[{"editor":[{"first_name":"Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0686-0365","last_name":"Bogomolov","full_name":"Bogomolov, Sergiy"},{"full_name":"Martel, Matthieu","last_name":"Martel","first_name":"Matthieu"},{"full_name":"Prabhakar, Pavithra","last_name":"Prabhakar","first_name":"Pavithra"}],"date_created":"2018-12-11T11:47:38Z","article_processing_charge":"No","status":"public","oa_version":"None","quality_controlled":"1","doi":"10.1007/978-3-319-54292-8","title":"Numerical Software Verification","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"conference":{"end_date":"2016-07-18","start_date":"2016-07-17","name":"NSV: Numerical Software Verification","location":"Toronto, ON, Canada"},"volume":10152,"month":"01","intvolume":"     10152","publist_id":"7150","_id":"638","year":"2017","abstract":[{"text":"This book constitutes the refereed proceedings of the 9th InternationalWorkshop on Numerical Software Verification, NSV 2016, held in Toronto, ON, Canada in July 2011 - colocated with CAV 2016, the 28th International Conference on Computer Aided Verification.\r\nThe NSV workshop is dedicated to the development of logical and mathematical techniques for the reasoning about programmability and reliability.","lang":"eng"}],"type":"conference_editor","date_published":"2017-01-01T00:00:00Z","citation":{"apa":"Bogomolov, S., Martel, M., &#38; Prabhakar, P. (Eds.). (2017). <i>Numerical Software Verification</i> (Vol. 10152). Presented at the NSV: Numerical Software Verification, Toronto, ON, Canada: Springer. <a href=\"https://doi.org/10.1007/978-3-319-54292-8\">https://doi.org/10.1007/978-3-319-54292-8</a>","mla":"Bogomolov, Sergiy, et al., editors. <i>Numerical Software Verification</i>. Vol. 10152, Springer, 2017, doi:<a href=\"https://doi.org/10.1007/978-3-319-54292-8\">10.1007/978-3-319-54292-8</a>.","ista":"Bogomolov S, Martel M, Prabhakar P eds. 2017. Numerical Software Verification, Springer,p.","ama":"Bogomolov S, Martel M, Prabhakar P, eds. <i>Numerical Software Verification</i>. Vol 10152. Springer; 2017. doi:<a href=\"https://doi.org/10.1007/978-3-319-54292-8\">10.1007/978-3-319-54292-8</a>","chicago":"Bogomolov, Sergiy, Matthieu Martel, and Pavithra Prabhakar, eds. <i>Numerical Software Verification</i>. Vol. 10152. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-54292-8\">https://doi.org/10.1007/978-3-319-54292-8</a>.","ieee":"S. Bogomolov, M. Martel, and P. Prabhakar, Eds., <i>Numerical Software Verification</i>, vol. 10152. Springer, 2017.","short":"S. Bogomolov, M. Martel, P. Prabhakar, eds., Numerical Software Verification, Springer, 2017."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","publication_identifier":{"issn":["0302-9743"],"eisbn":["978-3-319-54292-8"]},"publication_status":"published","department":[{"_id":"ToHe"}],"date_updated":"2026-03-31T12:28:01Z","day":"01"},{"publist_id":"7123","intvolume":"      2184","_id":"649","year":"2017","citation":{"apa":"Maas, J. (2017). Entropic Ricci curvature for discrete spaces. In L. Najman &#38; P. Romon (Eds.), <i>Modern Approaches to Discrete Curvature</i> (Vol. 2184, pp. 159–174). Springer. <a href=\"https://doi.org/10.1007/978-3-319-58002-9_5\">https://doi.org/10.1007/978-3-319-58002-9_5</a>","mla":"Maas, Jan. “Entropic Ricci Curvature for Discrete Spaces.” <i>Modern Approaches to Discrete Curvature</i>, edited by Laurent Najman and Pascal Romon, vol. 2184, Springer, 2017, pp. 159–74, doi:<a href=\"https://doi.org/10.1007/978-3-319-58002-9_5\">10.1007/978-3-319-58002-9_5</a>.","ama":"Maas J. Entropic Ricci curvature for discrete spaces. In: Najman L, Romon P, eds. <i>Modern Approaches to Discrete Curvature</i>. Vol 2184. Lecture Notes in Mathematics. Springer; 2017:159-174. doi:<a href=\"https://doi.org/10.1007/978-3-319-58002-9_5\">10.1007/978-3-319-58002-9_5</a>","chicago":"Maas, Jan. “Entropic Ricci Curvature for Discrete Spaces.” In <i>Modern Approaches to Discrete Curvature</i>, edited by Laurent Najman and Pascal Romon, 2184:159–74. Lecture Notes in Mathematics. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-58002-9_5\">https://doi.org/10.1007/978-3-319-58002-9_5</a>.","ieee":"J. Maas, “Entropic Ricci curvature for discrete spaces,” in <i>Modern Approaches to Discrete Curvature</i>, vol. 2184, L. Najman and P. Romon, Eds. Springer, 2017, pp. 159–174.","ista":"Maas J. 2017.Entropic Ricci curvature for discrete spaces. In: Modern Approaches to Discrete Curvature. vol. 2184, 159–174.","short":"J. Maas, in:, L. Najman, P. Romon (Eds.), Modern Approaches to Discrete Curvature, Springer, 2017, pp. 159–174."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"05","date_updated":"2026-04-03T11:05:20Z","editor":[{"full_name":"Najman, Laurent","last_name":"Najman","first_name":"Laurent"},{"last_name":"Romon","full_name":"Romon, Pascal","first_name":"Pascal"}],"quality_controlled":"1","oa_version":"None","doi":"10.1007/978-3-319-58002-9_5","volume":2184,"month":"10","scopus_import":"1","publisher":"Springer","abstract":[{"lang":"eng","text":"We give a short overview on a recently developed notion of Ricci curvature for discrete spaces. This notion relies on geodesic convexity properties of the relative entropy along geodesics in the space of probability densities, for a metric which is similar to (but different from) the 2-Wasserstein metric. The theory can be considered as a discrete counterpart to the theory of Ricci curvature for geodesic measure spaces developed by Lott–Sturm–Villani."}],"type":"book_chapter","date_published":"2017-10-05T00:00:00Z","department":[{"_id":"JaMa"}],"publication_status":"published","publication_identifier":{"isbn":["978-3-319-58001-2"],"eisbn":["978-3-319-58002-9"]},"author":[{"full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","last_name":"Maas","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"}],"page":"159 - 174","status":"public","article_processing_charge":"No","date_created":"2018-12-11T11:47:42Z","publication":"Modern Approaches to Discrete Curvature","title":"Entropic Ricci curvature for discrete spaces","corr_author":"1","language":[{"iso":"eng"}],"series_title":"Lecture Notes in Mathematics"},{"project":[{"call_identifier":"FWF","name":"The biochemical basis of PAR polarization","_id":"25985A36-B435-11E9-9278-68D0E5697425","grant_number":"T00817-B21"},{"call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451238/","open_access":"1"}],"external_id":{"pmid":["28504646"],"isi":["000402620800008"]},"publisher":"American Society for Clinical Investigation","scopus_import":"1","type":"journal_article","date_published":"2017-06-01T00:00:00Z","abstract":[{"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.","lang":"eng"}],"related_material":{"record":[{"id":"12401","status":"public","relation":"dissertation_contains"}]},"oa":1,"department":[{"_id":"MiSi"}],"publication_identifier":{"issn":["0021-9738"]},"publication_status":"published","author":[{"first_name":"Florian","full_name":"Ebner, Florian","last_name":"Ebner"},{"first_name":"Vitaly","full_name":"Sedlyarov, Vitaly","last_name":"Sedlyarov"},{"orcid":"0000-0003-1671-393X","last_name":"Tasciyan","full_name":"Tasciyan, Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","first_name":"Saren"},{"full_name":"Ivin, Masa","last_name":"Ivin","first_name":"Masa"},{"first_name":"Franz","last_name":"Kratochvill","full_name":"Kratochvill, Franz"},{"last_name":"Gratz","full_name":"Gratz, Nina","first_name":"Nina"},{"first_name":"Lukas","last_name":"Kenner","full_name":"Kenner, Lukas"},{"full_name":"Villunger, Andreas","last_name":"Villunger","first_name":"Andreas"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Pavel","last_name":"Kovarik","full_name":"Kovarik, Pavel"}],"page":"2051 - 2065","pmid":1,"status":"public","date_created":"2018-12-11T11:47:53Z","article_processing_charge":"No","publication":"The Journal of Clinical Investigation","title":"The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection","language":[{"iso":"eng"}],"publist_id":"7038","intvolume":"       127","_id":"679","year":"2017","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"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>","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>.","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.","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.","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."