[{"year":"2013","publist_id":"3929","publication":"Neuron","status":"public","project":[{"_id":"257A4776-B435-11E9-9278-68D0E5697425","grant_number":"281511","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","call_identifier":"FP7"}],"ec_funded":1,"date_published":"2013-03-21T00:00:00Z","acknowledgement":"D.D. and J.C. were supported by a MRC Intramural Programme Grant U138197111","doi":"10.1016/j.neuron.2013.01.033","publisher":"Elsevier","_id":"2860","date_updated":"2021-01-12T07:00:19Z","type":"journal_article","page":"166 - 180","ddc":["570"],"quality_controlled":"1","month":"03","department":[{"_id":"JoCs"}],"file":[{"relation":"main_file","checksum":"0e18cb8561153ddb50bb5af16e7c9e97","file_name":"2013_Neuron_Dupret.pdf","content_type":"application/pdf","access_level":"open_access","file_id":"5877","date_created":"2019-01-23T08:08:07Z","file_size":2637837,"date_updated":"2020-07-14T12:45:52Z","creator":"dernst"}],"oa":1,"language":[{"iso":"eng"}],"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>.","ista":"Dupret D, O’Neill J, Csicsvari JL. 2013. Dynamic reconfiguration of hippocampal interneuron circuits during spatial learning. Neuron. 78(1), 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>.","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>","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>","short":"D. Dupret, J. O’Neill, J.L. Csicsvari, Neuron 78 (2013) 166–180.","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."},"issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"day":"21","author":[{"full_name":"Dupret, David","last_name":"Dupret","first_name":"David"},{"first_name":"Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87","full_name":"O'Neill, Joseph","last_name":"O'Neill"},{"orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"title":"Dynamic reconfiguration of hippocampal interneuron circuits during spatial learning","oa_version":"Published Version","volume":78,"date_created":"2018-12-11T11:59:59Z","has_accepted_license":"1","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."}],"license":"https://creativecommons.org/licenses/by/4.0/","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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        78","file_date_updated":"2020-07-14T12:45:52Z","publication_status":"published"},{"intvolume":"        46","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"}],"publication_status":"published","quality_controlled":"1","author":[{"id":"421234E8-F248-11E8-B48F-1D18A9856A87","full_name":"Botella Soler, Vicente","last_name":"Botella Soler","first_name":"Vicente","orcid":"0000-0002-8790-1914"},{"first_name":"José","last_name":"Oteo","full_name":"Oteo, José"},{"last_name":"Ros","full_name":"Ros, Javier","first_name":"Javier"},{"last_name":"Glendinning","full_name":"Glendinning, Paul","first_name":"Paul"}],"doi":"10.1088/1751-8113/46/12/125101","scopus_import":1,"day":"29","title":"Lyapunov exponent and topological entropy plateaus in piecewise linear maps","publisher":"IOP Publishing Ltd.","oa_version":"None","date_updated":"2021-01-12T07:00:19Z","volume":46,"_id":"2861","type":"journal_article","date_created":"2018-12-11T11:59:59Z","publication":"Journal of Physics A: Mathematical and Theoretical","language":[{"iso":"eng"}],"status":"public","issue":"12","citation":{"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.","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>","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>.","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>","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.","short":"V. Botella Soler, J. Oteo, J. Ros, P. Glendinning, Journal of Physics A: Mathematical and Theoretical 46 (2013)."},"date_published":"2013-03-29T00:00:00Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2013","month":"03","department":[{"_id":"GaTk"}],"publist_id":"3928","article_number":"125101"},{"status":"public","publication":"Development","date_published":"2013-04-01T00:00:00Z","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.","pmid":1,"external_id":{"pmid":["23482490"]},"year":"2013","publist_id":"3927","page":"1550 - 1559","quality_controlled":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596994/","open_access":"1"}],"publisher":"Company of Biologists","doi":"10.1242/dev.087130","type":"journal_article","date_updated":"2021-01-12T07:00:20Z","_id":"2862","language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"7","citation":{"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>","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>.","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.","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.","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.","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>"},"month":"04","department":[{"_id":"CaHe"}],"intvolume":"       140","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."}],"publication_status":"published","oa_version":"Submitted Version","title":"Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle","author":[{"first_name":"Hwee","full_name":"Tay, Hwee","last_name":"Tay"},{"first_name":"Sabrina","last_name":"Schulze","full_name":"Schulze, Sabrina"},{"full_name":"Compagnon, Julien","id":"2E3E0988-F248-11E8-B48F-1D18A9856A87","last_name":"Compagnon","first_name":"Julien"},{"full_name":"Foley, Fiona","last_name":"Foley","first_name":"Fiona"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"},{"full_name":"Yost, H Joseph","last_name":"Yost","first_name":"H Joseph"},{"last_name":"Abdelilah Seyfried","full_name":"Abdelilah Seyfried, Salim","first_name":"Salim"},{"full_name":"Amack, Jeffrey","last_name":"Amack","first_name":"Jeffrey"}],"day":"01","scopus_import":1,"date_created":"2018-12-11T11:59:59Z","volume":140},{"year":"2013","publist_id":"3926","publication":"PLoS Computational Biology","status":"public","date_published":"2013-03-01T00:00:00Z","doi":"10.1371/journal.pcbi.1002922","publisher":"Public Library of Science","_id":"2863","date_updated":"2021-01-12T07:00:20Z","type":"journal_article","ddc":["570"],"quality_controlled":"1","month":"03","department":[{"_id":"GaTk"}],"file":[{"date_updated":"2020-07-14T12:45:52Z","creator":"system","file_size":1548120,"date_created":"2018-12-12T10:14:45Z","file_id":"5099","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2013-120-v1+1_journal.pcbi.1002922.pdf","checksum":"5a30876c193209fa05b26db71845dd16","relation":"main_file"}],"article_number":"e1002922","oa":1,"language":[{"iso":"eng"}],"pubrep_id":"120","citation":{"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>","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>.","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>.","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.","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.","short":"E. Granot Atedgi, G. Tkačik, R. Segev, E. Schneidman, PLoS Computational Biology 9 (2013).","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>"},"issue":"3","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","scopus_import":1,"author":[{"first_name":"Einat","full_name":"Granot Atedgi, Einat","last_name":"Granot Atedgi"},{"first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","last_name":"Tkacik"},{"full_name":"Segev, Ronen","last_name":"Segev","first_name":"Ronen"},{"first_name":"Elad","full_name":"Schneidman, Elad","last_name":"Schneidman"}],"oa_version":"Published Version","title":"Stimulus-dependent maximum entropy models of neural population codes","volume":9,"date_created":"2018-12-11T12:00:00Z","has_accepted_license":"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"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"}],"intvolume":"         9","file_date_updated":"2020-07-14T12:45:52Z","publication_status":"published"},{"publist_id":"3882","external_id":{"pmid":["23178590"]},"year":"2013","date_published":"2013-01-09T00:00:00Z","pmid":1,"ec_funded":1,"project":[{"call_identifier":"FP7","grant_number":"207362","name":"Hormonal cross-talk in plant organogenesis","_id":"253FCA6A-B435-11E9-9278-68D0E5697425"}],"publication":"EMBO Journal","status":"public","type":"journal_article","date_updated":"2021-01-12T07:00:27Z","_id":"2880","publisher":"Wiley-Blackwell","doi":"10.1038/emboj.2012.303","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545298/"}],"page":"149 - 158","department":[{"_id":"EvBe"}],"month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"1","citation":{"ieee":"P. Marhavý <i>et al.