[{"file":[{"date_created":"2018-12-12T10:14:45Z","content_type":"application/pdf","creator":"system","access_level":"open_access","relation":"main_file","file_name":"IST-2013-120-v1+1_journal.pcbi.1002922.pdf","checksum":"5a30876c193209fa05b26db71845dd16","file_size":1548120,"file_id":"5099","date_updated":"2020-07-14T12:45:52Z"}],"publication_status":"published","intvolume":"         9","month":"03","language":[{"iso":"eng"}],"ddc":["570"],"day":"01","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"e1002922","file_date_updated":"2020-07-14T12:45:52Z","quality_controlled":"1","scopus_import":1,"date_updated":"2021-01-12T07:00:20Z","doi":"10.1371/journal.pcbi.1002922","date_published":"2013-03-01T00:00:00Z","pubrep_id":"120","author":[{"last_name":"Granot Atedgi","first_name":"Einat","full_name":"Granot Atedgi, Einat"},{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455"},{"full_name":"Segev, Ronen","first_name":"Ronen","last_name":"Segev"},{"full_name":"Schneidman, Elad","last_name":"Schneidman","first_name":"Elad"}],"year":"2013","has_accepted_license":"1","_id":"2863","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":9,"citation":{"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.","short":"E. Granot Atedgi, G. Tkačik, R. Segev, E. Schneidman, PLoS Computational Biology 9 (2013).","mla":"Granot Atedgi, Einat, et al. “Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.” <i>PLoS Computational Biology</i>, vol. 9, no. 3, e1002922, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1002922\">10.1371/journal.pcbi.1002922</a>.","ama":"Granot Atedgi E, Tkačik G, Segev R, Schneidman E. Stimulus-dependent maximum entropy models of neural population codes. <i>PLoS Computational Biology</i>. 2013;9(3). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1002922\">10.1371/journal.pcbi.1002922</a>","apa":"Granot Atedgi, E., Tkačik, G., Segev, R., &#38; Schneidman, E. (2013). Stimulus-dependent maximum entropy models of neural population codes. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1002922\">https://doi.org/10.1371/journal.pcbi.1002922</a>","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."},"issue":"3","oa":1,"status":"public","publist_id":"3926","date_created":"2018-12-11T12:00:00Z","oa_version":"Published Version","publisher":"Public Library of Science","publication":"PLoS Computational Biology","department":[{"_id":"GaTk"}],"title":"Stimulus-dependent maximum entropy models of neural population codes","abstract":[{"lang":"eng","text":"Neural populations encode information about their stimulus in a collective fashion, by joint activity patterns of spiking and silence. A full account of this mapping from stimulus to neural activity is given by the conditional probability distribution over neural codewords given the sensory input. For large populations, direct sampling of these distributions is impossible, and so we must rely on constructing appropriate models. We show here that in a population of 100 retinal ganglion cells in the salamander retina responding to temporal white-noise stimuli, dependencies between cells play an important encoding role. We introduce the stimulus-dependent maximum entropy (SDME) model—a minimal extension of the canonical linear-nonlinear model of a single neuron, to a pairwise-coupled neural population. We find that the SDME model gives a more accurate account of single cell responses and in particular significantly outperforms uncoupled models in reproducing the distributions of population codewords emitted in response to a stimulus. We show how the SDME model, in conjunction with static maximum entropy models of population vocabulary, can be used to estimate information-theoretic quantities like average surprise and information transmission in a neural population."}]},{"publisher":"Botanical Society of America","publication":"American Journal of Botany","title":"Brassinosteroid control of shoot gravitropism interacts with ethylene and depends on auxin signaling components","publist_id":"3883","date_created":"2018-12-11T12:00:06Z","doi":"10.3732/ajb.1200264","date_updated":"2021-01-12T07:00:25Z","date_published":"2013-01-01T00:00:00Z","author":[{"first_name":"Filip","last_name":"Vandenbussche","full_name":"Vandenbussche, Filip"},{"last_name":"Callebert","first_name":"Pieter","full_name":"Callebert, Pieter"},{"full_name":"Žádníková, Petra","first_name":"Petra","last_name":"Žádníková"},{"orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Eva Benková"},{"first_name":"Dominique","last_name":"Van Der Straeten","full_name":"Van Der Straeten, Dominique"}],"quality_controlled":0,"extern":1,"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"}],"type":"journal_article","volume":100,"page":"215 - 225","year":"2013","publication_status":"published","_id":"2877","intvolume":"       100","issue":"1","day":"01","status":"public","month":"01","citation":{"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>","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>.","short":"F. Vandenbussche, P. Callebert, P. Žádníková, E. Benková, D. Van Der Straeten, American Journal of Botany 100 (2013) 215–225.","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.","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.","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>.","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>"}},{"citation":{"ista":"Marhavý P, Vanstraelen M, De Rybel B, Zhaojun D, Bennett M, Beeckman T, Benková E. 2013. Auxin reflux between the endodermis and pericycle promotes lateral root initiation. EMBO Journal. 