[{"publication":"Nature Neuroscience","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","day":"03","article_processing_charge":"No","publist_id":"3936","year":"2013","_id":"2856","external_id":{"isi":["000316723700023"],"pmid":["23455609"]},"date_published":"2013-03-03T00:00:00Z","pmid":1,"date_created":"2018-12-11T11:59:57Z","oa":1,"date_updated":"2025-09-29T13:39:33Z","status":"public","doi":"10.1038/nn.3346","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681425/","open_access":"1"}],"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."}],"title":"Optical control of metabotropic glutamate receptors","quality_controlled":"1","publisher":"Nature Publishing Group","month":"03","volume":16,"author":[{"last_name":"Levitz","full_name":"Levitz, Joshua","first_name":"Joshua"},{"first_name":"Carlos","full_name":"Pantoja, Carlos","last_name":"Pantoja"},{"first_name":"Benjamin","last_name":"Gaub","full_name":"Gaub, Benjamin"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","last_name":"Janovjak"},{"last_name":"Reiner","full_name":"Reiner, Andreas","first_name":"Andreas"},{"first_name":"Adam","last_name":"Hoagland","full_name":"Hoagland, Adam"},{"full_name":"Schoppik, David","last_name":"Schoppik","first_name":"David"},{"full_name":"Kane, Brian","last_name":"Kane","first_name":"Brian"},{"first_name":"Philipp","last_name":"Stawski","full_name":"Stawski, Philipp"},{"first_name":"Alexander","last_name":"Schier","full_name":"Schier, Alexander"},{"last_name":"Trauner","full_name":"Trauner, Dirk","first_name":"Dirk"},{"full_name":"Isacoff, Ehud","last_name":"Isacoff","first_name":"Ehud"}],"department":[{"_id":"HaJa"}],"isi":1,"publication_status":"published","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.)","scopus_import":"1","intvolume":" 16","oa_version":"Submitted Version","page":"507 - 516","language":[{"iso":"eng"}],"citation":{"apa":"Levitz, J., Pantoja, C., Gaub, B., Janovjak, H. L., Reiner, A., Hoagland, A., … Isacoff, E. (2013). Optical control of metabotropic glutamate receptors. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3346","ama":"Levitz J, Pantoja C, Gaub B, et al. Optical control of metabotropic glutamate receptors. Nature Neuroscience. 2013;16:507-516. doi:10.1038/nn.3346","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.” Nature Neuroscience, vol. 16, Nature Publishing Group, 2013, pp. 507–16, doi:10.1038/nn.3346.","ieee":"J. Levitz et al., “Optical control of metabotropic glutamate receptors,” Nature Neuroscience, 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.” Nature Neuroscience. Nature Publishing Group, 2013. https://doi.org/10.1038/nn.3346.","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."}},{"publist_id":"3932","year":"2013","file_date_updated":"2020-07-14T12:45:51Z","date_created":"2018-12-11T11:59:57Z","_id":"2857","date_published":"2013-02-22T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","publication":"Methods in Molecular Biology","day":"22","quality_controlled":"1","title":"Optical control of ligand-gated ion channels","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","file":[{"file_name":"IST-2017-834-v1+1_szobota.pdf","date_created":"2018-12-12T10:12:34Z","relation":"main_file","access_level":"open_access","file_size":336734,"creator":"system","file_id":"4952","content_type":"application/pdf","checksum":"1701f0d989f27ddac471b19a894ec0d1","date_updated":"2020-07-14T12:45:51Z"}],"oa":1,"date_updated":"2025-04-15T06:43:12Z","status":"public","doi":"10.1007/978-1-62703-351-0_32","project":[{"name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors","grant_number":"RGY0084/2012","_id":"255BFFFA-B435-11E9-9278-68D0E5697425"},{"_id":"25548C20-B435-11E9-9278-68D0E5697425","name":"Microbial Ion Channels for Synthetic Neurobiology","grant_number":"303564","call_identifier":"FP7"}],"language":[{"iso":"eng"}],"oa_version":"Submitted Version","page":"417 - 435","pubrep_id":"834","author":[{"full_name":"Szobota, Stephanie","last_name":"Szobota","first_name":"Stephanie"},{"id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","first_name":"Catherine","full_name":"Mckenzie, Catherine","last_name":"Mckenzie"},{"last_name":"Janovjak","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"HaJa"}],"publication_status":"published","month":"02","volume":998,"scopus_import":1,"intvolume":" 998","ddc":["570"],"citation":{"short":"S. Szobota, C. Mckenzie, H.L. Janovjak, Methods in Molecular Biology 998 (2013) 417–435.","ama":"Szobota S, Mckenzie C, Janovjak HL. Optical control of ligand-gated ion channels. Methods in Molecular Biology. 2013;998:417-435. doi:10.1007/978-1-62703-351-0_32","apa":"Szobota, S., Mckenzie, C., & Janovjak, H. L. (2013). Optical control of ligand-gated ion channels. Methods in Molecular Biology. Springer. https://doi.org/10.1007/978-1-62703-351-0_32","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,” Methods in Molecular Biology, vol. 998. Springer, pp. 417–435, 2013.","chicago":"Szobota, Stephanie, Catherine Mckenzie, and Harald L Janovjak. “Optical Control of Ligand-Gated Ion Channels.” Methods in Molecular Biology. Springer, 2013. https://doi.org/10.1007/978-1-62703-351-0_32.","mla":"Szobota, Stephanie, et al. “Optical Control of Ligand-Gated Ion Channels.” Methods in Molecular Biology, vol. 998, Springer, 2013, pp. 417–35, doi:10.1007/978-1-62703-351-0_32."},"has_accepted_license":"1","alternative_title":["MIMB"],"ec_funded":1},{"oa":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"project":[{"call_identifier":"FP7","_id":"257A4776-B435-11E9-9278-68D0E5697425","grant_number":"281511","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex"}],"doi":"10.1016/j.neuron.2013.01.033","status":"public","date_updated":"2025-09-29T13:37:37Z","file":[{"file_name":"2013_Neuron_Dupret.pdf","date_created":"2019-01-23T08:08:07Z","relation":"main_file","creator":"dernst","access_level":"open_access","file_size":2637837,"checksum":"0e18cb8561153ddb50bb5af16e7c9e97","content_type":"application/pdf","file_id":"5877","date_updated":"2020-07-14T12:45:52Z"}],"publisher":"Elsevier","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."}],"title":"Dynamic reconfiguration of hippocampal interneuron circuits during spatial learning","quality_controlled":"1","publication":"Neuron","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","article_processing_charge":"No","day":"21","file_date_updated":"2020-07-14T12:45:52Z","year":"2013","publist_id":"3929","date_published":"2013-03-21T00:00:00Z","_id":"2860","external_id":{"isi":["000317556000015"]},"license":"https://creativecommons.org/licenses/by/4.0/","date_created":"2018-12-11T11:59:59Z","issue":"1","corr_author":"1","citation":{"apa":"Dupret, D., O’Neill, J., & Csicsvari, J. L. (2013). Dynamic reconfiguration of hippocampal interneuron circuits during spatial learning. