[{"issue":"7","oa":1,"isi":1,"oa_version":"Published Version","date_created":"2018-12-11T11:47:58Z","type":"journal_article","article_number":"e1005609","date_published":"2017-07-18T00:00:00Z","citation":{"ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” <i>PLoS Computational Biology</i>, vol. 13, no. 7. Public Library of Science, 2017.","ama":"Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. 2017;13(7). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” <i>PLoS Computational Biology</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">https://doi.org/10.1371/journal.pcbi.1005609</a>.","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 13(7), e1005609.","apa":"Lukacisinova, M., Novak, S., &#38; Paixao, T. (2017). Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">https://doi.org/10.1371/journal.pcbi.1005609</a>","short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).","mla":"Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” <i>PLoS Computational Biology</i>, vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>."},"department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"abstract":[{"text":"Mutator strains are expected to evolve when the availability and effect of beneficial mutations are high enough to counteract the disadvantage from deleterious mutations that will inevitably accumulate. As the population becomes more adapted to its environment, both availability and effect of beneficial mutations necessarily decrease and mutation rates are predicted to decrease. It has been shown that certain molecular mechanisms can lead to increased mutation rates when the organism finds itself in a stressful environment. While this may be a correlated response to other functions, it could also be an adaptive mechanism, raising mutation rates only when it is most advantageous. Here, we use a mathematical model to investigate the plausibility of the adaptive hypothesis. We show that such a mechanism can be mantained if the population is subjected to diverse stresses. By simulating various antibiotic treatment schemes, we find that combination treatments can reduce the effectiveness of second-order selection on stress-induced mutagenesis. We discuss the implications of our results to strategies of antibiotic therapy.","lang":"eng"}],"_id":"696","date_updated":"2026-04-25T22:31:24Z","has_accepted_license":"1","language":[{"iso":"eng"}],"author":[{"id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisinova, Marta","first_name":"Marta","last_name":"Lukacisinova","orcid":"0000-0002-2519-8004"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","first_name":"Sebastian","last_name":"Novak","orcid":"0000-0002-2519-824X"},{"full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","last_name":"Paixao","first_name":"Tiago"}],"intvolume":"        13","article_type":"original","related_material":{"record":[{"relation":"research_data","status":"public","id":"9849"},{"status":"public","id":"9850","relation":"research_data"},{"relation":"research_data","status":"public","id":"9851"},{"relation":"research_data","status":"public","id":"9852"},{"relation":"dissertation_contains","status":"public","id":"6263"}]},"year":"2017","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","scopus_import":"1","ec_funded":1,"publist_id":"7004","corr_author":"1","doi":"10.1371/journal.pcbi.1005609","file_date_updated":"2020-07-14T12:47:46Z","pubrep_id":"894","project":[{"grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"month":"07","quality_controlled":"1","external_id":{"isi":["000406619800014"]},"ddc":["576"],"day":"18","status":"public","file":[{"file_size":3775716,"access_level":"open_access","file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","creator":"system","date_updated":"2020-07-14T12:47:46Z","checksum":"9143c290fa6458ed2563bff4b295554a","content_type":"application/pdf","file_id":"5117","date_created":"2018-12-12T10:15:01Z","relation":"main_file"}],"publication_identifier":{"issn":["1553-734X"]},"publication":"PLoS Computational Biology","volume":13,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publisher":"Public Library of Science","publication_status":"published"},{"scopus_import":"1","title":"PirB regulates asymmetries in hippocampal circuitry","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","year":"2017","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"51"}]},"article_type":"original","author":[{"first_name":"Hikari","last_name":"Ukai","full_name":"Ukai, Hikari"},{"full_name":"Kawahara, Aiko","first_name":"Aiko","last_name":"Kawahara"},{"full_name":"Hirayama, Keiko","first_name":"Keiko","last_name":"Hirayama"},{"id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Case, Matthew J","first_name":"Matthew J","last_name":"Case"},{"full_name":"Aino, Shotaro","last_name":"Aino","first_name":"Shotaro"},{"last_name":"Miyabe","first_name":"Masahiro","full_name":"Miyabe, Masahiro"},{"first_name":"Ken","last_name":"Wakita","full_name":"Wakita, Ken"},{"full_name":"Oogi, Ryohei","last_name":"Oogi","first_name":"Ryohei"},{"last_name":"Kasayuki","first_name":"Michiyo","full_name":"Kasayuki, Michiyo"},{"full_name":"Kawashima, Shihomi","first_name":"Shihomi","last_name":"Kawashima"},{"full_name":"Sugimoto, Shunichi","last_name":"Sugimoto","first_name":"Shunichi"},{"last_name":"Chikamatsu","first_name":"Kanako","full_name":"Chikamatsu, Kanako"},{"full_name":"Nitta, Noritaka","first_name":"Noritaka","last_name":"Nitta"},{"last_name":"Koga","first_name":"Tsuneyuki","full_name":"Koga, Tsuneyuki"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","first_name":"Ryuichi"},{"last_name":"Takai","first_name":"Toshiyuki","full_name":"Takai, Toshiyuki"},{"last_name":"Ito","first_name":"Isao","full_name":"Ito, Isao"}],"intvolume":"        12","language":[{"iso":"eng"}],"has_accepted_license":"1","_id":"682","abstract":[{"text":"Left-right asymmetry is a fundamental feature of higher-order brain structure; however, the molecular basis of brain asymmetry remains unclear. We recently identified structural and functional asymmetries in mouse hippocampal circuitry that result from the asymmetrical distribution of two distinct populations of pyramidal cell synapses that differ in the density of the NMDA receptor subunit GluRε2 (also known as NR2B, GRIN2B or GluN2B). By examining the synaptic distribution of ε2 subunits, we previously found that β2-microglobulin-deficient mice, which lack cell surface expression of the vast majority of major histocompatibility complex class I (MHCI) proteins, do not exhibit circuit asymmetry. In the present study, we conducted electrophysiological and anatomical analyses on the hippocampal circuitry of mice with a knockout of the paired immunoglobulin-like receptor B (PirB), an MHCI receptor. As in β2-microglobulin-deficient mice, the PirB-deficient hippocampus lacked circuit asymmetries. This finding that MHCI loss-of-function mice and PirB knockout mice have identical phenotypes suggests that MHCI signals that produce hippocampal asymmetries are transduced through PirB. Our results provide evidence for a critical role of the MHCI/PirB signaling system in the generation of asymmetries in hippocampal circuitry.","lang":"eng"}],"date_updated":"2026-04-25T22:31:25Z","department":[{"_id":"RySh"}],"date_published":"2017-06-01T00:00:00Z","citation":{"apa":"Ukai, H., Kawahara, A., Hirayama, K., Case, M. J., Aino, S., Miyabe, M., … Ito, I. (2017). PirB regulates asymmetries in hippocampal circuitry. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0179377\">https://doi.org/10.1371/journal.pone.0179377</a>","mla":"Ukai, Hikari, et al. “PirB Regulates Asymmetries in Hippocampal Circuitry.” <i>PLoS One</i>, vol. 12, no. 6, e0179377, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pone.0179377\">10.1371/journal.pone.0179377</a>.","short":"H. Ukai, A. Kawahara, K. Hirayama, M.J. Case, S. Aino, M. Miyabe, K. Wakita, R. Oogi, M. Kasayuki, S. Kawashima, S. Sugimoto, K. Chikamatsu, N. Nitta, T. Koga, R. Shigemoto, T. Takai, I. Ito, PLoS One 12 (2017).","chicago":"Ukai, Hikari, Aiko Kawahara, Keiko Hirayama, Matthew J Case, Shotaro Aino, Masahiro Miyabe, Ken Wakita, et al. “PirB Regulates Asymmetries in Hippocampal Circuitry.” <i>PLoS One</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pone.0179377\">https://doi.org/10.1371/journal.pone.0179377</a>.","ista":"Ukai H, Kawahara A, Hirayama K, Case MJ, Aino S, Miyabe M, Wakita K, Oogi R, Kasayuki M, Kawashima S, Sugimoto S, Chikamatsu K, Nitta N, Koga T, Shigemoto R, Takai T, Ito I. 2017. PirB regulates asymmetries in hippocampal circuitry. PLoS One. 12(6), e0179377.","ama":"Ukai H, Kawahara A, Hirayama K, et al. PirB regulates asymmetries in hippocampal circuitry. <i>PLoS One</i>. 2017;12(6). doi:<a href=\"https://doi.org/10.1371/journal.pone.0179377\">10.1371/journal.pone.0179377</a>","ieee":"H. Ukai <i>et al.</i>, “PirB regulates asymmetries in hippocampal circuitry,” <i>PLoS One</i>, vol. 12, no. 6. Public Library of Science, 2017."},"article_number":"e0179377","type":"journal_article","date_created":"2018-12-11T11:47:54Z","oa_version":"Published Version","isi":1,"oa":1,"issue":"6","publication_status":"published","publisher":"Public Library of Science","volume":12,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication":"PLoS One","publication_identifier":{"issn":["1932-6203"]},"file":[{"file_size":5798454,"file_name":"IST-2017-897-v1+1_journal.pone.0179377.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:40Z","creator":"system","content_type":"application/pdf","checksum":"24dd19c46fb1c761b0bcbbcd1025a3a8","file_id":"4934","date_created":"2018-12-12T10:12:16Z","relation":"main_file"}],"status":"public","day":"01","external_id":{"isi":["000402923200125"]},"ddc":["571"],"quality_controlled":"1","month":"06","file_date_updated":"2020-07-14T12:47:40Z","pubrep_id":"897","doi":"10.1371/journal.pone.0179377","publist_id":"7034"},{"status":"public","day":"01","file":[{"file_size":858338,"success":1,"file_name":"2017_CurrentOpinion_Lukaciinova.pdf","access_level":"open_access","creator":"dernst","date_updated":"2019-01-18T09:57:57Z","content_type":"application/pdf","file_id":"5846","date_created":"2019-01-18T09:57:57Z","relation":"main_file"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"volume":46,"publication":"Current Opinion in Biotechnology","publication_status":"published","publisher":"Elsevier","quality_controlled":"1","external_id":{"isi":["000408077400015"]},"ddc":["570"],"pubrep_id":"801","file_date_updated":"2019-01-18T09:57:57Z","doi":"10.1016/j.copbio.2017.02.013","project":[{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","call_identifier":"FWF"},{"_id":"25E83C2C-B435-11E9-9278-68D0E5697425","grant_number":"303507","name":"Optimality principles in responses to antibiotics","call_identifier":"FP7"},{"grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"}],"month":"08","ec_funded":1,"publist_id":"6364","corr_author":"1","title":"Toward a quantitative understanding of antibiotic resistance evolution","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","intvolume":"        46","author":[{"full_name":"Lukacisinova, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","first_name":"Marta","last_name":"Lukacisinova","orcid":"0000-0002-2519-8004"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X"}],"article_type":"original","related_material":{"record":[{"relation":"dissertation_contains","id":"6263","status":"public"}]},"article_processing_charge":"Yes (in subscription journal)","year":"2017","_id":"1027","date_updated":"2026-04-25T22:31:24Z","abstract":[{"lang":"eng","text":"The rising prevalence of antibiotic resistant bacteria is an increasingly serious public health challenge. To address this problem, recent work ranging from clinical studies to theoretical modeling has provided valuable insights into the mechanisms of resistance, its emergence and spread, and ways to counteract it. A deeper understanding of the underlying dynamics of resistance evolution will require a combination of experimental and theoretical expertise from different disciplines and new technology for studying evolution in the laboratory. Here, we review recent advances in the quantitative understanding of the mechanisms and evolution of antibiotic resistance. We focus on key theoretical concepts and new technology that enables well-controlled experiments. We further highlight key challenges that can be met in the near future to ultimately develop effective strategies for combating resistance."