[{"title":"Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks","doi":"10.1016/j.tpb.2013.03.001","day":"01","date_updated":"2021-01-12T07:00:09Z","has_accepted_license":"1","ec_funded":1,"year":"2013","oa":1,"month":"08","file_date_updated":"2020-07-14T12:45:50Z","file":[{"date_created":"2018-12-12T10:17:33Z","date_updated":"2020-07-14T12:45:50Z","access_level":"open_access","file_id":"5288","file_size":1554712,"checksum":"9bf9d9a6fd03dd9df50906891f393bf8","creator":"system","file_name":"IST-2016-558-v1+1_inference_revised3101NB.pdf","relation":"main_file","content_type":"application/pdf"},{"content_type":"application/pdf","creator":"system","checksum":"2bceddb76edacd0cd5fad73051e2a928","relation":"main_file","file_name":"IST-2016-558-v1+2_inference_revised3101NBApp.pdf","file_id":"5289","file_size":822964,"date_created":"2018-12-12T10:17:34Z","date_updated":"2020-07-14T12:45:50Z","access_level":"open_access"}],"author":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Etheridge, Alison","first_name":"Alison","last_name":"Etheridge"},{"full_name":"Kelleher, Jerome","last_name":"Kelleher","first_name":"Jerome"},{"first_name":"Amandine","last_name":"Véber","full_name":"Véber, Amandine"}],"citation":{"short":"N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population Biology 87 (2013) 105–119.","mla":"Barton, Nicholas H., et al. “Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence Blocks.” <i>Theoretical Population Biology</i>, vol. 87, no. 1, Elsevier, 2013, pp. 105–19, doi:<a href=\"https://doi.org/10.1016/j.tpb.2013.03.001\">10.1016/j.tpb.2013.03.001</a>.","ieee":"N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks,” <i>Theoretical Population Biology</i>, vol. 87, no. 1. Elsevier, pp. 105–119, 2013.","chicago":"Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber. “Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence Blocks.” <i>Theoretical Population Biology</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.tpb.2013.03.001\">https://doi.org/10.1016/j.tpb.2013.03.001</a>.","apa":"Barton, N. H., Etheridge, A., Kelleher, J., &#38; Véber, A. (2013). Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. <i>Theoretical Population Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tpb.2013.03.001\">https://doi.org/10.1016/j.tpb.2013.03.001</a>","ista":"Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. 87(1), 105–119.","ama":"Barton NH, Etheridge A, Kelleher J, Véber A. Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. <i>Theoretical Population Biology</i>. 2013;87(1):105-119. doi:<a href=\"https://doi.org/10.1016/j.tpb.2013.03.001\">10.1016/j.tpb.2013.03.001</a>"},"ddc":["570"],"page":"105 - 119","issue":"1","_id":"2842","pubrep_id":"558","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"project":[{"call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","publication_status":"published","publisher":"Elsevier","volume":87,"type":"journal_article","oa_version":"Submitted Version","scopus_import":1,"date_created":"2018-12-11T11:59:53Z","abstract":[{"lang":"eng","text":"We outline two approaches to inference of neighbourhood size, N, and dispersal rate, σ2, based on either allele frequencies or on the lengths of sequence blocks that are shared between genomes. Over intermediate timescales (10-100 generations, say), populations that live in two dimensions approach a quasi-equilibrium that is independent of both their local structure and their deeper history. Over such scales, the standardised covariance of allele frequencies (i.e. pairwise FS T) falls with the logarithm of distance, and depends only on neighbourhood size, N, and a 'local scale', κ; the rate of gene flow, σ2, cannot be inferred. We show how spatial correlations can be accounted for, assuming a Gaussian distribution of allele frequencies, giving maximum likelihood estimates of N and κ. Alternatively, inferences can be based on the distribution of the lengths of sequence that are identical between blocks of genomes: long blocks (&gt;0.1 cM, say) tell us about intermediate timescales, over which we assume a quasi-equilibrium. For large neighbourhood size, the distribution of long blocks is given directly by the classical Wright-Malécot formula; this relationship can be used to infer both N and σ2. With small neighbourhood size, there is an appreciable chance that recombinant lineages will coalesce back before escaping into the distant past. For this case, we show that if genomes are sampled from some distance apart, then the distribution of lengths of blocks that are identical in state is geometric, with a mean that depends on N and σ2."}],"date_published":"2013-08-01T00:00:00Z","status":"public","publist_id":"3953","publication":"Theoretical Population Biology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        87"},{"doi":"10.1007/978-3-642-37067-0","title":"Stable length estimates of tube-like shapes","department":[{"_id":"HeEd"}],"quality_controlled":"1","day":"21","publication_status":"published","date_updated":"2023-02-23T10:35:00Z","publisher":"Springer","conference":{"location":"Seville, Spain","name":"DGCI: Discrete Geometry for Computer Imagery","start_date":"2013-03-20","end_date":"2013-03-22"},"related_material":{"record":[{"relation":"later_version","id":"2255","status":"public"}]},"year":"2013","type":"conference","volume":7749,"author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"},{"full_name":"Pausinger, Florian","orcid":"0000-0002-8379-3768","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","last_name":"Pausinger","first_name":"Florian"}],"oa_version":"None","month":"02","scopus_import":1,"alternative_title":["LNCS"],"date_created":"2018-12-11T11:59:53Z","citation":{"short":"H. Edelsbrunner, F. Pausinger, in:, 17th IAPR International Conference on Discrete Geometry for Computer Imagery, Springer, 2013, pp. XV–XIX.","mla":"Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like Shapes.” <i>17th IAPR International Conference on Discrete Geometry for Computer Imagery</i>, vol. 7749, Springer, 2013, pp. XV–XIX, doi:<a href=\"https://doi.org/10.1007/978-3-642-37067-0\">10.1007/978-3-642-37067-0</a>.","chicago":"Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like Shapes.” In <i>17th IAPR International Conference on Discrete Geometry for Computer Imagery</i>, 7749:XV–XIX. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-37067-0\">https://doi.org/10.1007/978-3-642-37067-0</a>.","ieee":"H. Edelsbrunner and F. Pausinger, “Stable length estimates of tube-like shapes,” in <i>17th IAPR International Conference on Discrete Geometry for Computer Imagery</i>, Seville, Spain, 2013, vol. 7749, pp. XV–XIX.","ista":"Edelsbrunner H, Pausinger F. 2013. Stable length estimates of tube-like shapes. 17th IAPR International Conference on Discrete Geometry for Computer Imagery. DGCI: Discrete Geometry for Computer Imagery, LNCS, vol. 7749, XV–XIX.","apa":"Edelsbrunner, H., &#38; Pausinger, F. (2013). Stable length estimates of tube-like shapes. In <i>17th IAPR International Conference on Discrete Geometry for Computer Imagery</i> (Vol. 7749, pp. XV–XIX). Seville, Spain: Springer. <a href=\"https://doi.org/10.1007/978-3-642-37067-0\">https://doi.org/10.1007/978-3-642-37067-0</a>","ama":"Edelsbrunner H, Pausinger F. Stable length estimates of tube-like shapes. In: <i>17th IAPR International Conference on Discrete Geometry for Computer Imagery</i>. Vol 7749. Springer; 2013:XV-XIX. doi:<a href=\"https://doi.org/10.1007/978-3-642-37067-0\">10.1007/978-3-642-37067-0</a>"},"page":"XV - XIX","abstract":[{"lang":"eng","text":"Mathematical objects can be measured unambiguously, but not so objects from our physical world. Even the total length of tubelike shapes has its difficulties. We introduce a combination of geometric, probabilistic, and topological methods to design a stable length estimate for tube-like shapes; that is: one that is insensitive to small shape changes."}],"publist_id":"3952","publication":"17th IAPR International Conference on Discrete Geometry for Computer Imagery","status":"public","date_published":"2013-02-21T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2843","intvolume":"      7749","language":[{"iso":"eng"}]},{"author":[{"full_name":"Rosquete, Michel","last_name":"Rosquete","first_name":"Michel"},{"last_name":"Von Wangenheim","first_name":"Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247","full_name":"Von Wangenheim, Daniel"},{"id":"3F45B078-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavy","first_name":"Peter","full_name":"Marhavy, Peter","orcid":"0000-0001-5227-5741"},{"full_name":"Barbez, Elke","first_name":"Elke","last_name":"Barbez"},{"last_name":"Stelzer","first_name":"Ernst","full_name":"Stelzer, Ernst"},{"first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"},{"last_name":"Maizel","first_name":"Alexis","full_name":"Maizel, Alexis"},{"last_name":"Kleine Vehn","first_name":"Jürgen","full_name":"Kleine Vehn, Jürgen"}],"oa_version":"None","month":"05","scopus_import":1,"date_created":"2018-12-11T11:59:53Z","citation":{"ama":"Rosquete M, von Wangenheim D, Marhavý P, et al. An auxin transport mechanism restricts positive orthogravitropism in lateral roots. <i>Current Biology</i>. 2013;23(9):817-822. doi:<a href=\"https://doi.org/10.1016/j.cub.2013.03.064\">10.1016/j.cub.2013.03.064</a>","apa":"Rosquete, M., von Wangenheim, D., Marhavý, P., Barbez, E., Stelzer, E., Benková, E., … Kleine Vehn, J. (2013). An auxin transport mechanism restricts positive orthogravitropism in lateral roots. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2013.03.064\">https://doi.org/10.1016/j.cub.2013.03.064</a>","ista":"Rosquete M, von Wangenheim D, Marhavý P, Barbez E, Stelzer E, Benková E, Maizel A, Kleine Vehn J. 2013. An auxin transport mechanism restricts positive orthogravitropism in lateral roots. Current Biology. 23(9), 817–822.","ieee":"M. Rosquete <i>et al.</i>, “An auxin transport mechanism restricts positive orthogravitropism in lateral roots,” <i>Current Biology</i>, vol. 23, no. 9. Cell Press, pp. 817–822, 2013.","chicago":"Rosquete, Michel, Daniel von Wangenheim, Peter Marhavý, Elke Barbez, Ernst Stelzer, Eva Benková, Alexis Maizel, and Jürgen Kleine Vehn. “An Auxin Transport Mechanism Restricts Positive Orthogravitropism in Lateral Roots.” <i>Current Biology</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1016/j.cub.2013.03.064\">https://doi.org/10.1016/j.cub.2013.03.064</a>.","mla":"Rosquete, Michel, et al. “An Auxin Transport Mechanism Restricts Positive Orthogravitropism in Lateral Roots.” <i>Current Biology</i>, vol. 23, no. 9, Cell Press, 2013, pp. 817–22, doi:<a href=\"https://doi.org/10.1016/j.cub.2013.03.064\">10.1016/j.cub.2013.03.064</a>.","short":"M. Rosquete, D. von Wangenheim, P. Marhavý, E. Barbez, E. Stelzer, E. Benková, A. Maizel, J. Kleine Vehn, Current Biology 23 (2013) 817–822."