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2013.01.033","ama":"Dupret D, O’Neill J, Csicsvari JL. Dynamic reconfiguration of hippocampal interneuron circuits during spatial learning. Neuron. 2013;78(1):166-180. doi:10.1016/j.neuron.2013.01.033","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.” Neuron, vol. 78, no. 1, Elsevier, 2013, pp. 166–80, doi:10.1016/j.neuron.2013.01.033.","chicago":"Dupret, David, Joseph O’Neill, and Jozsef L Csicsvari. “Dynamic Reconfiguration of Hippocampal Interneuron Circuits during Spatial Learning.” Neuron. Elsevier, 2013. https://doi.org/10.1016/j.neuron.2013.01.033.","ieee":"D. Dupret, J. O’Neill, and J. L. Csicsvari, “Dynamic reconfiguration of hippocampal interneuron circuits during spatial learning,” Neuron, vol. 78, no. 1. Elsevier, pp. 166–180, 2013.","ista":"Dupret D, O’Neill J, Csicsvari JL. 2013. Dynamic reconfiguration of hippocampal interneuron circuits during spatial learning. Neuron. 78(1), 166–180."},"ec_funded":1,"has_accepted_license":"1","month":"03","volume":78,"publication_status":"published","isi":1,"department":[{"_id":"JoCs"}],"author":[{"last_name":"Dupret","full_name":"Dupret, David","first_name":"David"},{"first_name":"Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87","last_name":"O'Neill","full_name":"O'Neill, Joseph"},{"first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L"}],"acknowledgement":"D.D. and J.C. were supported by a MRC Intramural Programme Grant U138197111","ddc":["570"],"intvolume":" 78","scopus_import":"1","page":"166 - 180","oa_version":"Published Version","language":[{"iso":"eng"}]},{"title":"Lyapunov exponent and topological entropy plateaus in piecewise linear maps","quality_controlled":"1","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"}],"publisher":"IOP Publishing","status":"public","doi":"10.1088/1751-8113/46/12/125101","date_updated":"2025-09-29T13:36:56Z","external_id":{"isi":["000316058200010"]},"_id":"2861","date_published":"2013-03-29T00:00:00Z","date_created":"2018-12-11T11:59:59Z","publist_id":"3928","year":"2013","day":"29","article_processing_charge":"No","publication":"Journal of Physics A: Mathematical and Theoretical","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","issue":"12","citation":{"mla":"Botella Soler, Vicente, et al. “Lyapunov Exponent and Topological Entropy Plateaus in Piecewise Linear Maps.” Journal of Physics A: Mathematical and Theoretical, vol. 46, no. 12, 125101, IOP Publishing, 2013, doi:10.1088/1751-8113/46/12/125101.","ieee":"V. Botella Soler, J. Oteo, J. Ros, and P. Glendinning, “Lyapunov exponent and topological entropy plateaus in piecewise linear maps,” Journal of Physics A: Mathematical and Theoretical, vol. 46, no. 12. IOP Publishing, 2013.","chicago":"Botella Soler, Vicente, José Oteo, Javier Ros, and Paul Glendinning. “Lyapunov Exponent and Topological Entropy Plateaus in Piecewise Linear Maps.” Journal of Physics A: Mathematical and Theoretical. IOP Publishing, 2013. https://doi.org/10.1088/1751-8113/46/12/125101.","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.","apa":"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. IOP Publishing. https://doi.org/10.1088/1751-8113/46/12/125101","ama":"Botella Soler V, Oteo J, Ros J, Glendinning P. Lyapunov exponent and topological entropy plateaus in piecewise linear maps. Journal of Physics A: Mathematical and Theoretical. 2013;46(12). doi:10.1088/1751-8113/46/12/125101","short":"V. Botella Soler, J. Oteo, J. Ros, P. Glendinning, Journal of Physics A: Mathematical and Theoretical 46 (2013)."},"corr_author":"1","article_number":"125101","oa_version":"None","language":[{"iso":"eng"}],"scopus_import":"1","intvolume":" 46","month":"03","volume":46,"author":[{"orcid":"0000-0002-8790-1914","last_name":"Botella Soler","full_name":"Botella Soler, Vicente","id":"421234E8-F248-11E8-B48F-1D18A9856A87","first_name":"Vicente"},{"first_name":"José","last_name":"Oteo","full_name":"Oteo, José"},{"last_name":"Ros","full_name":"Ros, Javier","first_name":"Javier"},{"full_name":"Glendinning, Paul","last_name":"Glendinning","first_name":"Paul"}],"department":[{"_id":"GaTk"}],"publication_status":"published","isi":1},{"title":"Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle","quality_controlled":"1","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."}],"publisher":"Company of Biologists","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596994/"}],"date_updated":"2025-09-29T13:36:20Z","doi":"10.1242/dev.087130","status":"public","oa":1,"date_created":"2018-12-11T11:59:59Z","pmid":1,"_id":"2862","external_id":{"pmid":["23482490"],"isi":["000316096400018"]},"date_published":"2013-04-01T00:00:00Z","publist_id":"3927","year":"2013","day":"01","article_processing_charge":"No","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Development","citation":{"ieee":"H. Tay et al., “Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle,” Development, vol. 140, no. 7. Company of Biologists, pp. 1550–1559, 2013.","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.” Development. Company of Biologists, 2013. https://doi.org/10.1242/dev.087130.","mla":"Tay, Hwee, et al. “Lethal Giant Larvae 2 Regulates Development of the Ciliated Organ Kupffer’s Vesicle.” Development, vol. 140, no. 7, Company of Biologists, 2013, pp. 1550–59, doi:10.1242/dev.087130.","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.","ama":"Tay H, Schulze S, Compagnon J, et al. Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle. Development. 2013;140(7):1550-1559. doi:10.1242/dev.087130","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. Development. Company of Biologists. https://doi.org/10.1242/dev.087130","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."