32(1), 149–158.","short":"P. Marhavý, M. Vanstraelen, B. De Rybel, D. Zhaojun, M. Bennett, T. Beeckman, E. Benková, EMBO Journal 32 (2013) 149–158.","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>.","ama":"Marhavý P, Vanstraelen M, De Rybel B, et al. Auxin reflux between the endodermis and pericycle promotes lateral root initiation. <i>EMBO Journal</i>. 2013;32(1):149-158. doi:<a href=\"https://doi.org/10.1038/emboj.2012.303\">10.1038/emboj.2012.303</a>","apa":"Marhavý, P., Vanstraelen, M., De Rybel, B., Zhaojun, D., Bennett, M., Beeckman, T., &#38; Benková, E. (2013). Auxin reflux between the endodermis and pericycle promotes lateral root initiation. <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/emboj.2012.303\">https://doi.org/10.1038/emboj.2012.303</a>","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.","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>."},"issue":"1","external_id":{"pmid":["23178590"]},"oa":1,"status":"public","year":"2013","_id":"2880","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":32,"page":"149 - 158","abstract":[{"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.","lang":"eng"}],"publist_id":"3882","ec_funded":1,"date_created":"2018-12-11T12:00:07Z","oa_version":"Submitted Version","publisher":"Wiley-Blackwell","publication":"EMBO Journal","title":"Auxin reflux between the endodermis and pericycle promotes lateral root initiation","department":[{"_id":"EvBe"}],"month":"01","project":[{"_id":"253FCA6A-B435-11E9-9278-68D0E5697425","name":"Hormonal cross-talk in plant organogenesis","grant_number":"207362","call_identifier":"FP7"}],"language":[{"iso":"eng"}],"day":"09","pmid":1,"publication_status":"published","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545298/"}],"intvolume":"        32","quality_controlled":"1","scopus_import":1,"date_updated":"2021-01-12T07:00:27Z","doi":"10.1038/emboj.2012.303","date_published":"2013-01-09T00:00:00Z","author":[{"first_name":"Peter","orcid":"0000-0001-5227-5741","last_name":"Marhavy","full_name":"Marhavy, Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marleen","last_name":"Vanstraelen","full_name":"Vanstraelen, Marleen"},{"first_name":"Bert","last_name":"De Rybel","full_name":"De Rybel, Bert"},{"full_name":"Zhaojun, Ding","first_name":"Ding","last_name":"Zhaojun"},{"first_name":"Malcolm","last_name":"Bennett","full_name":"Bennett, Malcolm"},{"full_name":"Beeckman, Tom","first_name":"Tom","last_name":"Beeckman"},{"first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}]},{"intvolume":"        23","_id":"2881","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3567823/","open_access":"1"}],"year":"2013","publication_status":"published","volume":23,"page":"290 - 299","type":"journal_article","citation":{"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>","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.","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>.","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.","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>.","short":"H. Li, T. Xu, D. Lin, M. Wen, M. Xie, J. Duclercq, A. Bielach, J. Kim, G.V. Reddy, J. Zuo, E. Benková, J. Friml, H. Guo, Z. Yang, Cell Research 23 (2013) 290–299.","ama":"Li H, Xu T, Lin D, et al. Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis. <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>"},"month":"02","status":"public","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.","oa":1,"issue":"2","day":"01","date_created":"2018-12-11T12:00:07Z","publist_id":"3881","publication":"Cell Research","title":"Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis","publisher":"Nature Publishing Group","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"}],"quality_controlled":0,"extern":1,"author":[{"orcid":"0000-0001-5039-9660","last_name":"Li","first_name":"Hongjiang","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","full_name":"Hongjiang Li"},{"last_name":"Xu","first_name":"Tongda","full_name":"Xu, Tongda"},{"full_name":"Lin, Deshu","last_name":"Lin","first_name":"Deshu"},{"first_name":"Mingzhang","last_name":"Wen","full_name":"Wen, Mingzhang"},{"first_name":"Mingtang","last_name":"Xie","full_name":"Xie, Mingtang"},{"full_name":"Duclercq, Jérôme","first_name":"Jérôme","last_name":"Duclercq"},{"first_name":"Agnieszka","last_name":"Bielach","full_name":"Bielach, Agnieszka"},{"full_name":"Kim, Jungmook","first_name":"Jungmook","last_name":"Kim"},{"full_name":"Reddy, G Venugopala","last_name":"Reddy","first_name":"G Venugopala"},{"full_name":"Zuo, Jianru","first_name":"Jianru","last_name":"Zuo"},{"full_name":"Eva Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml"},{"last_name":"Guo","first_name":"Hongwei","full_name":"Guo, Hongwei"},{"full_name":"Yang, Zhenbiao","first_name":"Zhenbiao","last_name":"Yang"}],"date_published":"2013-02-01T00:00:00Z","doi":"10.1038/cr.2012.146","date_updated":"2021-01-12T07:00:27Z"},{"date_updated":"2021-01-12T07:00:27Z","doi":"10.1073/pnas.1300107110","date_published":"2013-02-26T00:00:00Z","author":[{"first_name":"Christian","last_name":"Löfke","full_name":"Löfke, Christian"},{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"full_name":"Heilmann, Ingo","last_name":"Heilmann","first_name":"Ingo"},{"full_name":"Van Montagu, Marc","last_name":"Van Montagu","first_name":"Marc"},{"first_name":"Thomas","last_name":"Teichmann","full_name":"Teichmann, Thomas"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí"}],"quality_controlled":"1","scopus_import":1,"publication_status":"published","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587205/","open_access":"1"}],"intvolume":"       110","day":"26","pmid":1,"language":[{"iso":"eng"}],"month":"02","publisher":"National Academy of Sciences","department":[{"_id":"JiFr"}],"title":"Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism","publication":"PNAS","publist_id":"3879","oa_version":"Submitted Version","date_created":"2018-12-11T12:00:07Z","abstract":[{"lang":"eng","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."