[{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","citation":{"mla":"Barzanjeh, Shabir, et al. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” <i>Physical Review E</i>, vol. 96, no. 1, 012404, American Institute of Physics, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">10.1103/PhysRevE.96.012404</a>.","ama":"Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. Optomechanical proposal for monitoring microtubule mechanical vibrations. <i>Physical Review E</i>. 2017;96(1). doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">10.1103/PhysRevE.96.012404</a>","apa":"Barzanjeh, S., Salari, V., Tuszynski, J., Cifra, M., &#38; Simon, C. (2017). Optomechanical proposal for monitoring microtubule mechanical vibrations. <i>Physical Review E</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">https://doi.org/10.1103/PhysRevE.96.012404</a>","ista":"Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. 2017. Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E. 96(1), 012404.","short":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, C. Simon, Physical Review E 96 (2017).","chicago":"Barzanjeh, Shabir, Vahid Salari, Jack Tuszynski, Michal Cifra, and Christoph Simon. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” <i>Physical Review E</i>. American Institute of Physics, 2017. <a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">https://doi.org/10.1103/PhysRevE.96.012404</a>.","ieee":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, and C. Simon, “Optomechanical proposal for monitoring microtubule mechanical vibrations,” <i>Physical Review E</i>, vol. 96, no. 1. American Institute of Physics, 2017."},"volume":96,"article_number":"012404","doi":"10.1103/PhysRevE.96.012404","scopus_import":"1","publication_status":"published","day":"12","intvolume":"        96","_id":"700","publication_identifier":{"issn":["2470-0045"]},"oa_version":"Submitted Version","status":"public","publication":"Physical Review E","type":"journal_article","arxiv":1,"date_created":"2018-12-11T11:48:00Z","oa":1,"year":"2017","month":"07","isi":1,"language":[{"iso":"eng"}],"abstract":[{"text":"Microtubules provide the mechanical force required for chromosome separation during mitosis. However, little is known about the dynamic (high-frequency) mechanical properties of microtubules. Here, we theoretically propose to control the vibrations of a doubly clamped microtubule by tip electrodes and to detect its motion via the optomechanical coupling between the vibrational modes of the microtubule and an optical cavity. In the presence of a red-detuned strong pump laser, this coupling leads to optomechanical-induced transparency of an optical probe field, which can be detected with state-of-the art technology. The center frequency and line width of the transparency peak give the resonance frequency and damping rate of the microtubule, respectively, while the height of the peak reveals information about the microtubule-cavity field coupling. Our method opens the new possibilities to gain information about the physical properties of microtubules, which will enhance our capability to design physical cancer treatment protocols as alternatives to chemotherapeutic drugs.","lang":"eng"}],"publisher":"American Institute of Physics","project":[{"call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics"}],"date_updated":"2026-07-07T13:21:37Z","title":"Optomechanical proposal for monitoring microtubule mechanical vibrations","issue":"1","date_published":"2017-07-12T00:00:00Z","publist_id":"6997","author":[{"full_name":"Barzanjeh, Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir","last_name":"Barzanjeh","orcid":"0000-0003-0415-1423"},{"full_name":"Salari, Vahid","first_name":"Vahid","last_name":"Salari"},{"full_name":"Tuszynski, Jack","first_name":"Jack","last_name":"Tuszynski"},{"full_name":"Cifra, Michal","first_name":"Michal","last_name":"Cifra"},{"first_name":"Christoph","last_name":"Simon","full_name":"Simon, Christoph"}],"main_file_link":[{"url":"https://arxiv.org/abs/1612.07061","open_access":"1"}],"department":[{"_id":"JoFi"}],"article_processing_charge":"No","external_id":{"arxiv":["1612.07061"],"isi":["000405367200012"]},"das_tickbox":"1","ec_funded":1},{"type":"journal_article","status":"public","oa_version":"Preprint","publication":"ACM Transactions on Computational Logic","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5415"},{"status":"public","id":"5436","relation":"earlier_version"},{"id":"1656","status":"public","relation":"earlier_version"}]},"corr_author":"1","arxiv":1,"date_created":"2018-12-11T11:46:38Z","scopus_import":"1","_id":"467","publication_identifier":{"issn":["1529-3785"]},"publication_status":"published","intvolume":"        18","day":"01","article_number":"31","citation":{"ama":"Chatterjee K, Henzinger TA, Otop J. Nested weighted automata. <i>ACM Transactions on Computational Logic</i>. 