},"issue":"7","language":[{"iso":"eng"}],"oa_version":"Submitted Version","page":"1550 - 1559","scopus_import":"1","intvolume":" 140","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.","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","last_name":"Compagnon","first_name":"Julien","id":"2E3E0988-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Foley","full_name":"Foley, Fiona","first_name":"Fiona"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yost, H Joseph","last_name":"Yost","first_name":"H Joseph"},{"first_name":"Salim","last_name":"Abdelilah Seyfried","full_name":"Abdelilah Seyfried, Salim"},{"last_name":"Amack","full_name":"Amack, Jeffrey","first_name":"Jeffrey"}],"department":[{"_id":"CaHe"}],"publication_status":"published","isi":1,"month":"04","volume":140},{"intvolume":" 9","ddc":["570"],"scopus_import":"1","volume":9,"month":"03","publication_status":"published","isi":1,"department":[{"_id":"GaTk"}],"author":[{"full_name":"Granot Atedgi, Einat","last_name":"Granot Atedgi","first_name":"Einat"},{"orcid":"0000-0002-6699-1455","last_name":"Tkacik","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"first_name":"Ronen","full_name":"Segev, Ronen","last_name":"Segev"},{"full_name":"Schneidman, Elad","last_name":"Schneidman","first_name":"Elad"}],"pubrep_id":"120","oa_version":"Published Version","language":[{"iso":"eng"}],"has_accepted_license":"1","issue":"3","corr_author":"1","article_number":"e1002922","citation":{"mla":"Granot Atedgi, Einat, et al. “Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.” PLoS Computational Biology, vol. 9, no. 3, e1002922, Public Library of Science, 2013, doi:10.1371/journal.pcbi.1002922.","chicago":"Granot Atedgi, Einat, Gašper Tkačik, Ronen Segev, and Elad Schneidman. “Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.” PLoS Computational Biology. Public Library of Science, 2013. https://doi.org/10.1371/journal.pcbi.1002922.","ieee":"E. Granot Atedgi, G. Tkačik, R. Segev, and E. Schneidman, “Stimulus-dependent maximum entropy models of neural population codes,” PLoS Computational Biology, vol. 9, no. 3. Public Library of Science, 2013.","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.","apa":"Granot Atedgi, E., Tkačik, G., Segev, R., & Schneidman, E. (2013). Stimulus-dependent maximum entropy models of neural population codes. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1002922","ama":"Granot Atedgi E, Tkačik G, Segev R, Schneidman E. Stimulus-dependent maximum entropy models of neural population codes. PLoS Computational Biology. 2013;9(3). doi:10.1371/journal.pcbi.1002922","short":"E. Granot Atedgi, G. Tkačik, R. Segev, E. Schneidman, PLoS Computational Biology 9 (2013)."},"article_processing_charge":"No","day":"01","publication":"PLoS Computational Biology","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","date_published":"2013-03-01T00:00:00Z","_id":"2863","external_id":{"isi":["000316864200003"]},"date_created":"2018-12-11T12:00:00Z","file_date_updated":"2020-07-14T12:45:52Z","year":"2013","publist_id":"3926","status":"public","date_updated":"2025-09-29T13:35:44Z","doi":"10.1371/journal.pcbi.1002922","oa":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"content_type":"application/pdf","checksum":"5a30876c193209fa05b26db71845dd16","file_id":"5099","date_updated":"2020-07-14T12:45:52Z","file_name":"IST-2013-120-v1+1_journal.pcbi.1002922.pdf","access_level":"open_access","file_size":1548120,"creator":"system","relation":"main_file","date_created":"2018-12-12T10:14:45Z"}],"publisher":"Public Library of Science","quality_controlled":"1","title":"Stimulus-dependent maximum entropy models of neural population codes","abstract":[{"lang":"eng","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."}]},{"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.” American Journal of Botany. Botanical Society of America, 2013. https://doi.org/10.3732/ajb.1200264.","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,” American Journal of Botany, vol. 100, no. 1. Botanical Society of America, pp. 215–225, 2013.","mla":"Vandenbussche, Filip, et al. “Brassinosteroid Control of Shoot Gravitropism Interacts with Ethylene and Depends on Auxin Signaling Components.” American Journal of Botany, vol. 100, no. 1, Botanical Society of America, 2013, pp. 215–25, doi:10.3732/ajb.1200264.","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.","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. American Journal of Botany. 2013;100(1):215-225. doi:10.3732/ajb.1200264","apa":"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. Botanical Society of America. https://doi.org/10.3732/ajb.1200264","short":"F. Vandenbussche, P. Callebert, P. Žádníková, E. Benková, D. Van Der Straeten, American Journal of Botany 100 (2013) 215–225."},"issue":"1","title":"Brassinosteroid control of shoot gravitropism interacts with ethylene and depends on auxin signaling components","quality_controlled":0,"abstract":[{"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.","lang":"eng"}],"publisher":"Botanical Society of America","extern":1,"status":"public","date_updated":"2021-01-12T07:00:25Z","doi":"10.3732/ajb.1200264","publist_id":"3883","year":"2013","page":"215 - 225","date_created":"2018-12-11T12:00:06Z","_id":"2877","date_published":"2013-01-01T00:00:00Z","author":[{"first_name":"Filip","full_name":"Vandenbussche, Filip","last_name":"Vandenbussche"},{"first_name":"Pieter","full_name":"Callebert, Pieter","last_name":"Callebert"},{"first_name":"Petra","last_name":"Žádníková","full_name":"Žádníková, Petra"},{"orcid":"0000-0002-8510-9739","full_name":"Eva Benková","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Van Der Straeten, Dominique","last_name":"Van Der Straeten","first_name":"Dominique"}],"publication_status":"published","type":"journal_article","month":"01","volume":100,"publication":"American Journal of Botany","day":"01","intvolume":" 100"},{"project":[{"name":"Hormonal cross-talk in plant organogenesis","grant_number":"207362","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_updated":"2025-09-29T13:35:12Z","status":"public","doi":"10.1038/emboj.2012.303","oa":1,"publisher":"Wiley-Blackwell","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."}],"quality_controlled":"1","title":"Auxin reflux between the endodermis and pericycle promotes lateral root initiation","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545298/","open_access":"1"}],"article_processing_charge":"No","day":"09","publication":"EMBO Journal","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2013-01-09T00:00:00Z","_id":"2880","external_id":{"isi":["000314141900014"],"pmid":["23178590"]},"date_created":"2018-12-11T12:00:07Z","pmid":1,"year":"2013","publist_id":"3882","ec_funded":1,"issue":"1","citation":{"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.” EMBO Journal. Wiley-Blackwell, 2013. https://doi.org/10.1038/emboj.2012.303.","ieee":"P. Marhavý et al., “Auxin reflux between the endodermis and pericycle promotes lateral root initiation,” EMBO Journal, vol. 32, no. 1. Wiley-Blackwell, pp. 149–158, 2013.","mla":"Marhavý, Peter, et al. “Auxin Reflux between the Endodermis and Pericycle Promotes Lateral Root Initiation.” EMBO Journal, vol. 32, no. 1, Wiley-Blackwell, 2013, pp. 149–58, doi:10.1038/emboj.2012.303.","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. EMBO Journal. 