[{"abstract":[{"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.","lang":"eng"}],"citation":{"ieee":"J. Levitz <i>et al.</i>, “Optical control of metabotropic glutamate receptors,” <i>Nature Neuroscience</i>, vol. 16. Nature Publishing Group, pp. 507–516, 2013.","ama":"Levitz J, Pantoja C, Gaub B, et al. Optical control of metabotropic glutamate receptors. <i>Nature Neuroscience</i>. 2013;16:507-516. doi:<a href=\"https://doi.org/10.1038/nn.3346\">10.1038/nn.3346</a>","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.","chicago":"Levitz, Joshua, Carlos Pantoja, Benjamin Gaub, Harald L Janovjak, Andreas Reiner, Adam Hoagland, David Schoppik, et al. “Optical Control of Metabotropic Glutamate Receptors.” <i>Nature Neuroscience</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/nn.3346\">https://doi.org/10.1038/nn.3346</a>.","mla":"Levitz, Joshua, et al. “Optical Control of Metabotropic Glutamate Receptors.” <i>Nature Neuroscience</i>, vol. 16, Nature Publishing Group, 2013, pp. 507–16, doi:<a href=\"https://doi.org/10.1038/nn.3346\">10.1038/nn.3346</a>.","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.","apa":"Levitz, J., Pantoja, C., Gaub, B., Janovjak, H. L., Reiner, A., Hoagland, A., … Isacoff, E. (2013). Optical control of metabotropic glutamate receptors. <i>Nature Neuroscience</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nn.3346\">https://doi.org/10.1038/nn.3346</a>"},"oa_version":"Submitted Version","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.)","month":"03","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681425/","open_access":"1"}],"isi":1,"quality_controlled":"1","date_created":"2018-12-11T11:59:57Z","language":[{"iso":"eng"}],"oa":1,"year":"2013","_id":"2856","author":[{"full_name":"Levitz, Joshua","first_name":"Joshua","last_name":"Levitz"},{"last_name":"Pantoja","first_name":"Carlos","full_name":"Pantoja, Carlos"},{"first_name":"Benjamin","full_name":"Gaub, Benjamin","last_name":"Gaub"},{"first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315"},{"first_name":"Andreas","full_name":"Reiner, Andreas","last_name":"Reiner"},{"last_name":"Hoagland","full_name":"Hoagland, Adam","first_name":"Adam"},{"last_name":"Schoppik","full_name":"Schoppik, David","first_name":"David"},{"full_name":"Kane, Brian","first_name":"Brian","last_name":"Kane"},{"full_name":"Stawski, Philipp","first_name":"Philipp","last_name":"Stawski"},{"last_name":"Schier","first_name":"Alexander","full_name":"Schier, Alexander"},{"last_name":"Trauner","full_name":"Trauner, Dirk","first_name":"Dirk"},{"last_name":"Isacoff","full_name":"Isacoff, Ehud","first_name":"Ehud"}],"volume":16,"external_id":{"isi":["000316723700023"],"pmid":["23455609"]},"department":[{"_id":"HaJa"}],"date_published":"2013-03-03T00:00:00Z","publication":"Nature Neuroscience","page":"507 - 516","scopus_import":"1","type":"journal_article","day":"03","publication_status":"published","status":"public","doi":"10.1038/nn.3346","title":"Optical control of metabotropic glutamate receptors","publisher":"Nature Publishing Group","publist_id":"3936","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"intvolume":"        16","article_processing_charge":"No","date_updated":"2025-09-29T13:39:33Z"},{"ec_funded":1,"publication":"Methods in Molecular Biology","page":"417 - 435","scopus_import":1,"type":"journal_article","has_accepted_license":"1","status":"public","publication_status":"published","day":"22","doi":"10.1007/978-1-62703-351-0_32","publisher":"Springer","title":"Optical control of ligand-gated ion channels","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3932","intvolume":"       998","ddc":["570"],"date_updated":"2025-04-15T06:43:12Z","abstract":[{"lang":"eng","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."}],"citation":{"apa":"Szobota, S., Mckenzie, C., &#38; Janovjak, H. L. (2013). Optical control of ligand-gated ion channels. <i>Methods in Molecular Biology</i>. Springer. <a href=\"https://doi.org/10.1007/978-1-62703-351-0_32\">https://doi.org/10.1007/978-1-62703-351-0_32</a>","ista":"Szobota S, Mckenzie C, Janovjak HL. 2013. Optical control of ligand-gated ion channels. Methods in Molecular Biology. 998, 417–435.","mla":"Szobota, Stephanie, et al. “Optical Control of Ligand-Gated Ion Channels.” <i>Methods in Molecular Biology</i>, vol. 998, Springer, 2013, pp. 417–35, doi:<a href=\"https://doi.org/10.1007/978-1-62703-351-0_32\">10.1007/978-1-62703-351-0_32</a>.","chicago":"Szobota, Stephanie, Catherine Mckenzie, and Harald L Janovjak. “Optical Control of Ligand-Gated Ion Channels.” <i>Methods in Molecular Biology</i>. Springer, 2013. <a href=\"https://doi.org/10.1007/978-1-62703-351-0_32\">https://doi.org/10.1007/978-1-62703-351-0_32</a>.","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. <i>Methods in Molecular Biology</i>. 2013;998:417-435. doi:<a href=\"https://doi.org/10.1007/978-1-62703-351-0_32\">10.1007/978-1-62703-351-0_32</a>","ieee":"S. Szobota, C. Mckenzie, and H. L. Janovjak, “Optical control of ligand-gated ion channels,” <i>Methods in Molecular Biology</i>, vol. 998. Springer, pp. 417–435, 2013."},"alternative_title":["MIMB"],"oa_version":"Submitted Version","file":[{"content_type":"application/pdf","access_level":"open_access","checksum":"1701f0d989f27ddac471b19a894ec0d1","relation":"main_file","file_name":"IST-2017-834-v1+1_szobota.pdf","file_id":"4952","date_created":"2018-12-12T10:12:34Z","creator":"system","date_updated":"2020-07-14T12:45:51Z","file_size":336734}],"month":"02","file_date_updated":"2020-07-14T12:45:51Z","project":[{"grant_number":"RGY0084/2012","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors","_id":"255BFFFA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology"}],"quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:59:57Z","oa":1,"year":"2013","author":[{"first_name":"Stephanie","full_name":"Szobota, Stephanie","last_name":"Szobota"},{"last_name":"Mckenzie","full_name":"Mckenzie, Catherine","first_name":"Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Janovjak","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"_id":"2857","volume":998,"date_published