},"page":"817 - 822","abstract":[{"text":"As soon as a seed germinates, plant growth relates to gravity to ensure that the root penetrates the soil and the shoot expands aerially. Whereas mechanisms of positive and negative orthogravitropism of primary roots and shoots are relatively well understood [1-3], lateral organs often show more complex growth behavior [4]. Lateral roots (LRs) seemingly suppress positive gravitropic growth and show a defined gravitropic set-point angle (GSA) that allows radial expansion of the root system (plagiotropism) [3, 4]. Despite its eminent importance for root architecture, it so far remains completely unknown how lateral organs partially suppress positive orthogravitropism. Here we show that the phytohormone auxin steers GSA formation and limits positive orthogravitropism in LR. Low and high auxin levels/signaling lead to radial or axial root systems, respectively. At a cellular level, it is the auxin transport-dependent regulation of asymmetric growth in the elongation zone that determines GSA. Our data suggest that strong repression of PIN4/PIN7 and transient PIN3 expression limit auxin redistribution in young LR columella cells. We conclude that PIN activity, by temporally limiting the asymmetric auxin fluxes in the tip of LRs, induces transient, differential growth responses in the elongation zone and, consequently, controls root architecture.","lang":"eng"}],"publist_id":"3950","issue":"9","publication":"Current Biology","date_published":"2013-05-06T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"_id":"2844","intvolume":"        23","doi":"10.1016/j.cub.2013.03.064","title":"An auxin transport mechanism restricts positive orthogravitropism in lateral roots","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Hormonal cross-talk in plant organogenesis","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362"}],"day":"06","publication_status":"published","date_updated":"2021-01-12T07:00:10Z","publisher":"Cell Press","ec_funded":1,"year":"2013","type":"journal_article","volume":23},{"language":[{"iso":"eng"}],"_id":"2845","intvolume":"        77","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2013-03-20T00:00:00Z","status":"public","publist_id":"3949","issue":"6","publication":"Neuron","abstract":[{"text":"At synapses formed between dissociated neurons, about half of all synaptic vesicles are refractory to evoked release, forming the so-called &quot;resting pool.&quot; Here, we use optical measurements of vesicular pH to study developmental changes in pool partitioning and vesicle cycling in cultured hippocampal slices. Two-photon imaging of a genetically encoded two-color release sensor (ratio-sypHy) allowed us to perform calibrated measurements at individual Schaffer collateral boutons. Mature boutons released a large fraction of their vesicles during simulated place field activity, and vesicle retrieval rates were 7-fold higher compared to immature boutons. Saturating stimulation mobilized essentially all vesicles at mature synapses. Resting pool formation and a concomitant reduction in evoked release was induced by chronic depolarization but not by acute inhibition of the protein phosphatase calcineurin. We conclude that synapses in CA1 undergo a prominent refinement of vesicle use during early postnatal development that is not recapitulated in dissociated neuronal culture.","lang":"eng"}],"page":"1109 - 1121","citation":{"ieee":"T. Rose, P. Schönenberger, K. Jezek, and T. Oertner, “Developmental refinement of vesicle cycling at Schaffer collateral synapses,” <i>Neuron</i>, vol. 77, no. 6. Elsevier, pp. 1109–1121, 2013.","chicago":"Rose, Tobias, Philipp Schönenberger, Karel Jezek, and Thomas Oertner. “Developmental Refinement of Vesicle Cycling at Schaffer Collateral Synapses.” <i>Neuron</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.neuron.2013.01.021\">https://doi.org/10.1016/j.neuron.2013.01.021</a>.","short":"T. Rose, P. Schönenberger, K. Jezek, T. Oertner, Neuron 77 (2013) 1109–1121.","mla":"Rose, Tobias, et al. “Developmental Refinement of Vesicle Cycling at Schaffer Collateral Synapses.” <i>Neuron</i>, vol. 77, no. 6, Elsevier, 2013, pp. 1109–21, doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.01.021\">10.1016/j.neuron.2013.01.021</a>.","ama":"Rose T, Schönenberger P, Jezek K, Oertner T. Developmental refinement of vesicle cycling at Schaffer collateral synapses. <i>Neuron</i>. 2013;77(6):1109-1121. doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.01.021\">10.1016/j.neuron.2013.01.021</a>","apa":"Rose, T., Schönenberger, P., Jezek, K., &#38; Oertner, T. (2013). Developmental refinement of vesicle cycling at Schaffer collateral synapses. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2013.01.021\">https://doi.org/10.1016/j.neuron.2013.01.021</a>","ista":"Rose T, Schönenberger P, Jezek K, Oertner T. 2013. Developmental refinement of vesicle cycling at Schaffer collateral synapses. Neuron. 77(6), 1109–1121."},"date_created":"2018-12-11T11:59:54Z","scopus_import":1,"month":"03","oa_version":"None","author":[{"full_name":"Rose, Tobias","first_name":"Tobias","last_name":"Rose"},{"id":"3B9D816C-F248-11E8-B48F-1D18A9856A87","last_name":"Schönenberger","first_name":"Philipp","full_name":"Schönenberger, Philipp"},{"last_name":"Jezek","first_name":"Karel","full_name":"Jezek, Karel"},{"last_name":"Oertner","first_name":"Thomas","full_name":"Oertner, Thomas"}],"volume":77,"type":"journal_article","year":"2013","publisher":"Elsevier","date_updated":"2021-01-12T07:00:11Z","publication_status":"published","day":"20","quality_controlled":"1","title":"Developmental refinement of vesicle cycling at Schaffer collateral synapses","department":[{"_id":"JoCs"}],"doi":"10.1016/j.neuron.2013.01.021"},{"type":"journal_article","volume":16,"publisher":"Wiley-Blackwell","publication_status":"published","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"        16","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"3948","publication":"Ecology Letters","status":"public","date_published":"2013-04-04T00:00:00Z","abstract":[{"lang":"eng","text":"The Red Queen hypothesis proposes that coevolving parasites select for outcrossing in the host. Outcrossing relies on males, which often show lower immune investment due to, for example, sexual selection. Here, we demonstrate that such sex differences in immunity interfere with parasite-mediated selection for outcrossing. Two independent coevolution experiments with Caenorhabditis elegans and its microparasite Bacillus thuringiensis produced decreased yet stable frequencies of outcrossing male hosts. A subsequent systematic analysis verified that male C. elegans suffered from a direct selective disadvantage under parasite pressure (i.e. lower resistance, decreased sexual activity, increased escape behaviour), which can reduce outcrossing and thus male frequencies. At the same time, males offered an indirect selective benefit, because male-mediated outcrossing increased offspring resistance, thus favouring male persistence in the evolving populations. As sex differences in immunity are widespread, such interference of opposing selective constraints is likely of central importance during host adaptation to a coevolving parasite."}],"date_created":"2018-12-11T11:59:54Z","extern":"1","scopus_import":"1","oa_version":"Published Version","article_processing_charge":"No","oa":1,"year":"2013","has_accepted_license":"1","date_updated":"2022-08-25T14:51:57Z","day":"04","doi":"10.1111/ele.12068","title":"Sex differences in host defence interfere with parasite-mediated selection for outcrossing during host-parasite coevolution","pubrep_id":"404","_id":"2846","language":[{"iso":"eng"}],"issue":"4","page":"461 - 468","ddc":["570"],"citation":{"short":"L. El Masri, R. Schulte, N. Timmermeyer, S. Thanisch, L. Crummenerl, G. Jansen, N. Michiels, H. Schulenburg, Ecology Letters 16 (2013) 461–468.","mla":"El Masri, Leila, et al. “Sex Differences in Host Defence Interfere with Parasite-Mediated Selection for Outcrossing during Host-Parasite Coevolution.” <i>Ecology Letters</i>, vol. 16, no. 4, Wiley-Blackwell, 2013, pp. 461–68, doi:<a href=\"https://doi.org/10.1111/ele.12068\">10.1111/ele.12068</a>.","chicago":"El Masri, Leila, Rebecca Schulte, Nadine Timmermeyer, Stefanie Thanisch, Lena Crummenerl, Gunther Jansen, Nico Michiels, and Hinrich Schulenburg. “Sex Differences in Host Defence Interfere with Parasite-Mediated Selection for Outcrossing during Host-Parasite Coevolution.” <i>Ecology Letters</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/ele.12068\">https://doi.org/10.1111/ele.12068</a>.","ieee":"L. El Masri <i>et al.</i>, “Sex differences in host defence interfere with parasite-mediated selection for outcrossing during host-parasite coevolution,” <i>Ecology Letters</i>, vol. 16, no. 4. Wiley-Blackwell, pp. 461–468, 2013.","ista":"El Masri L, Schulte R, Timmermeyer N, Thanisch S, Crummenerl L, Jansen G, Michiels N, Schulenburg H. 2013. Sex differences in host defence interfere with parasite-mediated selection for outcrossing during host-parasite coevolution. Ecology Letters. 16(4), 461–468.","apa":"El Masri, L., Schulte, R., Timmermeyer, N., Thanisch, S., Crummenerl, L., Jansen, G., … Schulenburg, H. (2013). Sex differences in host defence interfere with parasite-mediated selection for outcrossing during host-parasite coevolution. <i>Ecology Letters</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/ele.12068\">https://doi.org/10.1111/ele.12068</a>","ama":"El Masri L, Schulte R, Timmermeyer N, et al. Sex differences in host defence interfere with parasite-mediated selection for outcrossing during host-parasite coevolution. <i>Ecology Letters</i>. 2013;16(4):461-468. doi:<a href=\"https://doi.org/10.1111/ele.12068\">10.1111/ele.12068</a>"},"file":[{"content_type":"application/pdf","checksum":"aa7db788f7da7d7f102539a249ebce50","creator":"system","relation":"main_file","file_name":"IST-2016-404-v1+1_ele12068.pdf","file_id":"5176","file_size":763731,"date_created":"2018-12-12T10:15:52Z","date_updated":"2020-07-14T12:45:50Z","access_level":"open_access"}],"author":[{"full_name":"El Masri, Leila","first_name":"Leila","last_name":"El Masri","id":"349A6E66-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schulte, Rebecca","first_name":"Rebecca","last_name":"Schulte"},{"full_name":"Timmermeyer, Nadine","first_name":"Nadine","last_name":"Timmermeyer"},{"first_name":"Stefanie","last_name":"Thanisch","full_name":"Thanisch, Stefanie"},{"full_name":"Crummenerl, Lena","last_name":"Crummenerl","first_name":"Lena"},{"full_name":"Jansen, Gunther","first_name":"Gunther","last_name":"Jansen"},{"last_name":"Michiels","first_name":"Nico","full_name":"Michiels, Nico"},{"first_name":"Hinrich","last_name":"Schulenburg","full_name":"Schulenburg, Hinrich"}],"file_date_updated":"2020-07-14T12:45:50Z","month":"04"},{"language":[{"iso":"eng"}],"_id":"2847","page":"62 - 77","citation":{"ieee":"K. Bansal, E. Koskinen, T. Wies, and D. Zufferey, “Structural Counter Abstraction,” vol. 7795. Springer, pp. 62–77, 2013.","chicago":"Bansal, Kshitij, Eric Koskinen, Thomas Wies, and Damien Zufferey. “Structural Counter Abstraction.” Edited by Nir Piterman and Scott Smolka. Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-36742-7_5\">https://doi.org/10.1007/978-3-642-36742-7_5</a>.","mla":"Bansal, Kshitij, et al. <i>Structural Counter Abstraction</i>. Edited by Nir Piterman and Scott Smolka, vol. 7795, Springer, 2013, pp. 62–77, doi:<a href=\"https://doi.org/10.1007/978-3-642-36742-7_5\">10.1007/978-3-642-36742-7_5</a>.","short":"K. Bansal, E. Koskinen, T. Wies, D. Zufferey, 7795 (2013) 62–77.","ama":"Bansal K, Koskinen E, Wies T, Zufferey D. Structural Counter Abstraction. Piterman N, Smolka S, eds. 2013;7795:62-77. doi:<a href=\"https://doi.org/10.1007/978-3-642-36742-7_5\">10.1007/978-3-642-36742-7_5</a>","apa":"Bansal, K., Koskinen, E., Wies, T., &#38; Zufferey, D. (2013). Structural Counter Abstraction. (N. Piterman &#38; S. Smolka, Eds.). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Rome, Italy: Springer. <a href=\"https://doi.org/10.1007/978-3-642-36742-7_5\">https://doi.org/10.1007/978-3-642-36742-7_5</a>","ista":"Bansal K, Koskinen E, Wies T, Zufferey D. 2013. Structural Counter Abstraction (eds. N. Piterman &#38; S. Smolka). 7795, 62–77."},"author":[{"first_name":"Kshitij","last_name":"Bansal","full_name":"Bansal, Kshitij"},{"full_name":"Koskinen, Eric","first_name":"Eric","last_name":"Koskinen"},{"full_name":"Wies, Thomas","last_name":"Wies","first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-3197-8736","full_name":"Zufferey, Damien","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","first_name":"Damien","last_name":"Zufferey"}],"month":"03","oa":1,"conference":{"location":"Rome, Italy","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","start_date":"2013-03-16","end_date":"2013-03-24"},"series_title":"Lecture Notes in Computer Science","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1405"}]},"ec_funded":1,"year":"2013","day":"01","date_updated":"2023-09-07T11:36:36Z","doi":"10.1007/978-3-642-36742-7_5","title":"Structural Counter Abstraction","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"      7795","abstract":[{"text":"Depth-Bounded Systems form an expressive class of well-structured transition systems. They can model a wide range of concurrent infinite-state systems including those with dynamic thread creation, dynamically changing communication topology, and complex shared heap structures. We present the first method to automatically prove fair termination of depth-bounded systems. Our method uses a numerical abstraction of the system, which we obtain by systematically augmenting an over-approximation of the system’s reachable states with a finite set of counters. This numerical abstraction can be analyzed with existing termination provers. What makes our approach unique is the way in which it exploits the well-structuredness of the analyzed system. We have implemented our work in a prototype tool and used it to automatically prove liveness properties of complex concurrent systems, including nonblocking algorithms such as Treiber’s stack and several distributed processes. Many of these examples are beyond the scope of termination analyses that are based on traditional counter abstractions.","lang":"eng"}],"publist_id":"3947","status":"public","date_published":"2013-03-01T00:00:00Z","scopus_import":1,"alternative_title":["LNCS"],"date_created":"2018-12-11T11:59:54Z","oa_version":"Submitted Version","type":"conference","volume":7795,"main_file_link":[{"open_access":"1","url":"http://arise.or.at/pubpdf/Structural_Counter_Abstraction.pdf"}],"publication_status":"published","publisher":"Springer","editor":[{"first_name":"Nir","last_name":"Piterman","full_name":"Piterman, Nir"},{"first_name":"Scott","last_name":"Smolka","full_name":"Smolka, Scott"}],"department":[{"_id":"ToHe"}],"quality_controlled":"1","project":[{"call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}]},{"oa_version":"Preprint","scopus_import":1,"date_created":"2018-12-11T11:59:55Z","abstract":[{"text":"Recent work emphasizes that the maximum entropy principle provides a bridge between statistical mechanics models for collective behavior in neural networks and experiments on networks of real neurons. Most of this work has focused on capturing the measured correlations among pairs of neurons. Here we suggest an alternative, constructing models that are consistent with the distribution of global network activity, i.e. the probability that K out of N cells in the network generate action potentials in the same small time bin. The inverse problem that we need to solve in constructing the model is analytically tractable, and provides a natural 'thermodynamics' for the network in the limit of large N. We analyze the responses of neurons in a small patch of the retina to naturalistic stimuli, and find that the implied thermodynamics is very close to an unusual critical point, in which the entropy (in proper units) is exactly equal to the energy. © 2013 IOP Publishing Ltd and SISSA Medialab srl.\r\n","lang":"eng"}],"date_published":"2013-03-12T00:00:00Z","status":"public","publication":"Journal of Statistical Mechanics Theory and Experiment","publist_id":"3942","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"      2013","department":[{"_id":"GaTk"}],"quality_controlled":"1","publication_status":"published","publisher":"IOP Publishing Ltd.","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1207.6319"}],"volume":2013,"type":"journal_article","month":"03","article_number":"P03011","author":[{"orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Marre","first_name":"Olivier","full_name":"Marre, Olivier"},{"first_name":"Thierry","last_name":"Mora","full_name":"Mora, Thierry"},{"last_name":"Amodei","first_name":"Dario","full_name":"Amodei, Dario"},{"first_name":"Michael","last_name":"Berry","full_name":"Berry, Michael"},{"full_name":"Bialek, William","first_name":"William","last_name":"Bialek"}],"article_type":"original","arxiv":1,"citation":{"apa":"Tkačik, G., Marre, O., Mora, T., Amodei, D., Berry, M., &#38; Bialek, W. (2013). The simplest maximum entropy model for collective behavior in a neural network. <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1742-5468/2013/03/P03011\">https://doi.org/10.1088/1742-5468/2013/03/P03011</a>","ista":"Tkačik G, Marre O, Mora T, Amodei D, Berry M, Bialek W. 2013. The simplest maximum entropy model for collective behavior in a neural network. Journal of Statistical Mechanics Theory and Experiment. 2013(3), P03011.","ama":"Tkačik G, Marre O, Mora T, Amodei D, Berry M, Bialek W. The simplest maximum entropy model for collective behavior in a neural network. <i>Journal of Statistical Mechanics Theory and Experiment</i>. 2013;2013(3). doi:<a href=\"https://doi.org/10.1088/1742-5468/2013/03/P03011\">10.1088/1742-5468/2013/03/P03011</a>","mla":"Tkačik, Gašper, et al. “The Simplest Maximum Entropy Model for Collective Behavior in a Neural Network.” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2013, no. 3, P03011, IOP Publishing Ltd., 2013, doi:<a href=\"https://doi.org/10.1088/1742-5468/2013/03/P03011\">10.1088/1742-5468/2013/03/P03011</a>.","short":"G. Tkačik, O. Marre, T. Mora, D. Amodei, M. Berry, W. Bialek, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).","ieee":"G. Tkačik, O. Marre, T. Mora, D. Amodei, M. Berry, and W. Bialek, “The simplest maximum entropy model for collective behavior in a neural network,” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2013, no. 3. IOP Publishing Ltd., 2013.","chicago":"Tkačik, Gašper, Olivier Marre, Thierry Mora, Dario Amodei, Michael Berry, and William Bialek. “The Simplest Maximum Entropy Model for Collective Behavior in a Neural Network.” <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing Ltd., 2013. <a href=\"https://doi.org/10.1088/1742-5468/2013/03/P03011\">https://doi.org/10.1088/1742-5468/2013/03/P03011</a>."},"issue":"3","acknowledgement":"his work was supported in part by NSF Grants IIS-0613435 and PHY-0957573, by NIH Grants R01 EY14196 and P50 GM071508, by the Fannie and John Hertz Foundation, by the Human Frontiers Science Program, by the Swartz Foundation, and by the WM Keck Foundation.\r\n","_id":"2850","language":[{"iso":"eng"}],"title":"The simplest maximum entropy model for collective behavior in a neural network","doi":"10.1088/1742-5468/2013/03/P03011","external_id":{"arxiv":["1207.6319"]},"day":"12","date_updated":"2021-01-12T07:00:14Z","year":"2013","oa":1,"article_processing_charge":"No"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"      2013","_id":"2851","language":[{"iso":"eng"}],"abstract":[{"text":"The number of possible activity patterns in a population of neurons grows exponentially with the size of the population. Typical experiments explore only a tiny fraction of the large space of possible activity patterns in the case of populations with more than 10 or 20 neurons. It is thus impossible, in this undersampled regime, to estimate the probabilities with which most of the activity patterns occur. As a result, the corresponding entropy - which is a measure of the computational power of the neural population - cannot be estimated directly. We propose a simple scheme for estimating the entropy in the undersampled regime, which bounds its value from both below and above. The lower bound is the usual 'naive' entropy of the experimental frequencies. The upper bound results from a hybrid approximation of the entropy which makes use of the naive estimate, a maximum entropy fit, and a coverage adjustment. We apply our simple scheme to artificial data, in order to check their accuracy; we also compare its performance to those of several previously defined entropy estimators. We then apply it to actual measurements of neural activity in populations with up to 100 cells. Finally, we discuss the similarities and differences between the proposed simple estimation scheme and various earlier methods. © 2013 IOP Publishing Ltd and SISSA Medialab srl.","lang":"eng"}],"date_published":"2013-03-12T00:00:00Z","status":"public","issue":"3","publication":"Journal of Statistical Mechanics Theory and Experiment","publist_id":"3941","scopus_import":1,"citation":{"chicago":"Berry, Michael, Gašper Tkačik, Julien Dubuis, Olivier Marre, and Ravá Da Silveira. “A Simple Method for Estimating the Entropy of Neural Activity.” <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing Ltd., 2013. <a href=\"https://doi.org/10.1088/1742-5468/2013/03/P03015\">https://doi.org/10.1088/1742-5468/2013/03/P03015</a>.","ieee":"M. Berry, G. Tkačik, J. Dubuis, O. Marre, and R. Da Silveira, “A simple method for estimating the entropy of neural activity,” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2013, no. 3. IOP Publishing Ltd., 2013.","short":"M. Berry, G. Tkačik, J. Dubuis, O. Marre, R. Da Silveira, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).","mla":"Berry, Michael, et al. “A Simple Method for Estimating the Entropy of Neural Activity.” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2013, no. 3, P03015, IOP Publishing Ltd., 2013, doi:<a href=\"https://doi.org/10.1088/1742-5468/2013/03/P03015\">10.1088/1742-5468/2013/03/P03015</a>.","ama":"Berry M, Tkačik G, Dubuis J, Marre O, Da Silveira R. A simple method for estimating the entropy of neural activity. <i>Journal of Statistical Mechanics Theory and Experiment</i>. 2013;2013(3). doi:<a href=\"https://doi.org/10.1088/1742-5468/2013/03/P03015\">10.1088/1742-5468/2013/03/P03015</a>","ista":"Berry M, Tkačik G, Dubuis J, Marre O, Da Silveira R. 2013. A simple method for estimating the entropy of neural activity. Journal of Statistical Mechanics Theory and Experiment. 2013(3), P03015.","apa":"Berry, M., Tkačik, G., Dubuis, J., Marre, O., &#38; Da Silveira, R. (2013). A simple method for estimating the entropy of neural activity. <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1742-5468/2013/03/P03015\">https://doi.org/10.1088/1742-5468/2013/03/P03015</a>"},"date_created":"2018-12-11T11:59:56Z","article_number":"P03015","month":"03","author":[{"last_name":"Berry","first_name":"Michael","full_name":"Berry, Michael"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper"},{"last_name":"Dubuis","first_name":"Julien","full_name":"Dubuis, Julien"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"},{"first_name":"Ravá","last_name":"Da Silveira","full_name":"Da Silveira, Ravá"}],"oa_version":"None","volume":2013,"type":"journal_article","year":"2013","publication_status":"published","day":"12","publisher":"IOP Publishing Ltd.","date_updated":"2021-01-12T07:00:14Z","title":"A simple method for estimating the entropy of neural activity","department":[{"_id":"GaTk"}],"doi":"10.1088/1742-5468/2013/03/P03015","quality_controlled":"1"},{"publication_status":"published","publisher":"The Royal Society","department":[{"_id":"CaGu"}],"quality_controlled":"1","pmid":1,"type":"journal_article","volume":280,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3619501/","open_access":"1"}],"scopus_import":"1","date_created":"2018-12-11T11:59:56Z","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       280","abstract":[{"text":"High relatedness among interacting individuals has generally been considered a precondition for the evolution of altruism. However, kin-selection theory also predicts the evolution of altruism when relatedness is low, as long as the cost of the altruistic act is minor compared with its benefit. Here, we demonstrate evidence for a low-cost altruistic act in bacteria. We investigated Escherichia coli responding to the attack of an obligately lytic phage by committing suicide in order to prevent parasite transmission to nearby relatives. We found that bacterial suicide provides large benefits to survivors at marginal costs to committers. The cost of suicide was low, because infected cells are moribund, rapidly dying upon phage infection, such that no more opportunity for reproduction remains. As a consequence of its marginal cost, host suicide was selectively favoured even when relatedness between committers and survivors approached zero. Altogether, our findings demonstrate that low-cost suicide can evolve with ease, represents an effective host-defence strategy, and seems to be widespread among microbes. Moreover, low-cost suicide might also occur in higher organisms as exemplified by infected social insect workers leaving the colony to die in isolation.","lang":"eng"}],"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","publist_id":"3939","date_published":"2013-05-22T00:00:00Z","status":"public","day":"22","publication_identifier":{"eissn":["1471-2954"]},"date_updated":"2023-10-18T06:43:23Z","doi":"10.1098/rspb.2012.3035","title":"Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection","external_id":{"pmid":["23516238"]},"oa":1,"article_processing_charge":"No","related_material":{"record":[{"status":"public","relation":"research_data","id":"9751"}]},"year":"2013","article_type":"original","citation":{"ieee":"D. Refardt, T. Bergmiller, and R. Kümmerli, “Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 280, no. 1759. The Royal Society, 2013.","chicago":"Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. The Royal Society, 2013. <a href=\"https://doi.org/10.1098/rspb.2012.3035\">https://doi.org/10.1098/rspb.2012.3035</a>.","mla":"Refardt, Dominik, et al. “Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 280, no. 1759, The Royal Society, 2013, doi:<a href=\"https://doi.org/10.1098/rspb.2012.3035\">10.1098/rspb.2012.3035</a>.","short":"D. Refardt, T. Bergmiller, R. Kümmerli, Proceedings of the Royal Society of London Series B Biological Sciences 280 (2013).","ama":"Refardt D, Bergmiller T, Kümmerli R. Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2013;280(1759). doi:<a href=\"https://doi.org/10.1098/rspb.2012.3035\">10.1098/rspb.2012.3035</a>","apa":"Refardt, D., Bergmiller, T., &#38; Kümmerli, R. (2013). Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2012.3035\">https://doi.org/10.1098/rspb.2012.3035</a>","ista":"Refardt D, Bergmiller T, Kümmerli R. 2013. Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection. Proceedings of the Royal Society of London Series B Biological Sciences. 280(1759)."},"author":[{"full_name":"Refardt, Dominik","last_name":"Refardt","first_name":"Dominik"},{"orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","last_name":"Bergmiller","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rolf","last_name":"Kümmerli","full_name":"Kümmerli, Rolf"}],"month":"05","_id":"2853","language":[{"iso":"eng"}],"issue":"1759"},{"acknowledgement":"This work was partially supported in part by the NSF grants CCR-0132780, CNS-0720884, CCR-0225610, by the Swiss National Science Foundation, ERC Start Grant Graph Games (Project No. 279307), FWF NFN Grant S11407-N23 (RiSE), and a Microsoft faculty fellows","language":[{"iso":"eng"}],"_id":"2854","pubrep_id":"388","page":"640 - 657","issue":"5","article_type":"original","citation":{"chicago":"Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “Strategy Improvement for Concurrent Reachability and Turn Based Stochastic Safety Games.” <i>Journal of Computer and System Sciences</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.jcss.2012.12.001\">https://doi.org/10.1016/j.jcss.2012.12.001</a>.","ieee":"K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “Strategy improvement for concurrent reachability and turn based stochastic safety games,” <i>Journal of Computer and System Sciences</i>, vol. 79, no. 5. Elsevier, pp. 640–657, 2013.","mla":"Chatterjee, Krishnendu, et al. “Strategy Improvement for Concurrent Reachability and Turn Based Stochastic Safety Games.” <i>Journal of Computer and System Sciences</i>, vol. 79, no. 5, Elsevier, 2013, pp. 640–57, doi:<a href=\"https://doi.org/10.1016/j.jcss.2012.12.001\">10.1016/j.jcss.2012.12.001</a>.","short":"K. Chatterjee, L. De Alfaro, T.A. Henzinger, Journal of Computer and System Sciences 79 (2013) 640–657.","ama":"Chatterjee K, De Alfaro L, Henzinger TA. Strategy improvement for concurrent reachability and turn based stochastic safety games. <i>Journal of Computer and System Sciences</i>. 2013;79(5):640-657. doi:<a href=\"https://doi.org/10.1016/j.jcss.2012.12.001\">10.1016/j.jcss.2012.12.001</a>","ista":"Chatterjee K, De Alfaro L, Henzinger TA. 2013. Strategy improvement for concurrent reachability and turn based stochastic safety games. Journal of Computer and System Sciences. 79(5), 640–657.","apa":"Chatterjee, K., De Alfaro, L., &#38; Henzinger, T. A. (2013). Strategy improvement for concurrent reachability and turn based stochastic safety games. <i>Journal of Computer and System Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcss.2012.12.001\">https://doi.org/10.1016/j.jcss.2012.12.001</a>"},"ddc":["000"],"month":"08","file_date_updated":"2020-07-14T12:45:51Z","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Luca","last_name":"De Alfaro","full_name":"De Alfaro, Luca"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"file":[{"content_type":"application/pdf","checksum":"6d3ee12cceb946a0abe69594b6a22409","creator":"system","relation":"main_file","file_name":"IST-2015-388-v1+1_1-s2.0-S0022000012001778-main.pdf","file_id":"5370","file_size":425488,"date_updated":"2020-07-14T12:45:51Z","date_created":"2018-12-12T10:18:48Z","access_level":"open_access"}],"oa":1,"article_processing_charge":"No","has_accepted_license":"1","ec_funded":1,"year":"2013","day":"01","date_updated":"2021-01-12T07:00:16Z","title":"Strategy improvement for concurrent reachability and turn based stochastic safety games","doi":"10.1016/j.jcss.2012.12.001","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        79","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"abstract":[{"text":"We consider concurrent games played on graphs. At every round of a game, each player simultaneously and independently selects a move; the moves jointly determine the transition to a successor state. Two basic objectives are the safety objective to stay forever in a given set of states, and its dual, the reachability objective to reach a given set of states. First, we present a simple proof of the fact that in concurrent reachability games, for all ε&gt;0, memoryless ε-optimal strategies exist. A memoryless strategy is independent of the history of plays, and an ε-optimal strategy achieves the objective with probability within ε of the value of the game. In contrast to previous proofs of this fact, our proof is more elementary and more combinatorial. Second, we present a strategy-improvement (a.k.a. policy-iteration) algorithm for concurrent games with reachability objectives. Finally, we present a strategy-improvement algorithm for turn-based stochastic games (where each player selects moves in turns) with safety objectives. Our algorithms yield sequences of player-1 strategies which ensure probabilities of