2013;32(1):149-158. doi:10.1038/emboj.2012.303","apa":"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. Wiley-Blackwell. https://doi.org/10.1038/emboj.2012.303"},"intvolume":" 32","scopus_import":"1","month":"01","volume":32,"isi":1,"publication_status":"published","author":[{"first_name":"Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","full_name":"Marhavy, Peter","last_name":"Marhavy","orcid":"0000-0001-5227-5741"},{"full_name":"Vanstraelen, Marleen","last_name":"Vanstraelen","first_name":"Marleen"},{"first_name":"Bert","last_name":"De Rybel","full_name":"De Rybel, 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"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva","last_name":"Benková","orcid":"0000-0002-8510-9739"}],"department":[{"_id":"EvBe"}],"page":"149 - 158","oa_version":"Submitted Version","language":[{"iso":"eng"}]},{"page":"290 - 299","year":"2013","publist_id":"3881","date_published":"2013-02-01T00:00:00Z","_id":"2881","date_created":"2018-12-11T12:00:07Z","month":"02","publication":"Cell Research","volume":23,"publication_status":"published","type":"journal_article","author":[{"full_name":"Hongjiang Li","last_name":"Li","orcid":"0000-0001-5039-9660","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongjiang"},{"last_name":"Xu","full_name":"Xu, Tongda","first_name":"Tongda"},{"last_name":"Lin","full_name":"Lin, Deshu","first_name":"Deshu"},{"full_name":"Wen, Mingzhang","last_name":"Wen","first_name":"Mingzhang"},{"first_name":"Mingtang","full_name":"Xie, Mingtang","last_name":"Xie"},{"first_name":"Jérôme","last_name":"Duclercq","full_name":"Duclercq, Jérôme"},{"first_name":"Agnieszka","last_name":"Bielach","full_name":"Bielach, Agnieszka"},{"last_name":"Kim","full_name":"Kim, Jungmook","first_name":"Jungmook"},{"last_name":"Reddy","full_name":"Reddy, G Venugopala","first_name":"G Venugopala"},{"last_name":"Zuo","full_name":"Zuo, Jianru","first_name":"Jianru"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","full_name":"Eva Benková"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","last_name":"Friml"},{"first_name":"Hongwei","last_name":"Guo","full_name":"Guo, Hongwei"},{"last_name":"Yang","full_name":"Yang, Zhenbiao","first_name":"Zhenbiao"}],"acknowledgement":"is work was supported by grants from the US National Institute of General Medical Sciences (GM081451 and GM081451-03S2) to ZY. We thank National Science Foundation grant (IOS-1147250) to GVR and MX. HL and DL were partially supported by the Chinese Scholarship Council.","intvolume":" 23","day":"01","issue":"2","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3567823/","open_access":"1"}],"citation":{"short":"H. Li, T. Xu, D. Lin, M. Wen, M. Xie, J. Duclercq, A. Bielach, J. Kim, G.V. Reddy, J. Zuo, E. Benková, J. Friml, H. Guo, Z. Yang, Cell Research 23 (2013) 290–299.","ama":"Li H, Xu T, Lin D, et al. Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis. Cell Research. 2013;23(2):290-299. doi:10.1038/cr.2012.146","apa":"Li, H., Xu, T., Lin, D., Wen, M., Xie, M., Duclercq, J., … Yang, Z. (2013). Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis. Cell Research. Nature Publishing Group. https://doi.org/10.1038/cr.2012.146","ista":"Li H, Xu T, Lin D, Wen M, Xie M, Duclercq J, Bielach A, Kim J, Reddy GV, Zuo J, Benková E, Friml J, Guo H, Yang Z. 2013. Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis. Cell Research. 23(2), 290–299.","ieee":"H. Li et al., “Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis,” Cell Research, vol. 23, no. 2. Nature Publishing Group, pp. 290–299, 2013.","chicago":"Li, Hongjiang, Tongda Xu, Deshu Lin, Mingzhang Wen, Mingtang Xie, Jérôme Duclercq, Agnieszka Bielach, et al. “Cytokinin Signaling Regulates Pavement Cell Morphogenesis in Arabidopsis.” Cell Research. Nature Publishing Group, 2013. https://doi.org/10.1038/cr.2012.146.","mla":"Li, Hongjiang, et al. “Cytokinin Signaling Regulates Pavement Cell Morphogenesis in Arabidopsis.” Cell Research, vol. 23, no. 2, Nature Publishing Group, 2013, pp. 290–99, doi:10.1038/cr.2012.146."},"publisher":"Nature Publishing Group","quality_controlled":0,"title":"Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis","abstract":[{"text":"The puzzle piece-shaped Arabidopsis leaf pavement cells (PCs) with interdigitated lobes and indents is a good model system to investigate the mechanisms that coordinate cell polarity and shape formation within a tissue. Auxin has been shown to coordinate the interdigitation by activating ROP GTPase-dependent signaling pathways. To identify additional components or mechanisms, we screened for mutants with abnormal PC morphogenesis and found that cytokinin signaling regulates the PC interdigitation pattern. Reduction in cytokinin accumulation and defects in cytokinin signaling (such as in ARR7-over-expressing lines, the ahk3cre1 cytokinin receptor mutant, and the ahp12345 cytokinin signaling mutant) enhanced PC interdigitation, whereas over-production of cytokinin and over-activation of cytokinin signaling in an ARR20 over-expression line delayed or abolished PC interdigitation throughout the cotyledon. Genetic and biochemical analyses suggest that cytokinin signaling acts upstream of ROPs to suppress the formation of interdigitated pattern. Our results provide novel mechanistic understanding of the pathways controlling PC shape and uncover a new role for cytokinin signaling in cell morphogenesis.","lang":"eng"}],"oa":1,"extern":1,"date_updated":"2021-01-12T07:00:27Z","status":"public","doi":"10.1038/cr.2012.146"},{"oa_version":"Submitted Version","page":"3627 - 3632","language":[{"iso":"eng"}],"month":"02","volume":110,"author":[{"full_name":"Löfke, Christian","last_name":"Löfke","first_name":"Christian"},{"first_name":"Marta","full_name":"Zwiewka, Marta","last_name":"Zwiewka"},{"first_name":"Ingo","full_name":"Heilmann, Ingo","last_name":"Heilmann"},{"last_name":"Van Montagu","full_name":"Van Montagu, Marc","first_name":"Marc"},{"last_name":"Teichmann","full_name":"Teichmann, Thomas","first_name":"Thomas"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"}],"department":[{"_id":"JiFr"}],"publication_status":"published","isi":1,"scopus_import":"1","intvolume":" 110","issue":"9","citation":{"apa":"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. National Academy of Sciences. https://doi.org/10.1073/pnas.1300107110","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. PNAS. 2013;110(9):3627-3632. doi:10.1073/pnas.1300107110","short":"C. Löfke, M. Zwiewka, I. Heilmann, M. Van Montagu, T. Teichmann, J. Friml, PNAS 110 (2013) 3627–3632.","mla":"Löfke, Christian, et al. “Asymmetric Gibberellin Signaling Regulates Vacuolar Trafficking of PIN Auxin Transporters during Root Gravitropism.” PNAS, vol. 110, no. 9, National Academy of Sciences, 2013, pp. 3627–32, doi:10.1073/pnas.1300107110.","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.