},"year":"2017"},{"intvolume":"       319","date_created":"2021-06-22T11:51:27Z","month":"10","status":"public","volume":319,"publisher":"Elsevier","article_type":"original","title":"Resilience for the Littlewood–Offord problem","publication":"Advances in Mathematics","oa":1,"_id":"9588","publication_status":"published","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."}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1609.08136"}],"citation":{"mla":"Bandeira, Afonso S., et al. “Resilience for the Littlewood–Offord Problem.” <i>Advances in Mathematics</i>, vol. 319, Elsevier, 2017, pp. 292–312, doi:<a href=\"https://doi.org/10.1016/j.aim.2017.08.031\">10.1016/j.aim.2017.08.031</a>.","apa":"Bandeira, A. S., Ferber, A., &#38; Kwan, M. A. (2017). Resilience for the Littlewood–Offord problem. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2017.08.031\">https://doi.org/10.1016/j.aim.2017.08.031</a>","ama":"Bandeira AS, Ferber A, Kwan MA. Resilience for the Littlewood–Offord problem. <i>Advances in Mathematics</i>. 2017;319:292-312. doi:<a href=\"https://doi.org/10.1016/j.aim.2017.08.031\">10.1016/j.aim.2017.08.031</a>","ieee":"A. S. Bandeira, A. Ferber, and M. A. Kwan, “Resilience for the Littlewood–Offord problem,” <i>Advances in Mathematics</i>, vol. 319. Elsevier, pp. 292–312, 2017.","ista":"Bandeira AS, Ferber A, Kwan MA. 2017. Resilience for the Littlewood–Offord problem. Advances in Mathematics. 319, 292–312.","chicago":"Bandeira, Afonso S., Asaf Ferber, and Matthew Alan Kwan. “Resilience for the Littlewood–Offord Problem.” <i>Advances in Mathematics</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.aim.2017.08.031\">https://doi.org/10.1016/j.aim.2017.08.031</a>.","short":"A.S. Bandeira, A. Ferber, M.A. Kwan, Advances in Mathematics 319 (2017) 292–312."},"author":[{"first_name":"Afonso S.","last_name":"Bandeira","full_name":"Bandeira, Afonso S."},{"full_name":"Ferber, Asaf","first_name":"Asaf","last_name":"Ferber"},{"id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","orcid":"0000-0002-4003-7567","full_name":"Kwan, Matthew Alan","first_name":"Matthew Alan","last_name":"Kwan"}],"quality_controlled":"1","extern":"1","year":"2017","publication_identifier":{"issn":["0001-8708"]},"scopus_import":"1","arxiv":1,"date_published":"2017-10-15T00:00:00Z","external_id":{"arxiv":["1609.08136"]},"page":"292-312","language":[{"iso":"eng"}],"doi":"10.1016/j.aim.2017.08.031","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","date_updated":"2023-02-23T14:01:57Z","type":"journal_article","oa_version":"Preprint","day":"15"},{"intvolume":"        63","month":"06","date_created":"2021-06-22T12:18:59Z","status":"public","volume":63,"article_type":"original","publisher":"Elsevier","publication":"European Journal of Combinatorics","title":"The average number of spanning trees in sparse graphs with given degrees","_id":"9589","oa":1,"abstract":[{"lang":"eng","text":"We give an asymptotic expression for the expected number of spanning trees in a random graph with a given degree sequence , provided that the number of edges is at least , where  is the maximum degree. A key part of our argument involves establishing a concentration result for a certain family of functions over random trees with given degrees, using Prüfer codes."}],"publication_status":"published","citation":{"apa":"Greenhill, C., Isaev, M., Kwan, M. A., &#38; McKay, B. D. (2017). The average number of spanning trees in sparse graphs with given degrees. <i>European Journal of Combinatorics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ejc.2017.02.003\">https://doi.org/10.1016/j.ejc.2017.02.003</a>","mla":"Greenhill, Catherine, et al. “The Average Number of Spanning Trees in Sparse Graphs with given Degrees.” <i>European Journal of Combinatorics</i>, vol. 63, Elsevier, 2017, pp. 6–25, doi:<a href=\"https://doi.org/10.1016/j.ejc.2017.02.003\">10.1016/j.ejc.2017.02.003</a>.","ieee":"C. Greenhill, M. Isaev, M. A. Kwan, and B. D. McKay, “The average number of spanning trees in sparse graphs with given degrees,” <i>European Journal of Combinatorics</i>, vol. 63. Elsevier, pp. 6–25, 2017.","ama":"Greenhill C, Isaev M, Kwan MA, McKay BD. The average number of spanning trees in sparse graphs with given degrees. <i>European Journal of Combinatorics</i>. 2017;63:6-25. doi:<a href=\"https://doi.org/10.1016/j.ejc.2017.02.003\">10.1016/j.ejc.2017.02.003</a>","short":"C. Greenhill, M. Isaev, M.A. Kwan, B.D. McKay, European Journal of Combinatorics 63 (2017) 6–25.","chicago":"Greenhill, Catherine, Mikhail Isaev, Matthew Alan Kwan, and Brendan D. McKay. “The Average Number of Spanning Trees in Sparse Graphs with given Degrees.” <i>European Journal of Combinatorics</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.ejc.2017.02.003\">https://doi.org/10.1016/j.ejc.2017.02.003</a>.","ista":"Greenhill C, Isaev M, Kwan MA, McKay BD. 2017. The average number of spanning trees in sparse graphs with given degrees. European Journal of Combinatorics. 63, 6–25."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.ejc.2017.02.003"}],"quality_controlled":"1","author":[{"full_name":"Greenhill, Catherine","first_name":"Catherine","last_name":"Greenhill"},{"last_name":"Isaev","first_name":"Mikhail","full_name":"Isaev, Mikhail"},{"first_name":"Matthew Alan","last_name":"Kwan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan","orcid":"0000-0002-4003-7567"},{"first_name":"Brendan D.","last_name":"McKay","full_name":"McKay, Brendan D."}],"extern":"1","year":"2017","scopus_import":"1","publication_identifier":{"issn":["0195-6698"]},"arxiv":1,"external_id":{"arxiv":["1606.01586"]},"date_published":"2017-06-01T00:00:00Z","page":"6-25","language":[{"iso":"eng"}],"doi":"10.1016/j.ejc.2017.02.003","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","oa_version":"Published Version","type":"journal_article","date_updated":"2023-02-23T14:02:00Z","day":"01"},{"date_published":"2017-06-28T00:00:00Z","external_id":{"isi":["000404546400004"]},"page":"062419","publication_identifier":{"issn":["24700045"]},"scopus_import":"1","type":"journal_article","date_updated":"2023-09-22T09:59:01Z","oa_version":"Submitted Version","day":"28","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","ec_funded":1,"doi":"10.1103/PhysRevE.95.062419","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"}],"publisher":"American Institute of Physics","volume":95,"issue":"6","date_created":"2018-12-11T11:49:25Z","month":"06","status":"public","intvolume":"        95","publist_id":"6446","isi":1,"year":"2017","main_file_link":[{"open_access":"1","url":"https://arxiv.org/pdf/1703.00853.pdf"}],"citation":{"ista":"De Martino D. 2017. Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics.  Physical Review E Statistical Nonlinear and Soft Matter Physics . 95(6), 062419.","chicago":"De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary Metabolic Network Models via Thermodynamics.” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. American Institute of Physics, 2017. <a href=\"https://doi.org/10.1103/PhysRevE.95.062419\">https://doi.org/10.1103/PhysRevE.95.062419</a>.","short":"D. De Martino,  Physical Review E Statistical Nonlinear and Soft Matter Physics  95 (2017) 062419.","ieee":"D. De Martino, “Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics,” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>, vol. 95, no. 6. American Institute of Physics, p. 062419, 2017.","ama":"De Martino D. Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. 2017;95(6):062419. doi:<a href=\"https://doi.org/10.1103/PhysRevE.95.062419\">10.1103/PhysRevE.95.062419</a>","apa":"De Martino, D. (2017). Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.95.062419\">https://doi.org/10.1103/PhysRevE.95.062419</a>","mla":"De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary Metabolic Network Models via Thermodynamics.” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>, vol. 95, no. 6, American Institute of Physics, 2017, p. 062419, doi:<a href=\"https://doi.org/10.1103/PhysRevE.95.062419\">10.1103/PhysRevE.95.062419</a>."},"author":[{"last_name":"De Martino","first_name":"Daniele","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publication_status":"published","abstract":[{"text":"In this work it is shown that scale-free tails in metabolic flux distributions inferred in stationary models are an artifact due to reactions involved in thermodynamically unfeasible cycles, unbounded by physical constraints and in principle able to perform work without expenditure of free energy. After implementing thermodynamic constraints by removing such loops, metabolic flux distributions scale meaningfully with the physical limiting factors, acquiring in turn a richer multimodal structure potentially leading to symmetry breaking while optimizing for objective functions.","lang":"eng"}],"publication":" Physical Review E Statistical Nonlinear and Soft Matter Physics ","title":"Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics","oa":1,"_id":"959"},{"year":"2017","citation":{"mla":"Krivelevich, Michael, et al. “Bounded-Degree Spanning Trees in Randomly Perturbed Graphs.” <i>SIAM Journal on Discrete Mathematics</i>, vol. 31, no. 1, Society for Industrial &#38; Applied Mathematics, 2017, pp. 155–71, doi:<a href=\"https://doi.org/10.1137/15m1032910\">10.1137/15m1032910</a>.","apa":"Krivelevich, M., Kwan, M. A., &#38; Sudakov, B. (2017). Bounded-degree spanning trees in randomly perturbed graphs. <i>SIAM Journal on Discrete Mathematics</i>. Society for Industrial &#38; Applied Mathematics. <a href=\"https://doi.org/10.1137/15m1032910\">https://doi.org/10.1137/15m1032910</a>","ieee":"M. Krivelevich, M. A. Kwan, and B. Sudakov, “Bounded-degree spanning trees in randomly perturbed graphs,” <i>SIAM Journal on Discrete Mathematics</i>, vol. 31, no. 1. Society for Industrial &#38; Applied Mathematics, pp. 155–171, 2017.","ama":"Krivelevich M, Kwan MA, Sudakov B. Bounded-degree spanning trees in randomly perturbed graphs. <i>SIAM Journal on Discrete Mathematics</i>. 2017;31(1):155-171. doi:<a href=\"https://doi.org/10.1137/15m1032910\">10.1137/15m1032910</a>","short":"M. Krivelevich, M.A. Kwan, B. Sudakov, SIAM Journal on Discrete Mathematics 31 (2017) 155–171.","chicago":"Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Bounded-Degree Spanning Trees in Randomly Perturbed Graphs.” <i>SIAM Journal on Discrete Mathematics</i>. Society for Industrial &#38; Applied Mathematics, 2017. <a href=\"https://doi.org/10.1137/15m1032910\">https://doi.org/10.1137/15m1032910</a>.","ista":"Krivelevich M, Kwan MA, Sudakov B. 2017. Bounded-degree spanning trees in randomly perturbed graphs. SIAM Journal on Discrete Mathematics. 31(1), 155–171."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1507.07960"}],"quality_controlled":"1","extern":"1","author":[{"full_name":"Krivelevich, Michael","first_name":"Michael","last_name":"Krivelevich"},{"last_name":"Kwan","first_name":"Matthew Alan","full_name":"Kwan, Matthew Alan","orcid":"0000-0002-4003-7567","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3"},{"last_name":"Sudakov","first_name":"Benny","full_name":"Sudakov, Benny"}],"publication_status":"published","abstract":[{"text":"We show that for any fixed dense graph G and bounded-degree tree T on the same number of vertices, a modest random perturbation of G will typically contain a copy of T . This combines the viewpoints of the well-studied problems of embedding trees into fixed dense graphs and into random graphs, and extends a sizeable body of existing research on randomly perturbed graphs. Specifically, we show that there is c=c(α,Δ) such that if G is an n-vertex graph with minimum degree at least αn, and T is an n-vertex tree with maximum degree at most Δ , then if we add cn uniformly random edges to G, the resulting graph will contain T asymptotically almost surely (as n→∞ ). Our proof uses a lemma concerning the decomposition of a dense graph into super-regular pairs of comparable sizes, which may be of independent interest.","lang":"eng"}],"title":"Bounded-degree spanning trees in randomly perturbed graphs","publication":"SIAM Journal on Discrete Mathematics","oa":1,"_id":"9590","article_type":"original","publisher":"Society for Industrial & Applied Mathematics","volume":31,"issue":"1","date_created":"2021-06-22T12:26:25Z","month":"01","status":"public","intvolume":"        31","type":"journal_article","date_updated":"2023-02-23T14:02:05Z","oa_version":"Preprint","day":"12","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","language":[{"iso":"eng"}],"doi":"10.1137/15m1032910","date_published":"2017-01-12T00:00:00Z","external_id":{"arxiv":["1507.07960"]},"page":"155-171","arxiv":1,"publication_identifier":{"eissn":["1095-7146"],"issn":["0895-4801"]},"scopus_import":"1"},{"day":"28","oa_version":"Published