},"date_updated":"2026-04-05T22:30:21Z","day":"01","isi":1,"issue":"6","quality_controlled":"1","oa_version":"Submitted Version","doi":"10.1172/JCI80631","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.","volume":127,"month":"06"},{"language":[{"iso":"eng"}],"corr_author":"1","title":"Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection","publication":"eLife","status":"public","article_processing_charge":"No","date_created":"2018-12-11T11:48:01Z","author":[{"orcid":"0000-0003-1229-9719","last_name":"Steinrück","full_name":"Steinrück, Magdalena","first_name":"Magdalena","id":"2C023F40-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6220-2052","last_name":"Guet","full_name":"Guet, Calin C","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"file_date_updated":"2020-07-14T12:47:48Z","related_material":{"record":[{"status":"public","relation":"popular_science","id":"5564"},{"relation":"dissertation_contains","status":"public","id":"26"}]},"publication_identifier":{"issn":["2050-084X"]},"publication_status":"published","department":[{"_id":"CaGu"}],"ddc":["576"],"publisher":"eLife Sciences Publications","scopus_import":"1","date_published":"2017-07-25T00:00:00Z","abstract":[{"lang":"eng","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."}],"type":"journal_article","external_id":{"isi":["000406183700001"]},"article_number":"e25100","file":[{"file_name":"IST-2017-890-v1+1_elife-25100-v1.pdf","file_id":"4975","access_level":"open_access","file_size":2092088,"relation":"main_file","date_created":"2018-12-12T10:12:54Z","creator":"system","date_updated":"2020-07-14T12:47:48Z","checksum":"6b908b5db9f61f6820ebd7f8fa815571","content_type":"application/pdf"},{"date_created":"2018-12-12T10:12:55Z","relation":"main_file","access_level":"open_access","file_size":3428681,"file_id":"4976","file_name":"IST-2017-890-v1+2_elife-25100-figures-v1.pdf","content_type":"application/pdf","checksum":"ca21530389b720243552678125fdba35","date_updated":"2020-07-14T12:47:48Z","creator":"system"}],"month":"07","volume":6,"pubrep_id":"890","doi":"10.7554/eLife.25100","quality_controlled":"1","oa_version":"Published Version","has_accepted_license":"1","day":"25","date_updated":"2026-04-05T22:30:40Z","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"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>","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>.","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>","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.","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>.","ista":"Steinrück M, Guet CC. 2017. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife. 6, e25100.","short":"M. Steinrück, C.C. Guet, ELife 6 (2017)."},"year":"2017","_id":"704","publist_id":"6990","intvolume":"         6"},{"external_id":{"isi":["000398154000038"]},"file":[{"creator":"dernst","date_updated":"2019-01-18T09:39:55Z","success":1,"content_type":"application/pdf","file_size":2614942,"access_level":"open_access","file_name":"2017_communications_Kainrath.pdf","file_id":"5845","relation":"main_file","date_created":"2019-01-18T09:39:55Z"}],"project":[{"call_identifier":"FP7","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets"}],"author":[{"full_name":"Kainrath, Stephanie","last_name":"Kainrath","orcid":"0000-0002-6709-2195","first_name":"Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Manuela","full_name":"Stadler, Manuela","last_name":"Stadler"},{"full_name":"Gschaider-Reichhart, Eva","orcid":"0000-0002-7218-7738","last_name":"Gschaider-Reichhart","first_name":"Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Distel","full_name":"Distel, Martin","first_name":"Martin"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"418"},{"status":"public","relation":"part_of_dissertation","id":"7680"}]},"oa":1,"file_date_updated":"2019-01-18T09:39:55Z","publication_status":"published","department":[{"_id":"CaGu"},{"_id":"HaJa"}],"publication_identifier":{"issn":["1433-7851"]},"ddc":["540"],"scopus_import":"1","publisher":"Wiley-Blackwell","abstract":[{"lang":"eng","text":"Optogenetics and photopharmacology provide spatiotemporally precise control over protein interactions and protein function in cells and animals. Optogenetic methods that are sensitive to green light and can be used to break protein complexes are not broadly available but would enable multichromatic experiments with previously inaccessible biological targets. Herein, we repurposed cobalamin (vitamin B12) binding domains of bacterial CarH transcription factors for green-light-induced receptor dissociation. In cultured cells, we observed oligomerization-induced cell signaling for the fibroblast growth factor receptor 1 fused to cobalamin-binding domains in the dark that was rapidly eliminated upon illumination. In zebrafish embryos expressing fusion receptors, green light endowed control over aberrant fibroblast growth factor signaling during development. Green-light-induced domain dissociation and light-inactivated receptors will critically expand the optogenetic toolbox for control of biological processes."}],"type":"journal_article","date_published":"2017-03-20T00:00:00Z","title":"Green-light-induced inactivation of receptor signaling using cobalamin-binding domains","publication":"Angewandte Chemie - International Edition","status":"public","date_created":"2018-12-11T11:49:46Z","article_processing_charge":"No","page":"4608-4611","corr_author":"1","language":[{"iso":"eng"}],"year":"2017","ec_funded":1,"_id":"1028","publist_id":"6362","intvolume":"        56","day":"20","date_updated":"2026-04-05T22:30:44Z","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Kainrath, Stephanie, et al. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” <i>Angewandte Chemie - International Edition</i>, vol. 56, no. 16, Wiley-Blackwell, 2017, pp. 4608–11, doi:<a href=\"https://doi.org/10.1002/anie.201611998\">10.1002/anie.201611998</a>.","apa":"Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., &#38; Janovjak, H. L. (2017). Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. <i>Angewandte Chemie - International Edition</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/anie.201611998\">https://doi.org/10.1002/anie.201611998</a>","short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie - International Edition 56 (2017) 4608–4611.","chicago":"Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” <i>Angewandte Chemie - International Edition</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1002/anie.201611998\">https://doi.org/10.1002/anie.201611998</a>.","ista":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. 56(16), 4608–4611.","ama":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. <i>Angewandte Chemie - International Edition</i>. 2017;56(16):4608-4611. doi:<a href=\"https://doi.org/10.1002/anie.201611998\">10.1002/anie.201611998</a>","ieee":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Green-light-induced inactivation of receptor signaling using cobalamin-binding domains,” <i>Angewandte Chemie - International Edition</i>, vol. 56, no. 16. Wiley-Blackwell, pp. 4608–4611, 2017."},"doi":"10.1002/anie.201611998","quality_controlled":"1","oa_version":"Published Version","has_accepted_license":"1","issue":"16","month":"03","volume":56,"acknowledgement":"This work was supported by a grant from the European Union􏰝s Seventh Framework Programme (CIG-303564). E.R. was supported by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF), W1232) and a FemTech fellowship (Austrian Research Promotion Agency, 3580812)"},{"language":[{"iso":"eng"}],"corr_author":"1","title":"An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate","publication":"Developmental Cell","article_processing_charge":"No","date_created":"2018-12-11T11:48:13Z","status":"public","page":"198 - 211","author":[{"full_name":"Barone, Vanessa","orcid":"0000-0003-2676-3367","last_name":"Barone","first_name":"Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87"},{"id":"29E0800A-F248-11E8-B48F-1D18A9856A87","first_name":"Moritz","full_name":"Lang, Moritz","last_name":"Lang"},{"first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel","last_name":"Krens","orcid":"0000-0003-4761-5996"},{"first_name":"Saurabh","full_name":"Pradhan, Saurabh","last_name":"Pradhan"},{"full_name":"Shamipour, Shayan","last_name":"Shamipour","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sako","orcid":"0000-0002-6453-8075","full_name":"Sako, Keisuke","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","first_name":"Keisuke"},{"id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","first_name":"Mateusz K","last_name":"Sikora","full_name":"Sikora, Mateusz K"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","last_name":"Guet","full_name":"Guet, Calin C"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"department":[{"_id":"CaHe"},{"_id":"CaGu"},{"_id":"GaTk"}],"publication_status":"published","publication_identifier":{"issn":["1534-5807"]},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"961"},{"status":"public","relation":"dissertation_contains","id":"8350"}]},"type":"journal_article","date_published":"2017-10-23T00:00:00Z","abstract":[{"lang":"eng","text":"Cell-cell contact formation constitutes an essential step in evolution, leading to the differentiation of specialized cell types. However, remarkably little is known about whether and how the interplay between contact formation and fate specification affects development. Here, we identify a positive feedback loop between cell-cell contact duration, morphogen signaling, and mesendoderm cell-fate specification during zebrafish gastrulation. We show that long-lasting cell-cell contacts enhance the competence of prechordal plate (ppl) progenitor cells to respond to Nodal signaling, required for ppl cell-fate specification. We further show that Nodal signaling promotes ppl cell-cell contact duration, generating a positive feedback loop between ppl cell-cell contact duration and cell-fate specification. Finally, by combining mathematical modeling and experimentation, we show that this feedback determines whether anterior axial mesendoderm cells become ppl or, instead, turn into endoderm. Thus, the interdependent activities of cell-cell signaling and contact formation control fate diversification within the developing embryo."}],"publisher":"Cell Press","scopus_import":"1","external_id":{"isi":["000413443700011"]},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"},{"_id":"252DD2A6-B435-11E9-9278-68D0E5697425","name":"Cell segregation in gastrulation: the role of cell fate specification","grant_number":"I2058","call_identifier":"FWF"}],"month":"10","volume":43,"doi":"10.1016/j.devcel.2017.09.014","oa_version":"None","quality_controlled":"1","issue":"2","isi":1,"day":"23","date_updated":"2026-04-05T22:30:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Barone, Vanessa, et al. “An Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling Determines Cell Fate.” <i>Developmental Cell</i>, vol. 43, no. 2, Cell Press, 2017, pp. 198–211, doi:<a href=\"https://doi.org/10.1016/j.devcel.2017.09.014\">10.1016/j.devcel.2017.09.014</a>.","apa":"Barone, V., Lang, M., Krens, G., Pradhan, S., Shamipour, S., Sako, K., … Heisenberg, C.-P. J. (2017). An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2017.09.014\">https://doi.org/10.1016/j.devcel.2017.09.014</a>","short":"V. Barone, M. Lang, G. Krens, S. Pradhan, S. Shamipour, K. Sako, M.K. Sikora, C.C. Guet, C.-P.J. Heisenberg, Developmental Cell 43 (2017) 198–211.","chicago":"Barone, Vanessa, Moritz Lang, Gabriel Krens, Saurabh Pradhan, Shayan Shamipour, Keisuke Sako, Mateusz K Sikora, Calin C Guet, and Carl-Philipp J Heisenberg. “An Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling Determines Cell Fate.” <i>Developmental Cell</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.devcel.2017.09.014\">https://doi.org/10.1016/j.devcel.2017.09.014</a>.","ieee":"V. Barone <i>et al.</i>, “An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate,” <i>Developmental Cell</i>, vol. 43, no. 2. Cell Press, pp. 198–211, 2017.","ama":"Barone V, Lang M, Krens G, et al. An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. <i>Developmental Cell</i>. 2017;43(2):198-211. doi:<a href=\"https://doi.org/10.1016/j.devcel.2017.09.014\">10.1016/j.devcel.2017.09.014</a>","ista":"Barone V, Lang M, Krens G, Pradhan S, Shamipour S, Sako K, Sikora MK, Guet CC, Heisenberg C-PJ. 2017. An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. Developmental Cell. 43(2), 198–211."},"ec_funded":1,"year":"2017","_id":"735","intvolume":"        43","publist_id":"6934"},{"pubrep_id":"897","volume":12,"month":"06","issue":"6","has_accepted_license":"1","quality_controlled":"1","oa_version":"Published Version","doi":"10.1371/journal.pone.0179377","citation":{"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>.","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>","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).","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.","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.","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>.","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>"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"01","date_updated":"2026-04-05T22:30:53Z","isi":1,"publist_id":"7034","intvolume":"        12","_id":"682","article_type":"original","year":"2017","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","date_created":"2018-12-11T11:47:54Z","publication":"PLoS One","title":"PirB regulates asymmetries in hippocampal circuitry","publisher":"Public Library of Science","scopus_import":"1","abstract":[{"lang":"eng","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."