[{"author":[{"first_name":"Christian","full_name":"Löfke, Christian","last_name":"Löfke"},{"first_name":"Marta","full_name":"Zwiewka, Marta","last_name":"Zwiewka"},{"full_name":"Heilmann, Ingo","first_name":"Ingo","last_name":"Heilmann"},{"last_name":"Van Montagu","first_name":"Marc","full_name":"Van Montagu, Marc"},{"last_name":"Teichmann","first_name":"Thomas","full_name":"Teichmann, Thomas"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"_id":"2882","volume":110,"external_id":{"pmid":["23391733"],"isi":["000315841900083"]},"department":[{"_id":"JiFr"}],"date_published":"2013-02-26T00:00:00Z","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":{"short":"C. Löfke, M. Zwiewka, I. Heilmann, M. Van Montagu, T. Teichmann, J. Friml, PNAS 110 (2013) 3627–3632.","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>","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.","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>"},"oa_version":"Submitted Version","month":"02","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587205/","open_access":"1"}],"isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:00:07Z","oa":1,"year":"2013","issue":"9","title":"Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism","publisher":"National Academy of Sciences","publist_id":"3879","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"       110","pmid":1,"article_processing_charge":"No","date_updated":"2025-09-29T13:34:38Z","publication":"PNAS","page":"3627 - 3632","scopus_import":"1","type":"journal_article","day":"26","publication_status":"published","status":"public","doi":"10.1073/pnas.1300107110"},{"day":"01","status":"public","publication_status":"published","doi":"10.1105/tpc.112.105999","page":"202 - 214","publication":"Plant Cell","type":"journal_article","scopus_import":"1","date_updated":"2025-09-29T13:34:07Z","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","intvolume":"        25","pmid":1,"date_created":"2018-12-11T12:00:08Z","language":[{"iso":"eng"}],"quality_controlled":"1","issue":"1","year":"2013","oa":1,"oa_version":"Submitted Version","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"}],"citation":{"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.","ama":"Wang B, Bailly A, Zwiewk M, et al. Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane. <i>Plant Cell</i>. 2013;25(1):202-214. doi:<a href=\"https://doi.org/10.1105/tpc.112.105999\">10.1105/tpc.112.105999</a>","short":"B. Wang, A. Bailly, M. Zwiewk, S. Henrichs, E. Azzarello, S. Mancuso, M. Maeshima, J. Friml, A. Schulz, M. Geisler, Plant Cell 25 (2013) 202–214.","chicago":"Wang, Bangjun, Aurélien Bailly, Marta Zwiewk, Sina Henrichs, Elisa Azzarello, Stefano Mancuso, Masayoshi Maeshima, Jiří Friml, Alexander Schulz, and Markus Geisler. “Arabidopsis TWISTED DWARF1 Functionally Interacts with Auxin Exporter ABCB1 on the Root Plasma Membrane.” <i>Plant Cell</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1105/tpc.112.105999\">https://doi.org/10.1105/tpc.112.105999</a>.","mla":"Wang, Bangjun, et al. “Arabidopsis TWISTED DWARF1 Functionally Interacts with Auxin Exporter ABCB1 on the Root Plasma Membrane.” <i>Plant Cell</i>, vol. 25, no. 1, American Society of Plant Biologists, 2013, pp. 202–14, doi:<a href=\"https://doi.org/10.1105/tpc.112.105999\">10.1105/tpc.112.105999</a>.","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.","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>"},"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.","external_id":{"isi":["000315572400017"],"pmid":["23321285"]},"volume":25,"date_published":"2013-01-01T00:00:00Z","department":[{"_id":"JiFr"}],"author":[{"full_name":"Wang, Bangjun","first_name":"Bangjun","last_name":"Wang"},{"full_name":"Bailly, Aurélien","first_name":"Aurélien","last_name":"Bailly"},{"full_name":"Zwiewk, Marta","first_name":"Marta","last_name":"Zwiewk"},{"first_name":"Sina","full_name":"Henrichs, Sina","last_name":"Henrichs"},{"full_name":"Azzarello, Elisa","first_name":"Elisa","last_name":"Azzarello"},{"last_name":"Mancuso","full_name":"Mancuso, Stefano","first_name":"Stefano"},{"first_name":"Masayoshi","full_name":"Maeshima, Masayoshi","last_name":"Maeshima"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"first_name":"Alexander","full_name":"Schulz, Alexander","last_name":"Schulz"},{"first_name":"Markus","full_name":"Geisler, Markus","last_name":"Geisler"}],"_id":"2883"},{"department":[{"_id":"CaHe"}],"date_published":"2013-02-01T00:00:00Z","volume":29,"external_id":{"isi":["000315749700011"]},"author":[{"orcid":"0000-0002-3688-1474","last_name":"Maître","full_name":"Maître, Jean-Léon","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","first_name":"Jean-Léon"},{"last_name":"Berthoumieux","full_name":"Berthoumieux, Hélène","first_name":"Hélène"},{"first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","last_name":"Krens"},{"first_name":"Guillaume","full_name":"Salbreux, Guillaume","last_name":"Salbreux"},{"last_name":"Julicher","full_name":"Julicher, Frank","first_name":"Frank"},{"last_name":"Paluch","first_name":"Ewa","full_name":"Paluch, Ewa"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"_id":"2884","issue":"2","year":"2013","date_created":"2018-12-11T12:00:08Z","language":[{"iso":"eng"}],"project":[{"name":"Analysis of the Formation and Function of Different Cell Protusion Types During Cell Migration in Vivo","grant_number":"HE_3231/6-1","_id":"252064B8-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","grant_number":"I812-B12","_id":"2527D5CC-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"month":"02","oa_version":"None","citation":{"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.","ama":"Maître J-L, Berthoumieux H, Krens G, et al. Cell adhesion mechanics of zebrafish gastrulation. <i>Medecine Sciences</i>. 2013;29(2):147-150. doi:<a href=\"https://doi.org/10.1051/medsci/2013292011\">10.1051/medsci/2013292011</a>","short":"J.-L. Maître, H. Berthoumieux, G. Krens, G. Salbreux, F. Julicher, E. Paluch, C.-P.J. Heisenberg, Medecine Sciences 29 (2013) 147–150.","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>","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>.","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>."},"date_updated":"2025-09-29T13:33:31Z","article_processing_charge":"No","intvolume":"        29","publist_id":"3877","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Cell adhesion mechanics of zebrafish gastrulation","publisher":"Éditions Médicales et Scientifiques","doi":"10.1051/medsci/2013292011","day":"01","publication_status":"published","status":"public","type":"journal_article","scopus_import":"1","page":"147 - 150","publication":"Medecine Sciences"},{"intvolume":"      7721","_id":"2885","publist_id":"3874","editor":[{"full_name":"Kucera, Antonin","first_name":"Antonin","last_name":"Kucera"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"},{"last_name":"Nesetril","full_name":"Nesetril, Jaroslav","first_name":"Jaroslav"},{"last_name":"Vojnar","full_name":"Vojnar, Tomas","first_name":"Tomas"},{"last_name":"Antos","full_name":"Antos, David","first_name":"David"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Mathematical and Engineering Methods in Computer Science","publisher":"Springer","date_updated":"2019-08-02T12:37:55Z","series_title":"Lecture Notes in Computer Science","department":[{"_id":"ToHe"}],"date_published":"2013-01-09T00:00:00Z","volume":7721,"type":"conference_editor","acknowledgement":"Red Hat Czech Republic, Y Soft","month":"01","page":"1 - 228","oa_version":"None","citation":{"short":"A. Kucera, T.A. Henzinger, J. Nesetril, T. Vojnar, D. Antos, eds., Mathematical and Engineering Methods in Computer Science, Springer, 2013.","apa":"Kucera, A., Henzinger, T. A., Nesetril, J., Vojnar, T., &#38; Antos, D. (Eds.). (2013). <i>Mathematical and Engineering Methods in Computer Science</i> (Vol. 7721, pp. 1–228). Presented at the MEMICS: Mathematical and Engineering methods in computer science, Znojmo, Czech Republic: Springer. <a href=\"https://doi.org/10.1007/978-3-642-36046-6\">https://doi.org/10.1007/978-3-642-36046-6</a>","mla":"Kucera, Antonin, et al., editors. <i>Mathematical and Engineering Methods in Computer Science</i>. Vol. 7721, Springer, 2013, pp. 1–228, doi:<a href=\"https://doi.org/10.1007/978-3-642-36046-6\">10.1007/978-3-642-36046-6</a>.","ista":"Kucera A, Henzinger TA, Nesetril J, Vojnar T, Antos D eds. 2013. Mathematical and Engineering Methods in Computer Science, Springer,p.","chicago":"Kucera, Antonin, Thomas A Henzinger, Jaroslav Nesetril, Tomas Vojnar, and David Antos, eds. <i>Mathematical and Engineering Methods in Computer Science</i>. Vol. 7721. Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-36046-6\">https://doi.org/10.1007/978-3-642-36046-6</a>.","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.","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>"},"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"],"doi":"10.1007/978-3-642-36046-6","year":"2013","publication_status":"published","conference":{"start_date":"2012-10-25","location":"Znojmo, Czech Republic","name":"MEMICS: Mathematical and Engineering methods in computer science","end_date":"2012-10-28"},"day":"09","status":"public","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:00:08Z","quality_controlled":"1"},{"department":[{"_id":"KrCh"}],"date_published":"2013-01-09T00:00:00Z","external_id":{"arxiv":["1209.4499"]},"volume":7721,"_id":"2886","author":[{"last_name":"Chmelik","full_name":"Chmelik, Martin","first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Řehák, Vojtěch","first_name":"Vojtěch","last_name":"Řehák"}],"oa":1,"year":"2013","quality_controlled":"1","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T12:00:09Z","month":"01","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1209.4499"}],"citation":{"ieee":"M. Chmelik and V. Řehák, “Controllable-choice message sequence graphs,” vol. 7721. Springer, pp. 118–130, 2013.","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>","short":"M. Chmelik, V. Řehák, 7721 (2013) 118–130.","chicago":"Chmelik, Martin, and Vojtěch Řehák. “Controllable-Choice Message Sequence Graphs.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-36046-6_12\">https://doi.org/10.1007/978-3-642-36046-6_12</a>.","apa":"Chmelik, M., &#38; Řehák, V. (2013). Controllable-choice message sequence graphs. Presented at the MEMICS: Mathematical and Engineering Methods in Computer Science, Znojmo, Czech Republic: Springer. <a href=\"https://doi.org/10.1007/978-3-642-36046-6_12\">https://doi.org/10.1007/978-3-642-36046-6_12</a>","mla":"Chmelik, Martin, and Vojtěch Řehák. <i>Controllable-Choice Message Sequence Graphs</i>. Vol. 7721, Springer, 2013, pp. 118–30, doi:<a href=\"https://doi.org/10.1007/978-3-642-36046-6_12\">10.1007/978-3-642-36046-6_12</a>.","ista":"Chmelik M, Řehák V. 2013. Controllable-choice message sequence graphs. 7721, 118–130."},"abstract":[{"lang":"eng","text":"We focus on the realizability problem of Message Sequence Graphs (MSG), i.e. the problem whether a given MSG specification is correctly distributable among parallel components communicating via messages. This fundamental problem of MSG is known to be undecidable. We introduce a well motivated restricted class of MSG, so called controllable-choice MSG, and show that all its models are realizable and moreover it is decidable whether a given MSG model is a member of this class. In more detail, this class of MSG specifications admits a deadlock-free realization by overloading existing messages with additional bounded control data. We also show that the presented class is the largest known subclass of MSG that allows for deadlock-free realization."}],"alternative_title":["LNCS"],"oa_version":"Submitted Version","date_updated":"2025-06-11T08:05:09Z","series_title":"Lecture Notes in Computer Science","arxiv":1,"intvolume":"      7721","article_processing_charge":"No","title":"Controllable-choice message sequence graphs","publisher":"Springer","corr_author":"1","publist_id":"3873","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-642-36046-6_12","status":"public","publication_status":"published","day":"09","conference":{"location":"Znojmo, Czech Republic","start_date":"2012-10-25","end_date":"2012-10-28","name":"MEMICS: Mathematical and Engineering Methods in Computer Science"},"scopus_import":"1","type":"conference","ec_funded":1,"page":"118 - 130"},{"department":[{"_id":"HeEd"}],"date_published":"2013-02-12T00:00:00Z","volume":110,"external_id":{"isi":["000315812800060"],"pmid":["23362379"]},"author":[{"last_name":"Fang","first_name":"Suqin","full_name":"Fang, Suqin"},{"last_name":"Clark","full_name":"Clark, Randy","first_name":"Randy"},{"first_name":"Ying","full_name":"Zheng, Ying","last_name":"Zheng"},{"last_name":"Iyer Pascuzzi","first_name":"Anjali","full_name":"Iyer Pascuzzi, Anjali"},{"last_name":"Weitz","full_name":"Weitz, Joshua","first_name":"Joshua"},{"last_name":"Kochian","full_name":"Kochian, Leon","first_name":"Leon"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833"},{"last_name":"Liao","first_name":"Hong","full_name":"Liao, Hong"},{"first_name":"Philip","full_name":"Benfey, Philip","last_name":"Benfey"}],"_id":"2887","issue":"7","oa":1,"year":"2013","date_created":"2018-12-11T12:00:09Z","language":[{"iso":"eng"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574932/"}],"isi":1,"month":"02","oa_version":"Published Version","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"}],"citation":{"chicago":"Fang, Suqin, Randy Clark, Ying Zheng, Anjali Iyer Pascuzzi, Joshua Weitz, Leon Kochian, Herbert Edelsbrunner, Hong Liao, and Philip Benfey. “Genotypic Recognition and Spatial Responses by Rice Roots.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1222821110\">https://doi.org/10.1073/pnas.1222821110</a>.","ista":"Fang S, Clark R, Zheng Y, Iyer Pascuzzi A, Weitz J, Kochian L, Edelsbrunner H, Liao H, Benfey P. 2013. Genotypic recognition and spatial responses by rice roots. PNAS. 110(7), 2670–2675.","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>.","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.","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>","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."},"article_type":"original","date_updated":"2025-09-29T13:32:25Z","article_processing_charge":"No","pmid":1,"intvolume":"       110","publist_id":"3872","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Genotypic recognition and spatial responses by rice roots","publisher":"National Academy of Sciences","doi":"10.1073/pnas.1222821110","status":"public","day":"12","publication_status":"published","type":"journal_article","scopus_import":"1","page":"2670 - 2675","publication":"PNAS"},{"date_updated":"2021-01-12T07:00:34Z","date_published":"2013-01-01T00:00:00Z","volume":10,"intvolume":"        10","_id":"2900","author":[{"full_name":"Azevedo, Ricardo B","first_name":"Ricardo","last_name":"Azevedo"},{"last_name":"Lohaus","first_name":"Rolf","full_name":"Lohaus, Rolf"},{"last_name":"Paixao","orcid":"0000-0003-2361-3953","full_name":"Tiago Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago"}],"publist_id":"3858","title":"Networking networks","publisher":"Wiley-Blackwell","issue":"5","year":"2013","extern":1,"date_created":"2018-12-11T12:00:14Z","publication_status":"published","day":"01","status":"public","quality_controlled":0,"type":"journal_article","main_file_link":[{"url":"http://onlinelibrary.wiley.com/doi/10.1111/j.1525-142X.2008.00265.x/abstract","open_access":"0"}],"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.","chicago":"Azevedo, Ricardo, Rolf Lohaus, and Tiago Paixao. “Networking Networks.” <i>Evolution &#38; Development</i>. Wiley-Blackwell, 2013.","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."