Version","date_updated":"2024-03-25T23:30:23Z","type":"journal_article","article_processing_charge":"Yes","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"SiHi"},{"_id":"MaLo"}],"has_accepted_license":"1","doi":"10.3389/fncel.2017.00176","language":[{"iso":"eng"}],"ec_funded":1,"external_id":{"isi":["000404486700001"]},"file":[{"file_name":"IST-2017-830-v1+1_2017_Hansen_CellPolarity.pdf","checksum":"dc1f5a475b918d09a0f9f587400b1626","access_level":"open_access","date_updated":"2020-07-14T12:48:16Z","file_id":"4764","file_size":2153858,"creator":"system","content_type":"application/pdf","relation":"main_file","date_created":"2018-12-12T10:09:40Z"}],"date_published":"2017-06-28T00:00:00Z","scopus_import":"1","publication_identifier":{"issn":["16625102"]},"year":"2017","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"last_name":"Hansen","first_name":"Andi H","full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Düllberg","first_name":"Christian F","orcid":"0000-0001-6335-9748","full_name":"Düllberg, Christian F","id":"459064DC-F248-11E8-B48F-1D18A9856A87"},{"id":"34CAE85C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1919-7416","full_name":"Mieck, Christine","last_name":"Mieck","first_name":"Christine"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose"},{"last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","citation":{"ieee":"A. H. Hansen, C. F. Düllberg, C. Mieck, M. Loose, and S. Hippenmeyer, “Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks,” <i>Frontiers in Cellular Neuroscience</i>, vol. 11. Frontiers Research Foundation, 2017.","ama":"Hansen AH, Düllberg CF, Mieck C, Loose M, Hippenmeyer S. Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. <i>Frontiers in Cellular Neuroscience</i>. 2017;11. doi:<a href=\"https://doi.org/10.3389/fncel.2017.00176\">10.3389/fncel.2017.00176</a>","short":"A.H. Hansen, C.F. Düllberg, C. Mieck, M. Loose, S. Hippenmeyer, Frontiers in Cellular Neuroscience 11 (2017).","chicago":"Hansen, Andi H, Christian F Düllberg, Christine Mieck, Martin Loose, and Simon Hippenmeyer. “Cell Polarity in Cerebral Cortex Development - Cellular Architecture Shaped by Biochemical Networks.” <i>Frontiers in Cellular Neuroscience</i>. Frontiers Research Foundation, 2017. <a href=\"https://doi.org/10.3389/fncel.2017.00176\">https://doi.org/10.3389/fncel.2017.00176</a>.","ista":"Hansen AH, Düllberg CF, Mieck C, Loose M, Hippenmeyer S. 2017. Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. 11, 176.","apa":"Hansen, A. H., Düllberg, C. F., Mieck, C., Loose, M., &#38; Hippenmeyer, S. (2017). Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. <i>Frontiers in Cellular Neuroscience</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fncel.2017.00176\">https://doi.org/10.3389/fncel.2017.00176</a>","mla":"Hansen, Andi H., et al. “Cell Polarity in Cerebral Cortex Development - Cellular Architecture Shaped by Biochemical Networks.” <i>Frontiers in Cellular Neuroscience</i>, vol. 11, 176, Frontiers Research Foundation, 2017, doi:<a href=\"https://doi.org/10.3389/fncel.2017.00176\">10.3389/fncel.2017.00176</a>."},"abstract":[{"text":"The human cerebral cortex is the seat of our cognitive abilities and composed of an extraordinary number of neurons, organized in six distinct layers. The establishment of specific morphological and physiological features in individual neurons needs to be regulated with high precision. Impairments in the sequential developmental programs instructing corticogenesis lead to alterations in the cortical cytoarchitecture which is thought to represent the major underlying cause for several neurological disorders including neurodevelopmental and psychiatric diseases. In this review we discuss the role of cell polarity at sequential stages during cortex development. We first provide an overview of morphological cell polarity features in cortical neural stem cells and newly-born postmitotic neurons. We then synthesize a conceptual molecular and biochemical framework how cell polarity is established at the cellular level through a break in symmetry in nascent cortical projection neurons. Lastly we provide a perspective how the molecular mechanisms applying to single cells could be probed and integrated in an in vivo and tissue-wide context.","lang":"eng"}],"publication_status":"published","project":[{"_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"618444","name":"Molecular Mechanisms of Cerebral Cortex Development"},{"grant_number":"RGP0053/2014","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","_id":"25D7962E-B435-11E9-9278-68D0E5697425"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"name":"The biochemical basis of PAR polarization","grant_number":"T00817-B21","call_identifier":"FWF","_id":"25985A36-B435-11E9-9278-68D0E5697425"}],"_id":"960","related_material":{"record":[{"id":"9962","relation":"dissertation_contains","status":"public"}]},"oa":1,"ddc":["570"],"publication":"Frontiers in Cellular Neuroscience","title":"Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks","publisher":"Frontiers Research Foundation","file_date_updated":"2020-07-14T12:48:16Z","pubrep_id":"830","volume":11,"article_number":"176","status":"public","month":"06","date_created":"2018-12-11T11:49:25Z","isi":1,"publist_id":"6445","intvolume":"        11"},{"pubrep_id":"825","file_date_updated":"2020-07-14T12:48:16Z","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","publist_id":"6444","month":"03","date_created":"2018-12-11T11:49:25Z","status":"public","citation":{"apa":"Barone, V. (2017). <i>Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_825\">https://doi.org/10.15479/AT:ISTA:th_825</a>","mla":"Barone, Vanessa. <i>Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_825\">10.15479/AT:ISTA:th_825</a>.","short":"V. Barone, Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation, Institute of Science and Technology Austria, 2017.","chicago":"Barone, Vanessa. “Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_825\">https://doi.org/10.15479/AT:ISTA:th_825</a>.","ista":"Barone V. 2017. Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. Institute of Science and Technology Austria.","ama":"Barone V. Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_825\">10.15479/AT:ISTA:th_825</a>","ieee":"V. Barone, “Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation,” Institute of Science and Technology Austria, 2017."