}],"date_published":"2017-08-01T00:00:00Z","department":[{"_id":"ToBo"}],"page":"90 - 97","citation":{"chicago":"Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative Understanding of Antibiotic Resistance Evolution.” <i>Current Opinion in Biotechnology</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.copbio.2017.02.013\">https://doi.org/10.1016/j.copbio.2017.02.013</a>.","ista":"Lukacisinova M, Bollenbach MT. 2017. Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. 46, 90–97.","ieee":"M. Lukacisinova and M. T. Bollenbach, “Toward a quantitative understanding of antibiotic resistance evolution,” <i>Current Opinion in Biotechnology</i>, vol. 46. Elsevier, pp. 90–97, 2017.","ama":"Lukacisinova M, Bollenbach MT. Toward a quantitative understanding of antibiotic resistance evolution. <i>Current Opinion in Biotechnology</i>. 2017;46:90-97. doi:<a href=\"https://doi.org/10.1016/j.copbio.2017.02.013\">10.1016/j.copbio.2017.02.013</a>","apa":"Lukacisinova, M., &#38; Bollenbach, M. T. (2017). Toward a quantitative understanding of antibiotic resistance evolution. <i>Current Opinion in Biotechnology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.copbio.2017.02.013\">https://doi.org/10.1016/j.copbio.2017.02.013</a>","mla":"Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative Understanding of Antibiotic Resistance Evolution.” <i>Current Opinion in Biotechnology</i>, vol. 46, Elsevier, 2017, pp. 90–97, doi:<a href=\"https://doi.org/10.1016/j.copbio.2017.02.013\">10.1016/j.copbio.2017.02.013</a>.","short":"M. Lukacisinova, M.T. Bollenbach, Current Opinion in Biotechnology 46 (2017) 90–97."},"language":[{"iso":"eng"}],"has_accepted_license":"1","oa":1,"isi":1,"oa_version":"Published Version","date_created":"2018-12-11T11:49:45Z","type":"journal_article"},{"scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection","article_processing_charge":"No","year":"2017","related_material":{"record":[{"relation":"popular_science","id":"5564","status":"public"},{"status":"public","id":"26","relation":"dissertation_contains"}]},"intvolume":"         6","author":[{"full_name":"Steinrück, Magdalena","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1229-9719","last_name":"Steinrück","first_name":"Magdalena"},{"first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","_id":"704","abstract":[{"text":"How the organization of genes on a chromosome shapes adaptation is essential for understanding evolutionary paths. Here, we investigate how adaptation to rapidly increasing levels of antibiotic depends on the chromosomal neighborhood of a drug-resistance gene inserted at different positions of the Escherichia coli chromosome. Using a dual-fluorescence reporter that allows us to distinguish gene amplifications from other up-mutations, we track in real-time adaptive changes in expression of the drug-resistance gene. We find that the relative contribution of several mutation types differs systematically between loci due to properties of neighboring genes: essentiality, expression, orientation, termination, and presence of duplicates. These properties determine rate and fitness effects of gene amplification, deletions, and mutations compromising transcriptional termination. Thus, the adaptive potential of a gene under selection is a system-property with a complex genetic basis that is specific for each chromosomal locus, and it can be inferred from detailed functional and genomic data.","lang":"eng"}],"date_updated":"2026-04-25T22:31:29Z","department":[{"_id":"CaGu"}],"date_published":"2017-07-25T00:00:00Z","citation":{"mla":"Steinrück, Magdalena, and Calin C. Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” <i>ELife</i>, vol. 6, e25100, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/eLife.25100\">10.7554/eLife.25100</a>.","short":"M. Steinrück, C.C. Guet, ELife 6 (2017).","apa":"Steinrück, M., &#38; Guet, C. C. (2017). Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.25100\">https://doi.org/10.7554/eLife.25100</a>","ieee":"M. Steinrück and C. C. Guet, “Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017.","ama":"Steinrück M, Guet CC. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/eLife.25100\">10.7554/eLife.25100</a>","ista":"Steinrück M, Guet CC. 2017. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife. 6, e25100.","chicago":"Steinrück, Magdalena, and Calin C Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/eLife.25100\">https://doi.org/10.7554/eLife.25100</a>."},"article_number":"e25100","type":"journal_article","oa_version":"Published Version","date_created":"2018-12-11T11:48:01Z","isi":1,"oa":1,"publication_status":"published","publisher":"eLife Sciences Publications","volume":6,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication":"eLife","publication_identifier":{"issn":["2050-084X"]},"file":[{"file_id":"4975","date_created":"2018-12-12T10:12:54Z","relation":"main_file","access_level":"open_access","file_name":"IST-2017-890-v1+1_elife-25100-v1.pdf","file_size":2092088,"checksum":"6b908b5db9f61f6820ebd7f8fa815571","content_type":"application/pdf","creator":"system","date_updated":"2020-07-14T12:47:48Z"},{"file_id":"4976","relation":"main_file","date_created":"2018-12-12T10:12:55Z","access_level":"open_access","file_name":"IST-2017-890-v1+2_elife-25100-figures-v1.pdf","file_size":3428681,"content_type":"application/pdf","checksum":"ca21530389b720243552678125fdba35","date_updated":"2020-07-14T12:47:48Z","creator":"system"}],"status":"public","day":"25","ddc":["576"],"external_id":{"isi":["000406183700001"]},"quality_controlled":"1","month":"07","pubrep_id":"890","file_date_updated":"2020-07-14T12:47:48Z","doi":"10.7554/eLife.25100","corr_author":"1","publist_id":"6990"},{"year":"2017","article_processing_charge":"No","author":[{"id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","full_name":"Hurny, Andrej","orcid":"0000-0003-3638-1426","last_name":"Hurny","first_name":"Andrej"},{"first_name":"Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"}],"intvolume":"      1569","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"539"}]},"alternative_title":["Methods in Molecular Biology"],"title":"Methodological advances in auxin and cytokinin biology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","date_created":"2018-12-11T11:49:45Z","oa_version":"Submitted Version","type":"journal_article","oa":1,"page":"1 - 29","citation":{"ieee":"A. Hurny and E. Benková, “Methodological advances in auxin and cytokinin biology,” <i>Auxins and Cytokinins in Plant Biology</i>, vol. 1569. Springer, pp. 1–29, 2017.","ama":"Hurny A, Benková E. Methodological advances in auxin and cytokinin biology. <i>Auxins and Cytokinins in Plant Biology</i>. 2017;1569:1-29. doi:<a href=\"https://doi.org/10.1007/978-1-4939-6831-2_1\">10.1007/978-1-4939-6831-2_1</a>","chicago":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” <i>Auxins and Cytokinins in Plant Biology</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/978-1-4939-6831-2_1\">https://doi.org/10.1007/978-1-4939-6831-2_1</a>.","ista":"Hurny A, Benková E. 2017. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 1569, 1–29.","apa":"Hurny, A., &#38; Benková, E. (2017). Methodological advances in auxin and cytokinin biology. <i>Auxins and Cytokinins in Plant Biology</i>. Springer. <a href=\"https://doi.org/10.1007/978-1-4939-6831-2_1\">https://doi.org/10.1007/978-1-4939-6831-2_1</a>","mla":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” <i>Auxins and Cytokinins in Plant Biology</i>, vol. 1569, Springer, 2017, pp. 1–29, doi:<a href=\"https://doi.org/10.1007/978-1-4939-6831-2_1\">10.1007/978-1-4939-6831-2_1</a>.","short":"A. Hurny, E. Benková, Auxins and Cytokinins in Plant Biology 1569 (2017) 1–29."},"department":[{"_id":"EvBe"}],"date_published":"2017-03-17T00:00:00Z","_id":"1024","abstract":[{"lang":"eng","text":"The history of auxin and cytokinin biology including the initial discoveries by father–son duo Charles Darwin and Francis Darwin (1880), and Gottlieb Haberlandt (1919) is a beautiful demonstration of unceasing continuity of research. Novel findings are integrated into existing hypotheses and models and deepen our understanding of biological principles. At the same time new questions are triggered and hand to hand with this new methodologies are developed to address these new challenges."}],"date_updated":"2026-04-25T22:31:28Z","has_accepted_license":"1","language":[{"iso":"eng"}],"quality_controlled":"1","ddc":["575"],"publication":"Auxins and Cytokinins in Plant Biology","volume":1569,"publisher":"Springer","publication_status":"published","day":"17","status":"public","file":[{"creator":"system","date_updated":"2019-10-15T07:47:05Z","content_type":"application/pdf","file_size":840646,"access_level":"open_access","file_name":"IST-2018-1019-v1+1_Hurny_MethodsMolBiol_2017.pdf","date_created":"2018-12-12T10:14:18Z","relation":"main_file","file_id":"5068"}],"publication_identifier":{"issn":["1064-3745"]},"publist_id":"6369","corr_author":"1","month":"03","doi":"10.1007/978-1-4939-6831-2_1","pubrep_id":"1019","file_date_updated":"2019-10-15T07:47:05Z","project":[{"_id":"2542D156-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Hormone cross-talk drives nutrient dependent plant development","grant_number":"I 1774-B16"}]},{"intvolume":"       127","author":[{"full_name":"Ebner, Florian","last_name":"Ebner","first_name":"Florian"},{"full_name":"Sedlyarov, Vitaly","first_name":"Vitaly","last_name":"Sedlyarov"},{"id":"4323B49C-F248-11E8-B48F-1D18A9856A87","full_name":"Tasciyan, Saren","first_name":"Saren","orcid":"0000-0003-1671-393X","last_name":"Tasciyan"},{"first_name":"Masa","last_name":"Ivin","full_name":"Ivin, Masa"},{"full_name":"Kratochvill, Franz","first_name":"Franz","last_name":"Kratochvill"},{"full_name":"Gratz, Nina","last_name":"Gratz","first_name":"Nina"},{"last_name":"Kenner","first_name":"Lukas","full_name":"Kenner, Lukas"},{"last_name":"Villunger","first_name":"Andreas","full_name":"Villunger, Andreas"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179"},{"last_name":"Kovarik","first_name":"Pavel","full_name":"Kovarik, Pavel"}],"related_material":{"record":[{"status":"public","id":"12401","relation":"dissertation_contains"}]},"article_processing_charge":"No","year":"2017","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection","scopus_import":"1","issue":"6","oa":1,"isi":1,"oa_version":"Submitted Version","date_created":"2018-12-11T11:47:53Z","type":"journal_article","date_updated":"2026-04-25T22:31:31Z","_id":"679","abstract":[{"lang":"eng","text":"Protective responses against pathogens require a rapid mobilization of resting neutrophils and the timely removal of activated ones. Neutrophils are exceptionally short-lived leukocytes, yet it remains unclear whether the lifespan of pathogen-engaged neutrophils is regulated differently from that in the circulating steady-state pool. Here, we have found that under homeostatic conditions, the mRNA-destabilizing protein tristetraprolin (TTP) regulates apoptosis and the numbers of activated infiltrating murine neutrophils but not neutrophil cellularity. Activated TTP-deficient neutrophils exhibited decreased apoptosis and enhanced accumulation at the infection site. In the context of myeloid-specific deletion of Ttp, the potentiation of neutrophil deployment protected mice against lethal soft tissue infection with Streptococcus pyogenes and prevented bacterial dissemination. Neutrophil transcriptome analysis revealed that decreased apoptosis of TTP-deficient neutrophils was specifically associated with elevated expression of myeloid cell leukemia 1 (Mcl1) but not other antiapoptotic B cell leukemia/ lymphoma 2 (Bcl2) family members. Higher Mcl1 expression resulted from stabilization of Mcl1 mRNA in the absence of TTP. The low apoptosis rate of infiltrating TTP-deficient neutrophils was comparable to that of transgenic Mcl1-overexpressing neutrophils. Our study demonstrates that posttranscriptional gene regulation by TTP schedules the termination of the antimicrobial engagement of neutrophils. The balancing role of TTP comes at the cost of an increased risk of bacterial infections."