winning that converge monotonically (from below) to the value of the game. © 2012 Elsevier Inc.","lang":"eng"}],"status":"public","date_published":"2013-08-01T00:00:00Z","publication":"Journal of Computer and System Sciences","publist_id":"3938","scopus_import":1,"date_created":"2018-12-11T11:59:57Z","oa_version":"Published Version","volume":79,"type":"journal_article","publication_status":"published","publisher":"Elsevier","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"project":[{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"call_identifier":"FWF","grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1"},{"date_published":"2013-03-28T00:00:00Z","status":"public","publist_id":"3937","publication":"Cell Reports","abstract":[{"lang":"eng","text":"Genomic imprinting leads to preferred expression of either the maternal or paternal alleles of a subset of genes. Imprinting is essential for mammalian development, and its deregulation causes many diseases. However, the functional relevance of imprinting at the cellular level is poorly understood for most imprinted genes. We used mosaic analysis with double markers (MADM) in mice to create uniparental disomies (UPDs) and to visualize imprinting effects with single-cell resolution. Although chromosome 12 UPD did not produce detectable phenotypes, chromosome 7 UPD caused highly significant paternal growth dominance in the liver and lung, but not in the brain or heart. A single gene on chromosome 7, encoding the secreted insulin-like growth factor 2 (IGF2), accounts for most of the paternal dominance effect. Mosaic analyses implied additional imprinted loci on chromosome 7 acting cell autonomously to transmit the IGF2 signal. Our study reveals chromosome- and cell-type specificity of genomic imprinting effects."}],"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"intvolume":"         3","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","date_created":"2018-12-11T11:59:57Z","scopus_import":1,"volume":3,"type":"journal_article","quality_controlled":"1","department":[{"_id":"SiHi"}],"publisher":"Cell Press","publication_status":"published","issue":"3","page":"960 - 967","_id":"2855","pubrep_id":"405","language":[{"iso":"eng"}],"month":"03","file_date_updated":"2020-07-14T12:45:51Z","author":[{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer"},{"full_name":"Johnson, Randy","first_name":"Randy","last_name":"Johnson"},{"last_name":"Luo","first_name":"Liqun","full_name":"Luo, Liqun"}],"file":[{"content_type":"application/pdf","creator":"system","checksum":"6e977b918e81384cd571ec5a9d812289","relation":"main_file","file_name":"IST-2016-405-v1+1_1-s2.0-S2211124713000612-main.pdf","file_id":"5274","file_size":1907211,"date_updated":"2020-07-14T12:45:51Z","date_created":"2018-12-12T10:17:20Z","access_level":"open_access"}],"citation":{"ieee":"S. Hippenmeyer, R. Johnson, and L. Luo, “Mosaic analysis with double markers reveals cell type specific paternal growth dominance,” <i>Cell Reports</i>, vol. 3, no. 3. Cell Press, pp. 960–967, 2013.","chicago":"Hippenmeyer, Simon, Randy Johnson, and Liqun Luo. “Mosaic Analysis with Double Markers Reveals Cell Type Specific Paternal Growth Dominance.” <i>Cell Reports</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1016/j.celrep.2013.02.002\">https://doi.org/10.1016/j.celrep.2013.02.002</a>.","short":"S. Hippenmeyer, R. Johnson, L. Luo, Cell Reports 3 (2013) 960–967.","mla":"Hippenmeyer, Simon, et al. “Mosaic Analysis with Double Markers Reveals Cell Type Specific Paternal Growth Dominance.” <i>Cell Reports</i>, vol. 3, no. 3, Cell Press, 2013, pp. 960–67, doi:<a href=\"https://doi.org/10.1016/j.celrep.2013.02.002\">10.1016/j.celrep.2013.02.002</a>.","ama":"Hippenmeyer S, Johnson R, Luo L. Mosaic analysis with double markers reveals cell type specific paternal growth dominance. <i>Cell Reports</i>. 2013;3(3):960-967. doi:<a href=\"https://doi.org/10.1016/j.celrep.2013.02.002\">10.1016/j.celrep.2013.02.002</a>","apa":"Hippenmeyer, S., Johnson, R., &#38; Luo, L. (2013). Mosaic analysis with double markers reveals cell type specific paternal growth dominance. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2013.02.002\">https://doi.org/10.1016/j.celrep.2013.02.002</a>","ista":"Hippenmeyer S, Johnson R, Luo L. 2013. Mosaic analysis with double markers reveals cell type specific paternal growth dominance. Cell Reports. 3(3), 960–967."},"ddc":["570"],"year":"2013","has_accepted_license":"1","oa":1,"title":"Mosaic analysis with double markers reveals cell type specific paternal growth dominance","doi":"10.1016/j.celrep.2013.02.002","date_updated":"2021-01-12T07:00:16Z","day":"28"},{"oa_version":"Submitted Version","date_created":"2018-12-11T11:59:57Z","scopus_import":1,"status":"public","date_published":"2013-03-03T00:00:00Z","publication":"Nature Neuroscience","publist_id":"3936","abstract":[{"lang":"eng","text":"G protein–coupled receptors (GPCRs), the largest family of membrane signaling proteins, respond to neurotransmitters, hormones and small environmental molecules. The neuronal function of many GPCRs has been difficult to resolve because of an inability to gate them with subtype specificity, spatial precision, speed and reversibility. To address this, we developed an approach for opto-chemical engineering of native GPCRs. We applied this to the metabotropic glutamate receptors (mGluRs) to generate light-agonized and light-antagonized mGluRs (LimGluRs). The light-agonized LimGluR2, on which we focused, was fast, bistable and supported multiple rounds of on/off switching. Light gated two of the primary neuronal functions of mGluR2: suppression of excitability and inhibition of neurotransmitter release. We found that the light-antagonized tool LimGluR2-block was able to manipulate negative feedback of synaptically released glutamate on transmitter release. We generalized the optical control to two additional family members: mGluR3 and mGluR6. This system worked in rodent brain slices and in zebrafish in vivo, where we found that mGluR2 modulated the threshold for escape behavior. These light-gated mGluRs pave the way for determining the roles of mGluRs in synaptic plasticity, memory and disease."}],"intvolume":"        16","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"quality_controlled":"1","department":[{"_id":"HaJa"}],"publisher":"Nature Publishing Group","publication_status":"published","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681425/","open_access":"1"}],"volume":16,"type":"journal_article","month":"03","author":[{"last_name":"Levitz","first_name":"Joshua","full_name":"Levitz, Joshua"},{"last_name":"Pantoja","first_name":"Carlos","full_name":"Pantoja, Carlos"},{"first_name":"Benjamin","last_name":"Gaub","full_name":"Gaub, Benjamin"},{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Reiner, Andreas","last_name":"Reiner","first_name":"Andreas"},{"last_name":"Hoagland","first_name":"Adam","full_name":"Hoagland, Adam"},{"full_name":"Schoppik, David","last_name":"Schoppik","first_name":"David"},{"last_name":"Kane","first_name":"Brian","full_name":"Kane, Brian"},{"full_name":"Stawski, Philipp","last_name":"Stawski","first_name":"Philipp"},{"last_name":"Schier","first_name":"Alexander","full_name":"Schier, Alexander"},{"first_name":"Dirk","last_name":"Trauner","full_name":"Trauner, Dirk"},{"first_name":"Ehud","last_name":"Isacoff","full_name":"Isacoff, Ehud"}],"citation":{"short":"J. Levitz, C. Pantoja, B. Gaub, H.L. Janovjak, A. Reiner, A. Hoagland, D. Schoppik, B. Kane, P. Stawski, A. Schier, D. Trauner, E. Isacoff, Nature Neuroscience 16 (2013) 507–516.","mla":"Levitz, Joshua, et al. “Optical Control of Metabotropic Glutamate Receptors.” <i>Nature Neuroscience</i>, vol. 16, Nature Publishing Group, 2013, pp. 507–16, doi:<a href=\"https://doi.org/10.1038/nn.3346\">10.1038/nn.3346</a>.","ieee":"J. Levitz <i>et al.</i>, “Optical control of metabotropic glutamate receptors,” <i>Nature Neuroscience</i>, vol. 16. Nature Publishing Group, pp. 507–516, 2013.","chicago":"Levitz, Joshua, Carlos Pantoja, Benjamin Gaub, Harald L Janovjak, Andreas Reiner, Adam Hoagland, David Schoppik, et al. “Optical Control of Metabotropic Glutamate Receptors.” <i>Nature Neuroscience</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/nn.3346\">https://doi.org/10.1038/nn.3346</a>.","apa":"Levitz, J., Pantoja, C., Gaub, B., Janovjak, H. L., Reiner, A., Hoagland, A., … Isacoff, E. (2013). Optical control of metabotropic glutamate receptors. <i>Nature Neuroscience</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nn.3346\">https://doi.org/10.1038/nn.3346</a>","ista":"Levitz J, Pantoja C, Gaub B, Janovjak HL, Reiner A, Hoagland A, Schoppik D, Kane B, Stawski P, Schier A, Trauner D, Isacoff E. 2013. Optical control of metabotropic glutamate receptors. Nature Neuroscience. 16, 507–516.","ama":"Levitz J, Pantoja C, Gaub B, et al. Optical control of metabotropic glutamate receptors. <i>Nature Neuroscience</i>. 2013;16:507-516. doi:<a href=\"https://doi.org/10.1038/nn.3346\">10.1038/nn.3346</a>"},"page":"507 - 516","acknowledgement":"National Science Foundation grants CHE-0233882 and CHE-0840505 (to the College of Chemistry at the University of California, Berkeley), a postdoctoral fellowship of the European Molecular Biology Organization (H.J.)","_id":"2856","language":[{"iso":"eng"}],"external_id":{"pmid":["23455609"]},"title":"Optical control of metabotropic glutamate receptors","doi":"10.1038/nn.3346","date_updated":"2021-01-12T07:00:16Z","day":"03","year":"2013","oa":1},{"ddc":["570"],"citation":{"ama":"Szobota S, Mckenzie C, Janovjak HL. Optical control of ligand-gated ion channels. <i>Methods in Molecular Biology</i>. 2013;998:417-435. doi:<a href=\"https://doi.org/10.1007/978-1-62703-351-0_32\">10.1007/978-1-62703-351-0_32</a>","apa":"Szobota, S., Mckenzie, C., &#38; Janovjak, H. L. (2013). Optical control of ligand-gated ion channels. <i>Methods in Molecular Biology</i>. Springer. <a href=\"https://doi.org/10.1007/978-1-62703-351-0_32\">https://doi.org/10.1007/978-1-62703-351-0_32</a>","ista":"Szobota S, Mckenzie C, Janovjak HL. 2013. Optical control of ligand-gated ion channels. Methods in Molecular Biology. 998, 417–435.","ieee":"S. Szobota, C. Mckenzie, and H. L. Janovjak, “Optical control of ligand-gated ion channels,” <i>Methods in Molecular Biology</i>, vol. 998. Springer, pp. 417–435, 2013.","chicago":"Szobota, Stephanie, Catherine Mckenzie, and Harald L Janovjak. “Optical Control of Ligand-Gated Ion Channels.” <i>Methods in Molecular Biology</i>. Springer, 2013. <a href=\"https://doi.org/10.1007/978-1-62703-351-0_32\">https://doi.org/10.1007/978-1-62703-351-0_32</a>.","mla":"Szobota, Stephanie, et al. “Optical Control of Ligand-Gated Ion Channels.” <i>Methods in Molecular Biology</i>, vol. 998, Springer, 2013, pp. 417–35, doi:<a href=\"https://doi.org/10.1007/978-1-62703-351-0_32\">10.1007/978-1-62703-351-0_32</a>.","short":"S. Szobota, C. Mckenzie, H.L. Janovjak, Methods in Molecular Biology 998 (2013) 417–435."