</i>, “Auxin reflux between the endodermis and pericycle promotes lateral root initiation,” <i>EMBO Journal</i>, vol. 32, no. 1. Wiley-Blackwell, pp. 149–158, 2013.","short":"P. Marhavý, M. Vanstraelen, B. De Rybel, D. Zhaojun, M. Bennett, T. Beeckman, E. Benková, EMBO Journal 32 (2013) 149–158.","ama":"Marhavý P, Vanstraelen M, De Rybel B, et al. Auxin reflux between the endodermis and pericycle promotes lateral root initiation. <i>EMBO Journal</i>. 2013;32(1):149-158. doi:<a href=\"https://doi.org/10.1038/emboj.2012.303\">10.1038/emboj.2012.303</a>","apa":"Marhavý, P., Vanstraelen, M., De Rybel, B., Zhaojun, D., Bennett, M., Beeckman, T., &#38; Benková, E. (2013). Auxin reflux between the endodermis and pericycle promotes lateral root initiation. <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/emboj.2012.303\">https://doi.org/10.1038/emboj.2012.303</a>","mla":"Marhavý, Peter, et al. “Auxin Reflux between the Endodermis and Pericycle Promotes Lateral Root Initiation.” <i>EMBO Journal</i>, vol. 32, no. 1, Wiley-Blackwell, 2013, pp. 149–58, doi:<a href=\"https://doi.org/10.1038/emboj.2012.303\">10.1038/emboj.2012.303</a>.","ista":"Marhavý P, Vanstraelen M, De Rybel B, Zhaojun D, Bennett M, Beeckman T, Benková E. 2013. Auxin reflux between the endodermis and pericycle promotes lateral root initiation. EMBO Journal. 32(1), 149–158.","chicago":"Marhavý, Peter, Marleen Vanstraelen, Bert De Rybel, Ding Zhaojun, Malcolm Bennett, Tom Beeckman, and Eva Benková. “Auxin Reflux between the Endodermis and Pericycle Promotes Lateral Root Initiation.” <i>EMBO Journal</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1038/emboj.2012.303\">https://doi.org/10.1038/emboj.2012.303</a>."},"language":[{"iso":"eng"}],"oa":1,"date_created":"2018-12-11T12:00:07Z","volume":32,"oa_version":"Submitted Version","title":"Auxin reflux between the endodermis and pericycle promotes lateral root initiation","author":[{"full_name":"Marhavy, Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavy","orcid":"0000-0001-5227-5741","first_name":"Peter"},{"first_name":"Marleen","full_name":"Vanstraelen, Marleen","last_name":"Vanstraelen"},{"last_name":"De Rybel","full_name":"De Rybel, Bert","first_name":"Bert"},{"first_name":"Ding","full_name":"Zhaojun, Ding","last_name":"Zhaojun"},{"first_name":"Malcolm","full_name":"Bennett, Malcolm","last_name":"Bennett"},{"first_name":"Tom","last_name":"Beeckman","full_name":"Beeckman, Tom"},{"orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","last_name":"Benková"}],"day":"09","scopus_import":1,"publication_status":"published","abstract":[{"lang":"eng","text":"Lateral root (LR) formation is initiated when pericycle cells accumulate auxin, thereby acquiring founder cell (FC) status and triggering asymmetric cell divisions, giving rise to a new primordium. How this auxin maximum in pericycle cells builds up and remains focused is not understood. We report that the endodermis plays an active role in the regulation of auxin accumulation and is instructive for FCs to progress during the LR initiation (LRI) phase. We describe the functional importance of a PIN3 (PIN-formed) auxin efflux carrier-dependent hormone reflux pathway between overlaying endodermal and pericycle FCs. Disrupting this reflux pathway causes dramatic defects in the progress of FCs towards the next initiation phase. Our data identify an unexpected regulatory function for the endodermis in LRI as part of the fine-tuning mechanism that appears to act as a check point in LR organogenesis after FCs are specified."}],"intvolume":"        32"},{"publist_id":"3879","year":"2013","external_id":{"pmid":["23391733"]},"pmid":1,"date_published":"2013-02-26T00:00:00Z","publication":"PNAS","status":"public","_id":"2882","date_updated":"2021-01-12T07:00:27Z","type":"journal_article","doi":"10.1073/pnas.1300107110","publisher":"National Academy of Sciences","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587205/"}],"quality_controlled":"1","page":"3627 - 3632","department":[{"_id":"JiFr"}],"month":"02","citation":{"ama":"Löfke C, Zwiewka M, Heilmann I, Van Montagu M, Teichmann T, Friml J. Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism. <i>PNAS</i>. 2013;110(9):3627-3632. doi:<a href=\"https://doi.org/10.1073/pnas.1300107110\">10.1073/pnas.1300107110</a>","short":"C. Löfke, M. Zwiewka, I. Heilmann, M. Van Montagu, T. Teichmann, J. Friml, PNAS 110 (2013) 3627–3632.","ieee":"C. Löfke, M. Zwiewka, I. Heilmann, M. Van Montagu, T. Teichmann, and J. Friml, “Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism,” <i>PNAS</i>, vol. 110, no. 9. National Academy of Sciences, pp. 3627–3632, 2013.","chicago":"Löfke, Christian, Marta Zwiewka, Ingo Heilmann, Marc Van Montagu, Thomas Teichmann, and Jiří Friml. “Asymmetric Gibberellin Signaling Regulates Vacuolar Trafficking of PIN Auxin Transporters during Root Gravitropism.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1300107110\">https://doi.org/10.1073/pnas.1300107110</a>.","ista":"Löfke C, Zwiewka M, Heilmann I, Van Montagu M, Teichmann T, Friml J. 2013. Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism. PNAS. 110(9), 3627–3632.","mla":"Löfke, Christian, et al. “Asymmetric Gibberellin Signaling Regulates Vacuolar Trafficking of PIN Auxin Transporters during Root Gravitropism.” <i>PNAS</i>, vol. 110, no. 9, National Academy of Sciences, 2013, pp. 3627–32, doi:<a href=\"https://doi.org/10.1073/pnas.1300107110\">10.1073/pnas.1300107110</a>.","apa":"Löfke, C., Zwiewka, M., Heilmann, I., Van Montagu, M., Teichmann, T., &#38; Friml, J. (2013). Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1300107110\">https://doi.org/10.1073/pnas.1300107110</a>"},"issue":"9","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"volume":110,"date_created":"2018-12-11T12:00:07Z","day":"26","scopus_import":1,"author":[{"first_name":"Christian","full_name":"Löfke, Christian","last_name":"Löfke"},{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"first_name":"Ingo","last_name":"Heilmann","full_name":"Heilmann, Ingo"},{"first_name":"Marc","last_name":"Van Montagu","full_name":"Van Montagu, Marc"},{"first_name":"Thomas","last_name":"Teichmann","full_name":"Teichmann, Thomas"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Submitted Version","title":"Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism","publication_status":"published","abstract":[{"text":"Gravitropic bending of plant organs is mediated by an asymmetric signaling of the plant hormone auxin between the upper and lower side of the respective organ. Here, we show that also another plant hormone, gibberellic acid (GA), shows asymmetric action during gravitropic responses. Immunodetection using an antibody against GA and monitoring GA signaling output by downstream degradation of DELLA proteins revealed an asymmetric GA distribution and response with the maximum at the lower side of gravistimulated roots. Genetic or pharmacological manipulation of GA levels or response affects gravity-mediated auxin redistribution and root bending response. The higher GA levels at the lower side of the root correlate with increased amounts of PIN-FORMED2 (PIN2) auxin transporter at the plasma membrane. The observed increase in PIN2 stability is caused by a specific GA effect on trafficking of PIN proteins to lytic vacuoles that presumably occurs downstream of brefeldin A-sensitive endosomes. Our results suggest that asymmetric auxin distribution instructive for gravity-induced differential growth is consolidated by the asymmetric action of GA that stabilizes the PIN-dependent auxin stream along the lower side of gravistimulated roots.","lang":"eng"}],"intvolume":"       110"},{"publication_status":"published","intvolume":"        25","abstract":[{"lang":"eng","text":"Plant architecture is influenced by the polar, cell-to-cell transport of auxin that is primarily provided and regulated by plasma membrane efflux catalysts of the PIN-FORMED and B family of ABC transporter (ABCB) classes. The latter were shown to require the functionality of the FK506 binding protein42 TWISTED DWARF1 (TWD1), although underlying mechanisms are unclear. By genetic manipulation of TWD1 expression, we show here that TWD1 affects shootward root auxin reflux and, thus, downstream developmental traits, such as epidermal twisting and gravitropism of the root. Using immunological assays, we demonstrate a predominant lateral, mainly outward-facing, plasma membrane location for TWD1 in the root epidermis characterized by the lateral marker ABC transporter G36/PLEIOTROPIC DRUG-RESISTANCE8/PENETRATION3. At these epidermal plasma membrane domains, TWD1 colocalizes with nonpolar ABCB1. In planta bioluminescence resonance energy transfer analysis was used to verify specific ABC transporter B1 (ABCB1)-TWD1 interaction. Our data support a model in which TWD1 promotes lateral ABCB-mediated auxin efflux via protein-protein interaction at the plasma membrane, minimizing reflux from the root apoplast into the cytoplasm."