}],"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"3627 - 3632","volume":110,"year":"2013","_id":"2882","external_id":{"pmid":["23391733"]},"issue":"9","oa":1,"status":"public","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>","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.","short":"C. Löfke, M. Zwiewka, I. Heilmann, M. Van Montagu, T. Teichmann, J. Friml, PNAS 110 (2013) 3627–3632.","mla":"Löfke, Christian, et al. “Asymmetric Gibberellin Signaling Regulates Vacuolar Trafficking of PIN Auxin Transporters during Root Gravitropism.” <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>.","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>.","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.","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>"}},{"quality_controlled":"1","scopus_import":1,"date_updated":"2021-01-12T07:00:28Z","doi":"10.1105/tpc.112.105999","date_published":"2013-01-01T00:00:00Z","author":[{"last_name":"Wang","first_name":"Bangjun","full_name":"Wang, Bangjun"},{"full_name":"Bailly, Aurélien","first_name":"Aurélien","last_name":"Bailly"},{"full_name":"Zwiewk, Marta","first_name":"Marta","last_name":"Zwiewk"},{"first_name":"Sina","last_name":"Henrichs","full_name":"Henrichs, Sina"},{"full_name":"Azzarello, Elisa","last_name":"Azzarello","first_name":"Elisa"},{"full_name":"Mancuso, Stefano","first_name":"Stefano","last_name":"Mancuso"},{"last_name":"Maeshima","first_name":"Masayoshi","full_name":"Maeshima, Masayoshi"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"},{"full_name":"Schulz, Alexander","first_name":"Alexander","last_name":"Schulz"},{"full_name":"Geisler, Markus","first_name":"Markus","last_name":"Geisler"}],"language":[{"iso":"eng"}],"month":"01","day":"01","pmid":1,"publication_status":"published","intvolume":"        25","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584535/"}],"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"}],"publist_id":"3878","oa_version":"Submitted Version","date_created":"2018-12-11T12:00:08Z","publisher":"American Society of Plant Biologists","title":"Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane","department":[{"_id":"JiFr"}],"publication":"Plant Cell","citation":{"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>","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.","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>.","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.","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>"},"external_id":{"pmid":["23321285"]},"issue":"1","oa":1,"status":"public","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.","year":"2013","_id":"2883","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"202 - 214","volume":25},{"issue":"2","day":"01","status":"public","month":"02","language":[{"iso":"eng"}],"project":[{"grant_number":"HE_3231/6-1","name":"Analysis of the Formation and Function of Different Cell Protusion Types During Cell Migration in Vivo","_id":"252064B8-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","grant_number":"I 812-B12","_id":"2527D5CC-B435-11E9-9278-68D0E5697425"}],"citation":{"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>.","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.","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>","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>","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>.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":29,"page":"147 - 150","year":"2013","publication_status":"published","intvolume":"        29","_id":"2884","doi":"10.1051/medsci/2013292011","date_updated":"2021-01-12T07:00:28Z","author":[{"orcid":"0000-0002-3688-1474","last_name":"Maître","first_name":"Jean-Léon","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","full_name":"Maître, Jean-Léon"},{"full_name":"Berthoumieux, Hélène","last_name":"Berthoumieux","first_name":"Hélène"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","last_name":"Krens","first_name":"Gabriel"},{"full_name":"Salbreux, Guillaume","last_name":"Salbreux","first_name":"Guillaume"},{"last_name":"Julicher","first_name":"Frank","full_name":"Julicher, Frank"},{"full_name":"Paluch, Ewa","first_name":"Ewa","last_name":"Paluch"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"date_published":"2013-02-01T00:00:00Z","quality_controlled":"1","scopus_import":1,"publisher":"Éditions Médicales et Scientifiques","publication":"Medecine Sciences","department":[{"_id":"CaHe"}],"title":"Cell adhesion mechanics of zebrafish gastrulation","publist_id":"3877","date_created":"2018-12-11T12:00:08Z","oa_version":"None"},{"status":"public","acknowledgement":"Red Hat Czech Republic, Y Soft","day":"09","citation":{"ieee":"A. Kucera, T. A. Henzinger, J. Nesetril, T. Vojnar, and D. Antos, Eds., <i>Mathematical and Engineering Methods in Computer Science</i>, vol. 7721. Springer, 2013, pp. 1–228.","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>","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>","short":"A. Kucera, T.A. Henzinger, J. Nesetril, T. Vojnar, D. Antos, eds., Mathematical and Engineering Methods in Computer Science, Springer, 2013.","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."