},"author":[{"first_name":"Stephanie","last_name":"Szobota","full_name":"Szobota, Stephanie"},{"id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","last_name":"Mckenzie","first_name":"Catherine","full_name":"Mckenzie, Catherine"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"}],"file":[{"file_id":"4952","file_size":336734,"date_updated":"2020-07-14T12:45:51Z","date_created":"2018-12-12T10:12:34Z","access_level":"open_access","content_type":"application/pdf","creator":"system","checksum":"1701f0d989f27ddac471b19a894ec0d1","relation":"main_file","file_name":"IST-2017-834-v1+1_szobota.pdf"}],"month":"02","file_date_updated":"2020-07-14T12:45:51Z","pubrep_id":"834","_id":"2857","language":[{"iso":"eng"}],"page":"417 - 435","date_updated":"2021-01-12T07:00:17Z","day":"22","doi":"10.1007/978-1-62703-351-0_32","title":"Optical control of ligand-gated ion channels","oa":1,"ec_funded":1,"year":"2013","has_accepted_license":"1","date_created":"2018-12-11T11:59:57Z","scopus_import":1,"alternative_title":["MIMB"],"oa_version":"Submitted Version","intvolume":"       998","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3932","publication":"Methods in Molecular Biology","date_published":"2013-02-22T00:00:00Z","status":"public","abstract":[{"text":"In the vibrant field of optogenetics, optics and genetic targeting are combined to commandeer cellular functions, such as the neuronal action potential, by optically stimulating light-sensitive ion channels expressed in the cell membrane. One broadly applicable manifestation of this approach are covalently attached photochromic tethered ligands (PTLs) that allow activating ligand-gated ion channels with outstanding spatial and temporal resolution. Here, we describe all steps towards the successful development and application of PTL-gated ion channels in cell lines and primary cells. The basis for these experiments forms a combination of molecular modeling, genetic engineering, cell culture, and electrophysiology. The light-gated glutamate receptor (LiGluR), which consists of the PTL-functionalized GluK2 receptor, serves as a model.","lang":"eng"}],"publisher":"Springer","publication_status":"published","quality_controlled":"1","project":[{"name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","_id":"255BFFFA-B435-11E9-9278-68D0E5697425","grant_number":"RGY0084/2012"},{"grant_number":"303564","_id":"25548C20-B435-11E9-9278-68D0E5697425","name":"Microbial Ion Channels for Synthetic Neurobiology","call_identifier":"FP7"}],"department":[{"_id":"HaJa"}],"type":"journal_article","volume":998},{"publication_status":"published","publisher":"Wiley-Blackwell","department":[{"_id":"KrCh"}],"quality_controlled":"1","project":[{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF"}],"type":"journal_article","volume":6,"scopus_import":1,"date_created":"2018-12-11T11:59:58Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"         6","abstract":[{"lang":"eng","text":"Tumor growth is caused by the acquisition of driver mutations, which enhance the net reproductive rate of cells. Driver mutations may increase cell division, reduce cell death, or allow cells to overcome density-limiting effects. We study the dynamics of tumor growth as one additional driver mutation is acquired. Our models are based on two-type branching processes that terminate in either tumor disappearance or tumor detection. In our first model, both cell types grow exponentially, with a faster rate for cells carrying the additional driver. We find that the additional driver mutation does not affect the survival probability of the lesion, but can substantially reduce the time to reach the detectable size if the lesion is slow growing. In our second model, cells lacking the additional driver cannot exceed a fixed carrying capacity, due to density limitations. In this case, the time to detection depends strongly on this carrying capacity. Our model provides a quantitative framework for studying tumor dynamics during different stages of progression. We observe that early, small lesions need additional drivers, while late stage metastases are only marginally affected by them. These results help to explain why additional driver mutations are typically not detected in fast-growing metastases."}],"publist_id":"3931","publication":"Evolutionary Applications","status":"public","date_published":"2013-01-01T00:00:00Z","day":"01","date_updated":"2023-09-07T11:40:43Z","doi":"10.1111/eva.12020","title":"The effect of one additional driver mutation on tumor progression","oa":1,"has_accepted_license":"1","related_material":{"record":[{"id":"1400","relation":"dissertation_contains","status":"public"}]},"ec_funded":1,"year":"2013","ddc":["570"],"citation":{"ieee":"J. Reiter, I. Božić, B. Allen, K. Chatterjee, and M. Nowak, “The effect of one additional driver mutation on tumor progression,” <i>Evolutionary Applications</i>, vol. 6, no. 1. Wiley-Blackwell, pp. 34–45, 2013.","chicago":"Reiter, Johannes, Ivana Božić, Benjamin Allen, Krishnendu Chatterjee, and Martin Nowak. “The Effect of One Additional Driver Mutation on Tumor Progression.” <i>Evolutionary Applications</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/eva.12020\">https://doi.org/10.1111/eva.12020</a>.","short":"J. Reiter, I. Božić, B. Allen, K. Chatterjee, M. Nowak, Evolutionary Applications 6 (2013) 34–45.","mla":"Reiter, Johannes, et al. “The Effect of One Additional Driver Mutation on Tumor Progression.” <i>Evolutionary Applications</i>, vol. 6, no. 1, Wiley-Blackwell, 2013, pp. 34–45, doi:<a href=\"https://doi.org/10.1111/eva.12020\">10.1111/eva.12020</a>.","ama":"Reiter J, Božić I, Allen B, Chatterjee K, Nowak M. The effect of one additional driver mutation on tumor progression. <i>Evolutionary Applications</i>. 2013;6(1):34-45. doi:<a href=\"https://doi.org/10.1111/eva.12020\">10.1111/eva.12020</a>","apa":"Reiter, J., Božić, I., Allen, B., Chatterjee, K., &#38; Nowak, M. (2013). The effect of one additional driver mutation on tumor progression. <i>Evolutionary Applications</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/eva.12020\">https://doi.org/10.1111/eva.12020</a>","ista":"Reiter J, Božić I, Allen B, Chatterjee K, Nowak M. 2013. The effect of one additional driver mutation on tumor progression. Evolutionary Applications. 6(1), 34–45."},"author":[{"full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","last_name":"Reiter","first_name":"Johannes"},{"full_name":"Božić, Ivana","first_name":"Ivana","last_name":"Božić"},{"id":"135B5B70-E9D2-11E9-BD74-BB415DA2B523","last_name":"Allen","first_name":"Benjamin","full_name":"Allen, Benjamin"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"file":[{"date_updated":"2020-07-14T12:45:51Z","date_created":"2018-12-12T10:15:50Z","access_level":"open_access","file_id":"5173","file_size":1172037,"checksum":"e2955b3889f8a823c3d5a72cb16f8957","creator":"system","file_name":"IST-2016-415-v1+1_Reiter_et_al-2013-Evolutionary_Applications.pdf","relation":"main_file","content_type":"application/pdf"}],"file_date_updated":"2020-07-14T12:45:51Z","month":"01","_id":"2858","pubrep_id":"415","language":[{"iso":"eng"}],"page":"34 - 45","issue":"1"},{"oa":1,"year":"2013","day":"01","date_updated":"2021-01-12T07:00:18Z","title":"Homology and robustness of level and interlevel sets","doi":"10.4310/HHA.2013.v15.n1.a3","external_id":{"arxiv":["1102.3389"]},"_id":"2859","language":[{"iso":"eng"}],"page":"51 - 72","issue":"1","citation":{"short":"P. Bendich, H. Edelsbrunner, D. Morozov, A. Patel, Homology, Homotopy and Applications 15 (2013) 51–72.","mla":"Bendich, Paul, et al. “Homology and Robustness of Level and Interlevel Sets.” <i>Homology, Homotopy and Applications</i>, vol. 15, no. 1, International Press, 2013, pp. 51–72, doi:<a href=\"https://doi.org/10.4310/HHA.2013.v15.n1.a3\">10.4310/HHA.2013.v15.n1.a3</a>.","chicago":"Bendich, Paul, Herbert Edelsbrunner, Dmitriy Morozov, and Amit Patel. “Homology and Robustness of Level and Interlevel Sets.” <i>Homology, Homotopy and Applications</i>. International Press, 2013. <a href=\"https://doi.org/10.4310/HHA.2013.v15.n1.a3\">https://doi.org/10.4310/HHA.2013.v15.n1.a3</a>.","ieee":"P. Bendich, H. Edelsbrunner, D. Morozov, and A. Patel, “Homology and robustness of level and interlevel sets,” <i>Homology, Homotopy and Applications</i>, vol. 15, no. 1. International Press, pp. 51–72, 2013.","ista":"Bendich P, Edelsbrunner H, Morozov D, Patel A. 2013. Homology and robustness of level and interlevel sets. Homology, Homotopy and Applications. 15(1), 51–72.","apa":"Bendich, P., Edelsbrunner, H., Morozov, D., &#38; Patel, A. (2013). Homology and robustness of level and interlevel sets. <i>Homology, Homotopy and Applications</i>. International Press. <a href=\"https://doi.org/10.4310/HHA.2013.v15.n1.a3\">https://doi.org/10.4310/HHA.2013.v15.n1.a3</a>","ama":"Bendich P, Edelsbrunner H, Morozov D, Patel A. Homology and robustness of level and interlevel sets. <i>Homology, Homotopy and Applications</i>. 2013;15(1):51-72. doi:<a href=\"https://doi.org/10.4310/HHA.2013.v15.n1.a3\">10.4310/HHA.2013.v15.n1.a3</a>"},"arxiv":1,"month":"05","author":[{"full_name":"Bendich, Paul","last_name":"Bendich","first_name":"Paul","id":"43F6EC54-F248-11E8-B48F-1D18A9856A87"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"},{"last_name":"Morozov","first_name":"Dmitriy","full_name":"Morozov, Dmitriy"},{"first_name":"Amit","last_name":"Patel","id":"34A254A0-F248-11E8-B48F-1D18A9856A87","full_name":"Patel, Amit"}],"volume":15,"type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1102.3389v1","open_access":"1"}],"publication_status":"published","publisher":"International Press","department":[{"_id":"HeEd"}],"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        15","abstract":[{"lang":"eng","text":"Given a continuous function f:X-R on a topological space, we consider the preimages of intervals and their homology groups and show how to read the ranks of these groups from the extended persistence diagram of f. In addition, we quantify the robustness of the homology classes under perturbations of f using well groups, and we show how to read the ranks of these groups from the same extended persistence diagram. The special case X=R3 has ramifications in the fields of medical imaging and scientific visualization."