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1300107110.","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,” PNAS, vol. 110, no. 9. National Academy of Sciences, pp. 3627–3632, 2013.","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."},"publist_id":"3879","year":"2013","external_id":{"pmid":["23391733"],"isi":["000315841900083"]},"_id":"2882","date_published":"2013-02-26T00:00:00Z","pmid":1,"date_created":"2018-12-11T12:00:07Z","publication":"PNAS","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"26","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587205/"}],"title":"Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism","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"}],"quality_controlled":"1","publisher":"National Academy of Sciences","oa":1,"date_updated":"2025-09-29T13:34:38Z","status":"public","doi":"10.1073/pnas.1300107110"},{"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.” Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.112.105999.","ieee":"B. Wang et al., “Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane,” Plant Cell, vol. 25, no. 1. American Society of Plant Biologists, pp. 202–214, 2013.","mla":"Wang, Bangjun, et al. “Arabidopsis TWISTED DWARF1 Functionally Interacts with Auxin Exporter ABCB1 on the Root Plasma Membrane.” Plant Cell, vol. 25, no. 1, American Society of Plant Biologists, 2013, pp. 202–14, doi:10.1105/tpc.112.105999.","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.","ama":"Wang B, Bailly A, Zwiewk M, et al. Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane. Plant Cell. 2013;25(1):202-214. doi:10.1105/tpc.112.105999","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. Plant Cell. American Society of Plant Biologists. https://doi.org/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.","scopus_import":"1","intvolume":" 25","volume":25,"month":"01","department":[{"_id":"JiFr"}],"author":[{"last_name":"Wang","full_name":"Wang, Bangjun","first_name":"Bangjun"},{"last_name":"Bailly","full_name":"Bailly, Aurélien","first_name":"Aurélien"},{"first_name":"Marta","full_name":"Zwiewk, Marta","last_name":"Zwiewk"},{"last_name":"Henrichs","full_name":"Henrichs, Sina","first_name":"Sina"},{"first_name":"Elisa","last_name":"Azzarello","full_name":"Azzarello, Elisa"},{"first_name":"Stefano","full_name":"Mancuso, Stefano","last_name":"Mancuso"},{"last_name":"Maeshima","full_name":"Maeshima, Masayoshi","first_name":"Masayoshi"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"first_name":"Alexander","last_name":"Schulz","full_name":"Schulz, Alexander"},{"first_name":"Markus","last_name":"Geisler","full_name":"Geisler, Markus"}],"isi":1,"publication_status":"published","oa_version":"Submitted Version","page":"202 - 214","language":[{"iso":"eng"}],"status":"public","date_updated":"2025-09-29T13:34:07Z","doi":"10.1105/tpc.112.105999","oa":1,"title":"Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane","quality_controlled":"1","abstract":[{"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.","lang":"eng"}],"publisher":"American Society of Plant Biologists","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584535/"}],"day":"01","article_processing_charge":"No","publication":"Plant Cell","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","external_id":{"isi":["000315572400017"],"pmid":["23321285"]},"_id":"2883","date_published":"2013-01-01T00:00:00Z","pmid":1,"date_created":"2018-12-11T12:00:08Z","publist_id":"3878","year":"2013"},{"language":[{"iso":"eng"}],"page":"147 - 150","oa_version":"None","intvolume":" 29","scopus_import":"1","isi":1,"publication_status":"published","author":[{"id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","first_name":"Jean-Léon","orcid":"0000-0002-3688-1474","last_name":"Maître","full_name":"Maître, Jean-Léon"},{"full_name":"Berthoumieux, Hélène","last_name":"Berthoumieux","first_name":"Hélène"},{"first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel","last_name":"Krens"},{"first_name":"Guillaume","full_name":"Salbreux, Guillaume","last_name":"Salbreux"},{"first_name":"Frank","last_name":"Julicher","full_name":"Julicher, Frank"},{"last_name":"Paluch","full_name":"Paluch, Ewa","first_name":"Ewa"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"department":[{"_id":"CaHe"}],"volume":29,"month":"02","citation":{"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.” Medecine Sciences, vol. 29, no. 2, Éditions Médicales et Scientifiques, 2013, pp. 147–50, doi:10.1051/medsci/2013292011.","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.” Medecine Sciences. Éditions Médicales et Scientifiques, 2013. https://doi.org/10.1051/medsci/2013292011.","ieee":"J.-L. Maître et al., “Cell adhesion mechanics of zebrafish gastrulation,” Medecine Sciences, vol. 29, no. 2. Éditions Médicales et Scientifiques, pp. 147–150, 2013.","short":"J.-L. Maître, H. Berthoumieux, G. Krens, G. Salbreux, F. Julicher, E. Paluch, C.-P.J. Heisenberg, Medecine Sciences 29 (2013) 147–150.","apa":"Maître, J.-L., Berthoumieux, H., Krens, G., Salbreux, G., Julicher, F., Paluch, E., & Heisenberg, C.-P. J. (2013). Cell adhesion mechanics of zebrafish gastrulation. Medecine Sciences. Éditions Médicales et Scientifiques. https://doi.org/10.1051/medsci/2013292011","ama":"Maître J-L, Berthoumieux H, Krens G, et al. Cell adhesion mechanics of zebrafish gastrulation. Medecine Sciences. 