}],"citation":{"ista":"Ebner F, Sedlyarov V, Tasciyan S, Ivin M, Kratochvill F, Gratz N, Kenner L, Villunger A, Sixt MK, Kovarik P. 2017. The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. The Journal of Clinical Investigation. 127(6), 2051–2065.","chicago":"Ebner, Florian, Vitaly Sedlyarov, Saren Tasciyan, Masa Ivin, Franz Kratochvill, Nina Gratz, Lukas Kenner, Andreas Villunger, Michael K Sixt, and Pavel Kovarik. “The RNA-Binding Protein Tristetraprolin Schedules Apoptosis of Pathogen-Engaged Neutrophils during Bacterial Infection.” <i>The Journal of Clinical Investigation</i>. American Society for Clinical Investigation, 2017. <a href=\"https://doi.org/10.1172/JCI80631\">https://doi.org/10.1172/JCI80631</a>.","ama":"Ebner F, Sedlyarov V, Tasciyan S, et al. The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. <i>The Journal of Clinical Investigation</i>. 2017;127(6):2051-2065. doi:<a href=\"https://doi.org/10.1172/JCI80631\">10.1172/JCI80631</a>","ieee":"F. Ebner <i>et al.</i>, “The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection,” <i>The Journal of Clinical Investigation</i>, vol. 127, no. 6. American Society for Clinical Investigation, pp. 2051–2065, 2017.","short":"F. Ebner, V. Sedlyarov, S. Tasciyan, M. Ivin, F. Kratochvill, N. Gratz, L. Kenner, A. Villunger, M.K. Sixt, P. Kovarik, The Journal of Clinical Investigation 127 (2017) 2051–2065.","mla":"Ebner, Florian, et al. “The RNA-Binding Protein Tristetraprolin Schedules Apoptosis of Pathogen-Engaged Neutrophils during Bacterial Infection.” <i>The Journal of Clinical Investigation</i>, vol. 127, no. 6, American Society for Clinical Investigation, 2017, pp. 2051–65, doi:<a href=\"https://doi.org/10.1172/JCI80631\">10.1172/JCI80631</a>.","apa":"Ebner, F., Sedlyarov, V., Tasciyan, S., Ivin, M., Kratochvill, F., Gratz, N., … Kovarik, P. (2017). The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. <i>The Journal of Clinical Investigation</i>. American Society for Clinical Investigation. <a href=\"https://doi.org/10.1172/JCI80631\">https://doi.org/10.1172/JCI80631</a>"},"date_published":"2017-06-01T00:00:00Z","department":[{"_id":"MiSi"}],"page":"2051 - 2065","language":[{"iso":"eng"}],"quality_controlled":"1","acknowledgement":"This work was supported by grants from the Austrian Science Fund (FWF) (P27538-B21, I1621-B22, and SFB 43, to PK); by funding from the European Union Seventh Framework Programme Marie Curie Initial Training Networks (FP7-PEOPLE-2012-ITN) for the project INBIONET (INfection BIOlogy Training NETwork under grant agreement PITN-GA-2012-316682; and by a joint research cluster initiative of the University of Vienna and the Medical University of Vienna.","external_id":{"isi":["000402620800008"],"pmid":["28504646"]},"status":"public","pmid":1,"day":"01","publication_identifier":{"issn":["0021-9738"]},"volume":127,"publication":"The Journal of Clinical Investigation","publication_status":"published","publisher":"American Society for Clinical Investigation","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451238/","open_access":"1"}],"publist_id":"7038","doi":"10.1172/JCI80631","project":[{"_id":"25985A36-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"T00817-B21","name":"The biochemical basis of PAR polarization"},{"name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"}],"month":"06"},{"publist_id":"7047","corr_author":"1","month":"05","doi":"10.1242/dev.144964","file_date_updated":"2020-07-14T12:47:39Z","quality_controlled":"1","external_id":{"pmid":["28512197"],"isi":["000402275900007"]},"ddc":["570"],"publication":"Development","volume":144,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publisher":"Company of Biologists","publication_status":"published","day":"15","pmid":1,"status":"public","file":[{"file_size":8194516,"access_level":"open_access","file_name":"2017_Development_Krens.pdf","date_updated":"2020-07-14T12:47:39Z","creator":"dernst","content_type":"application/pdf","checksum":"bc25125fb664706cdf180e061429f91d","file_id":"6905","date_created":"2019-09-24T06:56:22Z","relation":"main_file"}],"publication_identifier":{"issn":["0950-1991"]},"date_created":"2018-12-11T11:47:52Z","oa_version":"Published Version","type":"journal_article","issue":"10","oa":1,"isi":1,"department":[{"_id":"Bio"},{"_id":"CaHe"}],"page":"1798 - 1806","citation":{"short":"G. Krens, J. Veldhuis, V. Barone, D. Capek, J.-L. Maître, W. Brodland, C.-P.J. Heisenberg, Development 144 (2017) 1798–1806.","mla":"Krens, Gabriel, et al. “Interstitial Fluid Osmolarity Modulates the Action of Differential Tissue Surface Tension in Progenitor Cell Segregation during Gastrulation.” <i>Development</i>, vol. 144, no. 10, Company of Biologists, 2017, pp. 1798–806, doi:<a href=\"https://doi.org/10.1242/dev.144964\">10.1242/dev.144964</a>.","apa":"Krens, G., Veldhuis, J., Barone, V., Capek, D., Maître, J.-L., Brodland, W., &#38; Heisenberg, C.-P. J. (2017). Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.144964\">https://doi.org/10.1242/dev.144964</a>","ieee":"G. Krens <i>et al.</i>, “Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation,” <i>Development</i>, vol. 144, no. 10. Company of Biologists, pp. 1798–1806, 2017.","ama":"Krens G, Veldhuis J, Barone V, et al. Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. <i>Development</i>. 2017;144(10):1798-1806. doi:<a href=\"https://doi.org/10.1242/dev.144964\">10.1242/dev.144964</a>","ista":"Krens G, Veldhuis J, Barone V, Capek D, Maître J-L, Brodland W, Heisenberg C-PJ. 2017. Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. Development. 144(10), 1798–1806.","chicago":"Krens, Gabriel, Jim Veldhuis, Vanessa Barone, Daniel Capek, Jean-Léon Maître, Wayne Brodland, and Carl-Philipp J Heisenberg. “Interstitial Fluid Osmolarity Modulates the Action of Differential Tissue Surface Tension in Progenitor Cell Segregation during Gastrulation.” <i>Development</i>. Company of Biologists, 2017. <a href=\"https://doi.org/10.1242/dev.144964\">https://doi.org/10.1242/dev.144964</a>."},"date_published":"2017-05-15T00:00:00Z","date_updated":"2026-04-25T22:31:36Z","_id":"676","abstract":[{"text":"The segregation of different cell types into distinct tissues is a fundamental process in metazoan development. Differences in cell adhesion and cortex tension are commonly thought to drive cell sorting by regulating tissue surface tension (TST). However, the role that differential TST plays in cell segregation within the developing embryo is as yet unclear. Here, we have analyzed the role of differential TST for germ layer progenitor cell segregation during zebrafish gastrulation. Contrary to previous observations that differential TST drives germ layer progenitor cell segregation in vitro, we show that germ layers display indistinguishable TST within the gastrulating embryo, arguing against differential TST driving germ layer progenitor cell segregation in vivo. We further show that the osmolarity of the interstitial fluid (IF) is an important factor that influences germ layer TST in vivo, and that lower osmolarity of the IF compared with standard cell culture medium can explain why germ layers display differential TST in culture but not in vivo. Finally, we show that directed migration of mesendoderm progenitors is required for germ layer progenitor cell segregation and germ layer formation.","lang":"eng"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"year":"2017","article_processing_charge":"No","intvolume":"       144","author":[{"orcid":"0000-0003-4761-5996","last_name":"Krens","first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel"},{"full_name":"Veldhuis, Jim","first_name":"Jim","last_name":"Veldhuis"},{"first_name":"Vanessa","last_name":"Barone","orcid":"0000-0003-2676-3367","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","full_name":"Barone, Vanessa"},{"last_name":"Capek","orcid":"0000-0001-5199-9940","first_name":"Daniel","full_name":"Capek, Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Maître, Jean-Léon","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3688-1474","last_name":"Maître","first_name":"Jean-Léon"},{"full_name":"Brodland, Wayne","first_name":"Wayne","last_name":"Brodland"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"related_material":{"record":[{"id":"961","status":"public","relation":"dissertation_contains"},{"status":"public","id":"50","relation":"dissertation_contains"}]},"article_type":"original","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation","scopus_import":"1"},{"external_id":{"pmid":["28346437"],"isi":["000397917000009"]},"quality_controlled":"1","publication_identifier":{"issn":["1465-7392"]},"pmid":1,"day":"27","status":"public","publisher":"Nature Publishing Group","publication_status":"published","publication":"Nature Cell Biology","volume":19,"ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://europepmc.org/articles/pmc5635970"}],"corr_author":"1","publist_id":"7074","project":[{"call_identifier":"FP7","grant_number":"306589","name":"Decoding the complexity of turbulence at its origin","_id":"25152F3A-B435-11E9-9278-68D0E5697425"},{"_id":"252ABD0A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I930-B20","name":"Control of Epithelial Cell Layer Spreading in Zebrafish"}],"doi":"10.1038/ncb3492","month":"03","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8350"},{"status":"public","id":"50","relation":"dissertation_contains"}]},"intvolume":"        19","author":[{"last_name":"Smutny","orcid":"0000-0002-5920-9090","first_name":"Michael","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","full_name":"Smutny, Michael"},{"first_name":"Zsuzsa","last_name":"Ákos","full_name":"Ákos, Zsuzsa"},{"first_name":"Silvia","last_name":"Grigolon","full_name":"Grigolon, Silvia"},{"full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan","last_name":"Shamipour"},{"full_name":"Ruprecht, Verena","last_name":"Ruprecht","first_name":"Verena"},{"full_name":"Capek, Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-9940","last_name":"Capek","first_name":"Daniel"},{"last_name":"Behrndt","first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","full_name":"Behrndt, Martin"},{"last_name":"Papusheva","first_name":"Ekaterina","id":"41DB591E-F248-11E8-B48F-1D18A9856A87","full_name":"Papusheva, Ekaterina"},{"first_name":"Masazumi","last_name":"Tada","full_name":"Tada, Masazumi"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754","last_name":"Hof"},{"first_name":"Tamás","last_name":"Vicsek","full_name":"Vicsek, Tamás"},{"last_name":"Salbreux","first_name":"Guillaume","full_name":"Salbreux, Guillaume"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566"}],"year":"2017","article_processing_charge":"No","scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Friction forces position the neural anlage","oa":1,"isi":1,"type":"journal_article","oa_version":"Submitted Version","date_created":"2018-12-11T11:47:46Z","acknowledged_ssus":[{"_id":"SSU"}],"language":[{"iso":"eng"}],"page":"306 - 317","department":[{"_id":"CaHe"},{"_id":"BjHo"},{"_id":"Bio"}],"citation":{"apa":"Smutny, M., Ákos, Z., Grigolon, S., Shamipour, S., Ruprecht, V., Capek, D., … Heisenberg, C.-P. J. (2017). Friction forces position the neural anlage. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb3492\">https://doi.org/10.1038/ncb3492</a>","mla":"Smutny, Michael, et al. “Friction Forces Position the Neural Anlage.” <i>Nature Cell Biology</i>, vol. 19, Nature Publishing Group, 2017, pp. 306–17, doi:<a href=\"https://doi.org/10.1038/ncb3492\">10.1038/ncb3492</a>.","short":"M. Smutny, Z. Ákos, S. Grigolon, S. Shamipour, V. Ruprecht, D. Capek, M. Behrndt, E. Papusheva, M. Tada, B. Hof, T. Vicsek, G. Salbreux, C.