}],"status":"public","date_published":"2013-05-01T00:00:00Z","publication":"Homology, Homotopy and Applications","publist_id":"3930","scopus_import":1,"date_created":"2018-12-11T11:59:58Z","oa_version":"Preprint"},{"scopus_import":1,"date_created":"2018-12-11T11:59:59Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"        78","abstract":[{"lang":"eng","text":"In the hippocampus, cell assemblies forming mnemonic representations of space are thought to arise as a result of changes in functional connections of pyramidal cells. We have found that CA1 interneuron circuits are also reconfigured during goal-oriented spatial learning through modification of inputs from pyramidal cells. As learning progressed, new pyramidal assemblies expressed in theta cycles alternated with previously established ones, and eventually overtook them. The firing patterns of interneurons developed a relationship to new, learning-related assemblies: some interneurons associated their activity with new pyramidal assemblies while some others dissociated from them. These firing associations were explained by changes in the weight of monosynaptic inputs received by interneurons from new pyramidal assemblies, as these predicted the associational changes. Spatial learning thus engages circuit modifications in the hippocampus that incorporate a redistribution of inhibitory activity that might assist in the segregation of competing pyramidal cell assembly patterns in space and time."}],"publication":"Neuron","publist_id":"3929","date_published":"2013-03-21T00:00:00Z","status":"public","publication_status":"published","publisher":"Elsevier","department":[{"_id":"JoCs"}],"quality_controlled":"1","project":[{"call_identifier":"FP7","grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex"}],"type":"journal_article","volume":78,"ddc":["570"],"citation":{"chicago":"Dupret, David, Joseph O’Neill, and Jozsef L Csicsvari. “Dynamic Reconfiguration of Hippocampal Interneuron Circuits during Spatial Learning.” <i>Neuron</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.neuron.2013.01.033\">https://doi.org/10.1016/j.neuron.2013.01.033</a>.","ieee":"D. Dupret, J. O’Neill, and J. L. Csicsvari, “Dynamic reconfiguration of hippocampal interneuron circuits during spatial learning,” <i>Neuron</i>, vol. 78, no. 1. Elsevier, pp. 166–180, 2013.","short":"D. Dupret, J. O’Neill, J.L. Csicsvari, Neuron 78 (2013) 166–180.","mla":"Dupret, David, et al. “Dynamic Reconfiguration of Hippocampal Interneuron Circuits during Spatial Learning.” <i>Neuron</i>, vol. 78, no. 1, Elsevier, 2013, pp. 166–80, doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.01.033\">10.1016/j.neuron.2013.01.033</a>.","ama":"Dupret D, O’Neill J, Csicsvari JL. Dynamic reconfiguration of hippocampal interneuron circuits during spatial learning. <i>Neuron</i>. 2013;78(1):166-180. doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.01.033\">10.1016/j.neuron.2013.01.033</a>","ista":"Dupret D, O’Neill J, Csicsvari JL. 2013. Dynamic reconfiguration of hippocampal interneuron circuits during spatial learning. Neuron. 78(1), 166–180.","apa":"Dupret, D., O’Neill, J., &#38; Csicsvari, J. L. (2013). Dynamic reconfiguration of hippocampal interneuron circuits during spatial learning. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2013.01.033\">https://doi.org/10.1016/j.neuron.2013.01.033</a>"},"author":[{"full_name":"Dupret, David","first_name":"David","last_name":"Dupret"},{"first_name":"Joseph","last_name":"O'Neill","id":"426376DC-F248-11E8-B48F-1D18A9856A87","full_name":"O'Neill, Joseph"},{"full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L"}],"file":[{"checksum":"0e18cb8561153ddb50bb5af16e7c9e97","creator":"dernst","file_name":"2013_Neuron_Dupret.pdf","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:45:52Z","date_created":"2019-01-23T08:08:07Z","access_level":"open_access","file_id":"5877","file_size":2637837}],"file_date_updated":"2020-07-14T12:45:52Z","month":"03","_id":"2860","language":[{"iso":"eng"}],"acknowledgement":"D.D. and J.C. were supported by a MRC Intramural Programme Grant U138197111","page":"166 - 180","issue":"1","day":"21","date_updated":"2021-01-12T07:00:19Z","doi":"10.1016/j.neuron.2013.01.033","title":"Dynamic reconfiguration of hippocampal interneuron circuits during spatial learning","oa":1,"has_accepted_license":"1","year":"2013","ec_funded":1},{"month":"03","article_number":"125101","author":[{"last_name":"Botella Soler","first_name":"Vicente","id":"421234E8-F248-11E8-B48F-1D18A9856A87","full_name":"Botella Soler, Vicente","orcid":"0000-0002-8790-1914"},{"full_name":"Oteo, José","last_name":"Oteo","first_name":"José"},{"full_name":"Ros, Javier","last_name":"Ros","first_name":"Javier"},{"last_name":"Glendinning","first_name":"Paul","full_name":"Glendinning, Paul"}],"oa_version":"None","scopus_import":1,"date_created":"2018-12-11T11:59:59Z","citation":{"mla":"Botella Soler, Vicente, et al. “Lyapunov Exponent and Topological Entropy Plateaus in Piecewise Linear Maps.” <i>Journal of Physics A: Mathematical and Theoretical</i>, vol. 46, no. 12, 125101, IOP Publishing Ltd., 2013, doi:<a href=\"https://doi.org/10.1088/1751-8113/46/12/125101\">10.1088/1751-8113/46/12/125101</a>.","short":"V. Botella Soler, J. Oteo, J. Ros, P. Glendinning, Journal of Physics A: Mathematical and Theoretical 46 (2013).","ieee":"V. Botella Soler, J. Oteo, J. Ros, and P. Glendinning, “Lyapunov exponent and topological entropy plateaus in piecewise linear maps,” <i>Journal of Physics A: Mathematical and Theoretical</i>, vol. 46, no. 12. IOP Publishing Ltd., 2013.","chicago":"Botella Soler, Vicente, José Oteo, Javier Ros, and Paul Glendinning. “Lyapunov Exponent and Topological Entropy Plateaus in Piecewise Linear Maps.” <i>Journal of Physics A: Mathematical and Theoretical</i>. IOP Publishing Ltd., 2013. <a href=\"https://doi.org/10.1088/1751-8113/46/12/125101\">https://doi.org/10.1088/1751-8113/46/12/125101</a>.","apa":"Botella Soler, V., Oteo, J., Ros, J., &#38; Glendinning, P. (2013). Lyapunov exponent and topological entropy plateaus in piecewise linear maps. <i>Journal of Physics A: Mathematical and Theoretical</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1751-8113/46/12/125101\">https://doi.org/10.1088/1751-8113/46/12/125101</a>","ista":"Botella Soler V, Oteo J, Ros J, Glendinning P. 2013. Lyapunov exponent and topological entropy plateaus in piecewise linear maps. Journal of Physics A: Mathematical and Theoretical. 46(12), 125101.","ama":"Botella Soler V, Oteo J, Ros J, Glendinning P. Lyapunov exponent and topological entropy plateaus in piecewise linear maps. <i>Journal of Physics A: Mathematical and Theoretical</i>. 2013;46(12). doi:<a href=\"https://doi.org/10.1088/1751-8113/46/12/125101\">10.1088/1751-8113/46/12/125101</a>"},"abstract":[{"text":"We consider a two-parameter family of piecewise linear maps in which the moduli of the two slopes take different values. We provide numerical evidence of the existence of some parameter regions in which the Lyapunov exponent and the topological entropy remain constant. Analytical proof of this phenomenon is also given for certain cases. Surprisingly however, the systems with that property are not conjugate as we prove by using kneading theory.","lang":"eng"}],"date_published":"2013-03-29T00:00:00Z","status":"public","publist_id":"3928","publication":"Journal of Physics A: Mathematical and Theoretical","issue":"12","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2861","intvolume":"        46","language":[{"iso":"eng"}],"title":"Lyapunov exponent and topological entropy plateaus in piecewise linear maps","department":[{"_id":"GaTk"}],"doi":"10.1088/1751-8113/46/12/125101","quality_controlled":"1","publication_status":"published","day":"29","publisher":"IOP Publishing Ltd.","date_updated":"2021-01-12T07:00:19Z","year":"2013","volume":46,"type":"journal_article"},{"oa_version":"Submitted Version","date_created":"2018-12-11T11:59:59Z","scopus_import":1,"status":"public","date_published":"2013-04-01T00:00:00Z","publist_id":"3927","publication":"Development","abstract":[{"lang":"eng","text":"Motile cilia perform crucial functions during embryonic development and throughout adult life. Development of organs containing motile cilia involves regulation of cilia formation (ciliogenesis) and formation of a luminal space (lumenogenesis) in which cilia generate fluid flows. Control of ciliogenesis and lumenogenesis is not yet fully understood, and it remains unclear whether these processes are coupled. In the zebrafish embryo, lethal giant larvae 2 (lgl2) is expressed prominently in ciliated organs. Lgl proteins are involved in establishing cell polarity and have been implicated in vesicle trafficking. Here, we identified a role for Lgl2 in development of ciliated epithelia in Kupffer's vesicle, which directs left-right asymmetry of the embryo; the otic vesicles, which give rise to the inner ear; and the pronephric ducts of the kidney. Using Kupffer's vesicle as a model ciliated organ, we found that depletion of Lgl2 disrupted lumen formation and reduced cilia number and length. Immunofluorescence and time-lapse imaging of Kupffer's vesicle morphogenesis in Lgl2-deficient embryos suggested cell adhesion defects and revealed loss of the adherens junction component E-cadherin at lateral membranes. Genetic interaction experiments indicate that Lgl2 interacts with Rab11a to regulate E-cadherin and mediate lumen formation that is uncoupled from cilia formation. These results uncover new roles and interactions for Lgl2 that are crucial for both lumenogenesis and ciliogenesis and indicate that these processes are genetically separable in zebrafish."}],"intvolume":"       140","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"quality_controlled":"1","department":[{"_id":"CaHe"}],"publisher":"Company of Biologists","publication_status":"published","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596994/","open_access":"1"}],"volume":140,"type":"journal_article","month":"04","author":[{"full_name":"Tay, Hwee","first_name":"Hwee","last_name":"Tay"},{"first_name":"Sabrina","last_name":"Schulze","full_name":"Schulze, Sabrina"},{"id":"2E3E0988-F248-11E8-B48F-1D18A9856A87","first_name":"Julien","last_name":"Compagnon","full_name":"Compagnon, Julien"},{"full_name":"Foley, Fiona","first_name":"Fiona","last_name":"Foley"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yost, H Joseph","last_name":"Yost","first_name":"H Joseph"},{"last_name":"Abdelilah Seyfried","first_name":"Salim","full_name":"Abdelilah Seyfried, Salim"},{"full_name":"Amack, Jeffrey","last_name":"Amack","first_name":"Jeffrey"}],"citation":{"mla":"Tay, Hwee, et al. “Lethal Giant Larvae 2 Regulates Development of the Ciliated Organ Kupffer’s Vesicle.” <i>Development</i>, vol. 140, no. 7, Company of Biologists, 2013, pp. 1550–59, doi:<a href=\"https://doi.org/10.1242/dev.087130\">10.1242/dev.087130</a>.","short":"H. Tay, S. Schulze, J. Compagnon, F. Foley, C.