}],"date_published":"2017-06-01T00:00:00Z","type":"journal_article","ddc":["571"],"related_material":{"record":[{"id":"51","relation":"dissertation_contains","status":"public"}]},"oa":1,"file_date_updated":"2020-07-14T12:47:40Z","publication_identifier":{"issn":["1932-6203"]},"department":[{"_id":"RySh"}],"publication_status":"published","author":[{"last_name":"Ukai","full_name":"Ukai, Hikari","first_name":"Hikari"},{"last_name":"Kawahara","full_name":"Kawahara, Aiko","first_name":"Aiko"},{"first_name":"Keiko","last_name":"Hirayama","full_name":"Hirayama, Keiko"},{"last_name":"Case","full_name":"Case, Matthew J","first_name":"Matthew J","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Aino, Shotaro","last_name":"Aino","first_name":"Shotaro"},{"last_name":"Miyabe","full_name":"Miyabe, Masahiro","first_name":"Masahiro"},{"last_name":"Wakita","full_name":"Wakita, Ken","first_name":"Ken"},{"first_name":"Ryohei","full_name":"Oogi, Ryohei","last_name":"Oogi"},{"last_name":"Kasayuki","full_name":"Kasayuki, Michiyo","first_name":"Michiyo"},{"last_name":"Kawashima","full_name":"Kawashima, Shihomi","first_name":"Shihomi"},{"first_name":"Shunichi","full_name":"Sugimoto, Shunichi","last_name":"Sugimoto"},{"full_name":"Chikamatsu, Kanako","last_name":"Chikamatsu","first_name":"Kanako"},{"full_name":"Nitta, Noritaka","last_name":"Nitta","first_name":"Noritaka"},{"first_name":"Tsuneyuki","last_name":"Koga","full_name":"Koga, Tsuneyuki"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi"},{"first_name":"Toshiyuki","full_name":"Takai, Toshiyuki","last_name":"Takai"},{"first_name":"Isao","full_name":"Ito, Isao","last_name":"Ito"}],"file":[{"date_updated":"2020-07-14T12:47:40Z","creator":"system","content_type":"application/pdf","checksum":"24dd19c46fb1c761b0bcbbcd1025a3a8","access_level":"open_access","file_size":5798454,"file_id":"4934","file_name":"IST-2017-897-v1+1_journal.pone.0179377.pdf","date_created":"2018-12-12T10:12:16Z","relation":"main_file"}],"article_number":"e0179377","external_id":{"isi":["000402923200125"]}},{"pubrep_id":"845","volume":10482,"month":"01","editor":[{"full_name":"D'Souza, Deepak","last_name":"D'Souza","first_name":"Deepak"}],"has_accepted_license":"1","quality_controlled":"1","oa_version":"Submitted Version","doi":"10.1007/978-3-319-68167-2_4","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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>.","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>","short":"K. Chatterjee, A.K. Goharshady, A. Pavlogiannis, in:, D. D’Souza (Ed.), Springer, 2017, pp. 59–66.","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>."},"date_updated":"2026-04-05T22:30:58Z","day":"01","isi":1,"publist_id":"6468","intvolume":"     10482","_id":"949","year":"2017","ec_funded":1,"language":[{"iso":"eng"}],"corr_author":"1","conference":{"location":"Pune, India","start_date":"2017-10-03","end_date":"2017-10-06","name":"ATVA: Automated Technology for Verification and Analysis"},"page":"59 - 66","status":"public","date_created":"2018-12-11T11:49:22Z","article_processing_charge":"No","alternative_title":["LNCS"],"title":"JTDec: A tool for tree decompositions in soot","publisher":"Springer","scopus_import":"1","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"}],"type":"conference","date_published":"2017-01-01T00:00:00Z","ddc":["005"],"related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"oa":1,"file_date_updated":"2020-07-14T12:48:16Z","publication_identifier":{"issn":["03029743"]},"publication_status":"published","department":[{"_id":"KrCh"}],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Goharshady, Amir","orcid":"0000-0003-1702-6584","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir"},{"full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"}],"project":[{"call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"file":[{"file_size":948514,"access_level":"open_access","file_name":"IST-2017-845-v1+1_2017_Chatterjee_JTDec.pdf","file_id":"4835","date_created":"2018-12-12T10:10:45Z","relation":"main_file","date_updated":"2020-07-14T12:48:16Z","creator":"system","content_type":"application/pdf","checksum":"a0d9f5f94dc594c4e71e78525c9942f1"}],"external_id":{"isi":["000723567800004"]}},{"alternative_title":["LNCS"],"title":"Non-polynomial worst case analysis of recursive programs","page":"41 - 63","status":"public","article_processing_charge":"No","date_created":"2018-12-11T11:47:39Z","language":[{"iso":"eng"}],"arxiv":1,"conference":{"location":"Heidelberg, Germany","name":"CAV: Computer Aided Verification","start_date":"2017-07-24","end_date":"2017-07-28"},"main_file_link":[{"url":"https://arxiv.org/abs/1705.00317","open_access":"1"}],"external_id":{"isi":["000431900900003"],"arxiv":["1705.00317"]},"project":[{"call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"related_material":{"record":[{"id":"7014","status":"public","relation":"later_version"},{"status":"public","relation":"dissertation_contains","id":"8934"}]},"oa":1,"department":[{"_id":"KrCh"}],"publication_status":"published","publication_identifier":{"isbn":["978-331963389-3"]},"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Fu","full_name":"Fu, Hongfei","first_name":"Hongfei"},{"first_name":"Amir","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir","last_name":"Goharshady","orcid":"0000-0003-1702-6584"}],"publisher":"Springer","scopus_import":"1","date_published":"2017-01-01T00:00:00Z","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","quality_controlled":"1","oa_version":"Submitted Version","doi":"10.1007/978-3-319-63390-9_3","editor":[{"last_name":"Majumdar","full_name":"Majumdar, Rupak","first_name":"Rupak"},{"last_name":"Kunčak","full_name":"Kunčak, Viktor","first_name":"Viktor"}],"volume":10427,"month":"01","year":"2017","ec_funded":1,"publist_id":"7149","intvolume":"     10427","_id":"639","date_updated":"2026-04-05T22:30:59Z","day":"01","isi":1,"citation":{"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>","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>.","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>","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.","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.","short":"K. Chatterjee, H. Fu, A.K. Goharshady, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 41–63."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"pubrep_id":"800","volume":12,"month":"03","issue":"3","has_accepted_license":"1","oa_version":"Published Version","quality_controlled":"1","doi":"10.1371/journal.pone.0174066","citation":{"short":"M. Lukacisin, M. Landon, R. Jajoo, PLoS One 12 (2017).","ama":"Lukacisin M, Landon M, Jajoo R. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. <i>PLoS One</i>. 2017;12(3). doi:<a href=\"https://doi.org/10.1371/journal.pone.0174066\">10.1371/journal.pone.0174066</a>","chicago":"Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” <i>PLoS One</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pone.0174066\">https://doi.org/10.1371/journal.pone.0174066</a>.","ista":"Lukacisin M, Landon M, Jajoo R. 2017. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. 