2017;18(4). doi:<a href=\"https://doi.org/10.1145/3152769\">10.1145/3152769</a>","short":"K. Chatterjee, T.A. Henzinger, J. Otop, ACM Transactions on Computational Logic 18 (2017).","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2017). Nested weighted automata. <i>ACM Transactions on Computational Logic</i>. ACM. <a href=\"https://doi.org/10.1145/3152769\">https://doi.org/10.1145/3152769</a>","ista":"Chatterjee K, Henzinger TA, Otop J. 2017. Nested weighted automata. ACM Transactions on Computational Logic. 18(4), 31.","mla":"Chatterjee, Krishnendu, et al. “Nested Weighted Automata.” <i>ACM Transactions on Computational Logic</i>, vol. 18, no. 4, 31, ACM, 2017, doi:<a href=\"https://doi.org/10.1145/3152769\">10.1145/3152769</a>.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted Automata.” <i>ACM Transactions on Computational Logic</i>. ACM, 2017. <a href=\"https://doi.org/10.1145/3152769\">https://doi.org/10.1145/3152769</a>.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted automata,” <i>ACM Transactions on Computational Logic</i>, vol. 18, no. 4. ACM, 2017."},"volume":18,"doi":"10.1145/3152769","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","ec_funded":1,"das_tickbox":"1","publist_id":"7354","date_published":"2017-12-01T00:00:00Z","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Otop, Jan","last_name":"Otop","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"}],"main_file_link":[{"url":"https://arxiv.org/abs/1606.03598","open_access":"1"}],"issue":"4","title":"Nested weighted automata","date_updated":"2026-07-07T14:01:10Z","article_processing_charge":"No","external_id":{"arxiv":["1606.03598"],"isi":["000419237100006"]},"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"ACM","abstract":[{"text":"Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata or in any other known decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata, which makes it possible to express important quantitative properties such as average response time. In nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in runtime verification. We establish an almost-complete decidability picture for the basic decision problems about nested weighted automata and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties.","lang":"eng"}],"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"oa":1,"isi":1,"language":[{"iso":"eng"}],"year":"2017","month":"12"},{"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/s00454-016-9843-x","article_type":"original","citation":{"ieee":"R. Connelly, M. Funkhouser, V. Z. Kuperberg, and E. Solomonides, “Packings of equal disks in a square torus,” <i>Discrete &#38; Computational Geometry</i>, vol. 58, no. 3. Springer Nature, pp. 614–642, 2017.","chicago":"Connelly, Robert, Matthew Funkhouser, Vivian Zieve Kuperberg, and Evan Solomonides. “Packings of Equal Disks in a Square Torus.” <i>Discrete &#38; Computational Geometry</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1007/s00454-016-9843-x\">https://doi.org/10.1007/s00454-016-9843-x</a>.","mla":"Connelly, Robert, et al. “Packings of Equal Disks in a Square Torus.” <i>Discrete &#38; Computational Geometry</i>, vol. 58, no. 3, Springer Nature, 2017, pp. 614–42, doi:<a href=\"https://doi.org/10.1007/s00454-016-9843-x\">10.1007/s00454-016-9843-x</a>.","ista":"Connelly R, Funkhouser M, Kuperberg VZ, Solomonides E. 2017. Packings of equal disks in a square torus. Discrete &#38; Computational Geometry. 58(3), 614–642.","short":"R. Connelly, M. Funkhouser, V.Z. Kuperberg, E. Solomonides, Discrete &#38; Computational Geometry 58 (2017) 614–642.","apa":"Connelly, R., Funkhouser, M., Kuperberg, V. Z., &#38; Solomonides, E. (2017). Packings of equal disks in a square torus. <i>Discrete &#38; Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-016-9843-x\">https://doi.org/10.1007/s00454-016-9843-x</a>","ama":"Connelly R, Funkhouser M, Kuperberg VZ, Solomonides E. Packings of equal disks in a square torus. <i>Discrete &#38; Computational Geometry</i>. 