2013;29(2):147-150. doi:10.1051/medsci/2013292011"},"issue":"2","date_created":"2018-12-11T12:00:08Z","date_published":"2013-02-01T00:00:00Z","_id":"2884","external_id":{"isi":["000315749700011"]},"year":"2013","publist_id":"3877","article_processing_charge":"No","day":"01","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Medecine Sciences","publisher":"Éditions Médicales et Scientifiques","title":"Cell adhesion mechanics of zebrafish gastrulation","quality_controlled":"1","project":[{"_id":"252064B8-B435-11E9-9278-68D0E5697425","name":"Analysis of the Formation and Function of Different Cell Protusion Types During Cell Migration in Vivo","grant_number":"HE_3231/6-1"},{"_id":"2527D5CC-B435-11E9-9278-68D0E5697425","grant_number":"I812-B12","name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","call_identifier":"FWF"}],"doi":"10.1051/medsci/2013292011","status":"public","date_updated":"2025-09-29T13:33:31Z"},{"month":"01","volume":7721,"department":[{"_id":"ToHe"}],"conference":{"name":"MEMICS: Mathematical and Engineering methods in computer science","end_date":"2012-10-28","start_date":"2012-10-25","location":"Znojmo, Czech Republic"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","type":"conference_editor","acknowledgement":"Red Hat Czech Republic, Y Soft","day":"09","intvolume":" 7721","oa_version":"None","page":"1 - 228","publist_id":"3874","language":[{"iso":"eng"}],"year":"2013","_id":"2885","editor":[{"last_name":"Kucera","full_name":"Kucera, Antonin","first_name":"Antonin"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"last_name":"Nesetril","full_name":"Nesetril, Jaroslav","first_name":"Jaroslav"},{"full_name":"Vojnar, Tomas","last_name":"Vojnar","first_name":"Tomas"},{"full_name":"Antos, David","last_name":"Antos","first_name":"David"}],"date_published":"2013-01-09T00:00:00Z","date_created":"2018-12-11T12:00:08Z","status":"public","date_updated":"2019-08-02T12:37:55Z","doi":"10.1007/978-3-642-36046-6","series_title":"Lecture Notes in Computer Science","citation":{"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. Mathematical and Engineering Methods in Computer Science. Vol 7721. Springer; 2013:1-228. doi:10.1007/978-3-642-36046-6","apa":"Kucera, A., Henzinger, T. A., Nesetril, J., Vojnar, T., & Antos, D. (Eds.). (2013). Mathematical and Engineering Methods in Computer Science (Vol. 7721, pp. 1–228). Presented at the MEMICS: Mathematical and Engineering methods in computer science, Znojmo, Czech Republic: Springer. https://doi.org/10.1007/978-3-642-36046-6","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. Mathematical and Engineering Methods in Computer Science. Vol. 7721. Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-36046-6.","ieee":"A. Kucera, T. A. Henzinger, J. Nesetril, T. Vojnar, and D. Antos, Eds., Mathematical and Engineering Methods in Computer Science, vol. 7721. Springer, 2013, pp. 1–228.","mla":"Kucera, Antonin, et al., editors. Mathematical and Engineering Methods in Computer Science. Vol. 7721, Springer, 2013, pp. 1–228, doi:10.1007/978-3-642-36046-6."},"alternative_title":["LNCS"],"title":"Mathematical and Engineering Methods in Computer Science","quality_controlled":"1","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"}],"publisher":"Springer"},{"language":[{"iso":"eng"}],"oa_version":"Submitted Version","page":"118 - 130","scopus_import":"1","intvolume":" 7721","department":[{"_id":"KrCh"}],"author":[{"first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin","last_name":"Chmelik"},{"first_name":"Vojtěch","full_name":"Řehák, Vojtěch","last_name":"Řehák"}],"conference":{"start_date":"2012-10-25","location":"Znojmo, Czech Republic","end_date":"2012-10-28","name":"MEMICS: Mathematical and Engineering Methods in Computer Science"},"publication_status":"published","month":"01","volume":7721,"alternative_title":["LNCS"],"ec_funded":1,"citation":{"ieee":"M. Chmelik and V. Řehák, “Controllable-choice message sequence graphs,” vol. 7721. Springer, pp. 118–130, 2013.","chicago":"Chmelik, Martin, and Vojtěch Řehák. “Controllable-Choice Message Sequence Graphs.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-36046-6_12.","mla":"Chmelik, Martin, and Vojtěch Řehák. Controllable-Choice Message Sequence Graphs. Vol. 7721, Springer, 2013, pp. 118–30, doi:10.1007/978-3-642-36046-6_12.","ista":"Chmelik M, Řehák V. 2013. Controllable-choice message sequence graphs. 7721, 118–130.","ama":"Chmelik M, Řehák V. Controllable-choice message sequence graphs. 2013;7721:118-130. doi:10.1007/978-3-642-36046-6_12","apa":"Chmelik, M., & Řehák, V. (2013). Controllable-choice message sequence graphs. Presented at the MEMICS: Mathematical and Engineering Methods in Computer Science, Znojmo, Czech Republic: Springer. https://doi.org/10.1007/978-3-642-36046-6_12","short":"M. Chmelik, V. Řehák, 7721 (2013) 118–130."},"corr_author":"1","date_created":"2018-12-11T12:00:09Z","external_id":{"arxiv":["1209.4499"]},"_id":"2886","date_published":"2013-01-09T00:00:00Z","publist_id":"3873","year":"2013","day":"09","article_processing_charge":"No","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Controllable-choice message sequence graphs","quality_controlled":"1","abstract":[{"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.","lang":"eng"}],"publisher":"Springer","series_title":"Lecture Notes in Computer Science","main_file_link":[{"url":"http://arxiv.org/abs/1209.4499","open_access":"1"}],"arxiv":1,"status":"public","date_updated":"2025-06-11T08:05:09Z","doi":"10.1007/978-3-642-36046-6_12","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"oa":1},{"date_created":"2018-12-11T12:00:09Z","pmid":1,"date_published":"2013-02-12T00:00:00Z","_id":"2887","external_id":{"isi":["000315812800060"],"pmid":["23362379"]},"year":"2013","publist_id":"3872","article_processing_charge":"No","day":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","publication":"PNAS","publisher":"National Academy of Sciences","abstract":[{"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.","lang":"eng"}],"title":"Genotypic recognition and spatial responses by rice roots","quality_controlled":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574932/","open_access":"1"}],"date_updated":"2026-06-18T18:36:41Z","status":"public","doi":"10.1073/pnas.1222821110","article_type":"original","oa":1,"language":[{"iso":"eng"}],"page":"2670 - 2675","oa_version":"Published Version","intvolume":" 110","ddc":["500"],"scopus_import":"1","publication_status":"published","isi":1,"department":[{"_id":"HeEd"}],"author":[{"full_name":"Fang, Suqin","last_name":"Fang","first_name":"Suqin"},{"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"},{"first_name":"Joshua","last_name":"Weitz","full_name":"Weitz, Joshua"},{"last_name":"Kochian","full_name":"Kochian, Leon","first_name":"Leon"},{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"full_name":"Liao, Hong","last_name":"Liao","first_name":"Hong"},{"last_name":"Benfey","full_name":"Benfey, Philip","first_name":"Philip"}],"volume":110,"month":"02","citation":{"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. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1222821110","ama":"Fang S, Clark R, Zheng Y, et al. Genotypic recognition and spatial responses by rice roots. PNAS. 2013;110(7):2670-2675. doi:10.1073/pnas.1222821110","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.","mla":"Fang, Suqin, et al. “Genotypic Recognition and Spatial Responses by Rice Roots.” PNAS, vol. 110, no. 7, National Academy of Sciences, 2013, pp. 2670–75, doi:10.1073/pnas.1222821110.","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.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1222821110.","ieee":"S. Fang et al., “Genotypic recognition and spatial responses by rice roots,” PNAS, vol. 110, no. 7. National Academy of Sciences, pp. 2670–2675, 2013.","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."},"issue":"7"},{"_id":"2900","date_published":"2013-01-01T00:00:00Z","date_created":"2018-12-11T12:00:14Z","page":"514 - 515","publist_id":"3858","year":"2013","day":"01","intvolume":" 10","month":"01","publication":"Evolution & Development","volume":10,"author":[{"last_name":"Azevedo","full_name":"Azevedo, Ricardo B","first_name":"Ricardo"},{"full_name":"Lohaus, Rolf","last_name":"Lohaus","first_name":"Rolf"},{"orcid":"0000-0003-2361-3953","full_name":"Tiago Paixao","last_name":"Paixao","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","type":"journal_article","title":"Networking networks","quality_controlled":0,"publisher":"Wiley-Blackwell","issue":"5","main_file_link":[{"url":"http://onlinelibrary.wiley.com/doi/10.1111/j.1525-142X.2008.00265.x/abstract","open_access":"0"}],"citation":{"short":"R. Azevedo, R. Lohaus, T. Paixao, Evolution & Development 10 (2013) 514–515.","apa":"Azevedo, R., Lohaus, R., & Paixao, T. (2013). Networking networks. Evolution & Development. Wiley-Blackwell.","ama":"Azevedo R, Lohaus R, Paixao T. Networking networks. Evolution & Development. 2013;10(5):514-515.","ista":"Azevedo R, Lohaus R, Paixao T. 2013. Networking networks. Evolution & Development. 10(5), 514–515.","mla":"Azevedo, Ricardo, et al. “Networking Networks.” Evolution & Development, vol. 10, no. 5, Wiley-Blackwell, 2013, pp. 514–15.","ieee":"R. Azevedo, R. Lohaus, and T. Paixao, “Networking networks,” Evolution & Development, vol. 10, no. 5. Wiley-Blackwell, pp. 514–515, 2013.","chicago":"Azevedo, Ricardo, Rolf Lohaus, and Tiago Paixao. “Networking Networks.” Evolution & Development. Wiley-Blackwell, 2013."},"status":"public","date_updated":"2021-01-12T07:00:34Z","extern":1},{"file":[{"date_updated":"2020-07-14T12:45:52Z","content_type":"application/pdf","checksum":"a15a3ba22df9445731507f3e06c9fcee","file_id":"4720","creator":"system","file_size":403013,"access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:08:57Z","file_name":"IST-2016-547-v1+1_2013-P-08-MedusaII.pdf"}],"title":"3D kinetic alpha complexes and their implementation","quality_controlled":"1","abstract":[{"lang":"eng","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."}],"publisher":"Society for Industrial and Applied Mathematics","status":"public","date_updated":"2025-06-03T11:47:11Z","doi":"10.1137/1.9781611972931.6","oa":1,"_id":"2906","date_published":"2013-01-01T00:00:00Z","date_created":"2018-12-11T12:00:16Z","file_date_updated":"2020-07-14T12:45:52Z","publist_id":"3841","year":"2013","day":"01","article_processing_charge":"No","publication":"2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","alternative_title":["ALENEX"],"has_accepted_license":"1","citation":{"mla":"Kerber, Michael, and Herbert Edelsbrunner. “3D Kinetic Alpha Complexes and Their Implementation.” 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments, Society for Industrial and Applied Mathematics, 2013, pp. 70–77, doi:10.1137/1.9781611972931.6.","chicago":"Kerber, Michael, and Herbert Edelsbrunner. “3D Kinetic Alpha Complexes and Their Implementation.” In 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments, 70–77. Society for Industrial and Applied Mathematics, 2013. https://doi.org/10.1137/1.9781611972931.6.","ieee":"M. Kerber and H. Edelsbrunner, “3D kinetic alpha complexes and their implementation,” in 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments, New Orleans, LA, United States, 2013, pp. 70–77.","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.","apa":"Kerber, M., & Edelsbrunner, H. (2013). 3D kinetic alpha complexes and their implementation. In 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments (pp. 70–77). New Orleans, LA, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611972931.6","ama":"Kerber M, Edelsbrunner H. 3D kinetic alpha complexes and their implementation. In: 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments. Society for Industrial and Applied Mathematics; 2013:70-77. doi:10.1137/1.9781611972931.6","short":"M. Kerber, H. Edelsbrunner, in:, 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments, Society for Industrial and Applied Mathematics, 2013, pp. 70–77."},"corr_author":"1","pubrep_id":"547","oa_version":"Submitted Version","page":"70 - 77","language":[{"iso":"eng"}],"scopus_import":"1","ddc":["500"],"month":"01","author":[{"first_name":"Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","full_name":"Kerber, Michael","last_name":"Kerber","orcid":"0000-0002-8030-9299"},{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"}],"department":[{"_id":"HeEd"}],"conference":{"end_date":"2013-01-07","location":"New Orleans, LA, United States","start_date":"2013-01-07","name":"ALENEX: Algorithm Engineering and Experiments"},"publication_status":"published"},{"pubrep_id":"119","oa_version":"Submitted Version","page":"328 - 333","language":[{"iso":"eng"}],"ddc":["576"],"month":"11","department":[{"_id":"NiBa"}],"author":[{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"publication_status":"published","has_accepted_license":"1","citation":{"short":"N.H. Barton, in:, The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–333.","ama":"Barton NH. Recombination and sex. In: The Princeton Guide to Evolution. Princeton University Press; 2013:328-333.","apa":"Barton, N. H. (2013). Recombination and sex. In The Princeton Guide to Evolution (pp. 328–333). Princeton University Press.","ista":"Barton NH. 2013.Recombination and sex. In: The Princeton Guide to Evolution. , 328–333.","ieee":"N. H. Barton, “Recombination and sex,” in The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–333.","chicago":"Barton, Nicholas H. “Recombination and Sex.” In The Princeton Guide to Evolution, 328–33. Princeton University Press, 2013.","mla":"Barton, Nicholas H. “Recombination and Sex.” The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–33."