":"2013-02-22T00:00:00Z","pubrep_id":"834","department":[{"_id":"HaJa"}]},{"volume":6,"external_id":{"isi":["000313878800004"]},"date_published":"2013-01-01T00:00:00Z","pubrep_id":"415","department":[{"_id":"KrCh"}],"related_material":{"record":[{"id":"1400","status":"public","relation":"dissertation_contains"}]},"_id":"2858","author":[{"first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","full_name":"Reiter, Johannes","last_name":"Reiter","orcid":"0000-0002-0170-7353"},{"last_name":"Božić","first_name":"Ivana","full_name":"Božić, Ivana"},{"last_name":"Allen","full_name":"Allen, Benjamin","id":"135B5B70-E9D2-11E9-BD74-BB415DA2B523","first_name":"Benjamin"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:59:58Z","file_date_updated":"2020-07-14T12:45:51Z","project":[{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"quality_controlled":"1","issue":"1","oa":1,"year":"2013","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"date_created":"2018-12-12T10:15:50Z","creator":"system","date_updated":"2020-07-14T12:45:51Z","file_size":1172037,"content_type":"application/pdf","checksum":"e2955b3889f8a823c3d5a72cb16f8957","relation":"main_file","access_level":"open_access","file_name":"IST-2016-415-v1+1_Reiter_et_al-2013-Evolutionary_Applications.pdf","file_id":"5173"}],"oa_version":"Published Version","citation":{"ieee":"J. Reiter, I. Božić, B. Allen, K. Chatterjee, and M. Nowak, “The effect of one additional driver mutation on tumor progression,” <i>Evolutionary Applications</i>, vol. 6, no. 1. Wiley-Blackwell, pp. 34–45, 2013.","ama":"Reiter J, Božić I, Allen B, Chatterjee K, Nowak M. The effect of one additional driver mutation on tumor progression. <i>Evolutionary Applications</i>. 2013;6(1):34-45. doi:<a href=\"https://doi.org/10.1111/eva.12020\">10.1111/eva.12020</a>","short":"J. Reiter, I. Božić, B. Allen, K. Chatterjee, M. Nowak, Evolutionary Applications 6 (2013) 34–45.","mla":"Reiter, Johannes, et al. “The Effect of One Additional Driver Mutation on Tumor Progression.” <i>Evolutionary Applications</i>, vol. 6, no. 1, Wiley-Blackwell, 2013, pp. 34–45, doi:<a href=\"https://doi.org/10.1111/eva.12020\">10.1111/eva.12020</a>.","ista":"Reiter J, Božić I, Allen B, Chatterjee K, Nowak M. 2013. The effect of one additional driver mutation on tumor progression. Evolutionary Applications. 6(1), 34–45.","apa":"Reiter, J., Božić, I., Allen, B., Chatterjee, K., &#38; Nowak, M. (2013). The effect of one additional driver mutation on tumor progression. <i>Evolutionary Applications</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/eva.12020\">https://doi.org/10.1111/eva.12020</a>","chicago":"Reiter, Johannes, Ivana Božić, Benjamin Allen, Krishnendu Chatterjee, and Martin Nowak. “The Effect of One Additional Driver Mutation on Tumor Progression.” <i>Evolutionary Applications</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/eva.12020\">https://doi.org/10.1111/eva.12020</a>."},"abstract":[{"text":"Tumor growth is caused by the acquisition of driver mutations, which enhance the net reproductive rate of cells. Driver mutations may increase cell division, reduce cell death, or allow cells to overcome density-limiting effects. We study the dynamics of tumor growth as one additional driver mutation is acquired. Our models are based on two-type branching processes that terminate in either tumor disappearance or tumor detection. In our first model, both cell types grow exponentially, with a faster rate for cells carrying the additional driver. We find that the additional driver mutation does not affect the survival probability of the lesion, but can substantially reduce the time to reach the detectable size if the lesion is slow growing. In our second model, cells lacking the additional driver cannot exceed a fixed carrying capacity, due to density limitations. In this case, the time to detection depends strongly on this carrying capacity. Our model provides a quantitative framework for studying tumor dynamics during different stages of progression. We observe that early, small lesions need additional drivers, while late stage metastases are only marginally affected by them. These results help to explain why additional driver mutations are typically not detected in fast-growing metastases.","lang":"eng"}],"isi":1,"month":"01","date_updated":"2025-09-29T13:38:52Z","ddc":["570"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"3931","corr_author":"1","publisher":"Wiley-Blackwell","title":"The effect of one additional driver mutation on tumor progression","article_processing_charge":"No","intvolume":"         6","day":"01","publication_status":"published","status":"public","doi":"10.1111/eva.12020","page":"34 - 45","ec_funded":1,"publication":"Evolutionary Applications","type":"journal_article","has_accepted_license":"1","scopus_import":"1"},{"_id":"2859","author":[{"last_name":"Bendich","full_name":"Bendich, Paul","first_name":"Paul","id":"43F6EC54-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"first_name":"Dmitriy","full_name":"Morozov, Dmitriy","last_name":"Morozov"},{"id":"34A254A0-F248-11E8-B48F-1D18A9856A87","first_name":"Amit","full_name":"Patel, Amit","last_name":"Patel"}],"department":[{"_id":"HeEd"}],"date_published":"2013-05-01T00:00:00Z","volume":15,"external_id":{"arxiv":["1102.3389"],"isi":["000322423600003"]},"month":"05","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1102.3389v1"}],"isi":1,"citation":{"short":"P. Bendich, H. Edelsbrunner, D. Morozov, A. Patel, Homology, Homotopy and Applications 15 (2013) 51–72.","chicago":"Bendich, Paul, Herbert Edelsbrunner, Dmitriy Morozov, and Amit Patel. “Homology and Robustness of Level and Interlevel Sets.” <i>Homology, Homotopy and Applications</i>. International Press, 2013. <a href=\"https://doi.org/10.4310/HHA.2013.v15.n1.a3\">https://doi.org/10.4310/HHA.2013.v15.n1.a3</a>.","ista":"Bendich P, Edelsbrunner H, Morozov D, Patel A. 2013. Homology and robustness of level and interlevel sets. Homology, Homotopy and Applications. 