-P.J. Heisenberg, Nature Cell Biology 19 (2017) 306–317.","chicago":"Smutny, Michael, Zsuzsa Ákos, Silvia Grigolon, Shayan Shamipour, Verena Ruprecht, Daniel Capek, Martin Behrndt, et al. “Friction Forces Position the Neural Anlage.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncb3492\">https://doi.org/10.1038/ncb3492</a>.","ista":"Smutny M, Ákos Z, Grigolon S, Shamipour S, Ruprecht V, Capek D, Behrndt M, Papusheva E, Tada M, Hof B, Vicsek T, Salbreux G, Heisenberg C-PJ. 2017. Friction forces position the neural anlage. Nature Cell Biology. 19, 306–317.","ama":"Smutny M, Ákos Z, Grigolon S, et al. Friction forces position the neural anlage. <i>Nature Cell Biology</i>. 2017;19:306-317. doi:<a href=\"https://doi.org/10.1038/ncb3492\">10.1038/ncb3492</a>","ieee":"M. Smutny <i>et al.</i>, “Friction forces position the neural anlage,” <i>Nature Cell Biology</i>, vol. 19. Nature Publishing Group, pp. 306–317, 2017."},"date_published":"2017-03-27T00:00:00Z","abstract":[{"lang":"eng","text":"During embryonic development, mechanical forces are essential for cellular rearrangements driving tissue morphogenesis. Here, we show that in the early zebrafish embryo, friction forces are generated at the interface between anterior axial mesoderm (prechordal plate, ppl) progenitors migrating towards the animal pole and neurectoderm progenitors moving in the opposite direction towards the vegetal pole of the embryo. These friction forces lead to global rearrangement of cells within the neurectoderm and determine the position of the neural anlage. Using a combination of experiments and simulations, we show that this process depends on hydrodynamic coupling between neurectoderm and ppl as a result of E-cadherin-mediated adhesion between those tissues. Our data thus establish the emergence of friction forces at the interface between moving tissues as a critical force-generating process shaping the embryo."}],"_id":"661","date_updated":"2026-04-25T22:31:36Z"},{"alternative_title":["LNCS"],"scopus_import":"1","conference":{"name":"CAV: Computer Aided Verification","end_date":"2017-07-28","location":"Heidelberg, Germany","start_date":"2017-07-24"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Non-polynomial worst case analysis of recursive programs","year":"2017","article_processing_charge":"No","related_material":{"record":[{"id":"7014","status":"public","relation":"later_version"},{"id":"8934","status":"public","relation":"dissertation_contains"}]},"editor":[{"full_name":"Majumdar, Rupak","last_name":"Majumdar","first_name":"Rupak"},{"full_name":"Kunčak, Viktor","first_name":"Viktor","last_name":"Kunčak"}],"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"first_name":"Hongfei","last_name":"Fu","full_name":"Fu, Hongfei"},{"first_name":"Amir","orcid":"0000-0003-1702-6584","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir"}],"intvolume":"     10427","language":[{"iso":"eng"}],"date_published":"2017-01-01T00:00:00Z","page":"41 - 63","department":[{"_id":"KrCh"}],"citation":{"chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Non-Polynomial Worst Case Analysis of Recursive Programs.” edited by Rupak Majumdar and Viktor Kunčak, 10427:41–63. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-63390-9_3\">https://doi.org/10.1007/978-3-319-63390-9_3</a>.","ista":"Chatterjee K, Fu H, Goharshady AK. 2017. Non-polynomial worst case analysis of recursive programs. CAV: Computer Aided Verification, LNCS, vol. 10427, 41–63.","ieee":"K. Chatterjee, H. Fu, and A. K. Goharshady, “Non-polynomial worst case analysis of recursive programs,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10427, pp. 41–63.","ama":"Chatterjee K, Fu H, Goharshady AK. Non-polynomial worst case analysis of recursive programs. In: Majumdar R, Kunčak V, eds. Vol 10427. Springer; 2017:41-63. doi:<a href=\"https://doi.org/10.1007/978-3-319-63390-9_3\">10.1007/978-3-319-63390-9_3</a>","apa":"Chatterjee, K., Fu, H., &#38; Goharshady, A. K. (2017). Non-polynomial worst case analysis of recursive programs. In R. Majumdar &#38; V. Kunčak (Eds.) (Vol. 10427, pp. 41–63). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. <a href=\"https://doi.org/10.1007/978-3-319-63390-9_3\">https://doi.org/10.1007/978-3-319-63390-9_3</a>","short":"K. Chatterjee, H. Fu, A.K. Goharshady, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 41–63.","mla":"Chatterjee, Krishnendu, et al. <i>Non-Polynomial Worst Case Analysis of Recursive Programs</i>. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10427, Springer, 2017, pp. 41–63, doi:<a href=\"https://doi.org/10.1007/978-3-319-63390-9_3\">10.1007/978-3-319-63390-9_3</a>."},"date_updated":"2026-04-25T22:31:40Z","_id":"639","abstract":[{"lang":"eng","text":"We study the problem of developing efficient approaches for proving worst-case bounds of non-deterministic recursive programs. Ranking functions are sound and complete for proving termination and worst-case bounds of non-recursive programs. First, we apply ranking functions to recursion, resulting in measure functions, and show that they provide a sound and complete approach to prove worst-case bounds of non-deterministic recursive programs. Our second contribution is the synthesis of measure functions in non-polynomial forms. We show that non-polynomial measure functions with logarithm and exponentiation can be synthesized through abstraction of logarithmic or exponentiation terms, Farkas’ Lemma, and Handelman’s Theorem using linear programming. While previous methods obtain worst-case polynomial bounds, our approach can synthesize bounds of the form O(n log n) as well as O(nr) where r is not an integer. We present experimental results to demonstrate that our approach can efficiently obtain worst-case bounds of classical recursive algorithms such as Merge-Sort, Closest-Pair, Karatsuba’s algorithm and Strassen’s algorithm."}],"type":"conference","oa_version":"Submitted Version","date_created":"2018-12-11T11:47:39Z","isi":1,"oa":1,"publisher":"Springer","publication_status":"published","volume":10427,"arxiv":1,"publication_identifier":{"isbn":["978-331963389-3"]},"day":"01","status":"public","external_id":{"isi":["000431900900003"],"arxiv":["1705.00317"]},"quality_controlled":"1","month":"01","project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"doi":"10.1007/978-3-319-63390-9_3","publist_id":"7149","ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.00317"}]},{"citation":{"apa":"Chatterjee, K., Goharshady, A. K., &#38; Pavlogiannis, A. (2017). JTDec: A tool for tree decompositions in soot. In D. D’Souza (Ed.) (Vol. 10482, pp. 59–66). Presented at the ATVA: Automated Technology for Verification and Analysis, Pune, India: Springer. <a href=\"https://doi.org/10.1007/978-3-319-68167-2_4\">https://doi.org/10.1007/978-3-319-68167-2_4</a>","mla":"Chatterjee, Krishnendu, et al. <i>JTDec: A Tool for Tree Decompositions in Soot</i>. Edited by Deepak D’Souza, vol. 10482, Springer, 2017, pp. 59–66, doi:<a href=\"https://doi.org/10.1007/978-3-319-68167-2_4\">10.1007/978-3-319-68167-2_4</a>.","short":"K. Chatterjee, A.K. Goharshady, A. Pavlogiannis, in:, D. D’Souza (Ed.), Springer, 2017, pp. 59–66.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Andreas Pavlogiannis. “JTDec: A Tool for Tree Decompositions in Soot.” edited by Deepak D’Souza, 10482:59–66. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-68167-2_4\">https://doi.org/10.1007/978-3-319-68167-2_4</a>.","ista":"Chatterjee K, Goharshady AK, Pavlogiannis A. 2017. JTDec: A tool for tree decompositions in soot. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 10482, 59–66.","ama":"Chatterjee K, Goharshady AK, Pavlogiannis A. JTDec: A tool for tree decompositions in soot. In: D’Souza D, ed. Vol 10482. Springer; 2017:59-66. doi:<a href=\"https://doi.org/10.1007/978-3-319-68167-2_4\">10.1007/978-3-319-68167-2_4</a>","ieee":"K. Chatterjee, A. K. Goharshady, and A. Pavlogiannis, “JTDec: A tool for tree decompositions in soot,” presented at the ATVA: Automated Technology for Verification and Analysis, Pune, India, 2017, vol. 10482, pp. 59–66."},"department":[{"_id":"KrCh"}],"page":"59 - 66","date_published":"2017-01-01T00:00:00Z","abstract":[{"text":"The notion of treewidth of graphs has been exploited for faster algorithms for several problems arising in verification and program analysis. Moreover, various notions of balanced tree decompositions have been used for improved algorithms supporting dynamic updates and analysis of concurrent programs. In this work, we present a tool for constructing tree-decompositions of CFGs obtained from Java methods, which is implemented as an extension to the widely used Soot framework. The experimental results show that our implementation on real-world Java benchmarks is very efficient. Our tool also provides the first implementation for balancing tree-decompositions. In summary, we present the first tool support for exploiting treewidth in the static analysis problems on Java programs.","lang":"eng"}],"_id":"949","date_updated":"2026-04-25T22:31:41Z","has_accepted_license":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:49:22Z","oa_version":"Submitted Version","type":"conference","oa":1,"isi":1,"alternative_title":["LNCS"],"conference":{"name":"ATVA: Automated Technology for Verification and Analysis","end_date":"2017-10-06","location":"Pune, India","start_date":"2017-10-03"},"title":"JTDec: A tool for tree decompositions in soot","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","scopus_import":"1","year":"2017","article_processing_charge":"No","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Amir","last_name":"Goharshady","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir"},{"full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","first_name":"Andreas"}],"intvolume":"     10482","related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"editor":[{"full_name":"D'Souza, Deepak","first_name":"Deepak","last_name":"D'Souza"}],"month":"01","doi":"10.1007/978-3-319-68167-2_4","file_date_updated":"2020-07-14T12:48:16Z","pubrep_id":"845","project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7"}],"publist_id":"6468","corr_author":"1","ec_funded":1,"volume":10482,"publisher":"Springer","publication_status":"published","day":"01","status":"public","file":[{"content_type":"application/pdf","checksum":"a0d9f5f94dc594c4e71e78525c9942f1","creator":"system","date_updated":"2020-07-14T12:48:16Z","access_level":"open_access","file_name":"IST-2017-845-v1+1_2017_Chatterjee_JTDec.pdf","file_size":948514,"date_created":"2018-12-12T10:10:45Z","relation":"main_file","file_id":"4835"}],"publication_identifier":{"issn":["0302-9743"]},"quality_controlled":"1","ddc":["005"],"external_id":{"isi":["000723567800004"]}},{"scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Enquiry into the topology of plasma membrane localized PIN auxin transport components","intvolume":"         9","author":[{"last_name":"Nodzyński","first_name":"Tomasz","full_name":"Nodzyński, Tomasz"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"full_name":"Pernisová, Markéta","first_name":"Markéta","last_name":"Pernisová"},{"full_name":"Hejátko, Jan","last_name":"Hejátko","first_name":"Jan"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí"}],"year":"2016","article_processing_charge":"No","has_accepted_license":"1","language":[{"iso":"eng"}],"date_published":"2016-11-07T00:00:00Z","page":"1504 - 1519","department":[{"_id":"JiFr"}],"citation":{"mla":"Nodzyński, Tomasz, et al. “Enquiry into the Topology of Plasma Membrane Localized PIN Auxin Transport Components.” <i>Molecular Plant</i>, vol. 9, no. 11, Cell Press, 2016, pp. 1504–19, doi:<a href=\"https://doi.org/10.1016/j.molp.2016.08.010\">10.1016/j.molp.2016.08.010</a>.","short":"T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, J. Friml, Molecular Plant 9 (2016) 1504–1519.","apa":"Nodzyński, T., Vanneste, S., Zwiewka, M., Pernisová, M., Hejátko, J., &#38; Friml, J. (2016). Enquiry into the topology of plasma membrane localized PIN auxin transport components. <i>Molecular Plant</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.molp.2016.08.010\">https://doi.org/10.1016/j.molp.2016.08.010</a>","ama":"Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. Enquiry into the topology of plasma membrane localized PIN auxin transport components. <i>Molecular Plant</i>. 