}},{"oa_version":"None","page":"161 - 169","citation":{"short":"C. Chen, V. Kolmogorov, Z. Yan, D. Metaxas, C. Lampert, in:, JMLR, 2013, pp. 161–169.","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.","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.","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.","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.","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."},"alternative_title":[" JMLR: W&CP"],"abstract":[{"lang":"eng","text":" We introduce the M-modes problem for graphical models: predicting the M label configurations of highest probability that are at the same time local maxima of the probability landscape. M-modes have multiple possible applications: because they are intrinsically diverse, they provide a principled alternative to non-maximum suppression techniques for structured prediction, they can act as codebook vectors for quantizing the configuration space, or they can form component centers for mixture model approximation. We present two algorithms for solving the M-modes problem. The first algorithm solves the problem in polynomial time when the underlying graphical model is a simple chain. The second algorithm solves the problem for junction chains. In synthetic and real dataset, we demonstrate how M-modes can improve the performance of prediction. We also use the generated modes as a tool to understand the topography of the probability distribution of configurations, for example with relation to the training set size and amount of noise in the data. "}],"type":"conference","main_file_link":[{"url":"http://jmlr.org/proceedings/papers/v31/chen13a.html","open_access":"1"}],"scopus_import":"1","month":"01","language":[{"iso":"eng"}],"status":"public","conference":{"end_date":"2013-05-01","name":"AISTATS: Conference on Uncertainty in Artificial Intelligence","start_date":"2013-04-29","location":"Scottsdale, AZ, United States"},"publication_status":"published","date_created":"2018-12-11T12:00:14Z","day":"01","quality_controlled":"1","oa":1,"year":"2013","publist_id":"3846","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Computing the M most probable modes of a graphical model","publisher":"JMLR","article_processing_charge":"No","intvolume":"        31","_id":"2901","author":[{"last_name":"Chen","full_name":"Chen, Chao","first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"},{"full_name":"Yan, Zhu","first_name":"Zhu","last_name":"Yan"},{"first_name":"Dimitris","full_name":"Metaxas, Dimitris","last_name":"Metaxas"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert"}],"volume":31,"date_updated":"2025-07-10T11:52:23Z","department":[{"_id":"HeEd"},{"_id":"VlKo"},{"_id":"ChLa"}],"date_published":"2013-01-01T00:00:00Z"},{"_id":"2906","author":[{"last_name":"Kerber","orcid":"0000-0002-8030-9299","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","full_name":"Kerber, Michael"},{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"}],"pubrep_id":"547","date_published":"2013-01-01T00:00:00Z","department":[{"_id":"HeEd"}],"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.","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>.","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.","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."},"abstract":[{"text":"Motivated by an application in cell biology, we describe an extension of the kinetic data structures framework from Delaunay triangulations to fixed-radius alpha complexes. Our algorithm is implemented\r\nusing CGAL, following the exact geometric computation paradigm. We report on several\r\ntechniques to accelerate the computation that turn our implementation applicable to the underlying biological\r\nproblem.","lang":"eng"}],"alternative_title":["ALENEX"],"oa_version":"Submitted Version","file":[{"date_created":"2018-12-12T10:08:57Z","creator":"system","date_updated":"2020-07-14T12:45:52Z","file_size":403013,"content_type":"application/pdf","access_level":"open_access","checksum":"a15a3ba22df9445731507f3e06c9fcee","relation":"main_file","file_id":"4720","file_name":"IST-2016-547-v1+1_2013-P-08-MedusaII.pdf"}],"month":"01","file_date_updated":"2020-07-14T12:45:52Z","quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:00:16Z","year":"2013","oa":1,"publisher":"Society for Industrial and Applied Mathematics","corr_author":"1","title":"3D kinetic alpha complexes and their implementation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3841","article_processing_charge":"No","ddc":["500"],"date_updated":"2025-06-03T11:47:11Z","publication":"2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments","page":"70 - 77","scopus_import":"1","type":"conference","has_accepted_license":"1","day":"01","status":"public","publication_status":"published","conference":{"end_date":"2013-01-07","name":"ALENEX: Algorithm Engineering and Experiments","start_date":"2013-01-07","location":"New Orleans, LA, United States"},"doi":"10.1137/1.9781611972931.6"},{"department":[{"_id":"NiBa"}],"pubrep_id":"119","date_published":"2013-11-04T00:00:00Z","publication_identifier":{"isbn":["9780691149776"]},"_id":"2907","author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"year":"2013","oa":1,"quality_controlled":"1","file_date_updated":"2020-07-14T12:45:52Z","date_created":"2018-12-11T12:00:16Z","language":[{"iso":"eng"}],"month":"11","citation":{"ama":"Barton NH. Recombination and sex. In: <i>The Princeton Guide to Evolution</i>. Princeton University Press; 2013:328-333.","ieee":"N. H. Barton, “Recombination and sex,” in <i>The Princeton Guide to Evolution</i>, Princeton University Press, 2013, pp. 328–333.","ista":"Barton NH. 2013.Recombination and sex. In: The Princeton Guide to Evolution. , 328–333.","mla":"Barton, Nicholas H. “Recombination and Sex.” <i>The Princeton Guide to Evolution</i>, Princeton University Press, 2013, pp. 328–33.","apa":"Barton, N. H. (2013). Recombination and sex. In <i>The Princeton Guide to Evolution</i> (pp. 328–333). Princeton University Press.","chicago":"Barton, Nicholas H. “Recombination and Sex.” In <i>The Princeton Guide to Evolution</i>, 328–33. Princeton University Press, 2013.","short":"N.H. Barton, in:, The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–333."},"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"}],"file":[{"creator":"system","date_created":"2018-12-12T10:16:47Z","file_size":79838,"date_updated":"2020-07-14T12:45:52Z","access_level":"open_access","checksum":"8332ca9cb40f7e66d1006b175ce36b60","relation":"main_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"IST-2013-119-v1+1_IV.4_Recombination_and_Sex_Barton_1-13-13-e.docx","file_id":"5237"},{"file_size":144131,"date_updated":"2020-07-14T12:45:52Z","creator":"system","date_created":"2018-12-12T10:16:48Z","file_name":"IST-2017-119-v1+2_Barton_Recombination_Sex.pdf","file_id":"5238","checksum":"849f418620fb78d6ba23bb4f488ee93f","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"oa_version":"Submitted Version","ddc":["576"],"date_updated":"2024-10-09T20:55:04Z","title":"Recombination and sex","publisher":"Princeton University Press","corr_author":"1","publist_id":"3839","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","day":"04","has_accepted_license":"1","type":"book_chapter","publication":"The Princeton Guide to Evolution","page":"328 - 333"},{"doi":"10.1111/jeb.12015","day":"17","status":"public","publication_status":"published","scopus_import":"1","type":"journal_article","has_accepted_license":"1","publication":"Journal of Evolutionary Biology","page":"267 - 269","ddc":["576"],"date_updated":"2025-09-29T13:31:43Z","intvolume":"        26","article_processing_charge":"No","corr_author":"1","publisher":"Wiley-Blackwell","title":"Does hybridisation influence speciation?  ","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"3835","oa":1,"year":"2013","issue":"2","file_date_updated":"2020-07-14T12:45:52Z","quality_controlled":"1","date_created":"2018-12-11T12:00:17Z","language":[{"iso":"eng"}],"month":"01","isi":1,"citation":{"short":"N.H. Barton, Journal of Evolutionary Biology 26 (2013) 267–269.","chicago":"Barton, Nicholas H. “Does Hybridisation Influence Speciation?  .” <i>Journal of Evolutionary Biology</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/jeb.12015\">https://doi.org/10.1111/jeb.12015</a>.","ista":"Barton NH. 2013. Does hybridisation influence speciation?  . Journal of Evolutionary Biology. 26(2), 267–269.","apa":"Barton, N. H. (2013). Does hybridisation influence speciation?  . <i>Journal of Evolutionary Biology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/jeb.12015\">https://doi.org/10.1111/jeb.12015</a>","mla":"Barton, Nicholas H. “Does Hybridisation Influence Speciation?  .” <i>Journal of Evolutionary Biology</i>, vol. 26, no. 2, Wiley-Blackwell, 2013, pp. 267–69, doi:<a href=\"https://doi.org/10.1111/jeb.12015\">10.1111/jeb.12015</a>.","ieee":"N. H. Barton, “Does hybridisation influence speciation?  ,” <i>Journal of Evolutionary Biology</i>, vol. 26, no. 2. Wiley-Blackwell, pp. 267–269, 2013.","ama":"Barton NH. Does hybridisation influence speciation?  . <i>Journal of Evolutionary Biology</i>. 2013;26(2):267-269. doi:<a href=\"https://doi.org/10.1111/jeb.12015\">10.1111/jeb.12015</a>"},"abstract":[{"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.","lang":"eng"}],"file":[{"content_type":"text/rtf","checksum":"716e88714c3411cd0bd70928b14ea692","access_level":"open_access","relation":"main_file","file_name":"IST-2013-111-v1+1_Hybridisation_and_speciation_revised.rtf","file_id":"4762","creator":"system","date_created":"2018-12-12T10:09:38Z","file_size":13339,"date_updated":"2020-07-14T12:45:52Z"},{"file_size":103437,"date_updated":"2020-07-14T12:45:52Z","creator":"system","date_created":"2018-12-12T10:09:39Z","file_id":"4763","file_name":"IST-2017-111-v1+2_Hybridisation_and_speciation_revised.pdf","content_type":"application/pdf","checksum":"957fd07c71c1b1eac2c65ae3311aca78","access_level":"open_access","relation":"main_file"}],"oa_version":"Submitted Version","date_published":"2013-01-17T00:00:00Z","pubrep_id":"111","department":[{"_id":"NiBa"}],"volume":26,"external_id":{"isi":["000313747600007"]},"_id":"2908","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}]},{"day":"16","publication_status":"published","status":"public","doi":"10.1088/1742-5468/2013/01/P01002","ec_funded":1,"publication":"Journal of Statistical Mechanics Theory and Experiment","scopus_import":"1","has_accepted_license":"1","type":"journal_article","ddc":["570"],"date_updated":"2025-09-29T13:31:08Z","title":"Modelling evolution in a spatial continuum","publisher":"IOP Publishing","corr_author":"1","publist_id":"3834","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"      2013","article_processing_charge":"No","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"quality_controlled":"1","file_date_updated":"2020-07-14T12:45:52Z","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:00:17Z","oa":1,"year":"2013","issue":"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"}],"citation":{"short":"N.H. Barton, A. Etheridge, A. Véber, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).","chicago":"Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “Modelling Evolution in a Spatial Continuum.” <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing, 2013. <a href=\"https://doi.org/10.1088/1742-5468/2013/01/P01002\">https://doi.org/10.1088/1742-5468/2013/01/P01002</a>.","mla":"Barton, Nicholas H., et al. “Modelling Evolution in a Spatial Continuum.” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2013, no. 1, IOP Publishing, 2013, doi:<a href=\"https://doi.org/10.1088/1742-5468/2013/01/P01002\">10.1088/1742-5468/2013/01/P01002</a>.","apa":"Barton, N. H., Etheridge, A., &#38; Véber, A. (2013). Modelling evolution in a spatial continuum. <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1742-5468/2013/01/P01002\">https://doi.org/10.1088/1742-5468/2013/01/P01002</a>","ista":"Barton NH, Etheridge A, Véber A. 2013. Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. 2013(1).","ieee":"N. H. Barton, A. Etheridge, and A. Véber, “Modelling evolution in a spatial continuum,” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2013, no. 1. IOP Publishing, 2013.","ama":"Barton NH, Etheridge A, Véber A. Modelling evolution in a spatial continuum. <i>Journal of Statistical Mechanics Theory and Experiment</i>. 2013;2013(1). doi:<a href=\"https://doi.org/10.1088/1742-5468/2013/01/P01002\">10.1088/1742-5468/2013/01/P01002</a>"},"file":[{"file_name":"IST-2016-557-v1+1_BEVrevised.pdf","file_id":"5242","relation":"main_file","access_level":"open_access","checksum":"ce8a4424385b3086138a1e054e16e0e3","content_type":"application/pdf","file_size":702583,"date_updated":"2020-07-14T12:45:52Z","creator":"system","date_created":"2018-12-12T10:16:52Z"}],"oa_version":"Submitted Version","month":"01","isi":1,"volume":2013,"external_id":{"isi":["000315410500003"]},"department":[{"_id":"NiBa"}],"pubrep_id":"557","date_published":"2013-01-16T00:00:00Z","_id":"2909","author":[{"last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"full_name":"Etheridge, Alison","first_name":"Alison","last_name":"Etheridge"},{"last_name":"Véber","full_name":"Véber, Amandine","first_name":"Amandine"}]},{"file_date_updated":"2020-07-14T12:45:52Z","quality_controlled":"1","project":[{"call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T12:00:17Z","language":[{"iso":"eng"}],"oa":1,"year":"2013","issue":"7","abstract":[{"lang":"eng","text":"Coalescent simulation has become an indispensable tool in population genetics and many complex evolutionary scenarios have been incorporated into the basic algorithm. Despite many years of intense interest in spatial structure, however, there are no available methods to simulate the ancestry of a sample of genes that occupy a spatial continuum. This is mainly due to the severe technical problems encountered by the classical model of isolation\r\nby distance. A recently introduced model solves these technical problems and provides a solid theoretical basis for the study of populations evolving in continuous space. We present a detailed algorithm to simulate the coalescent process in this model, and provide an efficient implementation of a generalised version of this algorithm as a freely available Python module."}],"citation":{"ama":"Kelleher J, Barton NH, Etheridge A. Coalescent simulation in continuous space. <i>Bioinformatics</i>. 2013;29(7):955-956. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btt067\">10.1093/bioinformatics/btt067</a>","ieee":"J. Kelleher, N. H. Barton, and A. Etheridge, “Coalescent simulation in continuous space,” <i>Bioinformatics</i>, vol. 29, no. 7. Oxford University Press, pp. 955–956, 2013.","apa":"Kelleher, J., Barton, N. H., &#38; Etheridge, A. (2013). Coalescent simulation in continuous space. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/btt067\">https://doi.org/10.1093/bioinformatics/btt067</a>","mla":"Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space.” <i>Bioinformatics</i>, vol. 29, no. 7, Oxford University Press, 2013, pp. 955–56, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btt067\">10.1093/bioinformatics/btt067</a>.","ista":"Kelleher J, Barton NH, Etheridge A. 2013. Coalescent simulation in continuous space. Bioinformatics. 29(7), 955–956.","chicago":"Kelleher, Jerome, Nicholas H Barton, and Alison Etheridge. “Coalescent Simulation in Continuous Space.” <i>Bioinformatics</i>. Oxford University Press, 2013. <a href=\"https://doi.org/10.1093/bioinformatics/btt067\">https://doi.org/10.1093/bioinformatics/btt067</a>.","short":"J. Kelleher, N.H. Barton, A. Etheridge, Bioinformatics 29 (2013) 955–956."