-P.J. Heisenberg, H.J. Yost, S. Abdelilah Seyfried, J. Amack, Development 140 (2013) 1550–1559.","chicago":"Tay, Hwee, Sabrina Schulze, Julien Compagnon, Fiona Foley, Carl-Philipp J Heisenberg, H Joseph Yost, Salim Abdelilah Seyfried, and Jeffrey Amack. “Lethal Giant Larvae 2 Regulates Development of the Ciliated Organ Kupffer’s Vesicle.” <i>Development</i>. Company of Biologists, 2013. <a href=\"https://doi.org/10.1242/dev.087130\">https://doi.org/10.1242/dev.087130</a>.","ieee":"H. Tay <i>et al.</i>, “Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle,” <i>Development</i>, vol. 140, no. 7. Company of Biologists, pp. 1550–1559, 2013.","ista":"Tay H, Schulze S, Compagnon J, Foley F, Heisenberg C-PJ, Yost HJ, Abdelilah Seyfried S, Amack J. 2013. Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle. Development. 140(7), 1550–1559.","apa":"Tay, H., Schulze, S., Compagnon, J., Foley, F., Heisenberg, C.-P. J., Yost, H. J., … Amack, J. (2013). Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.087130\">https://doi.org/10.1242/dev.087130</a>","ama":"Tay H, Schulze S, Compagnon J, et al. Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle. <i>Development</i>. 2013;140(7):1550-1559. doi:<a href=\"https://doi.org/10.1242/dev.087130\">10.1242/dev.087130</a>"},"issue":"7","page":"1550 - 1559","acknowledgement":"Deposited in PMC for release after 12 months. We thank members of the Amack lab for helpful discussions and Mahendra Sonawane for donating reagents.","_id":"2862","language":[{"iso":"eng"}],"external_id":{"pmid":["23482490"]},"title":"Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle","doi":"10.1242/dev.087130","date_updated":"2021-01-12T07:00:20Z","day":"01","year":"2013","oa":1},{"year":"2013","has_accepted_license":"1","oa":1,"title":"Stimulus-dependent maximum entropy models of neural population codes","doi":"10.1371/journal.pcbi.1002922","date_updated":"2021-01-12T07:00:20Z","day":"01","issue":"3","pubrep_id":"120","_id":"2863","language":[{"iso":"eng"}],"article_number":"e1002922","month":"03","file_date_updated":"2020-07-14T12:45:52Z","file":[{"content_type":"application/pdf","file_name":"IST-2013-120-v1+1_journal.pcbi.1002922.pdf","relation":"main_file","checksum":"5a30876c193209fa05b26db71845dd16","creator":"system","file_size":1548120,"file_id":"5099","access_level":"open_access","date_updated":"2020-07-14T12:45:52Z","date_created":"2018-12-12T10:14:45Z"}],"author":[{"full_name":"Granot Atedgi, Einat","first_name":"Einat","last_name":"Granot Atedgi"},{"last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"},{"full_name":"Segev, Ronen","first_name":"Ronen","last_name":"Segev"},{"full_name":"Schneidman, Elad","last_name":"Schneidman","first_name":"Elad"}],"citation":{"ieee":"E. Granot Atedgi, G. Tkačik, R. Segev, and E. Schneidman, “Stimulus-dependent maximum entropy models of neural population codes,” <i>PLoS Computational Biology</i>, vol. 9, no. 3. Public Library of Science, 2013.","chicago":"Granot Atedgi, Einat, Gašper Tkačik, Ronen Segev, and Elad Schneidman. “Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.” <i>PLoS Computational Biology</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pcbi.1002922\">https://doi.org/10.1371/journal.pcbi.1002922</a>.","short":"E. Granot Atedgi, G. Tkačik, R. Segev, E. Schneidman, PLoS Computational Biology 9 (2013).","mla":"Granot Atedgi, Einat, et al. “Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.” <i>PLoS Computational Biology</i>, vol. 9, no. 3, e1002922, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1002922\">10.1371/journal.pcbi.1002922</a>.","ama":"Granot Atedgi E, Tkačik G, Segev R, Schneidman E. Stimulus-dependent maximum entropy models of neural population codes. <i>PLoS Computational Biology</i>. 2013;9(3). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1002922\">10.1371/journal.pcbi.1002922</a>","apa":"Granot Atedgi, E., Tkačik, G., Segev, R., &#38; Schneidman, E. (2013). Stimulus-dependent maximum entropy models of neural population codes. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1002922\">https://doi.org/10.1371/journal.pcbi.1002922</a>","ista":"Granot Atedgi E, Tkačik G, Segev R, Schneidman E. 2013. Stimulus-dependent maximum entropy models of neural population codes. PLoS Computational Biology. 9(3), e1002922."},"ddc":["570"],"volume":9,"type":"journal_article","quality_controlled":"1","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","publication_status":"published","date_published":"2013-03-01T00:00:00Z","status":"public","publist_id":"3926","publication":"PLoS Computational Biology","abstract":[{"text":"Neural populations encode information about their stimulus in a collective fashion, by joint activity patterns of spiking and silence. A full account of this mapping from stimulus to neural activity is given by the conditional probability distribution over neural codewords given the sensory input. For large populations, direct sampling of these distributions is impossible, and so we must rely on constructing appropriate models. We show here that in a population of 100 retinal ganglion cells in the salamander retina responding to temporal white-noise stimuli, dependencies between cells play an important encoding role. We introduce the stimulus-dependent maximum entropy (SDME) model—a minimal extension of the canonical linear-nonlinear model of a single neuron, to a pairwise-coupled neural population. We find that the SDME model gives a more accurate account of single cell responses and in particular significantly outperforms uncoupled models in reproducing the distributions of population codewords emitted in response to a stimulus. We show how the SDME model, in conjunction with static maximum entropy models of population vocabulary, can be used to estimate information-theoretic quantities like average surprise and information transmission in a neural population.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"         9","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","date_created":"2018-12-11T12:00:00Z","scopus_import":1},{"publication_status":"published","day":"01","publisher":"Botanical Society of America","date_updated":"2021-01-12T07:00:25Z","title":"Brassinosteroid control of shoot gravitropism interacts with ethylene and depends on auxin signaling components","doi":"10.3732/ajb.1200264","quality_controlled":0,"volume":100,"type":"journal_article","year":"2013","extern":1,"date_created":"2018-12-11T12:00:06Z","citation":{"chicago":"Vandenbussche, Filip, Pieter Callebert, Petra Žádníková, Eva Benková, and Dominique Van Der Straeten. “Brassinosteroid Control of Shoot Gravitropism Interacts with Ethylene and Depends on Auxin Signaling Components.” <i>American Journal of Botany</i>. Botanical Society of America, 2013. <a href=\"https://doi.org/10.3732/ajb.1200264\">https://doi.org/10.3732/ajb.1200264</a>.","ieee":"F. Vandenbussche, P. Callebert, P. Žádníková, E. Benková, and D. Van Der Straeten, “Brassinosteroid control of shoot gravitropism interacts with ethylene and depends on auxin signaling components,” <i>American Journal of Botany</i>, vol. 100, no. 1. Botanical Society of America, pp. 215–225, 2013.","short":"F. Vandenbussche, P. Callebert, P. Žádníková, E. Benková, D. Van Der Straeten, American Journal of Botany 100 (2013) 215–225.","mla":"Vandenbussche, Filip, et al. “Brassinosteroid Control of Shoot Gravitropism Interacts with Ethylene and Depends on Auxin Signaling Components.” <i>American Journal of Botany</i>, vol. 100, no. 1, Botanical Society of America, 2013, pp. 215–25, doi:<a href=\"https://doi.org/10.3732/ajb.1200264\">10.3732/ajb.1200264</a>.","ama":"Vandenbussche F, Callebert P, Žádníková P, Benková E, Van Der Straeten D. Brassinosteroid control of shoot gravitropism interacts with ethylene and depends on auxin signaling components. <i>American Journal of Botany</i>. 2013;100(1):215-225. doi:<a href=\"https://doi.org/10.3732/ajb.1200264\">10.3732/ajb.1200264</a>","ista":"Vandenbussche F, Callebert P, Žádníková P, Benková E, Van Der Straeten D. 2013. Brassinosteroid control of shoot gravitropism interacts with ethylene and depends on auxin signaling components. American Journal of Botany. 100(1), 215–225.","apa":"Vandenbussche, F., Callebert, P., Žádníková, P., Benková, E., &#38; Van Der Straeten, D. (2013). Brassinosteroid control of shoot gravitropism interacts with ethylene and depends on auxin signaling components. <i>American Journal of Botany</i>. Botanical Society of America. <a href=\"https://doi.org/10.3732/ajb.1200264\">https://doi.org/10.3732/ajb.1200264</a>"},"month":"01","author":[{"full_name":"Vandenbussche, Filip","first_name":"Filip","last_name":"Vandenbussche"},{"full_name":"Callebert, Pieter","last_name":"Callebert","first_name":"Pieter"},{"full_name":"Žádníková, Petra","last_name":"Žádníková","first_name":"Petra"},{"orcid":"0000-0002-8510-9739","full_name":"Eva Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva"},{"last_name":"Van Der Straeten","first_name":"Dominique","full_name":"Van Der Straeten, Dominique"}],"intvolume":"       100","_id":"2877","abstract":[{"lang":"eng","text":"Premise of the study: To reach favorable conditions for photosynthesis, seedlings grow upward when deprived of light upon underground germination. To direct their growth, they use their negative gravitropic capacity. Negative gravitropism is under tight control of multiple hormones. • Methods: By counting the number of standing plants in a population or by real time monitoring of the reorientation of gravistimulated seedlings of Arabidopsis thaliana, we evaluated the negative gravitropism of ethylene or brassinosteroid (BR) treated plants. Meta-analysis of transcriptomic data on AUX / IAA genes was gathered, and subsequent mutant analysis was performed. • Key results: Ethylene and BR have opposite effects in regulating shoot gravitropism. Lack of BR enhances gravitropic reorientation in 2-d-old seedlings, whereas ethylene does not. Lack of ethylene signaling results in enhanced BR sensitivity. Ethylene and BRs regulate overlapping sets of AUX / IAA genes. BRs regulate a wider range of auxin signaling components than ethylene. • Conclusions: Upward growth in seedlings depends strongly on the internal hormonal balance. Endogenous ethylene stimulates, whereas BRs reduce negative gravitropism in a manner that depends on the function of different, yet overlapping sets of auxin signaling components."}],"page":"215 - 225","status":"public","date_published":"2013-01-01T00:00:00Z","issue":"1","publist_id":"3883","publication":"American Journal of Botany"}]