2016;9(11):1504-1519. doi:<a href=\"https://doi.org/10.1016/j.molp.2016.08.010\">10.1016/j.molp.2016.08.010</a>","ieee":"T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, and J. Friml, “Enquiry into the topology of plasma membrane localized PIN auxin transport components,” <i>Molecular Plant</i>, vol. 9, no. 11. Cell Press, pp. 1504–1519, 2016.","ista":"Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. 2016. Enquiry into the topology of plasma membrane localized PIN auxin transport components. Molecular Plant. 9(11), 1504–1519.","chicago":"Nodzyński, Tomasz, Steffen Vanneste, Marta Zwiewka, Markéta Pernisová, Jan Hejátko, and Jiří Friml. “Enquiry into the Topology of Plasma Membrane Localized PIN Auxin Transport Components.” <i>Molecular Plant</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.molp.2016.08.010\">https://doi.org/10.1016/j.molp.2016.08.010</a>."},"_id":"1145","abstract":[{"text":"Auxin directs plant ontogenesis via differential accumulation within tissues depending largely on the activity of PIN proteins that mediate auxin efflux from cells and its directional cell-to-cell transport. Regardless of the developmental importance of PINs, the structure of these transporters is poorly characterized. Here, we present experimental data concerning protein topology of plasma membrane-localized PINs. Utilizing approaches based on pH-dependent quenching of fluorescent reporters combined with immunolocalization techniques, we mapped the membrane topology of PINs and further cross-validated our results using available topology modeling software. We delineated the topology of PIN1 with two transmembrane (TM) bundles of five α-helices linked by a large intracellular loop and a C-terminus positioned outside the cytoplasm. Using constraints derived from our experimental data, we also provide an updated position of helical regions generating a verisimilitude model of PIN1. Since the canonical long PINs show a high degree of conservation in TM domains and auxin transport capacity has been demonstrated for Arabidopsis representatives of this group, this empirically enhanced topological model of PIN1 will be an important starting point for further studies on PIN structure–function relationships. In addition, we have established protocols that can be used to probe the topology of other plasma membrane proteins in plants. © 2016 The Authors","lang":"eng"}],"date_updated":"2025-09-22T14:08:07Z","oa":1,"isi":1,"issue":"11","type":"journal_article","oa_version":"Published Version","date_created":"2018-12-11T11:50:23Z","file":[{"date_updated":"2018-12-12T10:13:22Z","creator":"system","content_type":"application/pdf","file_size":5005876,"file_name":"IST-2017-746-v1+1_1-s2.0-S1674205216301915-main.pdf","access_level":"open_access","date_created":"2018-12-12T10:13:22Z","relation":"main_file","file_id":"5004"}],"day":"07","status":"public","publisher":"Cell Press","publication_status":"published","publication":"Molecular Plant","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"volume":9,"ddc":["581"],"external_id":{"isi":["000389594100008"]},"acknowledgement":"This research has been financially supported by the Ministry of Education, Youth and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) (T.N., M.Z., M.P., J.H.), Czech Science Foundation (13-40637S [J.F., M.Z.], 13-39982S [J.H.]); Research Foundation Flanders (Grant number FWO09/PDO/196) (S.V.) and the European Research Council (project ERC-2011-StG-20101109-PSDP) (J.F.). We thank David G. Robinson and Ranjan Swarup for sharing published material; Maria Šimášková, Mamoona Khan, Eva Benková for technical assistance; and R. Tejos, J. Kleine-Vehn, and E. Feraru for helpful discussions.","quality_controlled":"1","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"doi":"10.1016/j.molp.2016.08.010","file_date_updated":"2018-12-12T10:13:22Z","pubrep_id":"746","month":"11","ec_funded":1,"publist_id":"6213"},{"article_number":"35955","type":"journal_article","oa_version":"Published Version","date_created":"2018-12-11T11:50:24Z","oa":1,"isi":1,"language":[{"iso":"eng"}],"has_accepted_license":"1","abstract":[{"text":"Apical dominance is one of the fundamental developmental phenomena in plant biology, which determines the overall architecture of aerial plant parts. Here we show apex decapitation activated competition for dominance in adjacent upper and lower axillary buds. A two-nodal-bud pea (Pisum sativum L.) was used as a model system to monitor and assess auxin flow, auxin transport channels, and dormancy and initiation status of axillary buds. Auxin flow was manipulated by lateral stem wounds or chemically by auxin efflux inhibitors 2,3,5-triiodobenzoic acid (TIBA), 1-N-naphtylphtalamic acid (NPA), or protein synthesis inhibitor cycloheximide (CHX) treatments, which served to interfere with axillary bud competition. Redirecting auxin flow to different points influenced which bud formed the outgrowing and dominant shoot. The obtained results proved that competition between upper and lower axillary buds as secondary auxin sources is based on the same auxin canalization principle that operates between the shoot apex and axillary bud. © The Author(s) 2016.","lang":"eng"}],"_id":"1147","date_updated":"2025-09-22T09:59:19Z","department":[{"_id":"JiFr"}],"date_published":"2016-11-08T00:00:00Z","citation":{"mla":"Balla, Jozef, et al. “Auxin Flow Mediated Competition between Axillary Buds to Restore Apical Dominance.” <i>Scientific Reports</i>, vol. 6, 35955, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep35955\">10.1038/srep35955</a>.","short":"J. Balla, Z. Medved’Ová, P. Kalousek, N. Matiješčuková, J. Friml, V. Reinöhl, S. Procházka, Scientific Reports 6 (2016).","apa":"Balla, J., Medved’Ová, Z., Kalousek, P., Matiješčuková, N., Friml, J., Reinöhl, V., &#38; Procházka, S. (2016). Auxin flow mediated competition between axillary buds to restore apical dominance. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep35955\">https://doi.org/10.1038/srep35955</a>","ama":"Balla J, Medved’Ová Z, Kalousek P, et al. Auxin flow mediated competition between axillary buds to restore apical dominance. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep35955\">10.1038/srep35955</a>","ieee":"J. Balla <i>et al.</i>, “Auxin flow mediated competition between axillary buds to restore apical dominance,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016.","ista":"Balla J, Medved’Ová Z, Kalousek P, Matiješčuková N, Friml J, Reinöhl V, Procházka S. 2016. Auxin flow mediated competition between axillary buds to restore apical dominance. Scientific Reports. 6, 35955.","chicago":"Balla, Jozef, Zuzana Medved’Ová, Petr Kalousek, Natálie Matiješčuková, Jiří Friml, Vilém Reinöhl, and Stanislav Procházka. “Auxin Flow Mediated Competition between Axillary Buds to Restore Apical Dominance.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep35955\">https://doi.org/10.1038/srep35955</a>."},"article_processing_charge":"No","year":"2016","intvolume":"         6","author":[{"full_name":"Balla, Jozef","first_name":"Jozef","last_name":"Balla"},{"last_name":"Medved'Ová","first_name":"Zuzana","full_name":"Medved'Ová, Zuzana"},{"first_name":"Petr","last_name":"Kalousek","full_name":"Kalousek, Petr"},{"last_name":"Matiješčuková","first_name":"Natálie","full_name":"Matiješčuková, Natálie"},{"first_name":"Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"},{"first_name":"Vilém","last_name":"Reinöhl","full_name":"Reinöhl, Vilém"},{"last_name":"Procházka","first_name":"Stanislav","full_name":"Procházka, Stanislav"}],"scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Auxin flow mediated competition between axillary buds to restore apical dominance","publist_id":"6211","month":"11","file_date_updated":"2018-12-12T10:09:28Z","pubrep_id":"745","doi":"10.1038/srep35955","acknowledgement":"This research was carried out under the project CEITEC 2020 (LQ1601) with financial support from the Ministry of Education, Youth and Sports of the Czech Republic under the National Sustainability Programme II., supported by the project “CEITEC–Central European Institute of Technology” (CZ.1.05/1.1.00/02.0068) and the Agronomy faculty grant from Mendel University “IGA AF MENDELU” (IP 14/2013).","external_id":{"isi":["000387284700001"]},"ddc":["581"],"quality_controlled":"1","publication_status":"published","publisher":"Nature Publishing Group","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"volume":6,"publication":"Scientific Reports","file":[{"date_created":"2018-12-12T10:09:28Z","relation":"main_file","file_id":"4752","creator":"system","date_updated":"2018-12-12T10:09:28Z","content_type":"application/pdf","file_size":1587544,"access_level":"open_access","file_name":"IST-2017-745-v1+1_srep35955.pdf"}],"status":"public","day":"08"},{"date_created":"2018-12-11T11:50:24Z","oa_version":"None","type":"journal_article","isi":1,"_id":"1148","date_updated":"2025-09-23T07:44:57Z","abstract":[{"text":"Continuous-time Markov chain (CTMC) models have become a central tool for understanding the dynamics of complex reaction networks and the importance of stochasticity in the underlying biochemical processes. When such models are employed to answer questions in applications, in order to ensure that the model provides a sufficiently accurate representation of the real system, it is of vital importance that the model parameters are inferred from real measured data. This, however, is often a formidable task and all of the existing methods fail in one case or the other, usually because the underlying CTMC model is high-dimensional and computationally difficult to analyze. The parameter inference methods that tend to scale best in the dimension of the CTMC are based on so-called moment closure approximations. However, there exists a large number of different moment closure approximations and it is typically hard to say a priori which of the approximations is the most suitable for the inference procedure. Here, we propose a moment-based parameter inference method that automatically chooses the most appropriate moment closure method. Accordingly, contrary to existing methods, the user is not required to be experienced in moment closure techniques. In addition to that, our method adaptively changes the approximation during the parameter inference to ensure that always the best approximation is used, even in cases where different approximations are best in different regions of the parameter space. © 2016 Elsevier Ireland Ltd","lang":"eng"}],"date_published":"2016-11-01T00:00:00Z","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"page":"15 - 25","citation":{"apa":"Schilling, C., Bogomolov, S., Henzinger, T. A., Podelski, A., &#38; Ruess, J. (2016). Adaptive moment closure for parameter inference of biochemical reaction networks. <i>Biosystems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.biosystems.2016.07.005\">https://doi.org/10.1016/j.biosystems.2016.07.005</a>","short":"C. Schilling, S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, Biosystems 149 (2016) 15–25.","mla":"Schilling, Christian, et al. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” <i>Biosystems</i>, vol. 149, Elsevier, 2016, pp. 15–25, doi:<a href=\"https://doi.org/10.1016/j.biosystems.2016.07.005\">10.1016/j.biosystems.2016.07.005</a>.","ieee":"C. Schilling, S. Bogomolov, T. A. Henzinger, A. Podelski, and J. Ruess, “Adaptive moment closure for parameter inference of biochemical reaction networks,” <i>Biosystems</i>, vol. 149. Elsevier, pp. 15–25, 2016.","ama":"Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. Adaptive moment closure for parameter inference of biochemical reaction networks. <i>Biosystems</i>. 2016;149:15-25. doi:<a href=\"https://doi.org/10.1016/j.biosystems.2016.07.005\">10.1016/j.biosystems.2016.07.005</a>","chicago":"Schilling, Christian, Sergiy Bogomolov, Thomas A Henzinger, Andreas Podelski, and Jakob Ruess. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” <i>Biosystems</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.biosystems.2016.07.005\">https://doi.org/10.1016/j.biosystems.2016.07.005</a>.","ista":"Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. 2016. Adaptive moment closure for parameter inference of biochemical reaction networks. Biosystems. 149, 15–25."},"language":[{"iso":"eng"}],"article_processing_charge":"No","year":"2016","intvolume":"       149","author":[{"full_name":"Schilling, Christian","last_name":"Schilling","first_name":"Christian"},{"full_name":"Bogomolov, Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0686-0365","last_name":"Bogomolov","first_name":"Sergiy"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A"},{"first_name":"Andreas","last_name":"Podelski","full_name":"Podelski, Andreas"},{"last_name":"Ruess","orcid":"0000-0003-1615-3282","first_name":"Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","full_name":"Ruess, Jakob"}],"related_material":{"record":[{"status":"public","id":"1658","relation":"earlier_version"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Adaptive moment closure for parameter inference of biochemical reaction networks","scopus_import":"1","publist_id":"6210","ec_funded":1,"month":"11","doi":"10.1016/j.biosystems.2016.07.005","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","acknowledgement":"This work is based on the CMSB 2015 paper “Adaptive moment closure for parameter inference of biochemical reaction networks” (Bogomolov et al., 2015). The work was partly supported by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR 14 AVACS1), by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award). J.R. acknowledges support from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734.","external_id":{"isi":["000390743600003"]},"volume":149,"publication":"Biosystems","publication_status":"published","publisher":"Elsevier","status":"public","day":"01"},{"ec_funded":1,"publist_id":"6209","project":[{"_id":"255F06BE-B435-11E9-9278-68D0E5697425","grant_number":"622033","name":"Persistent Homology - Images, Data and Maps","call_identifier":"FP7"}],"doi":"10.1016/j.apnum.2016.04.005","month":"09","acknowledgement":"MG was partially supported by FAPESP grants 2013/07460-7 and 2010/00875-9, and by CNPq grants 305860/2013-5 and 306453/2009-6, Brazil. The work of HK was partially supported by Grant-in-Aid for Scientific Research (Nos.24654022, 25287029), Ministry of Education, Science, Technology, Culture and Sports, Japan. KM was supported by NSF grants NSF-DMS-0835621, 0915019, 1125174, 1248071, and contracts from AFOSR and DARPA. TM was supported by Grant-in-Aid for JSPS Fellows No. 245312. A part of the research of TM and HK was also supported by JST, CREST.\r\n\r\nResearch conducted by PP has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE – Programa Operacional Factores de Competitividade (POFC) and from the Portuguese national funds through Fundação para a Ciência e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (Ref. FCT PTDC/MAT/098871/2008); from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. 622033; and from the same sources as HK.\r\n\r\nThe authors express their gratitude to the Department of Mathematics of Kyoto University for making their server available for conducting the computations described in the paper, and to the reviewers for helpful comments that contributed towards increasing the quality of the paper.","external_id":{"isi":["000378447000003"]},"quality_controlled":"1","status":"public","day":"01","publication_status":"published","publisher":"Elsevier","volume":107,"publication":"Applied Numerical Mathematics","isi":1,"type":"journal_article","date_created":"2018-12-11T11:50:25Z","oa_version":"None","language":[{"iso":"eng"}],"_id":"1149","date_updated":"2025-09-22T09:58:16Z","abstract":[{"lang":"eng","text":"We study the usefulness of two most prominent publicly available rigorous ODE integrators: one provided by the CAPD group (capd.ii.uj.edu.pl), the other based on the COSY Infinity project (cosyinfinity.org). Both integrators are capable of handling entire sets of initial conditions and provide tight rigorous outer enclosures of the images under a time-T map. We conduct extensive benchmark computations using the well-known Lorenz system, and compare the computation time against the final accuracy achieved. We also discuss the effect of a few technical parameters, such as the order of the numerical integration method, the value of T, and the phase space resolution. We conclude that COSY may provide more precise results due to its ability of avoiding the variable dependency problem. However, the overall cost of computations conducted using CAPD is typically lower, especially when intervals of parameters are involved. Moreover, access to COSY is limited (registration required) and the rigorous ODE integrators are not publicly available, while CAPD is an open source free software project. Therefore, we recommend the latter integrator for this kind of computations. Nevertheless, proper choice of the various integration parameters turns out to be of even greater importance than the choice of the integrator itself. © 2016 IMACS. Published by Elsevier B.V. All rights reserved."}],"citation":{"ista":"Miyaji T, Pilarczyk P, Gameiro M, Kokubu H, Mischaikow K. 2016. A study of rigorous ODE integrators for multi scale set oriented computations. Applied Numerical Mathematics. 107, 34–47.","chicago":"Miyaji, Tomoyuki, Pawel Pilarczyk, Marcio Gameiro, Hiroshi Kokubu, and Konstantin Mischaikow. “A Study of Rigorous ODE Integrators for Multi Scale Set Oriented Computations.” <i>Applied Numerical Mathematics</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.apnum.2016.04.005\">https://doi.org/10.1016/j.apnum.2016.04.005</a>.","ama":"Miyaji T, Pilarczyk P, Gameiro M, Kokubu H, Mischaikow K. A study of rigorous ODE integrators for multi scale set oriented computations. <i>Applied Numerical Mathematics</i>. 2016;107:34-47. doi:<a href=\"https://doi.org/10.1016/j.apnum.2016.04.005\">10.1016/j.apnum.2016.04.005</a>","ieee":"T. Miyaji, P. Pilarczyk, M. Gameiro, H. Kokubu, and K. Mischaikow, “A study of rigorous ODE integrators for multi scale set oriented computations,” <i>Applied Numerical Mathematics</i>, vol. 107. Elsevier, pp. 34–47, 2016.","short":"T. Miyaji, P. Pilarczyk, M. Gameiro, H. Kokubu, K. Mischaikow, Applied Numerical Mathematics 107 (2016) 34–47.","mla":"Miyaji, Tomoyuki, et al. “A Study of Rigorous ODE Integrators for Multi Scale Set Oriented Computations.” <i>Applied Numerical Mathematics</i>, vol. 107, Elsevier, 2016, pp. 34–47, doi:<a href=\"https://doi.org/10.1016/j.apnum.2016.04.005\">10.1016/j.apnum.2016.04.005</a>.","apa":"Miyaji, T., Pilarczyk, P., Gameiro, M., Kokubu, H., &#38; Mischaikow, K. (2016). A study of rigorous ODE integrators for multi scale set oriented computations. <i>Applied Numerical Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.apnum.2016.04.005\">https://doi.org/10.1016/j.apnum.2016.04.005</a>"},"page":"34 - 47","date_published":"2016-09-01T00:00:00Z","department":[{"_id":"HeEd"}],"intvolume":"       107","author":[{"full_name":"Miyaji, Tomoyuki","first_name":"Tomoyuki","last_name":"Miyaji"},{"id":"3768D56A-F248-11E8-B48F-1D18A9856A87","full_name":"Pilarczyk, Pawel","first_name":"Pawel","last_name":"Pilarczyk"},{"full_name":"Gameiro, Marcio","last_name":"Gameiro","first_name":"Marcio"},{"full_name":"Kokubu, Hiroshi","last_name":"Kokubu","first_name":"Hiroshi"},{"last_name":"Mischaikow","first_name":"Konstantin","full_name":"Mischaikow, Konstantin"}],"article_processing_charge":"No","year":"2016","scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"A study of rigorous ODE integrators for multi scale set oriented computations"},{"day":"12","status":"public","publication":"Developmental Cell","volume":38,"publisher":"Cell Press","publication_status":"published","quality_controlled":"1","external_id":{"isi":["000383413000003"]},"doi":"10.1016/j.devcel.2016.08.017","month":"09","publist_id":"6208","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"A Radical Break Restraining Neutrophil Migration","scopus_import":"1","author":[{"id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","full_name":"Renkawitz, Jörg","last_name":"Renkawitz","orcid":"0000-0003-2856-3369","first_name":"Jörg"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K"}],"intvolume":"        38","year":"2016","article_processing_charge":"No","date_published":"2016-09-12T00:00:00Z","department":[{"_id":"MiSi"}],"page":"448 - 450","citation":{"ama":"Renkawitz J, Sixt MK. A Radical Break Restraining Neutrophil Migration. <i>Developmental Cell</i>. 2016;38(5):448-450. doi:<a href=\"https://doi.org/10.1016/j.devcel.2016.08.017\">10.1016/j.devcel.2016.08.017</a>","ieee":"J. Renkawitz and M. K. Sixt, “A Radical Break Restraining Neutrophil Migration,” <i>Developmental Cell</i>, vol. 38, no. 5. Cell Press, pp. 448–450, 2016.","chicago":"Renkawitz, Jörg, and Michael K Sixt. “A Radical Break Restraining Neutrophil Migration.” <i>Developmental Cell</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.devcel.2016.08.017\">https://doi.org/10.1016/j.devcel.2016.08.017</a>.","ista":"Renkawitz J, Sixt MK. 2016. A Radical Break Restraining Neutrophil Migration. Developmental Cell. 38(5), 448–450.","apa":"Renkawitz, J., &#38; Sixt, M. K. (2016). A Radical Break Restraining Neutrophil Migration. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2016.08.017\">https://doi.org/10.1016/j.devcel.2016.08.017</a>","short":"J. Renkawitz, M.K. Sixt, Developmental Cell 38 (2016) 448–450.","mla":"Renkawitz, Jörg, and Michael K. Sixt. “A Radical Break Restraining Neutrophil Migration.” <i>Developmental Cell</i>, vol. 38, no. 5, Cell Press, 2016, pp. 448–50, doi:<a href=\"https://doi.org/10.1016/j.devcel.2016.08.017\">10.1016/j.devcel.2016.08.017</a>."},"_id":"1150","abstract":[{"text":"When neutrophils infiltrate a site of inflammation, they have to stop at the right place to exert their effector function. In this issue of Developmental Cell, Wang et al. (2016) show that neutrophils sense reactive oxygen species via the TRPM2 channel to arrest migration at their target site. © 2016 Elsevier Inc.","lang":"eng"}],"date_updated":"2025-09-22T09:57:46Z","language":[{"iso":"eng"}],"issue":"5","isi":1,"date_created":"2018-12-11T11:50:25Z","oa_version":"None","type":"journal_article"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis","scopus_import":"1","year":"2016","article_processing_charge":"No","intvolume":"        30","author":[{"full_name":"Simonini, Sara","first_name":"Sara","last_name":"Simonini"},{"last_name":"Deb","first_name":"Joyita","full_name":"Deb, Joyita"},{"full_name":"Moubayidin, Laila","first_name":"Laila","last_name":"Moubayidin"},{"full_name":"Stephenson, Pauline","last_name":"Stephenson","first_name":"Pauline"},{"last_name":"Valluru","first_name":"Manoj","full_name":"Valluru, Manoj"},{"full_name":"Freire Rios, Alejandra","last_name":"Freire Rios","first_name":"Alejandra"},{"full_name":"Sorefan, Karim","first_name":"Karim","last_name":"Sorefan"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"},{"first_name":"Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lars","last_name":"Östergaard","full_name":"Östergaard, Lars"}],"department":[{"_id":"JiFr"}],"date_published":"2016-10-15T00:00:00Z","citation":{"ama":"Simonini S, Deb J, Moubayidin L, et al. A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. <i>Genes and Development</i>. 2016;30(20):2286-2296. doi:<a href=\"https://doi.org/10.1101/gad.285361.116\">10.1101/gad.285361.116</a>","ieee":"S. Simonini <i>et al.</i>, “A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis,” <i>Genes and Development</i>, vol. 30, no. 20. Cold Spring Harbor Laboratory Press, pp. 2286–2296, 2016.","ista":"Simonini S, Deb J, Moubayidin L, Stephenson P, Valluru M, Freire Rios A, Sorefan K, Weijers D, Friml J, Östergaard L. 2016. A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. Genes and Development. 