15(1), 51–72.","mla":"Bendich, Paul, et al. “Homology and Robustness of Level and Interlevel Sets.” <i>Homology, Homotopy and Applications</i>, vol. 15, no. 1, International Press, 2013, pp. 51–72, doi:<a href=\"https://doi.org/10.4310/HHA.2013.v15.n1.a3\">10.4310/HHA.2013.v15.n1.a3</a>.","apa":"Bendich, P., Edelsbrunner, H., Morozov, D., &#38; Patel, A. (2013). Homology and robustness of level and interlevel sets. <i>Homology, Homotopy and Applications</i>. International Press. <a href=\"https://doi.org/10.4310/HHA.2013.v15.n1.a3\">https://doi.org/10.4310/HHA.2013.v15.n1.a3</a>","ieee":"P. Bendich, H. Edelsbrunner, D. Morozov, and A. Patel, “Homology and robustness of level and interlevel sets,” <i>Homology, Homotopy and Applications</i>, vol. 15, no. 1. International Press, pp. 51–72, 2013.","ama":"Bendich P, Edelsbrunner H, Morozov D, Patel A. Homology and robustness of level and interlevel sets. <i>Homology, Homotopy and Applications</i>. 2013;15(1):51-72. doi:<a href=\"https://doi.org/10.4310/HHA.2013.v15.n1.a3\">10.4310/HHA.2013.v15.n1.a3</a>"},"abstract":[{"lang":"eng","text":"Given a continuous function f:X-R on a topological space, we consider the preimages of intervals and their homology groups and show how to read the ranks of these groups from the extended persistence diagram of f. In addition, we quantify the robustness of the homology classes under perturbations of f using well groups, and we show how to read the ranks of these groups from the same extended persistence diagram. The special case X=R3 has ramifications in the fields of medical imaging and scientific visualization."}],"oa_version":"Preprint","year":"2013","oa":1,"issue":"1","quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:59:58Z","intvolume":"        15","article_processing_charge":"No","title":"Homology and robustness of level and interlevel sets","publisher":"International Press","publist_id":"3930","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-29T13:38:09Z","arxiv":1,"scopus_import":"1","type":"journal_article","publication":"Homology, Homotopy and Applications","page":"51 - 72","doi":"10.4310/HHA.2013.v15.n1.a3","status":"public","day":"01","publication_status":"published"},{"external_id":{"isi":["000317556000015"]},"volume":78,"date_published":"2013-03-21T00:00:00Z","department":[{"_id":"JoCs"}],"author":[{"last_name":"Dupret","first_name":"David","full_name":"Dupret, David"},{"last_name":"O'Neill","first_name":"Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87","full_name":"O'Neill, Joseph"},{"orcid":"0000-0002-5193-4036","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L"}],"_id":"2860","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:59:59Z","file_date_updated":"2020-07-14T12:45:52Z","quality_controlled":"1","project":[{"call_identifier":"FP7","_id":"257A4776-B435-11E9-9278-68D0E5697425","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","grant_number":"281511"}],"issue":"1","oa":1,"year":"2013","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa_version":"Published Version","file":[{"file_size":2637837,"date_updated":"2020-07-14T12:45:52Z","creator":"dernst","date_created":"2019-01-23T08:08:07Z","file_name":"2013_Neuron_Dupret.pdf","file_id":"5877","access_level":"open_access","checksum":"0e18cb8561153ddb50bb5af16e7c9e97","relation":"main_file","content_type":"application/pdf"}],"citation":{"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.","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.","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>.","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>","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>."},"abstract":[{"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.","lang":"eng"}],"isi":1,"month":"03","acknowledgement":"D.D. and J.C. were supported by a MRC Intramural Programme Grant U138197111","date_updated":"2025-09-29T13:37:37Z","ddc":["570"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"3929","corr_author":"1","publisher":"Elsevier","title":"Dynamic reconfiguration of hippocampal interneuron circuits during spatial learning","article_processing_charge":"No","intvolume":"        78","status":"public","publication_status":"published","day":"21","doi":"10.1016/j.neuron.2013.01.033","page":"166 - 180","publication":"Neuron","ec_funded":1,"type":"journal_article","has_accepted_license":"1","scopus_import":"1"},{"publication_status":"published","status":"public","day":"29","doi":"10.1088/1751-8113/46/12/125101","publication":"Journal of Physics A: Mathematical and Theoretical","scopus_import":"1","type":"journal_article","date_updated":"2025-09-29T13:36:56Z","corr_author":"1","publisher":"IOP Publishing","title":"Lyapunov exponent and topological entropy plateaus in piecewise linear maps","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"3928","intvolume":"        46","article_processing_charge":"No","quality_controlled":"1","date_created":"2018-12-11T11:59:59Z","language":[{"iso":"eng"}],"year":"2013","issue":"12","abstract":[{"lang":"eng","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."}],"citation":{"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, 2013.","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>","short":"V. Botella Soler, J. Oteo, J. Ros, P. Glendinning, Journal of Physics A: Mathematical and Theoretical 46 (2013).","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. <a href=\"https://doi.org/10.1088/1751-8113/46/12/125101\">https://doi.org/10.1088/1751-8113/46/12/125101</a>","ista":"Botella Soler V, Oteo J, Ros J, Glendinning P. 2013. Lyapunov exponent and topological entropy plateaus in piecewise linear maps. Journal of Physics A: Mathematical and Theoretical. 46(12), 125101.","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, 2013, doi:<a href=\"https://doi.org/10.1088/1751-8113/46/12/125101\">10.1088/1751-8113/46/12/125101</a>.","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, 2013. <a href=\"https://doi.org/10.1088/1751-8113/46/12/125101\">https://doi.org/10.1088/1751-8113/46/12/125101</a>."