},"author":[{"last_name":"Barone","first_name":"Vanessa","orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2017","title":"Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation","_id":"961","ddc":["570","590"],"related_material":{"record":[{"id":"1100","status":"public","relation":"part_of_dissertation"},{"id":"1537","status":"public","relation":"part_of_dissertation"},{"id":"1912","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"2926"},{"id":"3246","relation":"part_of_dissertation","status":"public"},{"id":"676","status":"public","relation":"part_of_dissertation"},{"id":"735","relation":"part_of_dissertation","status":"public"}]},"oa":1,"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","file":[{"access_level":"closed","file_name":"2017_Barone_thesis_final.docx","checksum":"242f88c87f2cf267bf05049fa26a687b","date_updated":"2020-07-14T12:48:16Z","file_id":"6205","file_size":14497822,"creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2019-04-05T08:36:52Z","relation":"source_file"},{"access_level":"open_access","checksum":"ba5b0613ed8bade73a409acdd880fb8a","file_name":"2017_Barone_thesis_.pdf","date_updated":"2020-07-14T12:48:16Z","file_id":"6206","creator":"dernst","content_type":"application/pdf","file_size":14995941,"date_created":"2019-04-05T08:36:52Z","relation":"main_file"}],"date_published":"2017-03-01T00:00:00Z","page":"109","alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","oa_version":"Published Version","type":"dissertation","date_updated":"2023-09-27T14:16:45Z","supervisor":[{"first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"day":"01","has_accepted_license":"1","department":[{"_id":"CaHe"}],"doi":"10.15479/AT:ISTA:th_825","language":[{"iso":"eng"}],"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!"},{"abstract":[{"lang":"eng","text":"We present a new algorithm for model counting of a class of string constraints. In addition to the classic operation of concatenation, our class includes some recursively defined operations such as Kleene closure, and replacement of substrings. Additionally, our class also includes length constraints on the string expressions, which means, by requiring reasoning about numbers, that we face a multi-sorted logic. In the end, our string constraints are motivated by their use in programming for web applications. Our algorithm comprises two novel features: the ability to use a technique of (1) partial derivatives for constraints that are already in a solved form, i.e. a form where its (string) satisfiability is clearly displayed, and (2) non-progression, where cyclic reasoning in the reduction process may be terminated (thus allowing for the algorithm to look elsewhere). Finally, we experimentally compare our model counter with two recent works on model counting of similar constraints, SMC [18] and ABC [5], to demonstrate its superior performance."}],"publication_status":"published","project":[{"grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"_id":"962","title":"Model counting for recursively-defined strings","year":"2017","author":[{"full_name":"Trinh, Minh","first_name":"Minh","last_name":"Trinh"},{"last_name":"Chu","first_name":"Duc Hiep","full_name":"Chu, Duc Hiep","id":"3598E630-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jaffar, Joxan","first_name":"Joxan","last_name":"Jaffar"}],"quality_controlled":"1","citation":{"ieee":"M. Trinh, D. H. Chu, and J. Jaffar, “Model counting for recursively-defined strings,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10427, pp. 399–418.","ama":"Trinh M, Chu DH, Jaffar J. Model counting for recursively-defined strings. In: Majumdar R, Kunčak V, eds. Vol 10427. Springer; 2017:399-418. doi:<a href=\"https://doi.org/10.1007/978-3-319-63390-9_21\">10.1007/978-3-319-63390-9_21</a>","ista":"Trinh M, Chu DH, Jaffar J. 2017. Model counting for recursively-defined strings. CAV: Computer Aided Verification, LNCS, vol. 10427, 399–418.","short":"M. Trinh, D.H. Chu, J. Jaffar, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 399–418.","chicago":"Trinh, Minh, Duc Hiep Chu, and Joxan Jaffar. “Model Counting for Recursively-Defined Strings.” edited by Rupak Majumdar and Viktor Kunčak, 10427:399–418. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-63390-9_21\">https://doi.org/10.1007/978-3-319-63390-9_21</a>.","mla":"Trinh, Minh, et al. <i>Model Counting for Recursively-Defined Strings</i>. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10427, Springer, 2017, pp. 399–418, doi:<a href=\"https://doi.org/10.1007/978-3-319-63390-9_21\">10.1007/978-3-319-63390-9_21</a>.","apa":"Trinh, M., Chu, D. H., &#38; Jaffar, J. (2017). Model counting for recursively-defined strings. In R. Majumdar &#38; V. Kunčak (Eds.) (Vol. 10427, pp. 399–418). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. <a href=\"https://doi.org/10.1007/978-3-319-63390-9_21\">https://doi.org/10.1007/978-3-319-63390-9_21</a>"},"status":"public","month":"01","conference":{"end_date":"2017-07-28","name":"CAV: Computer Aided Verification","start_date":"2017-07-24","location":"Heidelberg, Germany"},"date_created":"2018-12-11T11:49:26Z","isi":1,"publist_id":"6443","intvolume":"     10427","editor":[{"full_name":"Majumdar, Rupak","last_name":"Majumdar","first_name":"Rupak"},{"full_name":"Kunčak, Viktor","first_name":"Viktor","last_name":"Kunčak"}],"publisher":"Springer","volume":10427,"department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-63390-9_21","day":"01","oa_version":"None","date_updated":"2023-09-22T09:58:02Z","type":"conference","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","publication_identifier":{"issn":["03029743"]},"alternative_title":["LNCS"],"page":"399 - 418","external_id":{"isi":["000431900900021"]},"date_published":"2017-01-01T00:00:00Z"},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2020-07-14T12:48:18Z","volume":83,"pubrep_id":"829","article_number":"37","status":"public","date_created":"2018-12-11T11:49:26Z","conference":{"location":"Aalborg, Denmark","start_date":"2017-08-21","end_date":"2017-08-25","name":"MFCS: Mathematical Foundations of Computer Science (SG)"},"month":"06","publist_id":"6438","intvolume":"        83","year":"2017","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","first_name":"Guy"},{"full_name":"Guha, Shibashis","last_name":"Guha","first_name":"Shibashis"},{"last_name":"Kupferman","first_name":"Orna","full_name":"Kupferman, Orna"}],"quality_controlled":"1","citation":{"ieee":"G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark, 2017, vol. 83.","ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.37\">10.4230/LIPIcs.MFCS.2017.37</a>","short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.37\">https://doi.org/10.4230/LIPIcs.MFCS.2017.37</a>.","ista":"Avni G, Guha S, Kupferman O. 2017. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 37.","mla":"Avni, Guy, et al. <i>Timed Network Games with Clocks</i>. Vol. 83, 37, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.37\">10.4230/LIPIcs.MFCS.2017.37</a>.","apa":"Avni, G., Guha, S., &#38; Kupferman, O. (2017). Timed network games with clocks (Vol. 83). Presented at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.37\">https://doi.org/10.4230/LIPIcs.MFCS.2017.37</a>"},"publication_status":"published","abstract":[{"text":"Network games are widely used as a model for selfish resource-allocation problems. In the classical model, each player selects a path connecting her source and target vertex. The cost of traversing an edge depends on the number of players that traverse it. Thus, it abstracts the fact that different users may use a resource at different times and for different durations, which plays an important role in defining the costs of the users in reality. For example, when transmitting packets in a communication network, routing traffic in a road network, or processing a task in a production system, the traversal of the network involves an inherent delay, and so sharing and congestion of resources crucially depends on time. We study timed network games , which add a time component to network games. Each vertex v in the network is associated with a cost function, mapping the load on v to the price that a player pays for staying in v for one time unit with this load. In addition, each edge has a guard, describing time intervals in which the edge can be traversed, forcing the players to spend time on vertices. Unlike earlier work that add a time component to network games, the time in our model is continuous and cannot be discretized. In particular, players have uncountably many strategies, and a game may have uncountably many pure Nash equilibria. We study properties of timed network games with cost-sharing or congestion cost functions: their stability, equilibrium inefficiency, and complexity. In particular, we show that the answer to the question whether we can restrict attention to boundary strategies, namely ones in which edges are traversed only at the boundaries of guards, is mixed. ","lang":"eng"}],"project":[{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23"}],"ddc":["004"],"related_material":{"record":[{"id":"6005","relation":"later_version","status":"public"}]},"oa":1,"_id":"963","title":"Timed network games with clocks","date_published":"2017-06-01T00:00:00Z","file":[{"date_created":"2018-12-12T10:14:10Z","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":369730,"date_updated":"2020-07-14T12:48:18Z","file_id":"5059","access_level":"open_access","checksum":"f55eaf7f3c36ea07801112acfedd17d5","file_name":"IST-2017-829-v1+1_mfcs-cr.pdf"}],"publication_identifier":{"issn":["18688969"]},"scopus_import":1,"alternative_title":["LIPIcs"],"day":"01","type":"conference","date_updated":"2023-02-23T12:35:50Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.MFCS.2017.37","has_accepted_license":"1","department":[{"_id":"ToHe"}]},{"article_type":"original","publisher":"AIP Publishing","issue":"10","volume":147,"date_created":"2021-07-15T08:13:29Z","month":"09","status":"public","article_number":"104707","intvolume":"       147","year":"2017","main_file_link":[{"url":"https://pure.qub.ac.uk/en/publications/the-gibbs-free-energy-of-homogeneous-nucleation-from-atomistic-nuclei-to-the-planar-limit(4599cdb4-dcc4-4522-8763-7b2a165ebf12).html","open_access":"1"}],"citation":{"chicago":"Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “The Gibbs Free Energy of Homogeneous Nucleation: From Atomistic Nuclei to the Planar Limit.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2017. <a href=\"https://doi.org/10.1063/1.4997180\">https://doi.org/10.1063/1.4997180</a>.","short":"B. Cheng, G.A. Tribello, M. Ceriotti, The Journal of Chemical Physics 147 (2017).","ista":"Cheng B, Tribello GA, Ceriotti M. 2017. The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit. The Journal of Chemical Physics. 147(10), 104707.","ama":"Cheng B, Tribello GA, Ceriotti M. The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit. <i>The Journal of Chemical Physics</i>. 2017;147(10). doi:<a href=\"https://doi.org/10.1063/1.4997180\">10.1063/1.4997180</a>","ieee":"B. Cheng, G. A. Tribello, and M. Ceriotti, “The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit,” <i>The Journal of Chemical Physics</i>, vol. 147, no. 10. AIP Publishing, 2017.","apa":"Cheng, B., Tribello, G. A., &#38; Ceriotti, M. (2017). The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4997180\">https://doi.org/10.1063/1.4997180</a>","mla":"Cheng, Bingqing, et al. “The Gibbs Free Energy of Homogeneous Nucleation: From Atomistic Nuclei to the Planar Limit.” <i>The Journal of Chemical Physics</i>, vol. 147, no. 10, 104707, AIP Publishing, 2017, doi:<a href=\"https://doi.org/10.1063/1.4997180\">10.1063/1.4997180</a>."},"extern":"1","quality_controlled":"1","author":[{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","first_name":"Bingqing","last_name":"Cheng"},{"full_name":"Tribello, Gareth A.","first_name":"Gareth A.","last_name":"Tribello"},{"full_name":"Ceriotti, Michele","first_name":"Michele","last_name":"Ceriotti"}],"publication_status":"published","abstract":[{"lang":"eng","text":"In this paper we discuss how the information contained in atomistic simulations of homogeneous nucleation should be used when fitting the parameters in macroscopic nucleation models. We show how the number of solid and liquid atoms in such simulations can be determined unambiguously by using a Gibbs dividing surface and how the free energy as a function of the number of solid atoms in the nucleus can thus be extracted. We then show that the parameters (the chemical potential, the interfacial free energy, and a Tolman correction) of a model based on classical nucleation theory can be fitted using the information contained in these free-energy profiles but that the parameters in such models are highly correlated. This correlation is unfortunate as it ensures that small errors in the computed free energy surface can give rise to large errors in the extrapolated properties of the fitted model. To resolve this problem we thus propose a method for fitting macroscopic nucleation models that uses simulations of planar interfaces and simulations of three-dimensional nuclei in tandem. We show that when the chemical potentials and the interface energy are pinned to their planar-interface values, more precise estimates for the Tolman length are obtained. Extrapolating the free energy profile obtained from small simulation boxes to larger nuclei is thus more reliable."