12(3), e0174066.","ieee":"M. Lukacisin, M. Landon, and R. Jajoo, “Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast,” <i>PLoS One</i>, vol. 12, no. 3. Public Library of Science, 2017.","mla":"Lukacisin, Martin, et al. “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” <i>PLoS One</i>, vol. 12, no. 3, e0174066, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pone.0174066\">10.1371/journal.pone.0174066</a>.","apa":"Lukacisin, M., Landon, M., &#38; Jajoo, R. (2017). Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0174066\">https://doi.org/10.1371/journal.pone.0174066</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"isi":1,"day":"16","date_updated":"2026-04-05T22:30:59Z","intvolume":"        12","publist_id":"6361","_id":"1029","year":"2017","language":[{"iso":"eng"}],"article_processing_charge":"Yes","date_created":"2018-12-11T11:49:46Z","status":"public","publication":"PLoS One","title":"Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast","type":"journal_article","date_published":"2017-03-16T00:00:00Z","abstract":[{"text":"RNA Polymerase II pauses and backtracks during transcription, with many consequences for gene expression and cellular physiology. Here, we show that the energy required to melt double-stranded nucleic acids in the transcription bubble predicts pausing in Saccharomyces cerevisiae far more accurately than nucleosome roadblocks do. In addition, the same energy difference also determines when the RNA polymerase backtracks instead of continuing to move forward. This data-driven model corroborates—in a genome wide and quantitative manner—previous evidence that sequence-dependent thermodynamic features of nucleic acids influence both transcriptional pausing and backtracking.","lang":"eng"}],"publisher":"Public Library of Science","scopus_import":"1","ddc":["570"],"department":[{"_id":"ToBo"}],"publication_identifier":{"issn":["1932-6203"]},"publication_status":"published","oa":1,"file_date_updated":"2018-12-12T10:09:47Z","related_material":{"record":[{"relation":"popular_science","status":"public","id":"5556"},{"id":"6392","status":"public","relation":"dissertation_contains"}]},"author":[{"first_name":"Martin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisin","orcid":"0000-0001-6549-4177","full_name":"Lukacisin, Martin"},{"first_name":"Matthieu","full_name":"Landon, Matthieu","last_name":"Landon"},{"first_name":"Rishi","full_name":"Jajoo, Rishi","last_name":"Jajoo"}],"file":[{"content_type":"application/pdf","date_updated":"2018-12-12T10:09:47Z","creator":"system","date_created":"2018-12-12T10:09:47Z","relation":"main_file","access_level":"open_access","file_size":3429381,"file_name":"IST-2017-800-v1+1_journal.pone.0174066.pdf","file_id":"4772"}],"article_number":"e0174066","external_id":{"isi":["000396318300121"]}},{"year":"2017","_id":"1024","intvolume":"      1569","publist_id":"6369","date_updated":"2026-04-05T22:31:00Z","day":"17","citation":{"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>.","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.","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.","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>","short":"A. Hurny, E. Benková, Auxins and Cytokinins in Plant Biology 1569 (2017) 1–29."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-1-4939-6831-2_1","oa_version":"Submitted Version","quality_controlled":"1","has_accepted_license":"1","month":"03","volume":1569,"pubrep_id":"1019","file":[{"content_type":"application/pdf","creator":"system","date_updated":"2019-10-15T07:47:05Z","relation":"main_file","date_created":"2018-12-12T10:14:18Z","file_name":"IST-2018-1019-v1+1_Hurny_MethodsMolBiol_2017.pdf","file_id":"5068","access_level":"open_access","file_size":840646}],"project":[{"call_identifier":"FWF","_id":"2542D156-B435-11E9-9278-68D0E5697425","name":"Hormone cross-talk drives nutrient dependent plant development","grant_number":"I 1774-B16"}],"author":[{"full_name":"Hurny, Andrej","orcid":"0000-0003-3638-1426","last_name":"Hurny","first_name":"Andrej","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}],"publication_identifier":{"issn":["1064-3745"]},"department":[{"_id":"EvBe"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"539"}]},"file_date_updated":"2019-10-15T07:47:05Z","oa":1,"ddc":["575"],"date_published":"2017-03-17T00:00:00Z","abstract":[{"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.","lang":"eng"}],"type":"journal_article","scopus_import":"1","publisher":"Springer","title":"Methodological advances in auxin and cytokinin biology","alternative_title":["Methods in Molecular Biology"],"publication":"Auxins and Cytokinins in Plant Biology","article_processing_charge":"No","date_created":"2018-12-11T11:49:45Z","status":"public","page":"1 - 29","language":[{"iso":"eng"}],"corr_author":"1"},{"corr_author":"1","language":[{"iso":"eng"}],"page":"1798 - 1806","pmid":1,"status":"public","date_created":"2018-12-11T11:47:52Z","article_processing_charge":"No","publication":"Development","title":"Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation","publisher":"Company of Biologists","scopus_import":"1","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"}],"type":"journal_article","date_published":"2017-05-15T00:00:00Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:39Z","oa":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"961"},{"relation":"dissertation_contains","status":"public","id":"50"}]},"department":[{"_id":"Bio"},{"_id":"CaHe"}],"publication_status":"published","publication_identifier":{"issn":["09501991"]},"author":[{"full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","last_name":"Krens","first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jim","full_name":"Veldhuis, Jim","last_name":"Veldhuis"},{"full_name":"Barone, Vanessa","last_name":"Barone","orcid":"0000-0003-2676-3367","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa"},{"id":"31C42484-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","orcid":"0000-0001-5199-9940","last_name":"Capek","full_name":"Capek, Daniel"},{"id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","first_name":"Jean-Léon","full_name":"Maître, Jean-Léon","last_name":"Maître","orcid":"0000-0002-3688-1474"},{"last_name":"Brodland","full_name":"Brodland, Wayne","first_name":"Wayne"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"file":[{"content_type":"application/pdf","checksum":"bc25125fb664706cdf180e061429f91d","date_updated":"2020-07-14T12:47:39Z","creator":"dernst","date_created":"2019-09-24T06:56:22Z","relation":"main_file","access_level":"open_access","file_size":8194516,"file_name":"2017_Development_Krens.pdf","file_id":"6905"}],"external_id":{"pmid":["28512197"],"isi":["000402275900007"]},"volume":144,"month":"05","issue":"10","has_accepted_license":"1","quality_controlled":"1","oa_version":"Published Version","doi":"10.1242/dev.144964","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"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>","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>.","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.","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.","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>.","short":"G. Krens, J. Veldhuis, V. Barone, D. Capek, J.