},"corr_author":"1","_id":"2907","date_published":"2013-11-04T00:00:00Z","date_created":"2018-12-11T12:00:16Z","file_date_updated":"2020-07-14T12:45:52Z","publist_id":"3839","year":"2013","day":"04","publication":"The Princeton Guide to Evolution","type":"book_chapter","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":79838,"access_level":"open_access","creator":"system","date_created":"2018-12-12T10:16:47Z","relation":"main_file","file_name":"IST-2013-119-v1+1_IV.4_Recombination_and_Sex_Barton_1-13-13-e.docx","date_updated":"2020-07-14T12:45:52Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"5237","checksum":"8332ca9cb40f7e66d1006b175ce36b60"},{"date_updated":"2020-07-14T12:45:52Z","checksum":"849f418620fb78d6ba23bb4f488ee93f","file_id":"5238","content_type":"application/pdf","file_size":144131,"creator":"system","access_level":"open_access","date_created":"2018-12-12T10:16:48Z","relation":"main_file","file_name":"IST-2017-119-v1+2_Barton_Recombination_Sex.pdf"}],"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"}],"quality_controlled":"1","title":"Recombination and sex","publisher":"Princeton University Press","publication_identifier":{"isbn":["9780691149776"]},"status":"public","date_updated":"2024-10-09T20:55:04Z","oa":1},{"file":[{"file_id":"4762","content_type":"text/rtf","checksum":"716e88714c3411cd0bd70928b14ea692","date_updated":"2020-07-14T12:45:52Z","file_name":"IST-2013-111-v1+1_Hybridisation_and_speciation_revised.rtf","relation":"main_file","date_created":"2018-12-12T10:09:38Z","creator":"system","file_size":13339,"access_level":"open_access"},{"creator":"system","file_size":103437,"access_level":"open_access","date_created":"2018-12-12T10:09:39Z","relation":"main_file","file_name":"IST-2017-111-v1+2_Hybridisation_and_speciation_revised.pdf","date_updated":"2020-07-14T12:45:52Z","content_type":"application/pdf","checksum":"957fd07c71c1b1eac2c65ae3311aca78","file_id":"4763"}],"title":"Does hybridisation influence speciation? ","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."}],"quality_controlled":"1","publisher":"Wiley-Blackwell","date_updated":"2025-09-29T13:31:43Z","doi":"10.1111/jeb.12015","status":"public","oa":1,"external_id":{"isi":["000313747600007"]},"_id":"2908","date_published":"2013-01-17T00:00:00Z","date_created":"2018-12-11T12:00:17Z","file_date_updated":"2020-07-14T12:45:52Z","publist_id":"3835","year":"2013","day":"17","article_processing_charge":"No","publication":"Journal of Evolutionary Biology","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","issue":"2","citation":{"ista":"Barton NH. 2013. Does hybridisation influence speciation? . Journal of Evolutionary Biology. 26(2), 267–269.","mla":"Barton, Nicholas H. “Does Hybridisation Influence Speciation? .” Journal of Evolutionary Biology, vol. 26, no. 2, Wiley-Blackwell, 2013, pp. 267–69, doi:10.1111/jeb.12015.","ieee":"N. H. Barton, “Does hybridisation influence speciation? ,” Journal of Evolutionary Biology, vol. 26, no. 2. Wiley-Blackwell, pp. 267–269, 2013.","chicago":"Barton, Nicholas H. “Does Hybridisation Influence Speciation? .” Journal of Evolutionary Biology. Wiley-Blackwell, 2013. https://doi.org/10.1111/jeb.12015.","short":"N.H. Barton, Journal of Evolutionary Biology 26 (2013) 267–269.","apa":"Barton, N. H. (2013). Does hybridisation influence speciation? . Journal of Evolutionary Biology. Wiley-Blackwell. https://doi.org/10.1111/jeb.12015","ama":"Barton NH. Does hybridisation influence speciation? . Journal of Evolutionary Biology. 2013;26(2):267-269. doi:10.1111/jeb.12015"},"corr_author":"1","pubrep_id":"111","oa_version":"Submitted Version","page":"267 - 269","language":[{"iso":"eng"}],"scopus_import":"1","ddc":["576"],"intvolume":" 26","month":"01","volume":26,"department":[{"_id":"NiBa"}],"author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","isi":1},{"publist_id":"3834","year":"2013","file_date_updated":"2020-07-14T12:45:52Z","date_created":"2018-12-11T12:00:17Z","_id":"2909","external_id":{"isi":["000315410500003"]},"date_published":"2013-01-16T00:00:00Z","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Journal of Statistical Mechanics Theory and Experiment","day":"16","article_processing_charge":"No","quality_controlled":"1","abstract":[{"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.","lang":"eng"}],"title":"Modelling evolution in a spatial continuum","publisher":"IOP Publishing","file":[{"date_updated":"2020-07-14T12:45:52Z","content_type":"application/pdf","checksum":"ce8a4424385b3086138a1e054e16e0e3","file_id":"5242","relation":"main_file","date_created":"2018-12-12T10:16:52Z","access_level":"open_access","file_size":702583,"creator":"system","file_name":"IST-2016-557-v1+1_BEVrevised.pdf"}],"oa":1,"date_updated":"2025-09-29T13:31:08Z","status":"public","doi":"10.1088/1742-5468/2013/01/P01002","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"oa_version":"Submitted Version","pubrep_id":"557","department":[{"_id":"NiBa"}],"author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"first_name":"Alison","last_name":"Etheridge","full_name":"Etheridge, Alison"},{"first_name":"Amandine","last_name":"Véber","full_name":"Véber, Amandine"}],"isi":1,"publication_status":"published","volume":2013,"month":"01","scopus_import":"1","intvolume":" 2013","ddc":["570"],"citation":{"apa":"Barton, N. H., Etheridge, A., & Véber, A. (2013). Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/2013/01/P01002","ama":"Barton NH, Etheridge A, Véber A. Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. 2013;2013(1). doi:10.1088/1742-5468/2013/01/P01002","short":"N.H. Barton, A. Etheridge, A. Véber, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).","mla":"Barton, Nicholas H., et al. “Modelling Evolution in a Spatial Continuum.” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 1, IOP Publishing, 2013, doi:10.1088/1742-5468/2013/01/P01002.","ieee":"N. H. Barton, A. Etheridge, and A. Véber, “Modelling evolution in a spatial continuum,” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 1. 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