},"language":[{"iso":"eng"}],"month":"01","page":"1 - 228","volume":7721,"type":"conference_editor","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2885","intvolume":"      7721","publication_status":"published","year":"2013","editor":[{"first_name":"Antonin","last_name":"Kucera","full_name":"Kucera, Antonin"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"},{"full_name":"Nesetril, Jaroslav","first_name":"Jaroslav","last_name":"Nesetril"},{"first_name":"Tomas","last_name":"Vojnar","full_name":"Vojnar, Tomas"},{"full_name":"Antos, David","first_name":"David","last_name":"Antos"}],"date_published":"2013-01-09T00:00:00Z","alternative_title":["LNCS"],"doi":"10.1007/978-3-642-36046-6","date_updated":"2019-08-02T12:37:55Z","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."}],"quality_controlled":"1","series_title":"Lecture Notes in Computer Science","department":[{"_id":"ToHe"}],"title":"Mathematical and Engineering Methods in Computer Science","publisher":"Springer","oa_version":"None","conference":{"start_date":"2012-10-25","location":"Znojmo, Czech Republic","end_date":"2012-10-28","name":"MEMICS: Mathematical and Engineering methods in computer science"},"date_created":"2018-12-11T12:00:08Z","publist_id":"3874"},{"publisher":"Springer","title":"Controllable-choice message sequence graphs","department":[{"_id":"KrCh"}],"publist_id":"3873","oa_version":"Submitted Version","ec_funded":1,"date_created":"2018-12-11T12:00:09Z","series_title":"Lecture Notes in Computer Science","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."}],"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"118 - 130","volume":7721,"year":"2013","_id":"2886","oa":1,"status":"public","citation":{"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>","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>.","ieee":"M. Chmelik and V. Řehák, “Controllable-choice message sequence graphs,” vol. 7721. Springer, pp. 118–130, 2013.","short":"M. Chmelik, V. Řehák, 7721 (2013) 118–130.","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.","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>"},"conference":{"end_date":"2012-10-28","name":"MEMICS: Mathematical and Engineering Methods in Computer Science","start_date":"2012-10-25","location":"Znojmo, Czech Republic"},"doi":"10.1007/978-3-642-36046-6_12","alternative_title":["LNCS"],"date_updated":"2020-08-11T10:09:52Z","date_published":"2013-01-09T00:00:00Z","author":[{"first_name":"Martin","last_name":"Chmelik","full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Řehák, Vojtěch","first_name":"Vojtěch","last_name":"Řehák"}],"quality_controlled":"1","scopus_import":1,"publication_status":"published","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1209.4499"}],"intvolume":"      7721","day":"09","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"month":"01"},{"status":"public","oa":1,"article_type":"original","external_id":{"pmid":["23362379"]},"issue":"7","citation":{"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.","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.","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>.","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.","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>"},"page":"2670 - 2675","volume":110,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2887","year":"2013","abstract":[{"text":"Root system growth and development is highly plastic and is influenced by the surrounding environment. Roots frequently grow in heterogeneous environments that include interactions from neighboring plants and physical impediments in the rhizosphere. To investigate how planting density and physical objects affect root system growth, we grew rice in a transparent gel system in close proximity with another plant or a physical object. Root systems were imaged and reconstructed in three dimensions. Root-root interaction strength was calculated using quantitative metrics that characterize the extent towhich the reconstructed root systems overlap each other. Surprisingly, we found the overlap of root systems of the same genotype was significantly higher than that of root systems of different genotypes. Root systems of the same genotype tended to grow toward each other but those of different genotypes appeared to avoid each other. Shoot separation experiments excluded the possibility of aerial interactions, suggesting root communication. Staggered plantings indicated that interactions likely occur at root tips in close proximity. Recognition of obstacles also occurred through root tips, but through physical contact in a size-dependent manner. These results indicate that root systems use two different forms of communication to recognize objects and alter root architecture: root-root recognition, possibly mediated through root exudates, and root-object recognition mediated by physical contact at the root tips. This finding suggests that root tips act as local sensors that integrate rhizosphere information into global root architectural changes.","lang":"eng"}],"title":"Genotypic recognition and spatial responses by rice roots","department":[{"_id":"HeEd"}],"publication":"PNAS","publisher":"National Academy of Sciences","oa_version":"Published Version","date_created":"2018-12-11T12:00:09Z","publist_id":"3872","pmid":1,"day":"12","language":[{"iso":"eng"}],"month":"02","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574932/"}],"intvolume":"       110","publication_status":"published","author":[{"first_name":"Suqin","last_name":"Fang","full_name":"Fang, Suqin"},{"full_name":"Clark, Randy","first_name":"Randy","last_name":"Clark"},{"last_name":"Zheng","first_name":"Ying","full_name":"Zheng, Ying"},{"first_name":"Anjali","last_name":"Iyer