},"oa_version":"None","month":"03","isi":1,"volume":46,"external_id":{"isi":["000316058200010"]},"article_number":"125101","date_published":"2013-03-29T00:00:00Z","department":[{"_id":"GaTk"}],"author":[{"full_name":"Botella Soler, Vicente","id":"421234E8-F248-11E8-B48F-1D18A9856A87","first_name":"Vicente","last_name":"Botella Soler","orcid":"0000-0002-8790-1914"},{"last_name":"Oteo","first_name":"José","full_name":"Oteo, José"},{"last_name":"Ros","full_name":"Ros, Javier","first_name":"Javier"},{"last_name":"Glendinning","first_name":"Paul","full_name":"Glendinning, Paul"}],"_id":"2861"},{"month":"04","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.","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596994/"}],"isi":1,"citation":{"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>","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.","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>.","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>","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>.","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."},"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."}],"oa_version":"Submitted Version","oa":1,"year":"2013","issue":"7","quality_controlled":"1","date_created":"2018-12-11T11:59:59Z","language":[{"iso":"eng"}],"author":[{"first_name":"Hwee","full_name":"Tay, Hwee","last_name":"Tay"},{"last_name":"Schulze","first_name":"Sabrina","full_name":"Schulze, Sabrina"},{"last_name":"Compagnon","full_name":"Compagnon, Julien","id":"2E3E0988-F248-11E8-B48F-1D18A9856A87","first_name":"Julien"},{"last_name":"Foley","first_name":"Fiona","full_name":"Foley, 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","first_name":"H Joseph","last_name":"Yost"},{"first_name":"Salim","full_name":"Abdelilah Seyfried, Salim","last_name":"Abdelilah Seyfried"},{"last_name":"Amack","first_name":"Jeffrey","full_name":"Amack, Jeffrey"}],"_id":"2862","department":[{"_id":"CaHe"}],"date_published":"2013-04-01T00:00:00Z","external_id":{"isi":["000316096400018"],"pmid":["23482490"]},"volume":140,"scopus_import":"1","type":"journal_article","publication":"Development","page":"1550 - 1559","doi":"10.1242/dev.087130","day":"01","status":"public","publication_status":"published","intvolume":"       140","pmid":1,"article_processing_charge":"No","title":"Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle","publisher":"Company of Biologists","publist_id":"3927","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-29T13:36:20Z"},{"file":[{"file_name":"IST-2013-120-v1+1_journal.pcbi.1002922.pdf","file_id":"5099","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"5a30876c193209fa05b26db71845dd16","date_updated":"2020-07-14T12:45:52Z","file_size":1548120,"date_created":"2018-12-12T10:14:45Z","creator":"system"}],"oa_version":"Published Version","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":{"short":"E. Granot Atedgi, G. Tkačik, R. Segev, E. Schneidman, PLoS Computational Biology 9 (2013).","mla":"Granot Atedgi, Einat, et al. “Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.” <i>PLoS Computational Biology</i>, vol. 9, no. 3, e1002922, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1002922\">10.1371/journal.pcbi.1002922</a>.","apa":"Granot Atedgi, E., Tkačik, G., Segev, R., &#38; Schneidman, E. (2013). Stimulus-dependent maximum entropy models of neural population codes. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1002922\">https://doi.org/10.1371/journal.pcbi.1002922</a>","ista":"Granot Atedgi E, Tkačik G, Segev R, Schneidman E. 2013. Stimulus-dependent maximum entropy models of neural population codes. PLoS Computational Biology. 9(3), e1002922.","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>.","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.","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>"},"isi":1,"month":"03","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:00:00Z","quality_controlled":"1","file_date_updated":"2020-07-14T12:45:52Z","issue":"3","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"year":"2013","_id":"2863","author":[{"first_name":"Einat","full_name":"Granot Atedgi, Einat","last_name":"Granot Atedgi"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","full_name":"Tkacik, Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455"},{"full_name":"Segev, Ronen","first_name":"Ronen","last_name":"Segev"},{"last_name":"Schneidman","full_name":"Schneidman, Elad","first_name":"Elad"}],"article_number":"e1002922","volume":9,"external_id":{"isi":["000316864200003"]},"department":[{"_id":"GaTk"}],"date_published":"2013-03-01T00:00:00Z","pubrep_id":"120","publication":"PLoS Computational Biology","has_accepted_license":"1","type":"journal_article","scopus_import":"1","publication_status":"published","day":"01","status":"public","doi":"10.1371/journal.pcbi.1002922","publist_id":"3926","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Stimulus-dependent maximum entropy models of neural population codes","publisher":"Public Library of Science","corr_author":"1","article_processing_charge":"No","intvolume":"         9","date_updated":"2025-09-29T13:35:44Z","ddc":["570"]},{"doi":"10.3732/ajb.1200264","issue":"1","year":"2013","extern":1,"date_created":"2018-12-11T12:00:06Z","status":"public","day":"01","publication_status":"published","quality_controlled":0,"type":"journal_article","month":"01","page":"215 - 225","publication":"American Journal of Botany","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"}],"citation":{"ieee":"F. Vandenbussche, P. Callebert, P. Žádníková, E. Benková, and D. Van Der Straeten, “Brassinosteroid control of shoot gravitropism interacts with ethylene and depends on auxin signaling components,” <i>American Journal of Botany</i>, vol. 100, no. 1. Botanical Society of America, pp. 215–225, 2013.","ama":"Vandenbussche F, Callebert P, Žádníková P, Benková E, Van Der Straeten D. Brassinosteroid control of shoot gravitropism interacts with ethylene and depends on auxin signaling components. <i>American Journal of Botany</i>. 