},"oa_version":"Published Version","file":[{"creator":"system","date_created":"2018-12-12T10:16:04Z","file_size":170197,"date_updated":"2020-07-14T12:45:52Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"a3b54d7477fac923815ac082403d9bd0","file_name":"IST-2016-556-v1+1_bioinformatics-2013.pdf","file_id":"5189"}],"month":"02","isi":1,"volume":29,"external_id":{"isi":["000316695700020"]},"date_published":"2013-02-07T00:00:00Z","pubrep_id":"556","department":[{"_id":"NiBa"}],"_id":"2910","author":[{"last_name":"Kelleher","full_name":"Kelleher, Jerome","first_name":"Jerome"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Etheridge","first_name":"Alison","full_name":"Etheridge, Alison"}],"publication_status":"published","day":"07","status":"public","doi":"10.1093/bioinformatics/btt067","publication":"Bioinformatics","ec_funded":1,"page":"955 - 956","scopus_import":"1","type":"journal_article","has_accepted_license":"1","ddc":["570"],"date_updated":"2025-09-29T13:30:36Z","publisher":"Oxford University Press","corr_author":"1","title":"Coalescent simulation in continuous space","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"3833","intvolume":"        29","article_processing_charge":"No"},{"status":"public","day":"28","publication_status":"published","doi":"10.1103/PhysRevLett.110.058104","publication":"Physical Review Letters","scopus_import":"1","type":"journal_article","arxiv":1,"date_updated":"2025-09-29T13:29:59Z","corr_author":"1","publisher":"American Physical Society","title":"Retinal metric: a stimulus distance measure derived from population neural responses","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"3830","intvolume":"       110","article_processing_charge":"No","quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:00:18Z","oa":1,"year":"2013","issue":"5","abstract":[{"text":"The ability of an organism to distinguish between various stimuli is limited by the structure and noise in the population code of its sensory neurons. Here we infer a distance measure on the stimulus space directly from the recorded activity of 100 neurons in the salamander retina. In contrast to previously used measures of stimulus similarity, this &quot;neural metric&quot; tells us how distinguishable a pair of stimulus clips is to the retina, based on the similarity between the induced distributions of population responses. We show that the retinal distance strongly deviates from Euclidean, or any static metric, yet has a simple structure: we identify the stimulus features that the neural population is jointly sensitive to, and show the support-vector-machine- like kernel function relating the stimulus and neural response spaces. We show that the non-Euclidean nature of the retinal distance has important consequences for neural decoding.","lang":"eng"}],"citation":{"short":"G. Tkačik, E. Granot Atedgi, R. Segev, E. Schneidman, Physical Review Letters 110 (2013).","chicago":"Tkačik, Gašper, Einat Granot Atedgi, Ronen Segev, and Elad Schneidman. “Retinal Metric: A Stimulus Distance Measure Derived from Population Neural Responses.” <i>Physical Review Letters</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevLett.110.058104\">https://doi.org/10.1103/PhysRevLett.110.058104</a>.","ista":"Tkačik G, Granot Atedgi E, Segev R, Schneidman E. 2013. Retinal metric: a stimulus distance measure derived from population neural responses. Physical Review Letters. 110(5), 058104.","apa":"Tkačik, G., Granot Atedgi, E., Segev, R., &#38; Schneidman, E. (2013). Retinal metric: a stimulus distance measure derived from population neural responses. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.110.058104\">https://doi.org/10.1103/PhysRevLett.110.058104</a>","mla":"Tkačik, Gašper, et al. “Retinal Metric: A Stimulus Distance Measure Derived from Population Neural Responses.” <i>Physical Review Letters</i>, vol. 110, no. 5, 058104, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.058104\">10.1103/PhysRevLett.110.058104</a>.","ieee":"G. Tkačik, E. Granot Atedgi, R. Segev, and E. Schneidman, “Retinal metric: a stimulus distance measure derived from population neural responses,” <i>Physical Review Letters</i>, vol. 110, no. 5. American Physical Society, 2013.","ama":"Tkačik G, Granot Atedgi E, Segev R, Schneidman E. Retinal metric: a stimulus distance measure derived from population neural responses. <i>Physical Review Letters</i>. 2013;110(5). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.058104\">10.1103/PhysRevLett.110.058104</a>"},"oa_version":"Preprint","month":"01","main_file_link":[{"url":"http://arxiv.org/abs/1205.6598","open_access":"1"}],"isi":1,"external_id":{"arxiv":["1205.6598"],"isi":["000314090300012"]},"volume":110,"article_number":"058104","date_published":"2013-01-28T00:00:00Z","department":[{"_id":"GaTk"}],"_id":"2913","author":[{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"},{"first_name":"Einat","full_name":"Granot Atedgi, Einat","last_name":"Granot Atedgi"},{"first_name":"Ronen","full_name":"Segev, Ronen","last_name":"Segev"},{"first_name":"Elad","full_name":"Schneidman, Elad","last_name":"Schneidman"}]},{"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)"},"language":[{"iso":"eng"}],"date_created":"2018-12-11T12:00:19Z","file_date_updated":"2020-07-14T12:45:53Z","quality_controlled":"1","isi":1,"acknowledgement":"This work was supported in part by NSF Grants No. IIS-0613435, No. IBN-0344678, and No. PHY-0957573, by NIH Grant No. T32 MH065214, by the Human Frontier Science Program, and by the Swartz Foundation.\r\nCC BY 3.0\r\n","month":"01","oa_version":"Published Version","file":[{"file_id":"5366","file_name":"IST-2016-401-v1+1_1281.full.pdf","checksum":"72bfbc2094c4680e8a8a6bed668cd06d","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:53Z","file_size":416965,"date_created":"2018-12-12T10:18:44Z","creator":"system"}],"citation":{"ieee":"G. Stephens, T. Mora, G. Tkačik, and W. Bialek, “Statistical thermodynamics of natural images,” <i>Physical Review Letters</i>, vol. 110, no. 1. American Physical Society, 2013.","ama":"Stephens G, Mora T, Tkačik G, Bialek W. Statistical thermodynamics of natural images. <i>Physical Review Letters</i>. 2013;110(1). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.018701\">10.1103/PhysRevLett.110.018701</a>","short":"G. Stephens, T. Mora, G. Tkačik, W. Bialek, Physical Review Letters 110 (2013).","ista":"Stephens G, Mora T, Tkačik G, Bialek W. 2013. Statistical thermodynamics of natural images. Physical Review Letters. 110(1), 018701.","mla":"Stephens, Greg, et al. “Statistical Thermodynamics of Natural Images.” <i>Physical Review Letters</i>, vol. 110, no. 1, 018701, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.018701\">10.1103/PhysRevLett.110.018701</a>.","apa":"Stephens, G., Mora, T., Tkačik, G., &#38; Bialek, W. (2013). Statistical thermodynamics of natural images. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.110.018701\">https://doi.org/10.1103/PhysRevLett.110.018701</a>","chicago":"Stephens, Greg, Thierry Mora, Gašper Tkačik, and William Bialek. “Statistical Thermodynamics of Natural Images.” <i>Physical Review Letters</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevLett.110.018701\">https://doi.org/10.1103/PhysRevLett.110.018701</a>."},"abstract":[{"lang":"eng","text":"The scale invariance of natural images suggests an analogy to the statistical mechanics of physical systems at a critical point. Here we examine the distribution of pixels in small image patches and show how to construct the corresponding thermodynamics. We find evidence for criticality in a diverging specific heat, which corresponds to large fluctuations in how &quot;surprising&quot; we find individual images, and in the quantitative form of the entropy vs energy. We identify special image configurations as local energy minima and show that average patches within each basin are interpretable as lines and edges in all orientations."