Pascuzzi","full_name":"Iyer Pascuzzi, Anjali"},{"last_name":"Weitz","first_name":"Joshua","full_name":"Weitz, Joshua"},{"last_name":"Kochian","first_name":"Leon","full_name":"Kochian, Leon"},{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"first_name":"Hong","last_name":"Liao","full_name":"Liao, Hong"},{"full_name":"Benfey, Philip","last_name":"Benfey","first_name":"Philip"}],"date_published":"2013-02-12T00:00:00Z","doi":"10.1073/pnas.1222821110","date_updated":"2021-01-12T07:00:29Z","article_processing_charge":"No","scopus_import":1,"quality_controlled":"1"},{"_id":"2900","main_file_link":[{"url":"http://onlinelibrary.wiley.com/doi/10.1111/j.1525-142X.2008.00265.x/abstract","open_access":"0"}],"intvolume":"        10","year":"2013","publication_status":"published","volume":10,"page":"514 - 515","type":"journal_article","citation":{"ama":"Azevedo R, Lohaus R, Paixao T. Networking networks. <i>Evolution &#38; Development</i>. 2013;10(5):514-515.","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.","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.","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.","apa":"Azevedo, R., Lohaus, R., &#38; Paixao, T. (2013). Networking networks. <i>Evolution &#38; Development</i>. 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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.","short":"C. Chen, V. Kolmogorov, Z. Yan, D. Metaxas, C. Lampert, in:, JMLR, 2013, pp. 161–169.","mla":"Chen, Chao, et al. <i>Computing the M Most Probable Modes of a Graphical Model</i>. Vol. 31, JMLR, 2013, pp. 161–69.","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.","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."},"month":"01","language":[{"iso":"eng"}],"volume":31,"page":"161 - 169","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","_id":"2901","intvolume":"        31","main_file_link":[{"open_access":"1","url":"http://jmlr.org/proceedings/papers/v31/chen13a.html"}],"year":"2013","publication_status":"published","date_published":"2013-01-01T00:00:00Z","author":[{"first_name":"Chao","last_name":"Chen","full_name":"Chen, Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir"},{"full_name":"Yan, Zhu","last_name":"Yan","first_name":"Zhu"},{"last_name":"Metaxas","first_name":"Dimitris","full_name":"Metaxas, Dimitris"},{"first_name":"Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2021-01-12T07:00:35Z","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. 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(2013). 3D kinetic alpha complexes and their implementation. In <i>2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments</i> (pp. 70–77). New Orleans, LA, United States: Society of Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611972931.6\">https://doi.org/10.1137/1.9781611972931.6</a>","chicago":"Kerber, Michael, and Herbert Edelsbrunner. “3D Kinetic Alpha Complexes and Their Implementation.” In <i>2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments</i>, 70–77. Society of Industrial and Applied Mathematics, 2013. <a href=\"https://doi.org/10.1137/1.9781611972931.6\">https://doi.org/10.1137/1.9781611972931.6</a>.","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.","short":"M. Kerber, H. Edelsbrunner, in:, 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments, Society of Industrial and Applied Mathematics, 2013, pp. 70–77.","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.","mla":"Kerber, Michael, and Herbert Edelsbrunner. “3D Kinetic Alpha Complexes and Their Implementation.” <i>2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments</i>, Society of Industrial and Applied Mathematics, 2013, pp. 70–77, doi:<a href=\"https://doi.org/10.1137/1.9781611972931.6\">10.1137/1.9781611972931.6</a>.","ama":"Kerber M, Edelsbrunner H. 3D kinetic alpha complexes and their implementation. In: <i>2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments</i>. Society of Industrial and Applied Mathematics; 2013:70-77. doi:<a href=\"https://doi.org/10.1137/1.9781611972931.6\">10.1137/1.9781611972931.6</a>"},"oa":1,"status":"public","_id":"2906","year":"2013","has_accepted_license":"1","page":"70 - 77","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","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."}],"date_created":"2018-12-11T12:00:16Z","oa_version":"Submitted Version","publist_id":"3841","publication":"2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments","title":"3D kinetic alpha complexes and their implementation","department":[{"_id":"HeEd"}],"publisher":"Society of Industrial and Applied Mathematics"},{"page":"328 - 333","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"book_chapter","_id":"2907","year":"2013","has_accepted_license":"1","file":[{"access_level":"open_access","creator":"system","relation":"main_file","date_created":"2018-12-12T10:16:47Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"5237","date_updated":"2020-07-14T12:45:52Z","checksum":"8332ca9cb40f7e66d1006b175ce36b60","file_name":"IST-2013-119-v1+1_IV.4_Recombination_and_Sex_Barton_1-13-13-e.docx","file_size":79838},{"file_id":"5238","date_updated":"2020-07-14T12:45:52Z","checksum":"849f418620fb78d6ba23bb4f488ee93f","file_name":"IST-2017-119-v1+2_Barton_Recombination_Sex.pdf","file_size":144131,"access_level":"open_access","creator":"system","relation":"main_file","date_created":"2018-12-12T10:16:48Z","content_type":"application/pdf"}],"publication_status":"published","oa":1,"status":"public","ddc":["576"],"day":"04","citation":{"apa":"Barton, N. H. (2013). Recombination