-L. Maître, W. Brodland, C.-P.J. Heisenberg, Development 144 (2017) 1798–1806."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"15","date_updated":"2026-04-05T22:31:01Z","isi":1,"publist_id":"7047","intvolume":"       144","_id":"676","article_type":"original","year":"2017"},{"language":[{"iso":"eng"}],"corr_author":"1","page":"306 - 317","pmid":1,"status":"public","article_processing_charge":"No","date_created":"2018-12-11T11:47:46Z","publication":"Nature Cell Biology","title":"Friction forces position the neural anlage","scopus_import":"1","publisher":"Nature Publishing Group","date_published":"2017-03-27T00:00:00Z","type":"journal_article","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"oa":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8350"},{"status":"public","relation":"dissertation_contains","id":"50"}]},"department":[{"_id":"CaHe"},{"_id":"BjHo"},{"_id":"Bio"}],"publication_status":"published","publication_identifier":{"issn":["1465-7392"]},"author":[{"full_name":"Smutny, Michael","last_name":"Smutny","orcid":"0000-0002-5920-9090","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","first_name":"Michael"},{"last_name":"Ákos","full_name":"Ákos, Zsuzsa","first_name":"Zsuzsa"},{"first_name":"Silvia","full_name":"Grigolon, Silvia","last_name":"Grigolon"},{"id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan","full_name":"Shamipour, Shayan","last_name":"Shamipour"},{"last_name":"Ruprecht","full_name":"Ruprecht, Verena","first_name":"Verena"},{"first_name":"Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87","full_name":"Capek, Daniel","last_name":"Capek","orcid":"0000-0001-5199-9940"},{"last_name":"Behrndt","full_name":"Behrndt, Martin","first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Papusheva, Ekaterina","last_name":"Papusheva","id":"41DB591E-F248-11E8-B48F-1D18A9856A87","first_name":"Ekaterina"},{"last_name":"Tada","full_name":"Tada, Masazumi","first_name":"Masazumi"},{"orcid":"0000-0003-2057-2754","last_name":"Hof","full_name":"Hof, Björn","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vicsek","full_name":"Vicsek, Tamás","first_name":"Tamás"},{"first_name":"Guillaume","full_name":"Salbreux, Guillaume","last_name":"Salbreux"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"project":[{"call_identifier":"FP7","grant_number":"306589","name":"Decoding the complexity of turbulence at its origin","_id":"25152F3A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"I930-B20","_id":"252ABD0A-B435-11E9-9278-68D0E5697425","name":"Control of Epithelial Cell Layer Spreading in Zebrafish"}],"main_file_link":[{"url":"https://europepmc.org/articles/pmc5635970","open_access":"1"}],"external_id":{"isi":["000397917000009"],"pmid":["28346437"]},"volume":19,"month":"03","quality_controlled":"1","oa_version":"Submitted Version","doi":"10.1038/ncb3492","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"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>.","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>","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>.","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.","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>","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."},"day":"27","date_updated":"2026-04-05T22:31:01Z","isi":1,"publist_id":"7074","intvolume":"        19","_id":"661","year":"2017","ec_funded":1},{"issue":"7","has_accepted_license":"1","quality_controlled":"1","oa_version":"Published Version","doi":"10.1371/journal.pcbi.1005609","pubrep_id":"894","volume":13,"month":"07","publist_id":"7004","intvolume":"        13","_id":"696","article_type":"original","year":"2017","ec_funded":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"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.","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>.","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.","short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).","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>","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>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-04-05T22:31:02Z","day":"18","isi":1,"status":"public","article_processing_charge":"No","date_created":"2018-12-11T11:47:58Z","publication":"PLoS Computational Biology","title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","language":[{"iso":"eng"}],"corr_author":"1","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","call_identifier":"FP7"}],"file":[{"date_updated":"2020-07-14T12:47:46Z","creator":"system","content_type":"application/pdf","checksum":"9143c290fa6458ed2563bff4b295554a","file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","file_id":"5117","access_level":"open_access","file_size":3775716,"date_created":"2018-12-12T10:15:01Z","relation":"main_file"}],"external_id":{"isi":["000406619800014"]},"article_number":"e1005609","scopus_import":"1","publisher":"Public Library of Science","type":"journal_article","abstract":[{"lang":"eng","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."}],"date_published":"2017-07-18T00:00:00Z","ddc":["576"],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9849"},{"relation":"research_data","status":"public","id":"9850"},{"id":"9851","relation":"research_data","status":"public"},{"relation":"research_data","status":"public","id":"9852"},{"id":"6263","relation":"dissertation_contains","status":"public"}]},"file_date_updated":"2020-07-14T12:47:46Z","oa":1,"publication_status":"published","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"publication_identifier":{"issn":["1553-734X"]},"author":[{"last_name":"Lukacisinova","orcid":"0000-0002-2519-8004","full_name":"Lukacisinova, Marta","first_name":"Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Novak","orcid":"0000-0002-2519-824X","full_name":"Novak, Sebastian"},{"first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","last_name":"Paixao"}]},{"pubrep_id":"801","volume":46,"month":"08","has_accepted_license":"1","quality_controlled":"1","oa_version":"Published Version","doi":"10.1016/j.copbio.2017.02.013","citation":{"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>.","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>","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.","short":"M. Lukacisinova, M.T. Bollenbach, Current Opinion in Biotechnology 46 (2017) 90–97."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"day":"01","date_updated":"2026-04-05T22:31:02Z","isi":1,"publist_id":"6364","intvolume":"        46","_id":"1027","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","year":"2017","article_type":"original","ec_funded":1,"language":[{"iso":"eng"}],"corr_author":"1","page":"90 - 97","status":"public","date_created":"2018-12-11T11:49:45Z","article_processing_charge":"Yes (in subscription journal)","publication":"Current Opinion in Biotechnology","title":"Toward a quantitative understanding of antibiotic resistance evolution","scopus_import":"1","publisher":"Elsevier","type":"journal_article","date_published":"2017-08-01T00:00:00Z","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."