}],"date_published":"2013-01-02T00:00:00Z","pubrep_id":"401","department":[{"_id":"GaTk"}],"article_number":"018701","external_id":{"isi":["000313006100058"],"arxiv":["0806.2694"]},"volume":110,"_id":"2914","author":[{"last_name":"Stephens","first_name":"Greg","full_name":"Stephens, Greg"},{"last_name":"Mora","first_name":"Thierry","full_name":"Mora, Thierry"},{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","full_name":"Tkacik, Gasper"},{"full_name":"Bialek, William","first_name":"William","last_name":"Bialek"}],"doi":"10.1103/PhysRevLett.110.018701","publication_status":"published","status":"public","day":"02","type":"journal_article","has_accepted_license":"1","publication":"Physical Review Letters","article_type":"original","date_updated":"2025-09-29T13:29:28Z","ddc":["530"],"arxiv":1,"article_processing_charge":"No","intvolume":"       110","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"3829","publisher":"American Physical Society","title":"Statistical thermodynamics of natural images"},{"publisher":"Nature Publishing Group","title":"Anthrax toxin receptor 2a controls mitotic spindle positioning","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"3819","intvolume":"        15","article_processing_charge":"No","date_updated":"2025-09-30T08:16:16Z","publication":"Nature Cell Biology","page":"28 - 39","scopus_import":"1","type":"journal_article","day":"01","status":"public","publication_status":"published","doi":"10.1038/ncb2632","author":[{"last_name":"Castanon","first_name":"Irinka","full_name":"Castanon, Irinka"},{"last_name":"Abrami","first_name":"Laurence","full_name":"Abrami, Laurence"},{"last_name":"Holtzer","first_name":"Laurent","full_name":"Holtzer, Laurent"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566"},{"first_name":"Françoise","full_name":"Van Der Goot, Françoise","last_name":"Van Der Goot"},{"full_name":"González Gaitán, Marcos","first_name":"Marcos","last_name":"González Gaitán"}],"_id":"2918","volume":15,"external_id":{"isi":["000312841300007"]},"date_published":"2013-01-01T00:00:00Z","department":[{"_id":"CaHe"}],"abstract":[{"text":"Oriented mitosis is essential during tissue morphogenesis. The Wnt/planar cell polarity (Wnt/PCP) pathway orients mitosis in a number of developmental systems, including dorsal epiblast cell divisions along the animal-vegetal (A-V) axis during zebrafish gastrulation. How Wnt signalling orients the mitotic plane is, however, unknown. Here we show that, in dorsal epiblast cells, anthrax toxin receptor 2a (Antxr2a) accumulates in a polarized cortical cap, which is aligned with the embryonic A-V axis and forecasts the division plane. Filamentous actin (F-actin) also forms an A-V polarized cap, which depends on Wnt/PCP and its effectors RhoA and Rock2. Antxr2a is recruited to the cap by interacting with actin. Antxr2a also interacts with RhoA and together they activate the diaphanous-related formin zDia2. Mechanistically, Antxr2a functions as a Wnt-dependent polarized determinant, which, through the action of RhoA and zDia2, exerts torque on the spindle to align it with the A-V axis.\r\n","lang":"eng"}],"citation":{"ista":"Castanon I, Abrami L, Holtzer L, Heisenberg C-PJ, Van Der Goot F, González Gaitán M. 2013. Anthrax toxin receptor 2a controls mitotic spindle positioning. Nature Cell Biology. 15(1), 28–39.","apa":"Castanon, I., Abrami, L., Holtzer, L., Heisenberg, C.-P. J., Van Der Goot, F., &#38; González Gaitán, M. (2013). Anthrax toxin receptor 2a controls mitotic spindle positioning. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb2632\">https://doi.org/10.1038/ncb2632</a>","mla":"Castanon, Irinka, et al. “Anthrax Toxin Receptor 2a Controls Mitotic Spindle Positioning.” <i>Nature Cell Biology</i>, vol. 15, no. 1, Nature Publishing Group, 2013, pp. 28–39, doi:<a href=\"https://doi.org/10.1038/ncb2632\">10.1038/ncb2632</a>.","chicago":"Castanon, Irinka, Laurence Abrami, Laurent Holtzer, Carl-Philipp J Heisenberg, Françoise Van Der Goot, and Marcos González Gaitán. “Anthrax Toxin Receptor 2a Controls Mitotic Spindle Positioning.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/ncb2632\">https://doi.org/10.1038/ncb2632</a>.","short":"I. Castanon, L. Abrami, L. Holtzer, C.-P.J. Heisenberg, F. Van Der Goot, M. González Gaitán, Nature Cell Biology 15 (2013) 28–39.","ama":"Castanon I, Abrami L, Holtzer L, Heisenberg C-PJ, Van Der Goot F, González Gaitán M. Anthrax toxin receptor 2a controls mitotic spindle positioning. <i>Nature Cell Biology</i>. 2013;15(1):28-39. doi:<a href=\"https://doi.org/10.1038/ncb2632\">10.1038/ncb2632</a>","ieee":"I. Castanon, L. Abrami, L. Holtzer, C.-P. J. Heisenberg, F. Van Der Goot, and M. González Gaitán, “Anthrax toxin receptor 2a controls mitotic spindle positioning,” <i>Nature Cell Biology</i>, vol. 15, no. 1. Nature Publishing Group, pp. 28–39, 2013."},"oa_version":"None","acknowledgement":"This work was supported by the SNSF, the Swiss SystemsX.ch initiative and LipidX-2008/011 (M.G-G. and F.G.v.d.G.), by the Fondation SANTE-Vaduz/Aide au Soutien des Nouvelles Thérapies (F.G.v.d.G.) and by the ERC, the NCCR Frontiers in Genetics and Chemical Biology programmes and the Polish–Swiss research program (M.G-G.).","month":"01","isi":1,"quality_controlled":"1","date_created":"2018-12-11T12:00:20Z","language":[{"iso":"eng"}],"year":"2013","issue":"1"},{"date_published":"2013-01-23T00:00:00Z","department":[{"_id":"JiFr"}],"volume":32,"external_id":{"isi":["000316464500009"],"pmid":["23211744"]},"_id":"2919","author":[{"last_name":"Baster","full_name":"Baster, Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel"},{"full_name":"Robert, Stéphanie","first_name":"Stéphanie","last_name":"Robert"},{"last_name":"Kleine Vehn","full_name":"Kleine Vehn, Jürgen","first_name":"Jürgen"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","first_name":"Urszula","full_name":"Kania, Urszula","last_name":"Kania"},{"last_name":"Grunewald","first_name":"Wim","full_name":"Grunewald, Wim"},{"first_name":"Bert","full_name":"De Rybel, Bert","last_name":"De Rybel"},{"full_name":"Beeckman, Tom","first_name":"Tom","last_name":"Beeckman"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"issue":"2","oa":1,"year":"2013","date_created":"2018-12-11T12:00:20Z","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3553380/","open_access":"1"}],"month":"01","oa_version":"Submitted Version","citation":{"chicago":"Baster, Pawel, Stéphanie Robert, Jürgen Kleine Vehn, Steffen Vanneste, Urszula Kania, Wim Grunewald, Bert De Rybel, Tom Beeckman, and Jiří Friml. “SCF^TIR1 AFB-Auxin Signalling Regulates PIN Vacuolar Trafficking and Auxin Fluxes during Root Gravitropism.” <i>EMBO Journal</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1038/emboj.2012.310\">https://doi.org/10.1038/emboj.2012.310</a>.","ista":"Baster P, Robert S, Kleine Vehn J, Vanneste S, Kania U, Grunewald W, De Rybel B, Beeckman T, Friml J. 2013. SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism. EMBO Journal. 32(2), 260–274.","mla":"Baster, Pawel, et al. “SCF^TIR1 AFB-Auxin Signalling Regulates PIN Vacuolar Trafficking and Auxin Fluxes during Root Gravitropism.” <i>EMBO Journal</i>, vol. 32, no. 2, Wiley-Blackwell, 2013, pp. 260–74, doi:<a href=\"https://doi.org/10.1038/emboj.2012.310\">10.1038/emboj.2012.310</a>.","apa":"Baster, P., Robert, S., Kleine Vehn, J., Vanneste, S., Kania, U., Grunewald, W., … Friml, J. (2013). SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism. <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/emboj.2012.310\">https://doi.org/10.1038/emboj.2012.310</a>","short":"P. Baster, S. Robert, J. Kleine Vehn, S. Vanneste, U. Kania, W. Grunewald, B. De Rybel, T. Beeckman, J. Friml, EMBO Journal 32 (2013) 260–274.","ama":"Baster P, Robert S, Kleine Vehn J, et al. SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism. <i>EMBO Journal</i>. 