2017;58(3):614-642. doi:<a href=\"https://doi.org/10.1007/s00454-016-9843-x\">10.1007/s00454-016-9843-x</a>"},"volume":58,"publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"_id":"22198","OA_place":"repository","intvolume":"        58","extern":"1","day":"09","publication_status":"published","OA_type":"green","scopus_import":"1","date_created":"2026-06-29T12:58:50Z","arxiv":1,"type":"journal_article","publication":"Discrete & Computational Geometry","status":"public","oa_version":"Preprint","language":[{"iso":"eng"}],"page":"614-642","month":"01","year":"2017","publisher":"Springer Nature","abstract":[{"text":"Packings of equal disks in the plane are known to have density at most\r\nπ/\r\n√\r\n12, although this density is never achieved in the square torus, which is what we\r\ncall the plane modulo the square lattice. We find packings of disks in a square torus\r\nthat we conjecture to be the most dense for certain numbers of packing disks, using\r\ncontinued fractions to approximate 1/\r\n√\r\n3 and 2 −\r\n√\r\n3. We also define a constant to\r\nmeasure the efficiency of a packing motived by a related constant due to Markov for\r\ncontinued fractions. One idea is to use the unique factorization property of Gaussian\r\nintegers to prove that there is an upper bound for the Markov constant for grid-like\r\npackings. By way of contrast, we show that an upper bound by Gruber [In many cases\r\noptimal configurations are almost regular hexagonal, vol. 65, pp. 121–145, 1999;Geom\r\nDedicata 84(1–3):271–320, 2001] for the error for the limiting density of a packing\r\nof equal disks in a planar square, which is on the order of 1/\r\n√\r\nN, is the best possible,\r\nwhereas for our examples for the square torus, the error for the limiting density is on\r\nthe order of 1/N, where N is the number of packing disks.","lang":"eng"}],"external_id":{"arxiv":["1512.08762"]},"article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1512.08762"}],"author":[{"first_name":"Robert","last_name":"Connelly","full_name":"Connelly, Robert"},{"last_name":"Funkhouser","first_name":"Matthew","full_name":"Funkhouser, Matthew"},{"full_name":"Kuperberg, Vivian Zieve","last_name":"Kuperberg","id":"c3bac823-112d-11f0-a3f5-c264f852e697","first_name":"Vivian Zieve"},{"first_name":"Evan","last_name":"Solomonides","full_name":"Solomonides, Evan"}],"date_published":"2017-01-09T00:00:00Z","date_updated":"2026-07-14T11:14:51Z","issue":"3","title":"Packings of equal disks in a square torus"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","volume":127,"citation":{"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>.","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.","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>.","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>","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>","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."},"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.","scopus_import":"1","publication_identifier":{"issn":["0021-9738"]},"_id":"679","intvolume":"       127","day":"01","publication_status":"published","type":"journal_article","status":"public","oa_version":"Submitted Version","publication":"The Journal of Clinical Investigation","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12401"}]},"pmid":1,"date_created":"2018-12-11T11:47:53Z","oa":1,"language":[{"iso":"eng"}],"isi":1,"page":"2051 - 2065","year":"2017","month":"06","publisher":"American Society for Clinical Investigation","abstract":[{"lang":"eng","text":"Protective responses against pathogens require a rapid mobilization of resting neutrophils and the timely removal of activated ones. Neutrophils are exceptionally short-lived leukocytes, yet it remains unclear whether the lifespan of pathogen-engaged neutrophils is regulated differently from that in the circulating steady-state pool. Here, we have found that under homeostatic conditions, the mRNA-destabilizing protein tristetraprolin (TTP) regulates apoptosis and the numbers of activated infiltrating murine neutrophils but not neutrophil cellularity. Activated TTP-deficient neutrophils exhibited decreased apoptosis and enhanced accumulation at the infection site. In the context of