and sex. In <i>The Princeton Guide to Evolution</i> (pp. 328–333). Princeton University Press.","ieee":"N. H. Barton, “Recombination and sex,” in <i>The Princeton Guide to Evolution</i>, Princeton University Press, 2013, pp. 328–333.","chicago":"Barton, Nicholas H. “Recombination and Sex.” In <i>The Princeton Guide to Evolution</i>, 328–33. Princeton University Press, 2013.","ista":"Barton NH. 2013.Recombination and sex. In: The Princeton Guide to Evolution. , 328–333.","short":"N.H. Barton, in:, The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–333.","mla":"Barton, Nicholas H. “Recombination and Sex.” <i>The Princeton Guide to Evolution</i>, Princeton University Press, 2013, pp. 328–33.","ama":"Barton NH. Recombination and sex. In: <i>The Princeton Guide to Evolution</i>. Princeton University Press; 2013:328-333."},"month":"11","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9780691149776"]},"publication":"The Princeton Guide to Evolution","title":"Recombination and sex","file_date_updated":"2020-07-14T12:45:52Z","department":[{"_id":"NiBa"}],"publisher":"Princeton University Press","date_created":"2018-12-11T12:00:16Z","oa_version":"Submitted Version","publist_id":"3839","author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"pubrep_id":"119","date_published":"2013-11-04T00:00:00Z","date_updated":"2021-01-12T07:00:37Z","abstract":[{"text":"Sex and recombination are among the most striking features of the living world, and they play a crucial role in allowing the evolution of complex adaptation. The sharing of genomes through the sexual union of different individuals requires elaborate behavioral and physiological adaptations. At the molecular level, the alignment of two DNA double helices, followed by their precise cutting and rejoining, is an extraordinary feat. Sex and recombination have diverse—and often surprising—evolutionary consequences: distinct sexes, elaborate mating displays, selfish genetic elements, and so on.","lang":"eng"}],"quality_controlled":"1"},{"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"}],"publist_id":"3835","date_created":"2018-12-11T12:00:17Z","oa_version":"Submitted Version","publisher":"Wiley-Blackwell","publication":"Journal of Evolutionary Biology","title":"Does hybridisation influence speciation?  ","department":[{"_id":"NiBa"}],"citation":{"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>","ista":"Barton NH. 2013. Does hybridisation influence speciation?  . Journal of Evolutionary Biology. 26(2), 267–269.","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>.","short":"N.H. Barton, Journal of Evolutionary Biology 26 (2013) 267–269.","ieee":"N. H. Barton, “Does hybridisation influence speciation?  ,” <i>Journal of Evolutionary Biology</i>, vol. 26, no. 2. Wiley-Blackwell, pp. 267–269, 2013.","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>.","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>"},"issue":"2","status":"public","oa":1,"year":"2013","has_accepted_license":"1","_id":"2908","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":26,"page":"267 - 269","quality_controlled":"1","scopus_import":1,"doi":"10.1111/jeb.12015","date_updated":"2021-01-12T07:00:37Z","date_published":"2013-01-17T00:00:00Z","pubrep_id":"111","author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"file_date_updated":"2020-07-14T12:45:52Z","month":"01","language":[{"iso":"eng"}],"ddc":["576"],"day":"17","file":[{"file_name":"IST-2013-111-v1+1_Hybridisation_and_speciation_revised.rtf","checksum":"716e88714c3411cd0bd70928b14ea692","file_size":13339,"date_updated":"2020-07-14T12:45:52Z","file_id":"4762","date_created":"2018-12-12T10:09:38Z","content_type":"text/rtf","access_level":"open_access","creator":"system","relation":"main_file"},{"content_type":"application/pdf","date_created":"2018-12-12T10:09:39Z","relation":"main_file","creator":"system","access_level":"open_access","file_size":103437,"checksum":"957fd07c71c1b1eac2c65ae3311aca78","file_name":"IST-2017-111-v1+2_Hybridisation_and_speciation_revised.pdf","file_id":"4763","date_updated":"2020-07-14T12:45:52Z"}],"publication_status":"published","intvolume":"        26"},{"doi":"10.1088/1742-5468/2013/01/P01002","date_updated":"2021-01-12T07:00:37Z","article_processing_charge":"No","date_published":"2013-01-16T00:00:00Z","pubrep_id":"557","author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"},{"full_name":"Etheridge, Alison","first_name":"Alison","last_name":"Etheridge"},{"full_name":"Véber, Amandine","first_name":"Amandine","last_name":"Véber"}],"quality_controlled":"1","scopus_import":1,"file_date_updated":"2020-07-14T12:45:52Z","day":"16","ddc":["570"],"language":[{"iso":"eng"}],"project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"month":"01","publication_status":"published","file":[{"access_level":"open_access","creator":"system","relation":"main_file","date_created":"2018-12-12T10:16:52Z","content_type":"application/pdf","file_id":"5242","date_updated":"2020-07-14T12:45:52Z","checksum":"ce8a4424385b3086138a1e054e16e0e3","file_name":"IST-2016-557-v1+1_BEVrevised.pdf","file_size":702583}],"intvolume":"      2013","abstract":[{"lang":"eng","text":"We survey a class of models for spatially structured populations\r\nwhich we have called spatial Λ-Fleming–Viot processes. They arise from a flexible\r\nframework for modelling in which the key innovation is that random genetic drift\r\nis driven by a Poisson point process of spatial ‘events’. We demonstrate how this\r\novercomes some of the obstructions to modelling populations which evolve in two-\r\n(and higher-) dimensional spatial continua, how its predictions match phenomena\r\nobserved in data and how it fits with classical models. Finally we outline some\r\ndirections for future research."