30(20), 2286–2296.","chicago":"Simonini, Sara, Joyita Deb, Laila Moubayidin, Pauline Stephenson, Manoj Valluru, Alejandra Freire Rios, Karim Sorefan, Dolf Weijers, Jiří Friml, and Lars Östergaard. “A Noncanonical Auxin Sensing Mechanism Is Required for Organ Morphogenesis in Arabidopsis.” <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press, 2016. <a href=\"https://doi.org/10.1101/gad.285361.116\">https://doi.org/10.1101/gad.285361.116</a>.","short":"S. Simonini, J. Deb, L. Moubayidin, P. Stephenson, M. Valluru, A. Freire Rios, K. Sorefan, D. Weijers, J. Friml, L. Östergaard, Genes and Development 30 (2016) 2286–2296.","mla":"Simonini, Sara, et al. “A Noncanonical Auxin Sensing Mechanism Is Required for Organ Morphogenesis in Arabidopsis.” <i>Genes and Development</i>, vol. 30, no. 20, Cold Spring Harbor Laboratory Press, 2016, pp. 2286–96, doi:<a href=\"https://doi.org/10.1101/gad.285361.116\">10.1101/gad.285361.116</a>.","apa":"Simonini, S., Deb, J., Moubayidin, L., Stephenson, P., Valluru, M., Freire Rios, A., … Östergaard, L. (2016). A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gad.285361.116\">https://doi.org/10.1101/gad.285361.116</a>"},"page":"2286 - 2296","date_updated":"2025-09-22T09:57:16Z","_id":"1151","abstract":[{"lang":"eng","text":"Tissue patterning in multicellular organisms is the output of precise spatio–temporal regulation of gene expression coupled with changes in hormone dynamics. In plants, the hormone auxin regulates growth and development at every stage of a plant’s life cycle. Auxin signaling occurs through binding of the auxin molecule to a TIR1/AFB F-box ubiquitin ligase, allowing interaction with Aux/IAA transcriptional repressor proteins. These are subsequently ubiquitinated and degraded via the 26S proteasome, leading to derepression of auxin response factors (ARFs). How auxin is able to elicit such a diverse range of developmental responses through a single signaling module has not yet been resolved. Here we present an alternative auxin-sensing mechanism in which the ARF ARF3/ETTIN controls gene expression through interactions with process-specific transcription factors. This noncanonical hormonesensing mechanism exhibits strong preference for the naturally occurring auxin indole 3-acetic acid (IAA) and is important for coordinating growth and patterning in diverse developmental contexts such as gynoecium morphogenesis, lateral root emergence, ovule development, and primary branch formation. Disrupting this IAA-sensing ability induces morphological aberrations with consequences for plant fitness. Therefore, our findings introduce a novel transcription factor-based mechanism of hormone perception in plants. © 2016 Simonini et al."}],"has_accepted_license":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:50:25Z","oa_version":"Published Version","type":"journal_article","issue":"20","oa":1,"isi":1,"publication":"Genes and Development","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"volume":30,"publisher":"Cold Spring Harbor Laboratory Press","publication_status":"published","pmid":1,"day":"15","status":"public","file":[{"success":1,"file_name":"2016_GeneDev_Simonini.pdf","access_level":"open_access","file_size":1419263,"content_type":"application/pdf","date_updated":"2019-01-25T09:32:55Z","creator":"dernst","file_id":"5882","date_created":"2019-01-25T09:32:55Z","relation":"main_file"}],"quality_controlled":"1","external_id":{"pmid":["27898393"],"isi":["000387814000005"]},"ddc":["570"],"acknowledgement":"We thank Norwich Research Park Bioimaging, Grant Calder, Roy\r\nDunford, Caroline Smith, Paul Thomas, and Mark Youles for\r\ntechnical support; Charlie Scutt, Alejandro Ferrando, and George\r\nLomonossoff for plasmids; Toshiro Ito for seeds; Brendan Davies\r\nand Barry Causier for the REGIA library; and Mark Buttner,\r\nSimona Masiero, Fabio Rossi, Doris Wagner, and Jun Xiao for\r\nhelp and material. We are also grateful to Stefano Bencivenga,\r\nMarie Brüser, Friederike Jantzen, Lukasz Langowski, Xinran Li,\r\nand Nicola Stacey for discussions and helpful comments on the\r\nmanuscript. This work was supported by grants BB/M004112/1\r\nand BB/I017232/1 (Crop Improvement Research Club) to L.Ø.\r\nfrom the Biotechnological and Biological Sciences Research\r\nCouncil, and Institute Strategic Programme grant (BB/J004553/\r\n1) to the John Innes Centre. S.S., J.D., and L.Ø conceived the ex-\r\nperiments. ","month":"10","doi":"10.1101/gad.285361.116","file_date_updated":"2019-01-25T09:32:55Z","publist_id":"6207"},{"year":"2016","article_processing_charge":"No","intvolume":"        28","author":[{"full_name":"Žádníková, Petra","first_name":"Petra","last_name":"Žádníková"},{"first_name":"Krzysztof T","last_name":"Wabnik","orcid":"0000-0001-7263-0560","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","full_name":"Wabnik, Krzysztof T"},{"last_name":"Abuzeineh","first_name":"Anas","full_name":"Abuzeineh, Anas"},{"last_name":"Gallemí","first_name":"Marçal","full_name":"Gallemí, Marçal"},{"full_name":"Van Der Straeten, Dominique","last_name":"Van Der Straeten","first_name":"Dominique"},{"full_name":"Smith, Richard","last_name":"Smith","first_name":"Richard"},{"full_name":"Inze, Dirk","first_name":"Dirk","last_name":"Inze"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"},{"full_name":"Prusinkiewicz, Przemysław","last_name":"Prusinkiewicz","first_name":"Przemysław"},{"orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"A model of differential growth guided apical hook formation in plants","type":"journal_article","date_created":"2018-12-11T11:50:26Z","oa_version":"Submitted Version","isi":1,"oa":1,"issue":"10","language":[{"iso":"eng"}],"citation":{"ama":"Žádníková P, Wabnik KT, Abuzeineh A, et al. A model of differential growth guided apical hook formation in plants. <i>Plant Cell</i>. 2016;28(10):2464-2477. doi:<a href=\"https://doi.org/10.1105/tpc.15.00569\">10.1105/tpc.15.00569</a>","ieee":"P. Žádníková <i>et al.</i>, “A model of differential growth guided apical hook formation in plants,” <i>Plant Cell</i>, vol. 28, no. 10. American Society of Plant Biologists, pp. 2464–2477, 2016.","chicago":"Žádníková, Petra, Krzysztof T Wabnik, Anas Abuzeineh, Marçal Gallemí, Dominique Van Der Straeten, Richard Smith, Dirk Inze, Jiří Friml, Przemysław Prusinkiewicz, and Eva Benková. “A Model of Differential Growth Guided Apical Hook Formation in Plants.” <i>Plant Cell</i>. American Society of Plant Biologists, 2016. <a href=\"https://doi.org/10.1105/tpc.15.00569\">https://doi.org/10.1105/tpc.15.00569</a>.","ista":"Žádníková P, Wabnik KT, Abuzeineh A, Gallemí M, Van Der Straeten D, Smith R, Inze D, Friml J, Prusinkiewicz P, Benková E. 2016. A model of differential growth guided apical hook formation in plants. Plant Cell. 28(10), 2464–2477.","apa":"Žádníková, P., Wabnik, K. T., Abuzeineh, A., Gallemí, M., Van Der Straeten, D., Smith, R., … Benková, E. (2016). A model of differential growth guided apical hook formation in plants. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.15.00569\">https://doi.org/10.1105/tpc.15.00569</a>","mla":"Žádníková, Petra, et al. “A Model of Differential Growth Guided Apical Hook Formation in Plants.” <i>Plant Cell</i>, vol. 28, no. 10, American Society of Plant Biologists, 2016, pp. 2464–77, doi:<a href=\"https://doi.org/10.1105/tpc.15.00569\">10.1105/tpc.15.00569</a>.","short":"P. Žádníková, K.T. Wabnik, A. Abuzeineh, M. Gallemí, D. Van Der Straeten, R. Smith, D. Inze, J. Friml, P. Prusinkiewicz, E. Benková, Plant Cell 28 (2016) 2464–2477."},"date_published":"2016-10-01T00:00:00Z","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"page":"2464 - 2477","date_updated":"2025-09-22T09:56:45Z","_id":"1153","abstract":[{"lang":"eng","text":"Differential cell growth enables flexible organ bending in the presence of environmental signals such as light or gravity. A prominent example of the developmental processes based on differential cell growth is the formation of the apical hook that protects the fragile shoot apical meristem when it breaks through the soil during germination. Here, we combined in silico and in vivo approaches to identify a minimal mechanism producing auxin gradient-guided differential growth during the establishment of the apical hook in the model plant Arabidopsis thaliana. Computer simulation models based on experimental data demonstrate that asymmetric expression of the PIN-FORMED auxin efflux carrier at the concave (inner) versus convex (outer) side of the hook suffices to establish an auxin maximum in the epidermis at the concave side of the apical hook. Furthermore, we propose a mechanism that translates this maximum into differential growth, and thus curvature, of the apical hook. Through a combination of experimental and in silico computational approaches, we have identified the individual contributions of differential cell elongation and proliferation to defining the apical hook and reveal the role of auxin-ethylene crosstalk in balancing these two processes. © 2016 American Society of Plant Biologists. All rights reserved."}],"external_id":{"isi":["000390135400013"]},"acknowledgement":"We thank Martine De Cock and Annick Bleys for help in preparing the manuscript, Daniel Van Damme for sharing material and stimulating discussion, and Rudiger Simon for support during revision of the manuscript.\r\nThis work was supported by grants from the European Research Council (StartingIndependentResearchGrantERC-2007-Stg-207362-HCPO)and the Czech Science Foundation (GACR CZ.1.07/2.3.00/20.0043) to E.B.\r\nand Natural Sciences and Engineering Research Council of Canada Discovery Grant 2014-05325 to P.P. K.W. acknowledges funding from a Human Frontier Science Program Long-Term Fellowship (LT-000209-2014).","quality_controlled":"1","publisher":"American Society of Plant Biologists","publication_status":"published","publication":"Plant Cell","volume":28,"day":"01","status":"public","corr_author":"1","publist_id":"6205","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5134968/"}],"ec_funded":1,"month":"10","project":[{"_id":"253FCA6A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Hormonal cross-talk in plant organogenesis","grant_number":"207362"}],"doi":"10.1105/tpc.15.00569"},{"year":"2016","article_processing_charge":"No","author":[{"last_name":"Schwarz","first_name":"Jan","full_name":"Schwarz, Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bierbaum, Veronika","id":"3FD04378-F248-11E8-B48F-1D18A9856A87","last_name":"Bierbaum","first_name":"Veronika"},{"full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","orcid":"0000-0001-5145-4609","first_name":"Jack"},{"full_name":"Frank, Tino","first_name":"Tino","last_name":"Frank"},{"last_name":"Hauschild","orcid":"0000-0001-9843-3522","first_name":"Robert","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","first_name":"Mark Tobias"},{"last_name":"Tay","first_name":"Savaş","full_name":"Tay, Savaş"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"},{"last_name":"Mehling","orcid":"0000-0001-8599-1226","first_name":"Matthias","full_name":"Mehling, Matthias","id":"3C23B994-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"         6","scopus_import":"1","title":"A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","article_number":"36440","oa_version":"Published Version","date_created":"2018-12-11T11:50:27Z","oa":1,"isi":1,"has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"ToBo"}],"date_published":"2016-11-07T00:00:00Z","citation":{"chicago":"Schwarz, Jan, Veronika Bierbaum, Jack Merrin, Tino Frank, Robert Hauschild, Mark Tobias Bollenbach, Savaş Tay, Michael K Sixt, and Matthias Mehling. “A Microfluidic Device for Measuring Cell Migration towards Substrate Bound and Soluble Chemokine Gradients.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep36440\">https://doi.org/10.1038/srep36440</a>.","ista":"Schwarz J, Bierbaum V, Merrin J, Frank T, Hauschild R, Bollenbach MT, Tay S, Sixt MK, Mehling M. 2016. A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. Scientific Reports. 6, 36440.","ieee":"J. Schwarz <i>et al.