2013;100(1):215-225. doi:<a href=\"https://doi.org/10.3732/ajb.1200264\">10.3732/ajb.1200264</a>","short":"F. Vandenbussche, P. Callebert, P. Žádníková, E. Benková, D. Van Der Straeten, American Journal of Botany 100 (2013) 215–225.","mla":"Vandenbussche, Filip, et al. “Brassinosteroid Control of Shoot Gravitropism Interacts with Ethylene and Depends on Auxin Signaling Components.” <i>American Journal of Botany</i>, vol. 100, no. 1, Botanical Society of America, 2013, pp. 215–25, doi:<a href=\"https://doi.org/10.3732/ajb.1200264\">10.3732/ajb.1200264</a>.","ista":"Vandenbussche F, Callebert P, Žádníková P, Benková E, Van Der Straeten D. 2013. Brassinosteroid control of shoot gravitropism interacts with ethylene and depends on auxin signaling components. American Journal of Botany. 100(1), 215–225.","apa":"Vandenbussche, F., Callebert, P., Žádníková, P., Benková, E., &#38; Van Der Straeten, D. (2013). Brassinosteroid control of shoot gravitropism interacts with ethylene and depends on auxin signaling components. <i>American Journal of Botany</i>. Botanical Society of America. <a href=\"https://doi.org/10.3732/ajb.1200264\">https://doi.org/10.3732/ajb.1200264</a>","chicago":"Vandenbussche, Filip, Pieter Callebert, Petra Žádníková, Eva Benková, and Dominique Van Der Straeten. “Brassinosteroid Control of Shoot Gravitropism Interacts with Ethylene and Depends on Auxin Signaling Components.” <i>American Journal of Botany</i>. Botanical Society of America, 2013. <a href=\"https://doi.org/10.3732/ajb.1200264\">https://doi.org/10.3732/ajb.1200264</a>."},"date_updated":"2021-01-12T07:00:25Z","date_published":"2013-01-01T00:00:00Z","volume":100,"intvolume":"       100","_id":"2877","author":[{"last_name":"Vandenbussche","first_name":"Filip","full_name":"Vandenbussche, Filip"},{"last_name":"Callebert","full_name":"Callebert, Pieter","first_name":"Pieter"},{"last_name":"Žádníková","first_name":"Petra","full_name":"Žádníková, Petra"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Eva Benková"},{"last_name":"Van Der Straeten","full_name":"Van Der Straeten, Dominique","first_name":"Dominique"}],"publist_id":"3883","title":"Brassinosteroid control of shoot gravitropism interacts with ethylene and depends on auxin signaling components","publisher":"Botanical Society of America"},{"_id":"2880","author":[{"orcid":"0000-0001-5227-5741","last_name":"Marhavy","full_name":"Marhavy, Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"full_name":"Vanstraelen, Marleen","first_name":"Marleen","last_name":"Vanstraelen"},{"last_name":"De Rybel","first_name":"Bert","full_name":"De Rybel, Bert"},{"last_name":"Zhaojun","first_name":"Ding","full_name":"Zhaojun, Ding"},{"full_name":"Bennett, Malcolm","first_name":"Malcolm","last_name":"Bennett"},{"last_name":"Beeckman","full_name":"Beeckman, Tom","first_name":"Tom"},{"orcid":"0000-0002-8510-9739","last_name":"Benková","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}],"date_published":"2013-01-09T00:00:00Z","department":[{"_id":"EvBe"}],"volume":32,"external_id":{"isi":["000314141900014"],"pmid":["23178590"]},"month":"01","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545298/"}],"isi":1,"citation":{"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>","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.","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>.","short":"P. Marhavý, M. Vanstraelen, B. De Rybel, D. Zhaojun, M. Bennett, T. Beeckman, E. Benková, EMBO Journal 32 (2013) 149–158."},"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."}],"oa_version":"Submitted Version","oa":1,"year":"2013","issue":"1","project":[{"call_identifier":"FP7","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","name":"Hormonal cross-talk in plant organogenesis","grant_number":"207362"}],"quality_controlled":"1","date_created":"2018-12-11T12:00:07Z","language":[{"iso":"eng"}],"intvolume":"        32","pmid":1,"article_processing_charge":"No","publisher":"Wiley-Blackwell","title":"Auxin reflux between the endodermis and pericycle promotes lateral root initiation","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"3882","date_updated":"2025-09-29T13:35:12Z","scopus_import":"1","type":"journal_article","ec_funded":1,"publication":"EMBO Journal","page":"149 - 158","doi":"10.1038/emboj.2012.303","publication_status":"published","status":"public","day":"09"},{"publist_id":"3881","title":"Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis","publisher":"Nature Publishing Group","intvolume":"        23","author":[{"last_name":"Li","orcid":"0000-0001-5039-9660","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongjiang","full_name":"Hongjiang Li"},{"last_name":"Xu","full_name":"Xu, Tongda","first_name":"Tongda"},{"full_name":"Lin, Deshu","first_name":"Deshu","last_name":"Lin"},{"full_name":"Wen, Mingzhang","first_name":"Mingzhang","last_name":"Wen"},{"last_name":"Xie","first_name":"Mingtang","full_name":"Xie, Mingtang"},{"last_name":"Duclercq","full_name":"Duclercq, Jérôme","first_name":"Jérôme"},{"last_name":"Bielach","full_name":"Bielach, Agnieszka","first_name":"Agnieszka"},{"full_name":"Kim, Jungmook","first_name":"Jungmook","last_name":"Kim"},{"last_name":"Reddy","full_name":"Reddy, G Venugopala","first_name":"G Venugopala"},{"first_name":"Jianru","full_name":"Zuo, Jianru","last_name":"Zuo"},{"full_name":"Eva Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","last_name":"Benková"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Jirí Friml"},{"last_name":"Guo","first_name":"Hongwei","full_name":"Guo, Hongwei"},{"full_name":"Yang, Zhenbiao","first_name":"Zhenbiao","last_name":"Yang"}],"_id":"2881","volume":23,"date_updated":"2021-01-12T07:00:27Z","date_published":"2013-02-01T00:00:00Z","page":"290 - 299","publication":"Cell Research","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"}],"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.","apa":"Li, H., Xu, T., Lin, D., Wen, M., Xie, M., Duclercq, J., … Yang, Z. (2013). Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis. <i>Cell Research</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/cr.2012.146\">https://doi.org/10.1038/cr.2012.146</a>","mla":"Li, Hongjiang, et al. “Cytokinin Signaling Regulates Pavement Cell Morphogenesis in Arabidopsis.” <i>Cell Research</i>, vol. 23, no. 2, Nature Publishing Group, 2013, pp. 290–99, doi:<a href=\"https://doi.org/10.1038/cr.2012.146\">10.1038/cr.2012.146</a>.","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.","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.” <i>Cell Research</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/cr.2012.146\">https://doi.org/10.1038/cr.2012.146</a>.","ieee":"H. Li <i>et al.