}],"date_created":"2018-12-11T12:00:08Z","volume":25,"title":"Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane","oa_version":"Submitted Version","author":[{"full_name":"Wang, Bangjun","last_name":"Wang","first_name":"Bangjun"},{"first_name":"Aurélien","full_name":"Bailly, Aurélien","last_name":"Bailly"},{"first_name":"Marta","full_name":"Zwiewk, Marta","last_name":"Zwiewk"},{"full_name":"Henrichs, Sina","last_name":"Henrichs","first_name":"Sina"},{"last_name":"Azzarello","full_name":"Azzarello, Elisa","first_name":"Elisa"},{"first_name":"Stefano","full_name":"Mancuso, Stefano","last_name":"Mancuso"},{"full_name":"Maeshima, Masayoshi","last_name":"Maeshima","first_name":"Masayoshi"},{"first_name":"Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schulz","full_name":"Schulz, Alexander","first_name":"Alexander"},{"last_name":"Geisler","full_name":"Geisler, Markus","first_name":"Markus"}],"scopus_import":1,"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"1","citation":{"ista":"Wang B, Bailly A, Zwiewk M, Henrichs S, Azzarello E, Mancuso S, Maeshima M, Friml J, Schulz A, Geisler M. 2013. Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane. Plant Cell. 25(1), 202–214.","chicago":"Wang, Bangjun, Aurélien Bailly, Marta Zwiewk, Sina Henrichs, Elisa Azzarello, Stefano Mancuso, Masayoshi Maeshima, Jiří Friml, Alexander Schulz, and Markus Geisler. “Arabidopsis TWISTED DWARF1 Functionally Interacts with Auxin Exporter ABCB1 on the Root Plasma Membrane.” <i>Plant Cell</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1105/tpc.112.105999\">https://doi.org/10.1105/tpc.112.105999</a>.","mla":"Wang, Bangjun, et al. “Arabidopsis TWISTED DWARF1 Functionally Interacts with Auxin Exporter ABCB1 on the Root Plasma Membrane.” <i>Plant Cell</i>, vol. 25, no. 1, American Society of Plant Biologists, 2013, pp. 202–14, doi:<a href=\"https://doi.org/10.1105/tpc.112.105999\">10.1105/tpc.112.105999</a>.","apa":"Wang, B., Bailly, A., Zwiewk, M., Henrichs, S., Azzarello, E., Mancuso, S., … Geisler, M. (2013). Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.112.105999\">https://doi.org/10.1105/tpc.112.105999</a>","ama":"Wang B, Bailly A, Zwiewk M, et al. Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane. <i>Plant Cell</i>. 2013;25(1):202-214. doi:<a href=\"https://doi.org/10.1105/tpc.112.105999\">10.1105/tpc.112.105999</a>","short":"B. Wang, A. Bailly, M. Zwiewk, S. Henrichs, E. Azzarello, S. Mancuso, M. Maeshima, J. Friml, A. Schulz, M. Geisler, Plant Cell 25 (2013) 202–214.","ieee":"B. Wang <i>et al.</i>, “Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane,” <i>Plant Cell</i>, vol. 25, no. 1. American Society of Plant Biologists, pp. 202–214, 2013."},"language":[{"iso":"eng"}],"oa":1,"department":[{"_id":"JiFr"}],"month":"01","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584535/"}],"page":"202 - 214","type":"journal_article","date_updated":"2021-01-12T07:00:28Z","_id":"2883","publisher":"American Society of Plant Biologists","doi":"10.1105/tpc.112.105999","acknowledgement":"We would thank Vincent Vincenzetti and Laurence Charrier for excellent technical assistance, A. von Arnim for the donation of BRET vectors, E. Spalding for TWD1-CFP, TWD1-CFP/29-1-GFP/ER-YFP, and ABCB4-GFP lines, M. Palmgren for discussion and support, and E. Martinoia for TT12 cDNA, support, and mentorship. Imaging data were partially collected at the Center for Advanced Bioimaging, University of Copenhagen, Denmark. This work was supported by grants from the Novartis Foundation (to M.G.), from the Danish Research School for Biotechnology (to M.G. and A.S.), from the Forschungskredit of the University of Zurich (to A.B.), from the Pool de Recherche of the University of Fribourg (to M.G.), and from the Swiss National Funds (to M.G.). M.G. dedicates this work to his father, who passed away during the resubmission process.","date_published":"2013-01-01T00:00:00Z","pmid":1,"status":"public","publication":"Plant Cell","publist_id":"3878","external_id":{"pmid":["23321285"]},"year":"2013"},{"project":[{"_id":"252064B8-B435-11E9-9278-68D0E5697425","grant_number":"HE_3231/6-1","name":"Analysis of the Formation and Function of Different Cell Protusion Types During Cell Migration in Vivo"},{"_id":"2527D5CC-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I 812-B12","name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation"}],"language":[{"iso":"eng"}],"publication":"Medecine Sciences","status":"public","issue":"2","citation":{"ama":"Maître J-L, Berthoumieux H, Krens G, et al. Cell adhesion mechanics of zebrafish gastrulation. <i>Medecine Sciences</i>. 2013;29(2):147-150. doi:<a href=\"https://doi.org/10.1051/medsci/2013292011\">10.1051/medsci/2013292011</a>","short":"J.-L. Maître, H. Berthoumieux, G. Krens, G. Salbreux, F. Julicher, E. Paluch, C.-P.J. Heisenberg, Medecine Sciences 29 (2013) 147–150.","ieee":"J.-L. Maître <i>et al.</i>, “Cell adhesion mechanics of zebrafish gastrulation,” <i>Medecine Sciences</i>, vol. 29, no. 2. Éditions Médicales et Scientifiques, pp. 147–150, 2013.","chicago":"Maître, Jean-Léon, Hélène Berthoumieux, Gabriel Krens, Guillaume Salbreux, Frank Julicher, Ewa Paluch, and Carl-Philipp J Heisenberg. “Cell Adhesion Mechanics of Zebrafish Gastrulation.” <i>Medecine Sciences</i>. Éditions Médicales et Scientifiques, 2013. <a href=\"https://doi.org/10.1051/medsci/2013292011\">https://doi.org/10.1051/medsci/2013292011</a>.","ista":"Maître J-L, Berthoumieux H, Krens G, Salbreux G, Julicher F, Paluch E, Heisenberg C-PJ. 2013. Cell adhesion mechanics of zebrafish gastrulation. Medecine Sciences. 29(2), 147–150.","mla":"Maître, Jean-Léon, et al. “Cell Adhesion Mechanics of Zebrafish Gastrulation.” <i>Medecine Sciences</i>, vol. 29, no. 2, Éditions Médicales et Scientifiques, 2013, pp. 147–50, doi:<a href=\"https://doi.org/10.1051/medsci/2013292011\">10.1051/medsci/2013292011</a>.","apa":"Maître, J.-L., Berthoumieux, H., Krens, G., Salbreux, G., Julicher, F., Paluch, E., &#38; Heisenberg, C.-P. J. (2013). Cell adhesion mechanics of zebrafish gastrulation. <i>Medecine Sciences</i>. Éditions Médicales et Scientifiques. <a href=\"https://doi.org/10.1051/medsci/2013292011\">https://doi.org/10.1051/medsci/2013292011</a>"},"date_published":"2013-02-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","month":"02","department":[{"_id":"CaHe"}],"publist_id":"3877","page":"147 - 150","intvolume":"        29","quality_controlled":"1","publication_status":"published","author":[{"orcid":"0000-0002-3688-1474","first_name":"Jean-Léon","last_name":"Maître","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","full_name":"Maître, Jean-Léon"},{"full_name":"Berthoumieux, Hélène","last_name":"Berthoumieux","first_name":"Hélène"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel","last_name":"Krens","orcid":"0000-0003-4761-5996","first_name":"Gabriel"},{"first_name":"Guillaume","last_name":"Salbreux","full_name":"Salbreux, Guillaume"},{"full_name":"Julicher, Frank","last_name":"Julicher","first_name":"Frank"},{"last_name":"Paluch","full_name":"Paluch, Ewa","first_name":"Ewa"},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1051/medsci/2013292011","day":"01","scopus_import":1,"title":"Cell adhesion mechanics of zebrafish gastrulation","publisher":"Éditions Médicales et Scientifiques","oa_version":"None","date_updated":"2021-01-12T07:00:28Z","volume":29,"_id":"2884","type":"journal_article","date_created":"2018-12-11T12:00:08Z"},{"quality_controlled":"1","publication_status":"published","page":"1 - 228","abstract":[{"text":"This volume contains the post-proceedings of the 8th Doctoral Workshop on Mathematical and Engineering Methods in Computer Science, MEMICS 2012, held in Znojmo, Czech Republic, in October, 2012. The 13 thoroughly revised papers were carefully selected out of 31 submissions and are presented together with 6 invited papers. The topics covered by the papers include: computer-aided analysis and verification, applications of game theory in computer science, networks and security, modern trends of graph theory in computer science, electronic systems design and testing, and quantum information processing.","lang":"eng"}],"intvolume":"      7721","date_updated":"2019-08-02T12:37:55Z","volume":7721,"_id":"2885","type":"conference_editor","series_title":"Lecture Notes in Computer