}],"ddc":["570"],"file_date_updated":"2019-01-18T09:57:57Z","oa":1,"related_material":{"record":[{"id":"6263","relation":"dissertation_contains","status":"public"}]},"department":[{"_id":"ToBo"}],"publication_status":"published","author":[{"last_name":"Lukacisinova","orcid":"0000-0002-2519-8004","full_name":"Lukacisinova, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","first_name":"Marta"},{"first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias"}],"project":[{"call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22"},{"call_identifier":"FP7","grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","name":"Optimality principles in responses to antibiotics"},{"grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"}],"file":[{"date_updated":"2019-01-18T09:57:57Z","creator":"dernst","content_type":"application/pdf","success":1,"file_id":"5846","file_name":"2017_CurrentOpinion_Lukaciinova.pdf","file_size":858338,"access_level":"open_access","date_created":"2019-01-18T09:57:57Z","relation":"main_file"}],"external_id":{"isi":["000408077400015"]}},{"isi":1,"date_updated":"2026-04-05T22:31:07Z","day":"18","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"apa":"Assen, F. P., &#38; Sixt, M. K. (2017). The dynamic cytokine niche. <i>Immunity</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.immuni.2017.04.006\">https://doi.org/10.1016/j.immuni.2017.04.006</a>","mla":"Assen, Frank P., and Michael K. Sixt. “The Dynamic Cytokine Niche.” <i>Immunity</i>, vol. 46, no. 4, Cell Press, 2017, pp. 519–20, doi:<a href=\"https://doi.org/10.1016/j.immuni.2017.04.006\">10.1016/j.immuni.2017.04.006</a>.","ieee":"F. P. Assen and M. K. Sixt, “The dynamic cytokine niche,” <i>Immunity</i>, vol. 46, no. 4. Cell Press, pp. 519–520, 2017.","chicago":"Assen, Frank P, and Michael K Sixt. “The Dynamic Cytokine Niche.” <i>Immunity</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.immuni.2017.04.006\">https://doi.org/10.1016/j.immuni.2017.04.006</a>.","ista":"Assen FP, Sixt MK. 2017. The dynamic cytokine niche. Immunity. 46(4), 519–520.","ama":"Assen FP, Sixt MK. The dynamic cytokine niche. <i>Immunity</i>. 2017;46(4):519-520. doi:<a href=\"https://doi.org/10.1016/j.immuni.2017.04.006\">10.1016/j.immuni.2017.04.006</a>","short":"F.P. Assen, M.K. Sixt, Immunity 46 (2017) 519–520."},"year":"2017","intvolume":"        46","publist_id":"7065","_id":"664","volume":46,"month":"04","oa_version":"None","quality_controlled":"1","doi":"10.1016/j.immuni.2017.04.006","issue":"4","department":[{"_id":"MiSi"}],"publication_identifier":{"issn":["1074-7613"]},"publication_status":"published","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6947"}]},"author":[{"full_name":"Assen, Frank P","orcid":"0000-0003-3470-6119","last_name":"Assen","first_name":"Frank P","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","date_published":"2017-04-18T00:00:00Z","abstract":[{"lang":"eng","text":"Immune cells communicate using cytokine signals, but the quantitative rules of this communication aren't clear. In this issue of Immunity, Oyler-Yaniv et al. (2017) suggest that the distribution of a cytokine within a lymphatic organ is primarily governed by the local density of cells consuming it."}],"scopus_import":"1","publisher":"Cell Press","external_id":{"isi":["000399451100002"]},"corr_author":"1","language":[{"iso":"eng"}],"publication":"Immunity","title":"The dynamic cytokine niche","page":"519 - 520","date_created":"2018-12-11T11:47:47Z","article_processing_charge":"No","status":"public"},{"file_date_updated":"2020-07-14T12:48:16Z","related_material":{"record":[{"id":"9962","relation":"dissertation_contains","status":"public"}]},"oa":1,"publication_status":"published","publication_identifier":{"issn":["1662-5102"]},"department":[{"_id":"SiHi"},{"_id":"MaLo"}],"author":[{"full_name":"Hansen, Andi H","last_name":"Hansen","first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Düllberg, Christian F","orcid":"0000-0001-6335-9748","last_name":"Düllberg","id":"459064DC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian F"},{"first_name":"Christine","id":"34CAE85C-F248-11E8-B48F-1D18A9856A87","full_name":"Mieck, Christine","orcid":"0000-0003-1919-7416","last_name":"Mieck"},{"last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"scopus_import":"1","publisher":"Frontiers Research Foundation","abstract":[{"text":"The human cerebral cortex is the seat of our cognitive abilities and composed of an extraordinary number of neurons, organized in six distinct layers. The establishment of specific morphological and physiological features in individual neurons needs to be regulated with high precision. Impairments in the sequential developmental programs instructing corticogenesis lead to alterations in the cortical cytoarchitecture which is thought to represent the major underlying cause for several neurological disorders including neurodevelopmental and psychiatric diseases. In this review we discuss the role of cell polarity at sequential stages during cortex development. We first provide an overview of morphological cell polarity features in cortical neural stem cells and newly-born postmitotic neurons. We then synthesize a conceptual molecular and biochemical framework how cell polarity is established at the cellular level through a break in symmetry in nascent cortical projection neurons. Lastly we provide a perspective how the molecular mechanisms applying to single cells could be probed and integrated in an in vivo and tissue-wide context.","lang":"eng"}],"date_published":"2017-06-28T00:00:00Z","type":"journal_article","ddc":["570"],"file":[{"content_type":"application/pdf","checksum":"dc1f5a475b918d09a0f9f587400b1626","date_updated":"2020-07-14T12:48:16Z","creator":"system","date_created":"2018-12-12T10:09:40Z","relation":"main_file","file_id":"4764","file_name":"IST-2017-830-v1+1_2017_Hansen_CellPolarity.pdf","access_level":"open_access","file_size":2153858}],"article_number":"176","external_id":{"isi":["000404486700001"]},"project":[{"call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development","_id":"25D61E48-B435-11E9-9278-68D0E5697425","grant_number":"618444"},{"_id":"25D7962E-B435-11E9-9278-68D0E5697425","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","grant_number":"RGP0053/2014"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"call_identifier":"FWF","name":"The biochemical basis of PAR polarization","_id":"25985A36-B435-11E9-9278-68D0E5697425","grant_number":"T00817-B21"}],"language":[{"iso":"eng"}],"publication":"Frontiers in Cellular Neuroscience","title":"Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks","status":"public","date_created":"2018-12-11T11:49:25Z","article_processing_charge":"Yes","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-04-05T22:31:11Z","day":"28","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"A.H. Hansen, C.F. Düllberg, C. Mieck, M. Loose, S. Hippenmeyer, Frontiers in Cellular Neuroscience 11 (2017).","ieee":"A. H. Hansen, C. F. Düllberg, C. Mieck, M. Loose, and S. Hippenmeyer, “Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks,” <i>Frontiers in Cellular Neuroscience</i>, vol. 11. Frontiers Research Foundation, 2017.","ista":"Hansen AH, Düllberg CF, Mieck C, Loose M, Hippenmeyer S. 2017. Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. 