</i>, “Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis,” <i>Cell Research</i>, vol. 23, no. 2. Nature Publishing Group, pp. 290–299, 2013.","ama":"Li H, Xu T, Lin D, et al. Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis. <i>Cell Research</i>. 2013;23(2):290-299. doi:<a href=\"https://doi.org/10.1038/cr.2012.146\">10.1038/cr.2012.146</a>"},"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3567823/","open_access":"1"}],"type":"journal_article","month":"02","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.","extern":1,"status":"public","publication_status":"published","day":"01","date_created":"2018-12-11T12:00:07Z","quality_controlled":0,"doi":"10.1038/cr.2012.146","issue":"2","year":"2013","oa":1},{"_id":"2882","author":[{"first_name":"Christian","full_name":"Löfke, Christian","last_name":"Löfke"},{"full_name":"Zwiewka, Marta","first_name":"Marta","last_name":"Zwiewka"},{"last_name":"Heilmann","first_name":"Ingo","full_name":"Heilmann, Ingo"},{"full_name":"Van Montagu, Marc","first_name":"Marc","last_name":"Van Montagu"},{"last_name":"Teichmann","full_name":"Teichmann, Thomas","first_name":"Thomas"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"volume":110,"external_id":{"isi":["000315841900083"],"pmid":["23391733"]},"date_published":"2013-02-26T00:00:00Z","department":[{"_id":"JiFr"}],"oa_version":"Submitted Version","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"}],"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>","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>.","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>.","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.","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>","short":"C. Löfke, M. Zwiewka, I. Heilmann, M. Van Montagu, T. Teichmann, J. Friml, PNAS 110 (2013) 3627–3632."},"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587205/"}],"isi":1,"month":"02","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:00:07Z","quality_controlled":"1","issue":"9","year":"2013","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"3879","publisher":"National Academy of Sciences","title":"Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism","article_processing_charge":"No","pmid":1,"intvolume":"       110","date_updated":"2025-09-29T13:34:38Z","page":"3627 - 3632","publication":"PNAS","type":"journal_article","scopus_import":"1","publication_status":"published","day":"26","status":"public","doi":"10.1073/pnas.1300107110"},{"page":"202 - 214","publication":"Plant Cell","type":"journal_article","scopus_import":"1","day":"01","status":"public","publication_status":"published","doi":"10.1105/tpc.112.105999","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"3878","publisher":"American Society of Plant Biologists","title":"Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane","article_processing_charge":"No","pmid":1,"intvolume":"        25","date_updated":"2025-09-29T13:34:07Z","oa_version":"Submitted Version","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.","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>","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>.","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. <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>","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."},"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"}],"isi":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584535/","open_access":"1"}],"month":"01","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_created":"2018-12-11T12:00:08Z","language":[{"iso":"eng"}],"quality_controlled":"1","issue":"1","oa":1,"year":"2013","author":[{"last_name":"Wang","full_name":"Wang, Bangjun","first_name":"Bangjun"},{"last_name":"Bailly","full_name":"Bailly, Aurélien","first_name":"Aurélien"},{"last_name":"Zwiewk","full_name":"Zwiewk, Marta","first_name":"Marta"},{"full_name":"Henrichs, Sina","first_name":"Sina","last_name":"Henrichs"},{"full_name":"Azzarello, Elisa","first_name":"Elisa","last_name":"Azzarello"},{"full_name":"Mancuso, Stefano","first_name":"Stefano","last_name":"Mancuso"},{"full_name":"Maeshima, Masayoshi","first_name":"Masayoshi","last_name":"Maeshima"},{"full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"last_name":"Schulz","full_name":"Schulz, Alexander","first_name":"Alexander"},{"last_name":"Geisler","first_name":"Markus","full_name":"Geisler, Markus"}],"_id":"2883","external_id":{"pmid":["23321285"],"isi":["000315572400017"]},"volume":25,"date_published":"2013-01-01T00:00:00Z","department":[{"_id":"JiFr"}]},{"author":[{"last_name":"Maître","orcid":"0000-0002-3688-1474","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","first_name":"Jean-Léon","full_name":"Maître, Jean-Léon"},{"first_name":"Hélène","full_name":"Berthoumieux, Hélène","last_name":"Berthoumieux"},{"orcid":"0000-0003-4761-5996","last_name":"Krens","first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel"},{"last_name":"Salbreux","full_name":"Salbreux, Guillaume","first_name":"Guillaume"},{"first_name":"Frank","full_name":"Julicher, Frank","last_name":"Julicher"},{"last_name":"Paluch","first_name":"Ewa","full_name":"Paluch, Ewa"},{"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"}],"_id":"2884","external_id":{"isi":["000315749700011"]},"volume":29,"department":[{"_id":"CaHe"}],"date_published":"2013-02-01T00:00:00Z","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>","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>.","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>.","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.","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>","short":"J.-L. Maître, H. Berthoumieux, G. Krens, G. Salbreux, F. Julicher, E. Paluch, C.-P.J. Heisenberg, Medecine Sciences 29 (2013) 147–150."