2013;32(2):260-274. doi:<a href=\"https://doi.org/10.1038/emboj.2012.310\">10.1038/emboj.2012.310</a>","ieee":"P. Baster <i>et al.</i>, “SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism,” <i>EMBO Journal</i>, vol. 32, no. 2. Wiley-Blackwell, pp. 260–274, 2013."},"abstract":[{"text":"The distribution of the phytohormone auxin regulates many aspects of plant development including growth response to gravity. Gravitropic root curvature involves coordinated and asymmetric cell elongation between the lower and upper side of the root, mediated by differential cellular auxin levels. The asymmetry in the auxin distribution is established and maintained by a spatio-temporal regulation of the PIN-FORMED (PIN) auxin transporter activity. We provide novel insights into the complex regulation of PIN abundance and activity during root gravitropism. We show that PIN2 turnover is differentially regulated on the upper and lower side of gravistimulated roots by distinct but partially overlapping auxin feedback mechanisms. In addition to regulating transcription and clathrin-mediated internalization, auxin also controls PIN abundance at the plasma membrane by promoting their vacuolar targeting and degradation. This effect of elevated auxin levels requires the activity of SKP-Cullin-F-box TIR1/AFB (SCF TIR1/AFB)-dependent pathway. Importantly, also suboptimal auxin levels mediate PIN degradation utilizing the same signalling pathway. These feedback mechanisms are functionally important during gravitropic response and ensure fine-tuning of auxin fluxes for maintaining as well as terminating asymmetric growth.","lang":"eng"}],"date_updated":"2025-09-29T13:28:19Z","article_processing_charge":"No","pmid":1,"intvolume":"        32","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"3818","publisher":"Wiley-Blackwell","corr_author":"1","title":"SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism","doi":"10.1038/emboj.2012.310","status":"public","day":"23","publication_status":"published","type":"journal_article","scopus_import":"1","page":"260 - 274","publication":"EMBO Journal"},{"scopus_import":"1","type":"journal_article","publication":"EMBO Journal","page":"1 - 3","doi":"10.1038/emboj.2012.325","publication_status":"published","day":"09","status":"public","pmid":1,"intvolume":"        32","article_processing_charge":"No","title":"Neurulation coordinating cell polarisation and lumen formation","corr_author":"1","publisher":"Wiley-Blackwell","publist_id":"3817","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-29T13:27:27Z","month":"01","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545307/"}],"isi":1,"abstract":[{"text":"Cell polarisation in development is a common and fundamental process underlying embryo patterning and morphogenesis, and has been extensively studied over the past years. Our current knowledge of cell polarisation in development is predominantly based on studies that have analysed polarisation of single cells, such as eggs, or cellular aggregates with a stable polarising interface, such as cultured epithelial cells (St Johnston and Ahringer, 2010). However, in embryonic development, particularly of vertebrates, cell polarisation processes often encompass large numbers of cells that are placed within moving and proliferating tissues, and undergo mesenchymal-to-epithelial transitions with a highly complex spatiotemporal choreography. How such intricate cell polarisation processes in embryonic development are achieved has only started to be analysed. By using live imaging of neurulation in the transparent zebrafish embryo, Buckley et al (2012) now describe a novel polarisation strategy by which cells assemble an apical domain in the part of their cell body that intersects with the midline of the forming neural rod. This mechanism, along with the previously described mirror-symmetric divisions (Tawk et al, 2007), is thought to trigger formation of both neural rod midline and lumen.","lang":"eng"}],"citation":{"mla":"Compagnon, Julien, and Carl-Philipp J. Heisenberg. “Neurulation Coordinating Cell Polarisation and Lumen Formation.” <i>EMBO Journal</i>, vol. 32, no. 1, Wiley-Blackwell, 2013, pp. 1–3, doi:<a href=\"https://doi.org/10.1038/emboj.2012.325\">10.1038/emboj.2012.325</a>.","apa":"Compagnon, J., &#38; Heisenberg, C.-P. J. (2013). Neurulation coordinating cell polarisation and lumen formation. <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/emboj.2012.325\">https://doi.org/10.1038/emboj.2012.325</a>","ista":"Compagnon J, Heisenberg C-PJ. 2013. Neurulation coordinating cell polarisation and lumen formation. EMBO Journal. 32(1), 1–3.","chicago":"Compagnon, Julien, and Carl-Philipp J Heisenberg. “Neurulation Coordinating Cell Polarisation and Lumen Formation.” <i>EMBO Journal</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1038/emboj.2012.325\">https://doi.org/10.1038/emboj.2012.325</a>.","short":"J. Compagnon, C.-P.J. Heisenberg, EMBO Journal 32 (2013) 1–3.","ama":"Compagnon J, Heisenberg C-PJ. Neurulation coordinating cell polarisation and lumen formation. <i>EMBO Journal</i>. 2013;32(1):1-3. doi:<a href=\"https://doi.org/10.1038/emboj.2012.325\">10.1038/emboj.2012.325</a>","ieee":"J. Compagnon and C.-P. J. Heisenberg, “Neurulation coordinating cell polarisation and lumen formation,” <i>EMBO Journal</i>, vol. 32, no. 1. Wiley-Blackwell, pp. 1–3, 2013."},"oa_version":"Submitted Version","year":"2013","oa":1,"issue":"1","quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:00:20Z","_id":"2920","author":[{"full_name":"Compagnon, Julien","id":"2E3E0988-F248-11E8-B48F-1D18A9856A87","first_name":"Julien","last_name":"Compagnon"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"CaHe"}],"date_published":"2013-01-09T00:00:00Z","external_id":{"isi":["000314141900001"],"pmid":["23211745"]},"volume":32},{"article_processing_charge":"No","intvolume":"        23","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"3811","publisher":"Cell Press","corr_author":"1","title":"Ants disinfect fungus-exposed brood by oral uptake and spread of their poison","date_updated":"2025-09-30T08:15:50Z","type":"journal_article","scopus_import":"1","page":"76 - 82","publication":"Current Biology","ec_funded":1,"doi":"10.1016/j.cub.2012.11.034","publication_status":"published","day":"07","status":"public","_id":"2926","author":[{"first_name":"Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87","full_name":"Tragust, Simon","last_name":"Tragust"},{"last_name":"Mitteregger","full_name":"Mitteregger, Barbara","id":"479DDAAC-E9CD-11E9-9B5F-82450873F7A1","first_name":"Barbara"},{"orcid":"0000-0003-2676-3367","last_name":"Barone","full_name":"Barone, Vanessa","first_name":"Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87"},{"id":"46528076-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","full_name":"Konrad, Matthias","last_name":"Konrad"},{"orcid":"0000-0003-1832-8883","last_name":"Ugelvig","first_name":"Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","full_name":"Ugelvig, Line V"},{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868"}],"related_material":{"record":[{"id":"9757","status":"public","relation":"research_data"},{"status":"public","relation":"dissertation_contains","id":"961"}]},"date_published":"2013-01-07T00:00:00Z","department":[{"_id":"SyCr"},{"_id":"CaHe"}],"external_id":{"isi":["000313383700026"]},"volume":23,"isi":1,"month":"01","acknowledgement":"Funding for this project was obtained by the German Research Foundation (DFG, to S.C.) and the European Research Council (ERC, through an ERC-Starting Grant to S.C. and an Individual Marie Curie IEF fellowship to L.V.U.).