11, 176.","chicago":"Hansen, Andi H, Christian F Düllberg, Christine Mieck, Martin Loose, and Simon Hippenmeyer. “Cell Polarity in Cerebral Cortex Development - Cellular Architecture Shaped by Biochemical Networks.” <i>Frontiers in Cellular Neuroscience</i>. Frontiers Research Foundation, 2017. <a href=\"https://doi.org/10.3389/fncel.2017.00176\">https://doi.org/10.3389/fncel.2017.00176</a>.","ama":"Hansen AH, Düllberg CF, Mieck C, Loose M, Hippenmeyer S. Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. <i>Frontiers in Cellular Neuroscience</i>. 2017;11. doi:<a href=\"https://doi.org/10.3389/fncel.2017.00176\">10.3389/fncel.2017.00176</a>","mla":"Hansen, Andi H., et al. “Cell Polarity in Cerebral Cortex Development - Cellular Architecture Shaped by Biochemical Networks.” <i>Frontiers in Cellular Neuroscience</i>, vol. 11, 176, Frontiers Research Foundation, 2017, doi:<a href=\"https://doi.org/10.3389/fncel.2017.00176\">10.3389/fncel.2017.00176</a>.","apa":"Hansen, A. H., Düllberg, C. F., Mieck, C., Loose, M., &#38; Hippenmeyer, S. (2017). Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. <i>Frontiers in Cellular Neuroscience</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fncel.2017.00176\">https://doi.org/10.3389/fncel.2017.00176</a>"},"year":"2017","ec_funded":1,"publist_id":"6445","intvolume":"        11","_id":"960","volume":11,"month":"06","pubrep_id":"830","quality_controlled":"1","oa_version":"Published Version","doi":"10.3389/fncel.2017.00176","has_accepted_license":"1"},{"author":[{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"first_name":"Markéta","last_name":"Pernisová","full_name":"Pernisová, Markéta"},{"full_name":"Hejátko, Jan","last_name":"Hejátko","first_name":"Jan"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"publication_status":"published","department":[{"_id":"JiFr"}],"file_date_updated":"2018-12-12T10:13:22Z","oa":1,"ddc":["581"],"type":"journal_article","date_published":"2016-11-07T00:00:00Z","abstract":[{"lang":"eng","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"}],"publisher":"Cell Press","scopus_import":"1","external_id":{"isi":["000389594100008"]},"file":[{"content_type":"application/pdf","creator":"system","date_updated":"2018-12-12T10:13:22Z","relation":"main_file","date_created":"2018-12-12T10:13:22Z","file_name":"IST-2017-746-v1+1_1-s2.0-S1674205216301915-main.pdf","file_id":"5004","file_size":5005876,"access_level":"open_access"}],"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7"}],"language":[{"iso":"eng"}],"title":"Enquiry into the topology of plasma membrane localized PIN auxin transport components","publication":"Molecular Plant","date_created":"2018-12-11T11:50:23Z","article_processing_charge":"No","status":"public","page":"1504 - 1519","isi":1,"day":"07","date_updated":"2025-09-22T14:08:07Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"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.","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.","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>","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>.","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>","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>."},"ec_funded":1,"year":"2016","_id":"1145","intvolume":"         9","publist_id":"6213","month":"11","volume":9,"pubrep_id":"746","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.","doi":"10.1016/j.molp.2016.08.010","oa_version":"Published Version","quality_controlled":"1","has_accepted_license":"1","issue":"11"},{"citation":{"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>.","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.","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>","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.","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>","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>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2025-09-22T09:59:19Z","day":"08","isi":1,"publist_id":"6211","intvolume":"         6","_id":"1147","year":"2016","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).","pubrep_id":"745","volume":6,"month":"11","has_accepted_license":"1","quality_controlled":"1","oa_version":"Published Version","doi":"10.1038/srep35955","publisher":"Nature Publishing Group","scopus_import":"1","date_published":"2016-11-08T00:00:00Z","type":"journal_article","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"}],"ddc":["581"],"oa":1,"file_date_updated":"2018-12-12T10:09:28Z","department":[{"_id":"JiFr"}],"publication_status":"published","author":[{"full_name":"Balla, Jozef","last_name":"Balla","first_name":"Jozef"},{"first_name":"Zuzana","full_name":"Medved'Ová, Zuzana","last_name":"Medved'Ová"},{"first_name":"Petr","last_name":"Kalousek","full_name":"Kalousek, Petr"},{"last_name":"Matiješčuková","full_name":"Matiješčuková, Natálie","first_name":"Natálie"},{"full_name":"Friml, Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Vilém","full_name":"Reinöhl, Vilém","last_name":"Reinöhl"},{"first_name":"Stanislav","full_name":"Procházka, Stanislav","last_name":"Procházka"}],"file":[{"date_updated":"2018-12-12T10:09:28Z","creator":"system","content_type":"application/pdf","file_id":"4752","file_name":"IST-2017-745-v1+1_srep35955.pdf","file_size":1587544,"access_level":"open_access","date_created":"2018-12-12T10:09:28Z","relation":"main_file"}],"article_number":"35955","external_id":{"isi":["000387284700001"]},"language":[{"iso":"eng"}],"status":"public","date_created":"2018-12-11T11:50:24Z","article_processing_charge":"No","publication":"Scientific Reports","title":"Auxin flow mediated competition between axillary buds to restore apical dominance"},{"author":[{"first_name":"Christian","full_name":"Schilling, Christian","last_name":"Schilling"},{"id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy","full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365","last_name":"Bogomolov"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"last_name":"Podelski","full_name":"Podelski, Andreas","first_name":"Andreas"},{"id":"4A245D00-F248-11E8-B48F-1D18A9856A87","first_name":"Jakob","full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282","last_name":"Ruess"}],"publication_status":"published","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"related_material":{"record":[{"id":"1658","status":"public","relation":"earlier_version"}]},"date_published":"2016-11-01T00:00:00Z","abstract":[{"lang":"eng","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"}],"type":"journal_article","publisher":"Elsevier","scopus_import":"1","external_id":{"isi":["000390743600003"]},"project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"language":[{"iso":"eng"}],"title":"Adaptive moment closure for parameter inference of biochemical reaction networks","publication":"Biosystems","date_created":"2018-12-11T11:50:24Z","article_processing_charge":"No","status":"public","page":"15 - 25","isi":1,"day":"01","date_updated":"2025-09-23T07:44:57Z","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>","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.","short":"C. Schilling, S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, Biosystems 149 (2016) 15–25."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"year":"2016","_id":"1148","intvolume":"       149","publist_id":"6210","month":"11","volume":149,"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.","doi":"10.1016/j.biosystems.2016.07.005","oa_version":"None","quality_controlled":"1"}]