Science","date_created":"2018-12-11T12:00:08Z","doi":"10.1007/978-3-642-36046-6","day":"09","alternative_title":["LNCS"],"editor":[{"last_name":"Kucera","full_name":"Kucera, Antonin","first_name":"Antonin"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A"},{"first_name":"Jaroslav","last_name":"Nesetril","full_name":"Nesetril, Jaroslav"},{"first_name":"Tomas","last_name":"Vojnar","full_name":"Vojnar, Tomas"},{"full_name":"Antos, David","last_name":"Antos","first_name":"David"}],"title":"Mathematical and Engineering Methods in Computer Science","oa_version":"None","publisher":"Springer","citation":{"ieee":"A. Kucera, T. A. Henzinger, J. Nesetril, T. Vojnar, and D. Antos, Eds., <i>Mathematical and Engineering Methods in Computer Science</i>, vol. 7721. Springer, 2013, pp. 1–228.","short":"A. Kucera, T.A. Henzinger, J. Nesetril, T. Vojnar, D. Antos, eds., Mathematical and Engineering Methods in Computer Science, Springer, 2013.","ama":"Kucera A, Henzinger TA, Nesetril J, Vojnar T, Antos D, eds. <i>Mathematical and Engineering Methods in Computer Science</i>. Vol 7721. Springer; 2013:1-228. doi:<a href=\"https://doi.org/10.1007/978-3-642-36046-6\">10.1007/978-3-642-36046-6</a>","apa":"Kucera, A., Henzinger, T. A., Nesetril, J., Vojnar, T., &#38; Antos, D. (Eds.). (2013). <i>Mathematical and Engineering Methods in Computer Science</i> (Vol. 7721, pp. 1–228). Presented at the MEMICS: Mathematical and Engineering methods in computer science, Znojmo, Czech Republic: Springer. <a href=\"https://doi.org/10.1007/978-3-642-36046-6\">https://doi.org/10.1007/978-3-642-36046-6</a>","mla":"Kucera, Antonin, et al., editors. <i>Mathematical and Engineering Methods in Computer Science</i>. Vol. 7721, Springer, 2013, pp. 1–228, doi:<a href=\"https://doi.org/10.1007/978-3-642-36046-6\">10.1007/978-3-642-36046-6</a>.","ista":"Kucera A, Henzinger TA, Nesetril J, Vojnar T, Antos D eds. 2013. Mathematical and Engineering Methods in Computer Science, Springer,p.","chicago":"Kucera, Antonin, Thomas A Henzinger, Jaroslav Nesetril, Tomas Vojnar, and David Antos, eds. <i>Mathematical and Engineering Methods in Computer Science</i>. Vol. 7721. Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-36046-6\">https://doi.org/10.1007/978-3-642-36046-6</a>."},"date_published":"2013-01-09T00:00:00Z","conference":{"name":"MEMICS: Mathematical and Engineering methods in computer science","end_date":"2012-10-28","start_date":"2012-10-25","location":"Znojmo, Czech Republic"},"acknowledgement":"Red Hat Czech Republic, Y Soft","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"publist_id":"3874","year":"2013","month":"01"},{"publisher":"Springer","alternative_title":["LNCS"],"doi":"10.1007/978-3-642-36046-6_12","series_title":"Lecture Notes in Computer Science","type":"conference","_id":"2886","date_updated":"2020-08-11T10:09:52Z","page":"118 - 130","quality_controlled":"1","main_file_link":[{"url":"http://arxiv.org/abs/1209.4499","open_access":"1"}],"year":"2013","publist_id":"3873","status":"public","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"conference":{"location":"Znojmo, Czech Republic","end_date":"2012-10-28","start_date":"2012-10-25","name":"MEMICS: Mathematical and Engineering Methods in Computer Science"},"date_published":"2013-01-09T00:00:00Z","ec_funded":1,"title":"Controllable-choice message sequence graphs","oa_version":"Submitted Version","day":"09","scopus_import":1,"author":[{"first_name":"Martin","full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik"},{"first_name":"Vojtěch","full_name":"Řehák, Vojtěch","last_name":"Řehák"}],"date_created":"2018-12-11T12:00:09Z","volume":7721,"abstract":[{"lang":"eng","text":"We focus on the realizability problem of Message Sequence Graphs (MSG), i.e. the problem whether a given MSG specification is correctly distributable among parallel components communicating via messages. This fundamental problem of MSG is known to be undecidable. We introduce a well motivated restricted class of MSG, so called controllable-choice MSG, and show that all its models are realizable and moreover it is decidable whether a given MSG model is a member of this class. In more detail, this class of MSG specifications admits a deadlock-free realization by overloading existing messages with additional bounded control data. We also show that the presented class is the largest known subclass of MSG that allows for deadlock-free realization."}],"intvolume":"      7721","publication_status":"published","month":"01","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Chmelik M, Řehák V. Controllable-choice message sequence graphs. 2013;7721:118-130. doi:<a href=\"https://doi.org/10.1007/978-3-642-36046-6_12\">10.1007/978-3-642-36046-6_12</a>","ieee":"M. Chmelik and V. Řehák, “Controllable-choice message sequence graphs,” vol. 7721. Springer, pp. 118–130, 2013.","short":"M. Chmelik, V. Řehák, 7721 (2013) 118–130.","chicago":"Chmelik, Martin, and Vojtěch Řehák. “Controllable-Choice Message Sequence Graphs.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-36046-6_12\">https://doi.org/10.1007/978-3-642-36046-6_12</a>.","ista":"Chmelik M, Řehák V. 2013. Controllable-choice message sequence graphs. 7721, 118–130.","apa":"Chmelik, M., &#38; Řehák, V. (2013). Controllable-choice message sequence graphs. Presented at the MEMICS: Mathematical and Engineering Methods in Computer Science, Znojmo, Czech Republic: Springer. <a href=\"https://doi.org/10.1007/978-3-642-36046-6_12\">https://doi.org/10.1007/978-3-642-36046-6_12</a>","mla":"Chmelik, Martin, and Vojtěch Řehák. <i>Controllable-Choice Message Sequence Graphs</i>. Vol. 7721, Springer, 2013, pp. 118–30, doi:<a href=\"https://doi.org/10.1007/978-3-642-36046-6_12\">10.1007/978-3-642-36046-6_12</a>."}},{"page":"2670 - 2675","quality_controlled":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574932/","open_access":"1"}],"publisher":"National Academy of Sciences","article_processing_charge":"No","doi":"10.1073/pnas.1222821110","type":"journal_article","_id":"2887","date_updated":"2021-01-12T07:00:29Z","publication":"PNAS","status":"public","date_published":"2013-02-12T00:00:00Z","pmid":1,"external_id":{"pmid":["23362379"]},"year":"2013","publist_id":"3872","intvolume":"       110","abstract":[{"lang":"eng","text":"Root system growth and development is highly plastic and is influenced by the surrounding environment. Roots frequently grow in heterogeneous environments that include interactions from neighboring plants and physical impediments in the rhizosphere. To investigate how planting density and physical objects affect root system growth, we grew rice in a transparent gel system in close proximity with another plant or a physical object. Root systems were imaged and reconstructed in three dimensions. Root-root interaction strength was calculated using quantitative metrics that characterize the extent towhich the reconstructed root systems overlap each other. Surprisingly, we found the overlap of root systems of the same genotype was significantly higher than that of root systems of different genotypes. Root systems of the same genotype tended to grow toward each other but those of different genotypes appeared to avoid each other. Shoot separation experiments excluded the possibility of aerial interactions, suggesting root communication. Staggered plantings indicated that interactions likely occur at root tips in close proximity. Recognition of obstacles also occurred through root tips, but through physical contact in a size-dependent manner. These results indicate that root systems use two different forms of communication to recognize objects and alter root architecture: root-root recognition, possibly mediated through root exudates, and root-object recognition mediated by physical contact at the root tips. This finding suggests that root tips act as local sensors that integrate rhizosphere information into global root architectural changes."}],"publication_status":"published","title":"Genotypic recognition and spatial responses by rice roots","oa_version":"Published Version","scopus_import":1,"day":"12","author":[{"first_name":"Suqin","full_name":"Fang, Suqin","last_name":"Fang"},{"first_name":"Randy","last_name":"Clark","full_name":"Clark, Randy"},{"first_name":"Ying","last_name":"Zheng","full_name":"Zheng, Ying"},{"last_name":"Iyer Pascuzzi","full_name":"Iyer Pascuzzi, Anjali","first_name":"Anjali"},{"full_name":"Weitz, Joshua","last_name":"Weitz","first_name":"Joshua"},{"first_name":"Leon","full_name":"Kochian, Leon","last_name":"Kochian"},{"orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"first_name":"Hong","last_name":"Liao","full_name":"Liao, Hong"},{"full_name":"Benfey, Philip","last_name":"Benfey","first_name":"Philip"}],"date_created":"2018-12-11T12:00:09Z","article_type":"original","volume":110,"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Fang, Suqin, et al. “Genotypic Recognition and Spatial Responses by Rice Roots.” <i>PNAS</i>, vol. 110, no. 7, National Academy of Sciences, 2013, pp. 2670–75, doi:<a href=\"https://doi.org/10.1073/pnas.1222821110\">10.1073/pnas.1222821110</a>.","apa":"Fang, S., Clark, R., Zheng, Y., Iyer Pascuzzi, A., Weitz, J., Kochian, L., … Benfey, P. (2013). Genotypic recognition and spatial responses by rice roots. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1222821110\">https://doi.org/10.1073/pnas.1222821110</a>","chicago":"Fang, Suqin, Randy Clark, Ying Zheng, Anjali Iyer Pascuzzi, Joshua Weitz, Leon Kochian, Herbert Edelsbrunner, Hong Liao, and Philip Benfey. “Genotypic Recognition and Spatial Responses by Rice Roots.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1222821110\">https://doi.org/10.1073/pnas.1222821110</a>.","ista":"Fang S, Clark R, Zheng Y, Iyer Pascuzzi A, Weitz J, Kochian L, Edelsbrunner H, Liao H, Benfey P. 2013. Genotypic recognition and spatial responses by rice roots. PNAS. 110(7), 2670–2675.","short":"S. Fang, R. Clark, Y. Zheng, A. Iyer Pascuzzi, J. Weitz, L. Kochian, H. Edelsbrunner, H. Liao, P. Benfey, PNAS 110 (2013) 2670–2675.","ieee":"S. Fang <i>et al.</i>, “Genotypic recognition and spatial responses by rice roots,” <i>PNAS</i>, vol. 110, no. 7. National Academy of Sciences, pp. 2670–2675, 2013.","ama":"Fang S, Clark R, Zheng Y, et al. Genotypic recognition and spatial responses by rice roots. <i>PNAS</i>. 2013;110(7):2670-2675. doi:<a href=\"https://doi.org/10.1073/pnas.1222821110\">10.1073/pnas.1222821110</a>"},"issue":"7","month":"02","department":[{"_id":"HeEd"}]},{"status":"public","language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"name":" AISTATS: Conference on Uncertainty in Artificial Intelligence","end_date":"2013-05-01","start_date":"2013-04-29","location":"Scottsdale, AZ, United States"},"date_published":"2013-01-01T00:00:00Z","citation":{"ama":"Chen C, Kolmogorov V, Yan Z, Metaxas D, Lampert C. Computing the M most probable modes of a graphical model. In: Vol 31. JMLR; 2013:161-169.","short":"C. Chen, V. Kolmogorov, Z. Yan, D. Metaxas, C. Lampert, in:, JMLR, 2013, pp. 161–169.","ieee":"C. Chen, V. Kolmogorov, Z. Yan, D. Metaxas, and C. Lampert, “Computing the M most probable modes of a graphical model,” presented at the  AISTATS: Conference on Uncertainty in Artificial Intelligence, Scottsdale, AZ, United States, 2013, vol. 31, pp. 161–169.","chicago":"Chen, Chao, Vladimir Kolmogorov, Zhu Yan, Dimitris Metaxas, and Christoph Lampert. “Computing the M Most Probable Modes of a Graphical Model,” 31:161–69. JMLR, 2013.","ista":"Chen C, Kolmogorov V, Yan Z, Metaxas D, Lampert C. 2013. Computing the M most probable modes of a graphical model.  AISTATS: Conference on Uncertainty in Artificial Intelligence,  JMLR: W&#38;CP, vol. 31, 161–169.","mla":"Chen, Chao, et al. <i>Computing the M Most Probable Modes of a Graphical Model</i>. Vol. 31, JMLR, 2013, pp. 161–69.","apa":"Chen, C., Kolmogorov, V., Yan, Z., Metaxas, D., &#38; Lampert, C. (2013). Computing the M most probable modes of a graphical model (Vol. 31, pp. 161–169). Presented at the  AISTATS: Conference on Uncertainty in Artificial Intelligence, Scottsdale, AZ, United States: JMLR."},"month":"01","year":"2013","publist_id":"3846","department":[{"_id":"HeEd"},{"_id":"VlKo"},{"_id":"ChLa"}],"intvolume":"        31","abstract":[{"lang":"eng","text":" We introduce the M-modes problem for graphical models: predicting the M label configurations of highest probability that are at the same time local maxima of the probability landscape. M-modes have multiple possible applications: because they are intrinsically diverse, they provide a principled alternative to non-maximum suppression techniques for structured prediction, they can act as codebook vectors for quantizing the configuration space, or they can form component centers for mixture model approximation. We present two algorithms for solving the M-modes problem. The first algorithm solves the problem in polynomial time when the underlying graphical model is a simple chain. The second algorithm solves the problem for junction chains. In synthetic and real dataset, we demonstrate how M-modes can improve the performance of prediction. We also use the generated modes as a tool to understand the topography of the probability distribution of configurations, for example with relation to the training set size and amount of noise in the data. "}],"page":"161 - 169","publication_status":"published","quality_controlled":"1","main_file_link":[{"url":"http://jmlr.org/proceedings/papers/v31/chen13a.html","open_access":"1"}],"title":"Computing the M most probable modes of a graphical model","oa_version":"None","publisher":"JMLR","day":"01","alternative_title":[" JMLR: W&CP"],"scopus_import":1,"author":[{"last_name":"Chen","full_name":"Chen, Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","first_name":"Chao"},{"first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"},{"last_name":"Yan","full_name":"Yan, Zhu","first_name":"Zhu"},{"last_name":"Metaxas","full_name":"Metaxas, Dimitris","first_name":"Dimitris"},{"last_name":"Lampert","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","orcid":"0000-0001-8622-7887"}],"date_created":"2018-12-11T12:00:14Z","type":"conference","_id":"2901","volume":31,"date_updated":"2021-01-12T07:00:35Z"},{"month":"01","department":[{"_id":"HeEd"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:45:52Z","file_size":403013,"date_created":"2018-12-12T10:08:57Z","file_id":"4720","content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-547-v1+1_2013-P-08-MedusaII.pdf","checksum":"a15a3ba22df9445731507f3e06c9fcee","relation":"main_file"}],"oa":1,"language":[{"iso":"eng"}],"pubrep_id":"547","citation":{"ista":"Kerber M, Edelsbrunner H. 2013. 3D kinetic alpha complexes and their implementation. 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments. ALENEX: Algorithm Engineering and Experiments, ALENEX, , 70–77.","chicago":"Kerber, Michael, and Herbert Edelsbrunner. “3D Kinetic Alpha Complexes and Their Implementation.” In <i>2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments</i>, 70–77. Society of Industrial and Applied Mathematics, 2013. <a href=\"https://doi.org/10.1137/1.9781611972931.6\">https://doi.org/10.1137/1.9781611972931.6</a>.","mla":"Kerber, Michael, and Herbert Edelsbrunner. “3D Kinetic Alpha Complexes and Their Implementation.” <i>2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments</i>, Society of Industrial and Applied Mathematics, 2013, pp. 70–77, doi:<a href=\"https://doi.org/10.1137/1.9781611972931.6\">10.1137/1.9781611972931.6</a>.","apa":"Kerber, M., &#38; Edelsbrunner, H. (2013). 3D kinetic alpha complexes and their implementation. In <i>2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments</i> (pp. 70–77). New Orleans, LA, United States: Society of Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611972931.6\">https://doi.org/10.1137/1.9781611972931.6</a>","ama":"Kerber M, Edelsbrunner H. 3D kinetic alpha complexes and their implementation. In: <i>2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments</i>. Society of Industrial and Applied Mathematics; 2013:70-77. doi:<a href=\"https://doi.org/10.1137/1.9781611972931.6\">10.1137/1.9781611972931.6</a>","short":"M. Kerber, H. Edelsbrunner, in:, 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments, Society of Industrial and Applied Mathematics, 2013, pp. 70–77.","ieee":"M. Kerber and H. Edelsbrunner, “3D kinetic alpha complexes and their implementation,” in <i>2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments</i>, New Orleans, LA, United States, 2013, pp. 70–77."