</i>, “A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016.","ama":"Schwarz J, Bierbaum V, Merrin J, et al. A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep36440\">10.1038/srep36440</a>","apa":"Schwarz, J., Bierbaum, V., Merrin, J., Frank, T., Hauschild, R., Bollenbach, M. T., … Mehling, M. (2016). A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep36440\">https://doi.org/10.1038/srep36440</a>","short":"J. Schwarz, V. Bierbaum, J. Merrin, T. Frank, R. Hauschild, M.T. Bollenbach, S. Tay, M.K. Sixt, M. Mehling, Scientific Reports 6 (2016).","mla":"Schwarz, Jan, et al. “A Microfluidic Device for Measuring Cell Migration towards Substrate Bound and Soluble Chemokine Gradients.” <i>Scientific Reports</i>, vol. 6, 36440, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep36440\">10.1038/srep36440</a>."},"abstract":[{"text":"Cellular locomotion is a central hallmark of eukaryotic life. It is governed by cell-extrinsic molecular factors, which can either emerge in the soluble phase or as immobilized, often adhesive ligands. To encode for direction, every cue must be present as a spatial or temporal gradient. Here, we developed a microfluidic chamber that allows measurement of cell migration in combined response to surface immobilized and soluble molecular gradients. As a proof of principle we study the response of dendritic cells to their major guidance cues, chemokines. The majority of data on chemokine gradient sensing is based on in vitro studies employing soluble gradients. Despite evidence suggesting that in vivo chemokines are often immobilized to sugar residues, limited information is available how cells respond to immobilized chemokines. We tracked migration of dendritic cells towards immobilized gradients of the chemokine CCL21 and varying superimposed soluble gradients of CCL19. Differential migratory patterns illustrate the potential of our setup to quantitatively study the competitive response to both types of gradients. Beyond chemokines our approach is broadly applicable to alternative systems of chemo- and haptotaxis such as cells migrating along gradients of adhesion receptor ligands vs. any soluble cue. \r\n","lang":"eng"}],"_id":"1154","date_updated":"2025-09-22T09:56:13Z","external_id":{"isi":["000387118300001"]},"ddc":["579"],"acknowledgement":"This work was supported by the Swiss National Science Foundation (Ambizione fellowship; PZ00P3-154733 to M.M.), the Swiss Multiple Sclerosis Society (research support to M.M.), a fellowship from the Boehringer Ingelheim Fonds (BIF) to J.S., the European Research Council (grant ERC GA 281556) and a START award from the Austrian Science Foundation (FWF) to M.S. #BioimagingFacility","quality_controlled":"1","publisher":"Nature Publishing Group","publication_status":"published","publication":"Scientific Reports","volume":6,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"content_type":"application/pdf","creator":"system","date_updated":"2018-12-12T10:09:32Z","access_level":"open_access","file_name":"IST-2017-744-v1+1_srep36440.pdf","file_size":2353456,"date_created":"2018-12-12T10:09:32Z","relation":"main_file","file_id":"4756"}],"day":"07","status":"public","publist_id":"6204","ec_funded":1,"month":"11","project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes"},{"_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Y 564-B12","name":"Cytoskeletal force generation and force transduction of migrating leukocytes"}],"doi":"10.1038/srep36440","file_date_updated":"2018-12-12T10:09:32Z","pubrep_id":"744"},{"type":"journal_article","date_created":"2018-12-11T11:50:27Z","oa_version":"Preprint","isi":1,"oa":1,"issue":"6","language":[{"iso":"eng"}],"page":"3786 - 3839","date_published":"2016-12-15T00:00:00Z","citation":{"ama":"Lee J, Schnelli K. Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. <i>Annals of Applied Probability</i>. 2016;26(6):3786-3839. doi:<a href=\"https://doi.org/10.1214/16-AAP1193\">10.1214/16-AAP1193</a>","ieee":"J. Lee and K. Schnelli, “Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population,” <i>Annals of Applied Probability</i>, vol. 26, no. 6. Institute of Mathematical Statistics, pp. 3786–3839, 2016.","ista":"Lee J, Schnelli K. 2016. Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. Annals of Applied Probability. 26(6), 3786–3839.","chicago":"Lee, Ji, and Kevin Schnelli. “Tracy-Widom Distribution for the Largest Eigenvalue of Real Sample Covariance Matrices with General Population.” <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2016. <a href=\"https://doi.org/10.1214/16-AAP1193\">https://doi.org/10.1214/16-AAP1193</a>.","mla":"Lee, Ji, and Kevin Schnelli. “Tracy-Widom Distribution for the Largest Eigenvalue of Real Sample Covariance Matrices with General Population.” <i>Annals of Applied Probability</i>, vol. 26, no. 6, Institute of Mathematical Statistics, 2016, pp. 3786–839, doi:<a href=\"https://doi.org/10.1214/16-AAP1193\">10.1214/16-AAP1193</a>.","short":"J. Lee, K. Schnelli, Annals of Applied Probability 26 (2016) 3786–3839.","apa":"Lee, J., &#38; Schnelli, K. (2016). Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/16-AAP1193\">https://doi.org/10.1214/16-AAP1193</a>"},"department":[{"_id":"LaEr"}],"_id":"1157","abstract":[{"lang":"eng","text":"We consider sample covariance matrices of the form Q = ( σ1/2X)(σ1/2X)∗, where the sample X is an M ×N random matrix whose entries are real independent random variables with variance 1/N and whereσ is an M × M positive-definite deterministic matrix. We analyze the asymptotic fluctuations of the largest rescaled eigenvalue of Q when both M and N tend to infinity with N/M →d ϵ (0,∞). For a large class of populations σ in the sub-critical regime, we show that the distribution of the largest rescaled eigenvalue of Q is given by the type-1 Tracy-Widom distribution under the additional assumptions that (1) either the entries of X are i.i.d. Gaussians or (2) that σ is diagonal and that the entries of X have a sub-exponential decay."}],"date_updated":"2025-09-22T09:55:43Z","year":"2016","article_processing_charge":"No","author":[{"last_name":"Lee","first_name":"Ji","full_name":"Lee, Ji"},{"first_name":"Kevin","orcid":"0000-0003-0954-3231","last_name":"Schnelli","full_name":"Schnelli, Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"        26","scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population","publist_id":"6201","main_file_link":[{"url":"https://arxiv.org/abs/1409.4979","open_access":"1"}],"ec_funded":1,"month":"12","project":[{"call_identifier":"FP7","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"doi":"10.1214/16-AAP1193","external_id":{"arxiv":["1409.4979"],"isi":["000391240100016"]},"acknowledgement":"We thank Horng-Tzer Yau for numerous discussions and remarks. We are grateful to Ben Adlam, Jinho Baik, Zhigang Bao, Paul Bourgade, László Erd ̋os, Iain Johnstone and Antti Knowles for comments. We are also grate-\r\nful to the anonymous referee for carefully reading our manuscript and suggesting several improvements.","quality_controlled":"1","publisher":"Institute of Mathematical Statistics","publication_status":"published","publication":"Annals of Applied Probability","volume":26,"arxiv":1,"day":"15","status":"public"},{"citation":{"mla":"Roux, Camille, et al. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” <i>PLoS Biology</i>, vol. 14, no. 12, e2000234, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234\">10.1371/journal.pbio.2000234</a>.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS Biology 14 (2016).","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Shedding light on the grey zone of speciation along a continuum of genomic divergence. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234\">https://doi.org/10.1371/journal.pbio.2000234</a>","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. 14(12), e2000234.","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” <i>PLoS Biology</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234\">https://doi.org/10.1371/journal.pbio.2000234</a>.","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Shedding light on the grey zone of speciation along a continuum of genomic divergence,” <i>PLoS Biology</i>, vol. 14, no. 12. Public Library of Science, 2016.","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Shedding light on the grey zone of speciation along a continuum of genomic divergence. <i>PLoS Biology</i>. 2016;14(12). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234\">10.1371/journal.pbio.2000234</a>"},"date_published":"2016-12-27T00:00:00Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"date_updated":"2025-09-22T09:55:10Z","_id":"1158","abstract":[{"lang":"eng","text":"Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids—the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of speciation thanks to a comparative analysis of genomic data from 61 pairs of populations/species of animals with variable levels of divergence. Gene flow between diverging gene pools is assessed under an approximate Bayesian computation (ABC) framework. We show that the intermediate &quot;grey zone&quot; of speciation, in which taxonomy is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective of species life history traits or ecology. Thanks to appropriate modeling of among-locus variation in genetic drift and introgression rate, we clarify the status of the majority of ambiguous cases and uncover a number of cryptic species. Our analysis also reveals the high incidence in animals of semi-isolated species (when some but not all loci are affected by barriers to gene flow) and highlights the intrinsic difficulty, both statistical and conceptual, of delineating species in the grey zone of speciation."}],"has_accepted_license":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","date_created":"2018-12-11T11:50:28Z","type":"journal_article","article_number":"e2000234","issue":"12","oa":1,"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Shedding light on the grey zone of speciation along a continuum of genomic divergence","scopus_import":"1","year":"2016","article_processing_charge":"No","intvolume":"        14","author":[{"full_name":"Roux, Camille","first_name":"Camille","last_name":"Roux"},{"first_name":"Christelle","last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Romiguier, Jonathan","last_name":"Romiguier","first_name":"Jonathan"},{"last_name":"Anciaux","first_name":"Youann","full_name":"Anciaux, Youann"},{"last_name":"Galtier","first_name":"Nicolas","full_name":"Galtier, Nicolas"},{"full_name":"Bierne, Nicolas","first_name":"Nicolas","last_name":"Bierne"}],"related_material":{"record":[{"id":"9862","status":"public","relation":"research_data"},{"status":"public","id":"9863","relation":"research_data"}]},"month":"12","doi":"10.1371/journal.pbio.2000234","file_date_updated":"2020-07-14T12:44:36Z","pubrep_id":"742","publist_id":"6200","publication":"PLoS Biology","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"volume":14,"publisher":"Public Library of Science","publication_status":"published","day":"27","status":"public","file":[{"relation":"main_file","date_created":"2018-12-12T10:15:42Z","file_id":"5164","creator":"system","date_updated":"2020-07-14T12:44:36Z","checksum":"2bab63b068a9840efd532b9ae583f9bb","content_type":"application/pdf","file_size":2494348,"file_name":"IST-2017-742-v1+1_journal.pbio.2000234.pdf","access_level":"open_access"}],"quality_controlled":"1","external_id":{"isi":["000392120100008"]},"ddc":["576"],"acknowledgement":"European Research Council (ERC) https://erc.europa.eu/ (grant number ERC grant 232971). PopPhyl project. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. French National Research Agency (ANR) http://www.agence-nationale-recherche.fr/en/project-based-funding-to-advance-french-research/ (grant number ANR-12-BSV7- 0011). HYSEA project.\r\nWe thank Aude Darracq, Vincent Castric, Pierre-Alexandre Gagnaire, Xavier Vekemans, and John Welch for insightful discussions. The computations were performed at the Vital-IT (http://www.vital-it.ch) Center for high-performance computing of the SIB Swiss Institute of Bioinformatics and the ISEM computing cluster at the platform Montpellier Bioinformatique et Biodiversité."}]