\r\nWe thank Jørgen Eilenberg, Bernhardt Steinwender, Miriam Stock, and Meghan L. Vyleta for the fungal strain and its characterization; Volker Witte for chemical information; Eva Sixt for ant drawings; and Robert Hauschild for help with image analysis. We further thank Martin Kaltenpoth, Michael Sixt, Jürgen Heinze, and Joachim Ruther for discussion and Daria Siekhaus, Sophie A.O. Armitage, and Leila Masri for comments on the manuscript. \r\n","oa_version":"None","citation":{"ama":"Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. <i>Current Biology</i>. 2013;23(1):76-82. doi:<a href=\"https://doi.org/10.1016/j.cub.2012.11.034\">10.1016/j.cub.2012.11.034</a>","ieee":"S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L. V. Ugelvig, and S. Cremer, “Ants disinfect fungus-exposed brood by oral uptake and spread of their poison,” <i>Current Biology</i>, vol. 23, no. 1. Cell Press, pp. 76–82, 2013.","mla":"Tragust, Simon, et al. “Ants Disinfect Fungus-Exposed Brood by Oral Uptake and Spread of Their Poison.” <i>Current Biology</i>, vol. 23, no. 1, Cell Press, 2013, pp. 76–82, doi:<a href=\"https://doi.org/10.1016/j.cub.2012.11.034\">10.1016/j.cub.2012.11.034</a>.","apa":"Tragust, S., Mitteregger, B., Barone, V., Konrad, M., Ugelvig, L. V., &#38; Cremer, S. (2013). Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2012.11.034\">https://doi.org/10.1016/j.cub.2012.11.034</a>","ista":"Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. 2013. Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. Current Biology. 23(1), 76–82.","chicago":"Tragust, Simon, Barbara Mitteregger, Vanessa Barone, Matthias Konrad, Line V Ugelvig, and Sylvia Cremer. “Ants Disinfect Fungus-Exposed Brood by Oral Uptake and Spread of Their Poison.” <i>Current Biology</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1016/j.cub.2012.11.034\">https://doi.org/10.1016/j.cub.2012.11.034</a>.","short":"S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L.V. Ugelvig, S. Cremer, Current Biology 23 (2013) 76–82."},"abstract":[{"lang":"eng","text":"To fight infectious diseases, host immune defenses are employed at multiple levels. Sanitary behavior, such as pathogen avoidance and removal, acts as a first line of defense to prevent infection [1] before activation of the physiological immune system. Insect societies have evolved a wide range of collective hygiene measures and intensive health care toward pathogen-exposed group members [2]. One of the most common behaviors is allogrooming, in which nestmates remove infectious particles from the body surfaces of exposed individuals [3]. Here we show that, in invasive garden ants, grooming of fungus-exposed brood is effective beyond the sheer mechanical removal of fungal conidiospores; it also includes chemical disinfection through the application of poison produced by the ants themselves. Formic acid is the main active component of the poison. It inhibits fungal growth of conidiospores remaining on the brood surface after grooming and also those collected in the mouth of the grooming ant. This dual function is achieved by uptake of the poison droplet into the mouth through acidopore self-grooming and subsequent application onto the infectious brood via brood grooming. This extraordinary behavior extends the current understanding of grooming and the establishment of social immunity in insect societies."}],"issue":"1","year":"2013","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:00:23Z","project":[{"_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","grant_number":"CR-118/3-1","name":"Host-Parasite Coevolution"},{"call_identifier":"FP7","grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","_id":"25DC711C-B435-11E9-9278-68D0E5697425"},{"grant_number":"302004","name":"Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach","_id":"25DDF0F0-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"quality_controlled":"1"},{"status":"public","publication_status":"published","day":"01","doi":"10.1016/j.comgeo.2012.02.010","page":"435 - 447","publication":"Computational Geometry: Theory and Applications","type":"journal_article","scopus_import":"1","date_updated":"2025-09-29T13:26:21Z","publist_id":"3796","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"An output sensitive algorithm for persistent homology","corr_author":"1","publisher":"Elsevier","article_processing_charge":"No","intvolume":"        46","date_created":"2018-12-11T12:00:27Z","language":[{"iso":"eng"}],"quality_controlled":"1","issue":"4","year":"2013","oa_version":"None","abstract":[{"text":"In this paper, we present the first output-sensitive algorithm to compute the persistence diagram of a filtered simplicial complex. For any Γ &gt; 0, it returns only those homology classes with persistence at least Γ. Instead of the classical reduction via column operations, our algorithm performs rank computations on submatrices of the boundary matrix. For an arbitrary constant δ ∈ (0, 1), the running time is O (C (1 - δ) Γ R d (n) log n), where C (1 - δ) Γ is the number of homology classes with persistence at least (1 - δ) Γ, n is the total number of simplices in the complex, d its dimension, and R d (n) is the complexity of computing the rank of an n × n matrix with O (d n) nonzero entries. Depending on the choice of the rank algorithm, this yields a deterministic O (C (1 - δ) Γ n 2.376) algorithm, an O (C (1 - δ) Γ n 2.28) Las-Vegas algorithm, or an O (C (1 - δ) Γ n 2 + ε{lunate}) Monte-Carlo algorithm for an arbitrary ε{lunate} &gt; 0. The space complexity of the Monte-Carlo version is bounded by O (d n) = O (n log n).","lang":"eng"}],"citation":{"ama":"Chen C, Kerber M. An output sensitive algorithm for persistent homology. <i>Computational Geometry: Theory and Applications</i>. 2013;46(4):435-447. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2012.02.010\">10.1016/j.comgeo.2012.02.010</a>","ieee":"C. Chen and M. Kerber, “An output sensitive algorithm for persistent homology,” <i>Computational Geometry: Theory and Applications</i>, vol. 46, no. 4. Elsevier, pp. 435–447, 2013.","mla":"Chen, Chao, and Michael Kerber. “An Output Sensitive Algorithm for Persistent Homology.” <i>Computational Geometry: Theory and Applications</i>, vol. 46, no. 4, Elsevier, 2013, pp. 435–47, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2012.02.010\">10.1016/j.comgeo.2012.02.010</a>.","ista":"Chen C, Kerber M. 2013. An output sensitive algorithm for persistent homology. Computational Geometry: Theory and Applications. 46(4), 435–447.","apa":"Chen, C., &#38; Kerber, M. (2013). An output sensitive algorithm for persistent homology. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2012.02.010\">https://doi.org/10.1016/j.comgeo.2012.02.010</a>","chicago":"Chen, Chao, and Michael Kerber. “An Output Sensitive Algorithm for Persistent Homology.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.comgeo.2012.02.010\">https://doi.org/10.1016/j.comgeo.2012.02.010</a>.","short":"C. Chen, M. Kerber, Computational Geometry: Theory and Applications 46 (2013) 435–447."},"isi":1,"acknowledgement":"The authors thank Herbert Edelsbrunner for many helpful discussions and suggestions. Moreover, they are grateful for the careful reviews that helped to improve the quality of the paper.","month":"05","volume":46,"external_id":{"isi":["000314437000004"]},"department":[{"_id":"HeEd"}],"date_published":"2013-05-01T00:00:00Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"3367"}]},"author":[{"full_name":"Chen, Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","first_name":"Chao","last_name":"Chen"},{"orcid":"0000-0002-8030-9299","last_name":"Kerber","first_name":"Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","full_name":"Kerber, Michael"}],"_id":"2939"}]