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Kerber, Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","last_name":"Kerber","orcid":"0000-0002-8030-9299","first_name":"Michael"},{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","first_name":"Herbert"}],"day":"01","scopus_import":1,"oa_version":"Submitted Version","title":"3D kinetic alpha complexes and their implementation","date_created":"2018-12-11T12:00:16Z","has_accepted_license":"1","abstract":[{"text":"Motivated by an application in cell biology, we describe an extension of the kinetic data structures framework from Delaunay triangulations to fixed-radius alpha complexes. Our algorithm is implemented\r\nusing CGAL, following the exact geometric computation paradigm. We report on several\r\ntechniques to accelerate the computation that turn our implementation applicable to the underlying biological\r\nproblem.","lang":"eng"}],"publication_status":"published","file_date_updated":"2020-07-14T12:45:52Z","year":"2013","publist_id":"3841","status":"public","publication":"2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments","date_published":"2013-01-01T00:00:00Z","conference":{"location":"New Orleans, LA, United States","name":"ALENEX: Algorithm Engineering and Experiments","end_date":"2013-01-07","start_date":"2013-01-07"},"doi":"10.1137/1.9781611972931.6","alternative_title":["ALENEX"],"publisher":"Society of Industrial and Applied Mathematics","date_updated":"2021-01-12T07:00:36Z","_id":"2906","type":"conference","page":"70 - 77","ddc":["500"],"quality_controlled":"1"},{"abstract":[{"text":"Sex and recombination are among the most striking features of the living world, and they play a crucial role in allowing the evolution of complex adaptation. The sharing of genomes through the sexual union of different individuals requires elaborate behavioral and physiological adaptations. At the molecular level, the alignment of two DNA double helices, followed by their precise cutting and rejoining, is an extraordinary feat. Sex and recombination have diverse—and often surprising—evolutionary consequences: distinct sexes, elaborate mating displays, selfish genetic elements, and so on.","lang":"eng"}],"ddc":["576"],"page":"328 - 333","has_accepted_license":"1","publication_status":"published","publication_identifier":{"isbn":["9780691149776"]},"quality_controlled":"1","file_date_updated":"2020-07-14T12:45:52Z","publisher":"Princeton University Press","oa_version":"Submitted Version","title":"Recombination and sex","author":[{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"}],"day":"04","type":"book_chapter","date_created":"2018-12-11T12:00:16Z","date_updated":"2021-01-12T07:00:37Z","_id":"2907","pubrep_id":"119","publication":"The Princeton Guide to Evolution","status":"public","language":[{"iso":"eng"}],"oa":1,"date_published":"2013-11-04T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Barton, Nicholas H. “Recombination and Sex.” In <i>The Princeton Guide to Evolution</i>, 328–33. Princeton University Press, 2013.","ista":"Barton NH. 2013.Recombination and sex. In: The Princeton Guide to Evolution. , 328–333.","mla":"Barton, Nicholas H. “Recombination and Sex.” <i>The Princeton Guide to Evolution</i>, Princeton University Press, 2013, pp. 328–33.","apa":"Barton, N. H. (2013). Recombination and sex. In <i>The Princeton Guide to Evolution</i> (pp. 328–333). Princeton University Press.","ama":"Barton NH. Recombination and sex. In: <i>The Princeton Guide to Evolution</i>. Princeton University Press; 2013:328-333.","short":"N.H. Barton, in:, The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–333.","ieee":"N. H. Barton, “Recombination and sex,” in <i>The Princeton Guide to Evolution</i>, Princeton University Press, 2013, pp. 328–333."},"month":"11","year":"2013","publist_id":"3839","file":[{"file_id":"5237","creator":"system","date_updated":"2020-07-14T12:45:52Z","file_size":79838,"date_created":"2018-12-12T10:16:47Z","checksum":"8332ca9cb40f7e66d1006b175ce36b60","relation":"main_file","access_level":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"IST-2013-119-v1+1_IV.4_Recombination_and_Sex_Barton_1-13-13-e.docx"},{"file_size":144131,"date_created":"2018-12-12T10:16:48Z","creator":"system","date_updated":"2020-07-14T12:45:52Z","file_id":"5238","file_name":"IST-2017-119-v1+2_Barton_Recombination_Sex.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"849f418620fb78d6ba23bb4f488ee93f"}],"department":[{"_id":"NiBa"}]},{"has_accepted_license":"1","abstract":[{"lang":"eng","text":"Hybridization is an almost inevitable component of speciation, and its study can tell us much about that process. However, hybridization itself may have a negligible influence on the origin of species: on the one hand, universally favoured alleles spread readily across hybrid zones, whilst on the other, spatially heterogeneous selection causes divergence despite gene flow. Thus, narrow hybrid zones or occasional hybridisation may hardly affect the process of divergence."}],"intvolume":"        26","file_date_updated":"2020-07-14T12:45:52Z","publication_status":"published","day":"17","scopus_import":1,"author":[{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton"}],"title":"Does hybridisation influence speciation?  ","oa_version":"Submitted Version","volume":26,"date_created":"2018-12-11T12:00:17Z","oa":1,"language":[{"iso":"eng"}],"pubrep_id":"111","citation":{"ieee":"N. H. Barton, “Does hybridisation influence speciation?  ,” <i>Journal of Evolutionary Biology</i>, vol. 26, no. 2. Wiley-Blackwell, pp. 267–269, 2013.","short":"N.H. Barton, Journal of Evolutionary Biology 26 (2013) 267–269.","ama":"Barton NH. Does hybridisation influence speciation?  . <i>Journal of Evolutionary Biology</i>. 2013;26(2):267-269. doi:<a href=\"https://doi.org/10.1111/jeb.12015\">10.1111/jeb.12015</a>","apa":"Barton, N. H. (2013). Does hybridisation influence speciation?  . <i>Journal of Evolutionary Biology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/jeb.12015\">https://doi.org/10.1111/jeb.12015</a>","mla":"Barton, Nicholas H. “Does Hybridisation Influence Speciation?  .” <i>Journal of Evolutionary Biology</i>, vol. 26, no. 2, Wiley-Blackwell, 2013, pp. 267–69, doi:<a href=\"https://doi.org/10.1111/jeb.12015\">10.1111/jeb.12015</a>.","chicago":"Barton, Nicholas H. “Does Hybridisation Influence Speciation?  .” <i>Journal of Evolutionary Biology</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/jeb.12015\">https://doi.org/10.1111/jeb.12015</a>.","ista":"Barton NH. 2013. Does hybridisation influence speciation?  . Journal of Evolutionary Biology. 26(2), 267–269."},"issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","department":[{"_id":"NiBa"}],"file":[{"content_type":"text/rtf","access_level":"open_access","file_name":"IST-2013-111-v1+1_Hybridisation_and_speciation_revised.rtf","checksum":"716e88714c3411cd0bd70928b14ea692","relation":"main_file","date_updated":"2020-07-14T12:45:52Z","creator":"system","date_created":"2018-12-12T10:09:38Z","file_size":13339,"file_id":"4762"},{"relation":"main_file","checksum":"957fd07c71c1b1eac2c65ae3311aca78","file_name":"IST-2017-111-v1+2_Hybridisation_and_speciation_revised.pdf","content_type":"application/pdf","access_level":"open_access","file_id":"4763","file_size":103437,"date_created":"2018-12-12T10:09:39Z","creator":"system","date_updated":"2020-07-14T12:45:52Z"}],"page":"267 - 269","ddc":["576"],"quality_controlled":"1","doi":"10.1111/jeb.12015","publisher":"Wiley-Blackwell","_id":"2908","date_updated":"2021-01-12T07:00:37Z","type":"journal_article","status":"public","publication":"Journal of Evolutionary Biology","date_published":"2013-01-17T00:00:00Z","year":"2013","publist_id":"3835"},{"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"status":"public","publication":"Journal of Statistical Mechanics Theory and Experiment","ec_funded":1,"date_published":"2013-01-16T00:00:00Z","year":"2013","publist_id":"3834","ddc":["570"],"quality_controlled":"1","doi":"10.1088/1742-5468/2013/01/P01002","article_processing_charge":"No","publisher":"IOP Publishing Ltd.","date_updated":"2021-01-12T07:00:37Z","_id":"2909","type":"journal_article","oa":1,"pubrep_id":"557","language":[{"iso":"eng"}],"issue":"1","citation":{"ista":"Barton NH, Etheridge A, Véber A. 2013. Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. 2013(1).","chicago":"Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “Modelling Evolution in a Spatial Continuum.” <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing Ltd., 2013. <a href=\"https://doi.org/10.1088/1742-5468/2013/01/P01002\">https://doi.org/10.1088/1742-5468/2013/01/P01002</a>.","mla":"Barton, Nicholas H., et al. “Modelling Evolution in a Spatial Continuum.” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2013, no. 1, IOP Publishing Ltd., 2013, doi:<a href=\"https://doi.org/10.1088/1742-5468/2013/01/P01002\">10.1088/1742-5468/2013/01/P01002</a>.","apa":"Barton, N. H., Etheridge, A., &#38; Véber, A. (2013). Modelling evolution in a spatial continuum. <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1742-5468/2013/01/P01002\">https://doi.org/10.1088/1742-5468/2013/01/P01002</a>","ama":"Barton NH, Etheridge A, Véber A. Modelling evolution in a spatial continuum. <i>Journal of Statistical Mechanics Theory and Experiment</i>. 