}],"title":"The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit","publication":"The Journal of Chemical Physics","pmid":1,"oa":1,"_id":"9660","date_published":"2017-09-14T00:00:00Z","external_id":{"pmid":["28915742"],"arxiv":["1703.06062"]},"arxiv":1,"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"scopus_import":"1","type":"journal_article","date_updated":"2023-02-23T14:04:02Z","oa_version":"Submitted Version","day":"14","article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","language":[{"iso":"eng"}],"doi":"10.1063/1.4997180"},{"oa_version":"Preprint","type":"journal_article","date_updated":"2021-08-09T12:31:57Z","day":"21","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","language":[{"iso":"eng"}],"doi":"10.1063/1.4973883","external_id":{"pmid":["28109231"],"arxiv":["1610.01322"]},"date_published":"2017-01-21T00:00:00Z","arxiv":1,"scopus_import":"1","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"year":"2017","main_file_link":[{"url":"https://arxiv.org/abs/1610.01322","open_access":"1"}],"citation":{"apa":"Cheng, B., &#38; Ceriotti, M. (2017). Bridging the gap between atomistic and macroscopic models of homogeneous nucleation. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4973883\">https://doi.org/10.1063/1.4973883</a>","mla":"Cheng, Bingqing, and Michele Ceriotti. “Bridging the Gap between Atomistic and Macroscopic Models of Homogeneous Nucleation.” <i>The Journal of Chemical Physics</i>, vol. 146, no. 3, 034106, AIP Publishing, 2017, doi:<a href=\"https://doi.org/10.1063/1.4973883\">10.1063/1.4973883</a>.","ieee":"B. Cheng and M. Ceriotti, “Bridging the gap between atomistic and macroscopic models of homogeneous nucleation,” <i>The Journal of Chemical Physics</i>, vol. 146, no. 3. AIP Publishing, 2017.","ama":"Cheng B, Ceriotti M. Bridging the gap between atomistic and macroscopic models of homogeneous nucleation. <i>The Journal of Chemical Physics</i>. 2017;146(3). doi:<a href=\"https://doi.org/10.1063/1.4973883\">10.1063/1.4973883</a>","ista":"Cheng B, Ceriotti M. 2017. Bridging the gap between atomistic and macroscopic models of homogeneous nucleation. The Journal of Chemical Physics. 146(3), 034106.","short":"B. Cheng, M. Ceriotti, The Journal of Chemical Physics 146 (2017).","chicago":"Cheng, Bingqing, and Michele Ceriotti. “Bridging the Gap between Atomistic and Macroscopic Models of Homogeneous Nucleation.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2017. <a href=\"https://doi.org/10.1063/1.4973883\">https://doi.org/10.1063/1.4973883</a>."},"extern":"1","quality_controlled":"1","author":[{"last_name":"Cheng","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing"},{"full_name":"Ceriotti, Michele","last_name":"Ceriotti","first_name":"Michele"}],"abstract":[{"lang":"eng","text":"Macroscopic theories of nucleation such as classical nucleation theory envision that clusters of the bulk stable phase form inside the bulk metastable phase. Molecular dynamics simulations are often used to elucidate nucleation mechanisms, by capturing the microscopic configurations of all the atoms. In this paper, we introduce a thermodynamic model that links macroscopic theories and atomic-scale simulations and thus provide a simple and elegant framework for testing the limits of classical nucleation theory."}],"publication_status":"published","pmid":1,"publication":"The Journal of Chemical Physics","title":"Bridging the gap between atomistic and macroscopic models of homogeneous nucleation","_id":"9661","oa":1,"article_type":"original","publisher":"AIP Publishing","issue":"3","volume":146,"month":"01","date_created":"2021-07-15T08:27:31Z","article_number":"034106","status":"public","intvolume":"       146"},{"date_published":"2017-01-14T00:00:00Z","publisher":"Dryad","status":"public","month":"01","date_created":"2021-07-23T09:39:34Z","author":[{"full_name":"Riccio, Paul","first_name":"Paul","last_name":"Riccio"},{"last_name":"Cebrián","first_name":"Christina","full_name":"Cebrián, Christina"},{"last_name":"Zong","first_name":"Hui","full_name":"Zong, Hui"},{"last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Costantini, Frank","first_name":"Frank","last_name":"Costantini"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"apa":"Riccio, P., Cebrián, C., Zong, H., Hippenmeyer, S., &#38; Costantini, F. (2017). Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. Dryad. <a href=\"https://doi.org/10.5061/dryad.pk16b\">https://doi.org/10.5061/dryad.pk16b</a>","mla":"Riccio, Paul, et al. <i>Data from: Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis</i>. Dryad, 2017, doi:<a href=\"https://doi.org/10.5061/dryad.pk16b\">10.5061/dryad.pk16b</a>.","chicago":"Riccio, Paul, Christina Cebrián, Hui Zong, Simon Hippenmeyer, and Frank Costantini. “Data from: Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis.” Dryad, 2017. <a href=\"https://doi.org/10.5061/dryad.pk16b\">https://doi.org/10.5061/dryad.pk16b</a>.","short":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, F. Costantini, (2017).","ista":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. 2017. Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis, Dryad, <a href=\"https://doi.org/10.5061/dryad.pk16b\">10.5061/dryad.pk16b</a>.","ieee":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, and F. Costantini, “Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis.” Dryad, 2017.","ama":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. 2017. doi:<a href=\"https://doi.org/10.5061/dryad.pk16b\">10.5061/dryad.pk16b</a>"},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.pk16b","open_access":"1"}],"year":"2017","day":"14","oa_version":"Published Version","date_updated":"2022-08-25T13:34:55Z","type":"research_data_reference","department":[{"_id":"SiHi"}],"_id":"9707","related_material":{"record":[{"id":"9702","relation":"used_in_publication","status":"deleted"}]},"doi":"10.5061/dryad.pk16b","oa":1,"title":"Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis","abstract":[{"text":"Branching morphogenesis of the epithelial ureteric bud forms the renal collecting duct system and is critical for normal nephron number, while low nephron number is implicated in hypertension and renal disease. Ureteric bud growth and branching requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling up-regulates transcription factors Etv4 and Etv5, which are also critical for branching. Despite extensive knowledge of the genetic control of these events, it is not understood, at the cellular level, how renal branching