},"oa_version":"None","month":"02","isi":1,"quality_controlled":"1","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"},{"name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","grant_number":"I812-B12","_id":"2527D5CC-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T12:00:08Z","year":"2013","issue":"2","title":"Cell adhesion mechanics of zebrafish gastrulation","publisher":"Éditions Médicales et Scientifiques","publist_id":"3877","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"        29","article_processing_charge":"No","date_updated":"2025-09-29T13:33:31Z","publication":"Medecine Sciences","page":"147 - 150","scopus_import":"1","type":"journal_article","day":"01","status":"public","publication_status":"published","doi":"10.1051/medsci/2013292011"},{"publist_id":"3874","editor":[{"first_name":"Antonin","full_name":"Kucera, Antonin","last_name":"Kucera"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"first_name":"Jaroslav","full_name":"Nesetril, Jaroslav","last_name":"Nesetril"},{"first_name":"Tomas","full_name":"Vojnar, Tomas","last_name":"Vojnar"},{"last_name":"Antos","first_name":"David","full_name":"Antos, David"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Mathematical and Engineering Methods in Computer Science","publisher":"Springer","intvolume":"      7721","_id":"2885","volume":7721,"date_updated":"2019-08-02T12:37:55Z","series_title":"Lecture Notes in Computer Science","department":[{"_id":"ToHe"}],"date_published":"2013-01-09T00:00:00Z","page":"1 - 228","oa_version":"None","citation":{"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>.","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>","ista":"Kucera A, Henzinger TA, Nesetril J, Vojnar T, Antos D eds. 2013. Mathematical and Engineering Methods in Computer Science, Springer,p.","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>.","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>","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."},"abstract":[{"lang":"eng","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."}],"alternative_title":["LNCS"],"type":"conference_editor","acknowledgement":"Red Hat Czech Republic, Y Soft","month":"01","publication_status":"published","status":"public","day":"09","conference":{"name":"MEMICS: Mathematical and Engineering methods in computer science","end_date":"2012-10-28","start_date":"2012-10-25","location":"Znojmo, Czech Republic"},"language":[{"iso":"eng"}],"date_created":"2018-12-11T12:00:08Z","quality_controlled":"1","doi":"10.1007/978-3-642-36046-6","year":"2013"},{"language":[{"iso":"eng"}],"date_created":"2018-12-11T12:00:09Z","project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"},{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","year":"2013","oa":1,"oa_version":"Submitted Version","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"}],"alternative_title":["LNCS"],"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.","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>.","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>.","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>","ista":"Chmelik M, Řehák V. 2013. Controllable-choice message sequence graphs. 7721, 118–130.","short":"M. Chmelik, V. Řehák, 7721 (2013) 118–130."},"main_file_link":[{"url":"http://arxiv.org/abs/1209.4499","open_access":"1"}],"month":"01","external_id":{"arxiv":["1209.4499"]},"volume":7721,"department":[{"_id":"KrCh"}],"date_published":"2013-01-09T00:00:00Z","author":[{"last_name":"Chmelik","first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin"},{"first_name":"Vojtěch","full_name":"Řehák, Vojtěch","last_name":"Řehák"}],"_id":"2886","day":"09","publication_status":"published","conference":{"start_date":"2012-10-25","location":"Znojmo, Czech Republic","end_date":"2012-10-28","name":"MEMICS: Mathematical and Engineering Methods in Computer Science"},"status":"public","doi":"10.1007/978-3-642-36046-6_12","page":"118 - 130","ec_funded":1,"type":"conference","scopus_import":"1","arxiv":1,"date_updated":"2025-06-11T08:05:09Z","series_title":"Lecture Notes in Computer Science","publist_id":"3873","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Controllable-choice message sequence graphs","publisher":"Springer","corr_author":"1","article_processing_charge":"No","intvolume":"      7721"},{"date_updated":"2025-09-29T13:32:25Z","article_type":"original","article_processing_charge":"No","pmid":1,"intvolume":"       110","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"3872","publisher":"National Academy of Sciences","title":"Genotypic recognition and spatial responses by rice roots","doi":"10.1073/pnas.1222821110","status":"public","publication_status":"published","day":"12","type":"journal_article","scopus_import":"1","page":"2670 - 2675","publication":"PNAS","date_published":"2013-02-12T00:00:00Z","department":[{"_id":"HeEd"}],"volume":110,"external_id":{"pmid":["23362379"],"isi":["000315812800060"]},"author":[{"full_name":"Fang, Suqin","first_name":"Suqin","last_name":"Fang"},{"last_name":"Clark","first_name":"Randy","full_name":"Clark, Randy"},{"last_name":"Zheng","first_name":"Ying","full_name":"Zheng, Ying"},{"full_name":"Iyer Pascuzzi, Anjali","first_name":"Anjali","last_name":"Iyer Pascuzzi"},{"last_name":"Weitz","full_name":"Weitz, Joshua","first_name":"Joshua"},{"last_name":"Kochian","first_name":"Leon","full_name":"Kochian, Leon"},{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Liao, Hong","first_name":"Hong","last_name":"Liao"},{"last_name":"Benfey","first_name":"Philip","full_name":"Benfey, Philip"}],"_id":"2887","issue":"7","oa":1,"year":"2013","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:00:09Z","quality_controlled":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574932/","open_access":"1"}],"isi":1,"month":"02","oa_version":"Published Version","citation":{"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>","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.","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>.","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>","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>.","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."