2013;2013(1). doi:<a href=\"https://doi.org/10.1088/1742-5468/2013/01/P01002\">10.1088/1742-5468/2013/01/P01002</a>","short":"N.H. Barton, A. Etheridge, A. Véber, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).","ieee":"N. H. Barton, A. Etheridge, and A. Véber, “Modelling evolution in a spatial continuum,” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2013, no. 1. IOP Publishing Ltd., 2013."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"01","department":[{"_id":"NiBa"}],"file":[{"file_name":"IST-2016-557-v1+1_BEVrevised.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"ce8a4424385b3086138a1e054e16e0e3","file_size":702583,"date_created":"2018-12-12T10:16:52Z","date_updated":"2020-07-14T12:45:52Z","creator":"system","file_id":"5242"}],"has_accepted_license":"1","intvolume":"      2013","abstract":[{"lang":"eng","text":"We survey a class of models for spatially structured populations\r\nwhich we have called spatial Λ-Fleming–Viot processes. They arise from a flexible\r\nframework for modelling in which the key innovation is that random genetic drift\r\nis driven by a Poisson point process of spatial ‘events’. We demonstrate how this\r\novercomes some of the obstructions to modelling populations which evolve in two-\r\n(and higher-) dimensional spatial continua, how its predictions match phenomena\r\nobserved in data and how it fits with classical models. Finally we outline some\r\ndirections for future research."}],"publication_status":"published","file_date_updated":"2020-07-14T12:45:52Z","author":[{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"last_name":"Etheridge","full_name":"Etheridge, Alison","first_name":"Alison"},{"first_name":"Amandine","last_name":"Véber","full_name":"Véber, Amandine"}],"scopus_import":1,"day":"16","title":"Modelling evolution in a spatial continuum","oa_version":"Submitted Version","volume":2013,"date_created":"2018-12-11T12:00:17Z"},{"publication_status":"published","file_date_updated":"2020-07-14T12:45:52Z","has_accepted_license":"1","intvolume":"        29","abstract":[{"text":"Coalescent simulation has become an indispensable tool in population genetics and many complex evolutionary scenarios have been incorporated into the basic algorithm. Despite many years of intense interest in spatial structure, however, there are no available methods to simulate the ancestry of a sample of genes that occupy a spatial continuum. This is mainly due to the severe technical problems encountered by the classical model of isolation\r\nby distance. A recently introduced model solves these technical problems and provides a solid theoretical basis for the study of populations evolving in continuous space. We present a detailed algorithm to simulate the coalescent process in this model, and provide an efficient implementation of a generalised version of this algorithm as a freely available Python module.","lang":"eng"}],"volume":29,"date_created":"2018-12-11T12:00:17Z","author":[{"first_name":"Jerome","full_name":"Kelleher, Jerome","last_name":"Kelleher"},{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"}],"day":"07","scopus_import":1,"title":"Coalescent simulation in continuous space","oa_version":"Published Version","issue":"7","citation":{"chicago":"Kelleher, Jerome, Nicholas H Barton, and Alison Etheridge. “Coalescent Simulation in Continuous Space.” <i>Bioinformatics</i>. Oxford University Press, 2013. <a href=\"https://doi.org/10.1093/bioinformatics/btt067\">https://doi.org/10.1093/bioinformatics/btt067</a>.","ista":"Kelleher J, Barton NH, Etheridge A. 2013. Coalescent simulation in continuous space. Bioinformatics. 29(7), 955–956.","mla":"Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space.” <i>Bioinformatics</i>, vol. 29, no. 7, Oxford University Press, 2013, pp. 955–56, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btt067\">10.1093/bioinformatics/btt067</a>.","apa":"Kelleher, J., Barton, N. H., &#38; Etheridge, A. (2013). Coalescent simulation in continuous space. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/btt067\">https://doi.org/10.1093/bioinformatics/btt067</a>","ama":"Kelleher J, Barton NH, Etheridge A. Coalescent simulation in continuous space. <i>Bioinformatics</i>. 2013;29(7):955-956. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btt067\">10.1093/bioinformatics/btt067</a>","short":"J. Kelleher, N.H. Barton, A. Etheridge, Bioinformatics 29 (2013) 955–956.","ieee":"J. Kelleher, N. H. Barton, and A. Etheridge, “Coalescent simulation in continuous space,” <i>Bioinformatics</i>, vol. 29, no. 7. Oxford University Press, pp. 955–956, 2013."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"pubrep_id":"556","department":[{"_id":"NiBa"}],"file":[{"access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-556-v1+1_bioinformatics-2013.pdf","checksum":"a3b54d7477fac923815ac082403d9bd0","relation":"main_file","creator":"system","date_updated":"2020-07-14T12:45:52Z","file_size":170197,"date_created":"2018-12-12T10:16:04Z","file_id":"5189"}],"month":"02","quality_controlled":"1","page":"955 - 956","ddc":["570"],"date_updated":"2021-01-12T07:00:38Z","_id":"2910","type":"journal_article","doi":"10.1093/bioinformatics/btt067","publisher":"Oxford University Press","ec_funded":1,"date_published":"2013-02-07T00:00:00Z","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"status":"public","publication":"Bioinformatics","publist_id":"3833","year":"2013"},{"year":"2013","month":"01","department":[{"_id":"GaTk"}],"publist_id":"3830","article_number":"058104","oa":1,"publication":"Physical Review Letters","language":[{"iso":"eng"}],"status":"public","issue":"5","citation":{"ista":"Tkačik G, Granot Atedgi E, Segev R, Schneidman E. 2013. Retinal metric: a stimulus distance measure derived from population neural responses. Physical Review Letters. 110(5), 058104.","chicago":"Tkačik, Gašper, Einat Granot Atedgi, Ronen Segev, and Elad Schneidman. “Retinal Metric: A Stimulus Distance Measure Derived from Population Neural Responses.” <i>Physical Review Letters</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevLett.110.058104\">https://doi.org/10.1103/PhysRevLett.110.058104</a>.","apa":"Tkačik, G., Granot Atedgi, E., Segev, R., &#38; Schneidman, E. (2013). Retinal metric: a stimulus distance measure derived from population neural responses. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.110.058104\">https://doi.org/10.1103/PhysRevLett.110.058104</a>","mla":"Tkačik, Gašper, et al. “Retinal Metric: A Stimulus Distance Measure Derived from Population Neural Responses.” <i>Physical Review Letters</i>, vol. 110, no. 5, 058104, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.058104\">10.1103/PhysRevLett.110.058104</a>.","ama":"Tkačik G, Granot Atedgi E, Segev R, Schneidman E. Retinal metric: a stimulus distance measure derived from population neural responses. <i>Physical Review Letters</i>. 2013;110(5). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.058104\">10.1103/PhysRevLett.110.058104</a>","ieee":"G. Tkačik, E. Granot Atedgi, R. Segev, and E. Schneidman, “Retinal metric: a stimulus distance measure derived from population neural responses,” <i>Physical Review Letters</i>, vol. 110, no. 5. American Physical Society, 2013.","short":"G. Tkačik, E. Granot Atedgi, R. Segev, E. Schneidman, Physical Review Letters 110 (2013)."},"date_published":"2013-01-28T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1103/PhysRevLett.110.058104","author":[{"orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"},{"first_name":"Einat","full_name":"Granot Atedgi, Einat","last_name":"Granot Atedgi"},{"first_name":"Ronen","last_name":"Segev","full_name":"Segev, Ronen"},{"full_name":"Schneidman, Elad","last_name":"Schneidman","first_name":"Elad"}],"day":"28","scopus_import":1,"oa_version":"Preprint","title":"Retinal metric: a stimulus distance measure derived from population neural responses","publisher":"American Physical Society","date_updated":"2021-01-12T07:00:39Z","volume":110,"_id":"2913","type":"journal_article","date_created":"2018-12-11T12:00:18Z","abstract":[{"text":"The ability of an organism to distinguish between various stimuli is limited by the structure and noise in the population code of its sensory neurons. Here we infer a distance measure on the stimulus space directly from the recorded activity of 100 neurons in the salamander retina. In contrast to previously used measures of stimulus similarity, this &quot;neural metric&quot; tells us how distinguishable a pair of stimulus clips is to the retina, based on the similarity between the induced distributions of population responses. We show that the retinal distance strongly deviates from Euclidean, or any static metric, yet has a simple structure: we identify the stimulus features that the neural population is jointly sensitive to, and show the support-vector-machine- like kernel function relating the stimulus and neural response spaces. We show that the non-Euclidean nature of the retinal distance has important consequences for neural decoding.","lang":"eng"}],"intvolume":"       110","main_file_link":[{"url":"http://arxiv.org/abs/1205.6598","open_access":"1"}],"publication_status":"published","quality_controlled":"1"},{"external_id":{"arxiv":["0806.2694"]},"year":"2013","publist_id":"3829","status":"public","publication":"Physical Review Letters","acknowledgement":"This work was supported in part by NSF Grants No. IIS-0613435, No. IBN-0344678, and No. PHY-0957573, by NIH Grant No. T32 MH065214, by the Human Frontier Science Program, and by the Swartz Foundation.