morphogenesis is achieved or how Ret signaling influences epithelial cell behaviors to promote this process. Analysis of chimeric embryos previously suggested a role for Ret signaling in promoting cell rearrangements in the nephric duct, but this method was unsuited to study individual cell behaviors during ureteric bud branching. Here, we use Mosaic Analysis with Double Markers (MADM), combined with organ culture and time-lapse imaging, to trace the movements and divisions of individual ureteric bud tip cells. We first examine wild-type clones and then Ret or Etv4 mutant/wild-type clones in which the mutant and wild-type sister cells are differentially and heritably marked by green and red fluorescent proteins. We find that, in normal kidneys, most individual tip cells behave as self-renewing progenitors, some of whose progeny remain at the tips while others populate the growing UB trunks. In Ret or Etv4 MADM clones, the wild-type cells generated at a UB tip are much more likely to remain at, or move to, the new tips during branching and elongation, while their Ret−/− or Etv4−/− sister cells tend to lag behind and contribute only to the trunks. By tracking successive mitoses in a cell lineage, we find that Ret signaling has little effect on proliferation, in contrast to its effects on cell movement. Our results show that Ret/Etv4 signaling promotes directed cell movements in the ureteric bud tips, and suggest a model in which these cell movements mediate branching morphogenesis.","lang":"eng"}]},{"publisher":"Dryad","date_published":"2017-10-18T00:00:00Z","status":"public","date_created":"2021-07-23T11:34:34Z","month":"10","day":"18","year":"2017","date_updated":"2023-02-21T16:34:41Z","type":"research_data_reference","oa_version":"Published Version","article_processing_charge":"No","author":[{"full_name":"Prentice, Jason","first_name":"Jason","last_name":"Prentice"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"},{"first_name":"Mark","last_name":"Ioffe","full_name":"Ioffe, Mark"},{"last_name":"Loback","first_name":"Adrianna","full_name":"Loback, Adrianna"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","first_name":"Gašper","last_name":"Tkačik"},{"first_name":"Michael","last_name":"Berry","full_name":"Berry, Michael"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ama":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Data from: Error-robust modes of the retinal population code. 2017. doi:<a href=\"https://doi.org/10.5061/dryad.1f1rc\">10.5061/dryad.1f1rc</a>","ieee":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Data from: Error-robust modes of the retinal population code.” Dryad, 2017.","chicago":"Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.” Dryad, 2017. <a href=\"https://doi.org/10.5061/dryad.1f1rc\">https://doi.org/10.5061/dryad.1f1rc</a>.","short":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017).","ista":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2017. Data from: Error-robust modes of the retinal population code, Dryad, <a href=\"https://doi.org/10.5061/dryad.1f1rc\">10.5061/dryad.1f1rc</a>.","apa":"Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., &#38; Berry, M. (2017). Data from: Error-robust modes of the retinal population code. Dryad. <a href=\"https://doi.org/10.5061/dryad.1f1rc\">https://doi.org/10.5061/dryad.1f1rc</a>","mla":"Prentice, Jason, et al. <i>Data from: Error-Robust Modes of the Retinal Population Code</i>. Dryad, 2017, doi:<a href=\"https://doi.org/10.5061/dryad.1f1rc\">10.5061/dryad.1f1rc</a>."},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.1f1rc","open_access":"1"}],"abstract":[{"text":"Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina.","lang":"eng"}],"related_material":{"record":[{"id":"1197","status":"public","relation":"used_in_publication"}]},"oa":1,"doi":"10.5061/dryad.1f1rc","_id":"9709","department":[{"_id":"GaTk"}],"title":"Data from: Error-robust modes of the retinal population code"},{"date_published":"2017-12-29T00:00:00Z","publisher":"Mendeley Data","status":"public","month":"12","date_created":"2021-08-09T13:18:55Z","author":[{"last_name":"Etheridge","first_name":"Alison","full_name":"Etheridge, Alison"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.17632/nw68fxzjpm.1","open_access":"1"}],"citation":{"mla":"Etheridge, Alison, and Nicholas H. Barton. <i>Data for: Establishment in a New Habitat by Polygenic Adaptation</i>. Mendeley Data, 2017, doi:<a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">10.17632/nw68fxzjpm.1</a>.","apa":"Etheridge, A., &#38; Barton, N. H. (2017). Data for: Establishment in a new habitat by polygenic adaptation. Mendeley Data. <a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">https://doi.org/10.17632/nw68fxzjpm.1</a>","chicago":"Etheridge, Alison, and Nicholas H Barton. “Data for: Establishment in a New Habitat by Polygenic Adaptation.” Mendeley Data, 2017. <a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">https://doi.org/10.17632/nw68fxzjpm.1</a>.","short":"A. Etheridge, N.H. Barton, (2017).","ista":"Etheridge A, Barton NH. 2017. Data for: Establishment in a new habitat by polygenic adaptation, Mendeley Data, <a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">10.17632/nw68fxzjpm.1</a>.","ama":"Etheridge A, Barton NH. Data for: Establishment in a new habitat by polygenic adaptation. 2017. doi:<a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">10.17632/nw68fxzjpm.1</a>","ieee":"A. Etheridge and N. H. Barton, “Data for: Establishment in a new habitat by polygenic adaptation.” Mendeley Data, 2017."},"year":"2017","day":"29","oa_version":"Published Version","date_updated":"2025-05-28T11:56:59Z","type":"research_data_reference","_id":"9842","department":[{"_id":"NiBa"}],"related_material":{"record":[{"id":"564","status":"public","relation":"used_in_publication"}]},"doi":"10.17632/nw68fxzjpm.1","oa":1,"title":"Data for: Establishment in a new habitat by polygenic adaptation","abstract":[{"text":"Mathematica notebooks used to generate figures.","lang":"eng"}]},{"_id":"9844","department":[{"_id":"CaGu"}],"doi":"10.1371/journal.pgen.1007122.s018","related_material":{"record":[{"id":"541","relation":"used_in_publication","status":"public"}]},"title":"Source data for figures and tables","article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090","last_name":"Nikolic","first_name":"Nela"},{"first_name":"Frank","last_name":"Schreiber","full_name":"Schreiber, Frank"},{"last_name":"Dal Co","first_name":"Alma","full_name":"Dal Co, Alma"},{"last_name":"Kiviet","first_name":"Daniel","full_name":"Kiviet, Daniel"},{"first_name":"Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"full_name":"Littmann, Sten","first_name":"Sten","last_name":"Littmann"},{"full_name":"Kuypers, Marcel","last_name":"Kuypers","first_name":"Marcel"},{"full_name":"Ackermann, Martin","last_name":"Ackermann","first_name":"Martin"}],"citation":{"ama":"Nikolic N, Schreiber F, Dal Co A, et al. Source data for figures and tables. 