},"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."}]},{"main_file_link":[{"open_access":"0","url":"http://onlinelibrary.wiley.com/doi/10.1111/j.1525-142X.2008.00265.x/abstract"}],"type":"journal_article","month":"01","page":"514 - 515","publication":"Evolution & Development","citation":{"ieee":"R. Azevedo, R. Lohaus, and T. Paixao, “Networking networks,” <i>Evolution &#38; Development</i>, vol. 10, no. 5. Wiley-Blackwell, pp. 514–515, 2013.","ama":"Azevedo R, Lohaus R, Paixao T. Networking networks. <i>Evolution &#38; Development</i>. 2013;10(5):514-515.","short":"R. Azevedo, R. Lohaus, T. Paixao, Evolution &#38; Development 10 (2013) 514–515.","apa":"Azevedo, R., Lohaus, R., &#38; Paixao, T. (2013). Networking networks. <i>Evolution &#38; Development</i>. Wiley-Blackwell.","ista":"Azevedo R, Lohaus R, Paixao T. 2013. Networking networks. Evolution &#38; Development. 10(5), 514–515.","mla":"Azevedo, Ricardo, et al. “Networking Networks.” <i>Evolution &#38; Development</i>, vol. 10, no. 5, Wiley-Blackwell, 2013, pp. 514–15.","chicago":"Azevedo, Ricardo, Rolf Lohaus, and Tiago Paixao. “Networking Networks.” <i>Evolution &#38; Development</i>. Wiley-Blackwell, 2013."},"issue":"5","year":"2013","extern":1,"status":"public","date_created":"2018-12-11T12:00:14Z","day":"01","publication_status":"published","quality_controlled":0,"intvolume":"        10","author":[{"first_name":"Ricardo","full_name":"Azevedo, Ricardo B","last_name":"Azevedo"},{"first_name":"Rolf","full_name":"Lohaus, Rolf","last_name":"Lohaus"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","full_name":"Tiago Paixao","orcid":"0000-0003-2361-3953","last_name":"Paixao"}],"_id":"2900","publist_id":"3858","title":"Networking networks","publisher":"Wiley-Blackwell","date_updated":"2021-01-12T07:00:34Z","date_published":"2013-01-01T00:00:00Z","volume":10},{"department":[{"_id":"HeEd"},{"_id":"VlKo"},{"_id":"ChLa"}],"date_published":"2013-01-01T00:00:00Z","date_updated":"2025-07-10T11:52:23Z","volume":31,"intvolume":"        31","author":[{"full_name":"Chen, Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","first_name":"Chao","last_name":"Chen"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov"},{"last_name":"Yan","full_name":"Yan, Zhu","first_name":"Zhu"},{"last_name":"Metaxas","first_name":"Dimitris","full_name":"Metaxas, Dimitris"},{"orcid":"0000-0001-8622-7887","last_name":"Lampert","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"_id":"2901","article_processing_charge":"No","title":"Computing the M most probable modes of a graphical model","publisher":"JMLR","publist_id":"3846","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"year":"2013","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","day":"01","conference":{"start_date":"2013-04-29","location":"Scottsdale, AZ, United States","end_date":"2013-05-01","name":"AISTATS: Conference on Uncertainty in Artificial Intelligence"},"publication_status":"published","date_created":"2018-12-11T12:00:14Z","scopus_import":"1","month":"01","main_file_link":[{"open_access":"1","url":"http://jmlr.org/proceedings/papers/v31/chen13a.html"}],"type":"conference","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.","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.","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.","mla":"Chen, Chao, et al. <i>Computing the M Most Probable Modes of a Graphical Model</i>. Vol. 31, JMLR, 2013, pp. 161–69.","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.","short":"C. Chen, V. Kolmogorov, Z. Yan, D. Metaxas, C. Lampert, in:, JMLR, 2013, pp. 161–169."},"alternative_title":[" JMLR: W&CP"],"abstract":[{"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. ","lang":"eng"}],"oa_version":"None","page":"161 - 169"},{"department":[{"_id":"HeEd"}],"pubrep_id":"547","date_published":"2013-01-01T00:00:00Z","author":[{"orcid":"0000-0002-8030-9299","last_name":"Kerber","full_name":"Kerber, Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","first_name":"Michael"},{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"}],"_id":"2906","year":"2013","oa":1,"quality_controlled":"1","file_date_updated":"2020-07-14T12:45:52Z","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:00:16Z","month":"01","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."}],"citation":{"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 for Industrial and Applied Mathematics; 2013:70-77. doi:<a href=\"https://doi.org/10.1137/1.9781611972931.6\">10.1137/1.9781611972931.6</a>","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.","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 for Industrial and Applied Mathematics. <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 for 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>.","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 for Industrial and Applied Mathematics, 2013. <a href=\"https://doi.org/10.1137/1.9781611972931.6\">https://doi.org/10.1137/1.9781611972931.6</a>.","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."},"alternative_title":["ALENEX"],"file":[{"date_created":"2018-12-12T10:08:57Z","creator":"system","date_updated":"2020-07-14T12:45:52Z","file_size":403013,"checksum":"a15a3ba22df9445731507f3e06c9fcee","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4720","file_name":"IST-2016-547-v1+1_2013-P-08-MedusaII.pdf"}],"oa_version":"Submitted Version","ddc":["500"],"date_updated":"2025-06-03T11:47:11Z","article_processing_charge":"No","title":"3D kinetic alpha complexes and their implementation","publisher":"Society for Industrial and Applied Mathematics","corr_author":"1","publist_id":"3841","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1137/1.9781611972931.6","status":"public","publication_status":"published","day":"01","conference":{"name":"ALENEX: Algorithm Engineering and Experiments","end_date":"2013-01-07","location":"New Orleans, LA, United States","start_date":"2013-01-07"},"scopus_import":"1","has_accepted_license":"1","type":"conference","publication":"2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments","page":"70 - 77"}]