}],"publisher":"IOP Publishing Ltd.","title":"Modelling evolution in a spatial continuum","department":[{"_id":"NiBa"}],"publication":"Journal of Statistical Mechanics Theory and Experiment","publist_id":"3834","oa_version":"Submitted Version","date_created":"2018-12-11T12:00:17Z","ec_funded":1,"issue":"1","status":"public","oa":1,"citation":{"ieee":"N. H. Barton, A. Etheridge, and A. Véber, “Modelling evolution in a spatial continuum,” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2013, no. 1. IOP Publishing Ltd., 2013.","chicago":"Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “Modelling Evolution in a Spatial Continuum.” <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing Ltd., 2013. <a href=\"https://doi.org/10.1088/1742-5468/2013/01/P01002\">https://doi.org/10.1088/1742-5468/2013/01/P01002</a>.","apa":"Barton, N. H., Etheridge, A., &#38; Véber, A. (2013). Modelling evolution in a spatial continuum. <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1742-5468/2013/01/P01002\">https://doi.org/10.1088/1742-5468/2013/01/P01002</a>","ama":"Barton NH, Etheridge A, Véber A. Modelling evolution in a spatial continuum. <i>Journal of Statistical Mechanics Theory and Experiment</i>. 2013;2013(1). doi:<a href=\"https://doi.org/10.1088/1742-5468/2013/01/P01002\">10.1088/1742-5468/2013/01/P01002</a>","ista":"Barton NH, Etheridge A, Véber A. 2013. Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. 2013(1).","mla":"Barton, Nicholas H., et al. “Modelling Evolution in a Spatial Continuum.” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2013, no. 1, IOP Publishing Ltd., 2013, doi:<a href=\"https://doi.org/10.1088/1742-5468/2013/01/P01002\">10.1088/1742-5468/2013/01/P01002</a>.","short":"N.H. Barton, A. Etheridge, A. Véber, Journal of Statistical Mechanics Theory and Experiment 2013 (2013)."},"type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":2013,"has_accepted_license":"1","year":"2013","_id":"2909"},{"intvolume":"        29","publication_status":"published","file":[{"access_level":"open_access","creator":"system","relation":"main_file","date_created":"2018-12-12T10:16:04Z","content_type":"application/pdf","file_id":"5189","date_updated":"2020-07-14T12:45:52Z","file_name":"IST-2016-556-v1+1_bioinformatics-2013.pdf","checksum":"a3b54d7477fac923815ac082403d9bd0","file_size":170197}],"day":"07","ddc":["570"],"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"month":"02","file_date_updated":"2020-07-14T12:45:52Z","author":[{"first_name":"Jerome","last_name":"Kelleher","full_name":"Kelleher, Jerome"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"},{"first_name":"Alison","last_name":"Etheridge","full_name":"Etheridge, Alison"}],"pubrep_id":"556","date_published":"2013-02-07T00:00:00Z","doi":"10.1093/bioinformatics/btt067","date_updated":"2021-01-12T07:00:38Z","scopus_import":1,"quality_controlled":"1","page":"955 - 956","volume":29,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2910","has_accepted_license":"1","year":"2013","oa":1,"status":"public","issue":"7","citation":{"chicago":"Kelleher, Jerome, Nicholas H Barton, and Alison Etheridge. “Coalescent Simulation in Continuous Space.” <i>Bioinformatics</i>. Oxford University Press, 2013. <a href=\"https://doi.org/10.1093/bioinformatics/btt067\">https://doi.org/10.1093/bioinformatics/btt067</a>.","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>","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>","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.","short":"J. Kelleher, N.H. Barton, A. Etheridge, Bioinformatics 29 (2013) 955–956."},"title":"Coalescent simulation in continuous space","department":[{"_id":"NiBa"}],"publication":"Bioinformatics","publisher":"Oxford University Press","oa_version":"Published Version","ec_funded":1,"date_created":"2018-12-11T12:00:17Z","publist_id":"3833","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."}]},{"volume":110,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1205.6598"}],"_id":"2913","intvolume":"       110","publication_status":"published","year":"2013","status":"public","oa":1,"day":"28","issue":"5","citation":{"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>.","short":"G. Tkačik, E. Granot Atedgi, R. Segev, E. Schneidman, Physical Review Letters 110 (2013).","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.","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>","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>","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>.","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."},"language":[{"iso":"eng"}],"month":"01","department":[{"_id":"GaTk"}],"title":"Retinal metric: a stimulus distance measure derived from population neural responses","publication":"Physical Review Letters","article_number":"058104","publisher":"American Physical Society","oa_version":"Preprint","date_created":"2018-12-11T12:00:18Z","publist_id":"3830","author":[{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik"},{"full_name":"Granot Atedgi, Einat","last_name":"Granot Atedgi","first_name":"Einat"},{"full_name":"Segev, Ronen","last_name":"Segev","first_name":"Ronen"},{"last_name":"Schneidman","first_name":"Elad","full_name":"Schneidman, Elad"}],"date_published":"2013-01-28T00:00:00Z","doi":"10.1103/PhysRevLett.110.058104","date_updated":"2021-01-12T07:00:39Z","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"}],"scopus_import":1,"quality_controlled":"1"},{"citation":{"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>","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.","chicago":"Stephens, Greg, Thierry Mora, Gašper Tkačik, and William Bialek. “Statistical Thermodynamics of Natural Images.” <i>Physical Review Letters</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevLett.110.018701\">https://doi.org/10.1103/PhysRevLett.110.018701</a>.","ista":"Stephens G, Mora T, Tkačik G, Bialek W. 2013. Statistical thermodynamics of natural images. Physical Review Letters. 