2017. doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007122.s018\">10.1371/journal.pgen.1007122.s018</a>","ieee":"N. Nikolic <i>et al.</i>, “Source data for figures and tables.” Public Library of Science, 2017.","short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017).","chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Source Data for Figures and Tables.” Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pgen.1007122.s018\">https://doi.org/10.1371/journal.pgen.1007122.s018</a>.","ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Source data for figures and tables, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pgen.1007122.s018\">10.1371/journal.pgen.1007122.s018</a>.","apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Source data for figures and tables. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1007122.s018\">https://doi.org/10.1371/journal.pgen.1007122.s018</a>","mla":"Nikolic, Nela, et al. <i>Source Data for Figures and Tables</i>. Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007122.s018\">10.1371/journal.pgen.1007122.s018</a>."},"year":"2017","day":"18","oa_version":"Published Version","date_updated":"2023-02-23T12:25:04Z","type":"research_data_reference","status":"public","month":"12","date_created":"2021-08-09T13:27:16Z","date_published":"2017-12-18T00:00:00Z","publisher":"Public Library of Science"},{"citation":{"ama":"Nikolic N, Schreiber F, Dal Co A, et al. Mathematical model. 2017. doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007122.s017\">10.1371/journal.pgen.1007122.s017</a>","ieee":"N. Nikolic <i>et al.</i>, “Mathematical model.” Public Library of Science, 2017.","ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Mathematical model, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pgen.1007122.s017\">10.1371/journal.pgen.1007122.s017</a>.","short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017).","chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Mathematical Model.” Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pgen.1007122.s017\">https://doi.org/10.1371/journal.pgen.1007122.s017</a>.","mla":"Nikolic, Nela, et al. <i>Mathematical Model</i>. Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007122.s017\">10.1371/journal.pgen.1007122.s017</a>.","apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Mathematical model. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1007122.s017\">https://doi.org/10.1371/journal.pgen.1007122.s017</a>"},"article_processing_charge":"No","author":[{"last_name":"Nikolic","first_name":"Nela","orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Frank","last_name":"Schreiber","full_name":"Schreiber, Frank"},{"full_name":"Dal Co, Alma","last_name":"Dal Co","first_name":"Alma"},{"full_name":"Kiviet, Daniel","last_name":"Kiviet","first_name":"Daniel"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","first_name":"Tobias","last_name":"Bergmiller"},{"first_name":"Sten","last_name":"Littmann","full_name":"Littmann, Sten"},{"last_name":"Kuypers","first_name":"Marcel","full_name":"Kuypers, Marcel"},{"full_name":"Ackermann, Martin","first_name":"Martin","last_name":"Ackermann"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T12:25:04Z","type":"research_data_reference","oa_version":"None","day":"18","year":"2017","title":"Mathematical model","doi":"10.1371/journal.pgen.1007122.s017","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"541"}]},"_id":"9845","department":[{"_id":"CaGu"}],"abstract":[{"text":"Estimates of 13 C-arabinose and 2 H-glucose uptake from the fractions of heavy isotopes measured\tin single cells","lang":"eng"}],"date_published":"2017-12-18T00:00:00Z","publisher":"Public Library of Science","date_created":"2021-08-09T13:31:51Z","month":"12","status":"public"},{"doi":"10.1371/journal.pgen.1007122.s016","related_material":{"record":[{"id":"541","status":"public","relation":"used_in_publication"}]},"department":[{"_id":"CaGu"}],"_id":"9846","title":"Supplementary methods","day":"18","year":"2017","date_updated":"2023-02-23T12:25:04Z","type":"research_data_reference","oa_version":"Published Version","article_processing_charge":"No","author":[{"id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090","first_name":"Nela","last_name":"Nikolic"},{"full_name":"Schreiber, Frank","first_name":"Frank","last_name":"Schreiber"},{"first_name":"Alma","last_name":"Dal Co","full_name":"Dal Co, Alma"},{"first_name":"Daniel","last_name":"Kiviet","full_name":"Kiviet, Daniel"},{"orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","first_name":"Tobias"},{"full_name":"Littmann, Sten","last_name":"Littmann","first_name":"Sten"},{"last_name":"Kuypers","first_name":"Marcel","full_name":"Kuypers, Marcel"},{"last_name":"Ackermann","first_name":"Martin","full_name":"Ackermann, Martin"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ieee":"N. Nikolic <i>et al.</i>, “Supplementary methods.” Public Library of Science, 2017.","ama":"Nikolic N, Schreiber F, Dal Co A, et al. Supplementary methods. 2017. doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007122.s016\">10.1371/journal.pgen.1007122.s016</a>","ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Supplementary methods, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pgen.1007122.s016\">10.1371/journal.pgen.1007122.s016</a>.","chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Supplementary Methods.” Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pgen.1007122.s016\">https://doi.org/10.1371/journal.pgen.1007122.s016</a>.","short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017).","apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Supplementary methods. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1007122.s016\">https://doi.org/10.1371/journal.pgen.1007122.s016</a>","mla":"Nikolic, Nela, et al. <i>Supplementary Methods</i>. Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007122.s016\">10.1371/journal.pgen.1007122.s016</a>."},"status":"public","date_created":"2021-08-09T13:35:17Z","month":"12","publisher":"Public Library of Science","date_published":"2017-12-18T00:00:00Z"}]