\r\nCC BY 3.0\r\n","date_published":"2013-01-02T00:00:00Z","publisher":"American Physical Society","doi":"10.1103/PhysRevLett.110.018701","article_processing_charge":"No","type":"journal_article","date_updated":"2023-09-04T11:47:51Z","_id":"2914","ddc":["530"],"quality_controlled":"1","month":"01","arxiv":1,"file":[{"file_id":"5366","creator":"system","date_updated":"2020-07-14T12:45:53Z","date_created":"2018-12-12T10:18:44Z","file_size":416965,"checksum":"72bfbc2094c4680e8a8a6bed668cd06d","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-401-v1+1_1281.full.pdf"}],"article_number":"018701","department":[{"_id":"GaTk"}],"pubrep_id":"401","language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"1","citation":{"mla":"Stephens, Greg, et al. “Statistical Thermodynamics of Natural Images.” <i>Physical Review Letters</i>, vol. 110, no. 1, 018701, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.018701\">10.1103/PhysRevLett.110.018701</a>.","apa":"Stephens, G., Mora, T., Tkačik, G., &#38; Bialek, W. (2013). Statistical thermodynamics of natural images. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.110.018701\">https://doi.org/10.1103/PhysRevLett.110.018701</a>","chicago":"Stephens, Greg, Thierry Mora, Gašper Tkačik, and William Bialek. “Statistical Thermodynamics of Natural Images.” <i>Physical Review Letters</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevLett.110.018701\">https://doi.org/10.1103/PhysRevLett.110.018701</a>.","ista":"Stephens G, Mora T, Tkačik G, Bialek W. 2013. Statistical thermodynamics of natural images. Physical Review Letters. 110(1), 018701.","short":"G. Stephens, T. Mora, G. Tkačik, W. Bialek, Physical Review Letters 110 (2013).","ieee":"G. Stephens, T. Mora, G. Tkačik, and W. Bialek, “Statistical thermodynamics of natural images,” <i>Physical Review Letters</i>, vol. 110, no. 1. American Physical Society, 2013.","ama":"Stephens G, Mora T, Tkačik G, Bialek W. Statistical thermodynamics of natural images. <i>Physical Review Letters</i>. 2013;110(1). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.018701\">10.1103/PhysRevLett.110.018701</a>"},"oa_version":"Published Version","title":"Statistical thermodynamics of natural images","author":[{"first_name":"Greg","full_name":"Stephens, Greg","last_name":"Stephens"},{"full_name":"Mora, Thierry","last_name":"Mora","first_name":"Thierry"},{"last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","first_name":"Gasper"},{"first_name":"William","full_name":"Bialek, William","last_name":"Bialek"}],"day":"02","article_type":"original","date_created":"2018-12-11T12:00:19Z","volume":110,"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"The scale invariance of natural images suggests an analogy to the statistical mechanics of physical systems at a critical point. Here we examine the distribution of pixels in small image patches and show how to construct the corresponding thermodynamics. We find evidence for criticality in a diverging specific heat, which corresponds to large fluctuations in how &quot;surprising&quot; we find individual images, and in the quantitative form of the entropy vs energy. We identify special image configurations as local energy minima and show that average patches within each basin are interpretable as lines and edges in all orientations.","lang":"eng"}],"intvolume":"       110","has_accepted_license":"1","publication_status":"published","file_date_updated":"2020-07-14T12:45:53Z"},{"issue":"1","citation":{"ieee":"I. Castanon, L. Abrami, L. Holtzer, C.-P. J. Heisenberg, F. Van Der Goot, and M. González Gaitán, “Anthrax toxin receptor 2a controls mitotic spindle positioning,” <i>Nature Cell Biology</i>, vol. 15, no. 1. Nature Publishing Group, pp. 28–39, 2013.","short":"I. Castanon, L. Abrami, L. Holtzer, C.-P.J. Heisenberg, F. Van Der Goot, M. González Gaitán, Nature Cell Biology 15 (2013) 28–39.","ama":"Castanon I, Abrami L, Holtzer L, Heisenberg C-PJ, Van Der Goot F, González Gaitán M. Anthrax toxin receptor 2a controls mitotic spindle positioning. <i>Nature Cell Biology</i>. 2013;15(1):28-39. doi:<a href=\"https://doi.org/10.1038/ncb2632\">10.1038/ncb2632</a>","apa":"Castanon, I., Abrami, L., Holtzer, L., Heisenberg, C.-P. J., Van Der Goot, F., &#38; González Gaitán, M. (2013). Anthrax toxin receptor 2a controls mitotic spindle positioning. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb2632\">https://doi.org/10.1038/ncb2632</a>","mla":"Castanon, Irinka, et al. “Anthrax Toxin Receptor 2a Controls Mitotic Spindle Positioning.” <i>Nature Cell Biology</i>, vol. 15, no. 1, Nature Publishing Group, 2013, pp. 28–39, doi:<a href=\"https://doi.org/10.1038/ncb2632\">10.1038/ncb2632</a>.","chicago":"Castanon, Irinka, Laurence Abrami, Laurent Holtzer, Carl-Philipp J Heisenberg, Françoise Van Der Goot, and Marcos González Gaitán. “Anthrax Toxin Receptor 2a Controls Mitotic Spindle Positioning.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/ncb2632\">https://doi.org/10.1038/ncb2632</a>.","ista":"Castanon I, Abrami L, Holtzer L, Heisenberg C-PJ, Van Der Goot F, González Gaitán M. 2013. Anthrax toxin receptor 2a controls mitotic spindle positioning. Nature Cell Biology. 15(1), 28–39."},"acknowledgement":"This work was supported by the SNSF, the Swiss SystemsX.ch initiative and LipidX-2008/011 (M.G-G. and F.G.v.d.G.), by the Fondation SANTE-Vaduz/Aide au Soutien des Nouvelles Thérapies (F.G.v.d.G.) and by the ERC, the NCCR Frontiers in Genetics and Chemical Biology programmes and the Polish–Swiss research program (M.G-G.).","date_published":"2013-01-01T00:00:00Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication":"Nature Cell Biology","status":"public","language":[{"iso":"eng"}],"department":[{"_id":"CaHe"}],"publist_id":"3819","year":"2013","month":"01","publication_status":"published","quality_controlled":"1","page":"28 - 39","abstract":[{"lang":"eng","text":"Oriented mitosis is essential during tissue morphogenesis. The Wnt/planar cell polarity (Wnt/PCP) pathway orients mitosis in a number of developmental systems, including dorsal epiblast cell divisions along the animal-vegetal (A-V) axis during zebrafish gastrulation. How Wnt signalling orients the mitotic plane is, however, unknown. Here we show that, in dorsal epiblast cells, anthrax toxin receptor 2a (Antxr2a) accumulates in a polarized cortical cap, which is aligned with the embryonic A-V axis and forecasts the division plane. Filamentous actin (F-actin) also forms an A-V polarized cap, which depends on Wnt/PCP and its effectors RhoA and Rock2. Antxr2a is recruited to the cap by interacting with actin. Antxr2a also interacts with RhoA and together they activate the diaphanous-related formin zDia2. Mechanistically, Antxr2a functions as a Wnt-dependent polarized determinant, which, through the action of RhoA and zDia2, exerts torque on the spindle to align it with the A-V axis.\r\n"}],"intvolume":"        15","date_updated":"2021-01-12T07:00:41Z","_id":"2918","volume":15,"type":"journal_article","date_created":"2018-12-11T12:00:20Z","author":[{"first_name":"Irinka","last_name":"Castanon","full_name":"Castanon, Irinka"},{"first_name":"Laurence","last_name":"Abrami","full_name":"Abrami, Laurence"},{"first_name":"Laurent","full_name":"Holtzer, Laurent","last_name":"Holtzer"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"first_name":"Françoise","full_name":"Van Der Goot, Françoise","last_name":"Van Der Goot"},{"last_name":"González Gaitán","full_name":"González Gaitán, Marcos","first_name":"Marcos"}],"doi":"10.1038/ncb2632","day":"01","scopus_import":1,"title":"Anthrax toxin receptor 2a controls mitotic spindle positioning","oa_version":"None","publisher":"Nature Publishing Group"}]