110(1), 018701.","short":"G. Stephens, T. Mora, G. Tkačik, W. Bialek, Physical Review Letters 110 (2013).","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>.","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>"},"issue":"1","article_type":"original","external_id":{"arxiv":["0806.2694"]},"status":"public","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","oa":1,"year":"2013","has_accepted_license":"1","_id":"2914","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":110,"abstract":[{"text":"The scale invariance of natural images suggests an analogy to the statistical mechanics of physical systems at a critical point. Here we examine the distribution of pixels in small image patches and show how to construct the corresponding thermodynamics. We find evidence for criticality in a diverging specific heat, which corresponds to large fluctuations in how &quot;surprising&quot; we find individual images, and in the quantitative form of the entropy vs energy. We identify special image configurations as local energy minima and show that average patches within each basin are interpretable as lines and edges in all orientations.","lang":"eng"}],"arxiv":1,"publist_id":"3829","date_created":"2018-12-11T12:00:19Z","oa_version":"Published Version","publisher":"American Physical Society","publication":"Physical Review Letters","title":"Statistical thermodynamics of natural images","department":[{"_id":"GaTk"}],"month":"01","language":[{"iso":"eng"}],"ddc":["530"],"day":"02","file":[{"file_id":"5366","date_updated":"2020-07-14T12:45:53Z","file_size":416965,"file_name":"IST-2016-401-v1+1_1281.full.pdf","checksum":"72bfbc2094c4680e8a8a6bed668cd06d","relation":"main_file","access_level":"open_access","creator":"system","content_type":"application/pdf","date_created":"2018-12-12T10:18:44Z"}],"publication_status":"published","intvolume":"       110","quality_controlled":"1","article_processing_charge":"No","doi":"10.1103/PhysRevLett.110.018701","date_updated":"2023-09-04T11:47:51Z","date_published":"2013-01-02T00:00:00Z","pubrep_id":"401","author":[{"last_name":"Stephens","first_name":"Greg","full_name":"Stephens, Greg"},{"full_name":"Mora, Thierry","first_name":"Thierry","last_name":"Mora"},{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"},{"last_name":"Bialek","first_name":"William","full_name":"Bialek, William"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"018701","file_date_updated":"2020-07-14T12:45:53Z"},{"doi":"10.1038/ncb2632","date_updated":"2021-01-12T07:00:41Z","date_published":"2013-01-01T00:00:00Z","author":[{"first_name":"Irinka","last_name":"Castanon","full_name":"Castanon, Irinka"},{"full_name":"Abrami, Laurence","last_name":"Abrami","first_name":"Laurence"},{"first_name":"Laurent","last_name":"Holtzer","full_name":"Holtzer, Laurent"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566"},{"full_name":"Van Der Goot, Françoise","first_name":"Françoise","last_name":"Van Der Goot"},{"full_name":"González Gaitán, Marcos","first_name":"Marcos","last_name":"González Gaitán"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"Oriented mitosis is essential during tissue morphogenesis. The Wnt/planar cell polarity (Wnt/PCP) pathway orients mitosis in a number of developmental systems, including dorsal epiblast cell divisions along the animal-vegetal (A-V) axis during zebrafish gastrulation. How Wnt signalling orients the mitotic plane is, however, unknown. Here we show that, in dorsal epiblast cells, anthrax toxin receptor 2a (Antxr2a) accumulates in a polarized cortical cap, which is aligned with the embryonic A-V axis and forecasts the division plane. Filamentous actin (F-actin) also forms an A-V polarized cap, which depends on Wnt/PCP and its effectors RhoA and Rock2. Antxr2a is recruited to the cap by interacting with actin. Antxr2a also interacts with RhoA and together they activate the diaphanous-related formin zDia2. Mechanistically, Antxr2a functions as a Wnt-dependent polarized determinant, which, through the action of RhoA and zDia2, exerts torque on the spindle to align it with the A-V axis.\r\n"}],"scopus_import":1,"publisher":"Nature Publishing Group","title":"Anthrax toxin receptor 2a controls mitotic spindle positioning","department":[{"_id":"CaHe"}],"publication":"Nature Cell Biology","publist_id":"3819","oa_version":"None","date_created":"2018-12-11T12:00:20Z","day":"01","issue":"1","status":"public","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.).","language":[{"iso":"eng"}],"month":"01","citation":{"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>","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>.","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.","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.","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.","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>.","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>"},"type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","page":"28 - 39","volume":15,"publication_status":"published","year":"2013","intvolume":"        15","_id":"2918"}]