myeloid-specific deletion of Ttp, the potentiation of neutrophil deployment protected mice against lethal soft tissue infection with Streptococcus pyogenes and prevented bacterial dissemination. Neutrophil transcriptome analysis revealed that decreased apoptosis of TTP-deficient neutrophils was specifically associated with elevated expression of myeloid cell leukemia 1 (Mcl1) but not other antiapoptotic B cell leukemia/ lymphoma 2 (Bcl2) family members. Higher Mcl1 expression resulted from stabilization of Mcl1 mRNA in the absence of TTP. The low apoptosis rate of infiltrating TTP-deficient neutrophils was comparable to that of transgenic Mcl1-overexpressing neutrophils. Our study demonstrates that posttranscriptional gene regulation by TTP schedules the termination of the antimicrobial engagement of neutrophils. The balancing role of TTP comes at the cost of an increased risk of bacterial infections."}],"project":[{"grant_number":"T00817-B21","name":"The biochemical basis of PAR polarization","_id":"25985A36-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"author":[{"first_name":"Florian","last_name":"Ebner","full_name":"Ebner, Florian"},{"full_name":"Sedlyarov, Vitaly","first_name":"Vitaly","last_name":"Sedlyarov"},{"full_name":"Tasciyan, Saren","first_name":"Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X","last_name":"Tasciyan"},{"last_name":"Ivin","first_name":"Masa","full_name":"Ivin, Masa"},{"full_name":"Kratochvill, Franz","first_name":"Franz","last_name":"Kratochvill"},{"full_name":"Gratz, Nina","first_name":"Nina","last_name":"Gratz"},{"full_name":"Kenner, Lukas","first_name":"Lukas","last_name":"Kenner"},{"first_name":"Andreas","last_name":"Villunger","full_name":"Villunger, Andreas"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kovarik","first_name":"Pavel","full_name":"Kovarik, Pavel"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451238/","open_access":"1"}],"publist_id":"7038","date_published":"2017-06-01T00:00:00Z","date_updated":"2026-07-22T22:30:09Z","title":"The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection","issue":"6","external_id":{"isi":["000402620800008"],"pmid":["28504646"]},"article_processing_charge":"No","department":[{"_id":"MiSi"}]},{"oa":1,"month":"07","year":"2017","isi":1,"language":[{"iso":"eng"}],"abstract":[{"text":"How the organization of genes on a chromosome shapes adaptation is essential for understanding evolutionary paths. Here, we investigate how adaptation to rapidly increasing levels of antibiotic depends on the chromosomal neighborhood of a drug-resistance gene inserted at different positions of the Escherichia coli chromosome. Using a dual-fluorescence reporter that allows us to distinguish gene amplifications from other up-mutations, we track in real-time adaptive changes in expression of the drug-resistance gene. We find that the relative contribution of several mutation types differs systematically between loci due to properties of neighboring genes: essentiality, expression, orientation, termination, and presence of duplicates. These properties determine rate and fitness effects of gene amplification, deletions, and mutations compromising transcriptional termination. Thus, the adaptive potential of a gene under selection is a system-property with a complex genetic basis that is specific for each chromosomal locus, and it can be inferred from detailed functional and genomic data.","lang":"eng"}],"pubrep_id":"890","publisher":"eLife Sciences Publications","title":"Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection","date_updated":"2026-07-22T22:30:11Z","author":[{"id":"2C023F40-F248-11E8-B48F-1D18A9856A87","first_name":"Magdalena","orcid":"0000-0003-1229-9719","last_name":"Steinrück","full_name":"Steinrück, Magdalena"},{"full_name":"Guet, Calin C","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","last_name":"Guet"}],"publist_id":"6990","date_published":"2017-07-25T00:00:00Z","department":[{"_id":"CaGu"}],"external_id":{"isi":["000406183700001"]},"article_processing_charge":"No","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"file_id":"4975","relation":"main_file","content_type":"application/pdf","checksum":"6b908b5db9f61f6820ebd7f8fa815571","date_updated":"2020-07-14T12:47:48Z","file_size":2092088,"file_name":"IST-2017-890-v1+1_elife-25100-v1.pdf","creator":"system","date_created":"2018-12-12T10:12:54Z","access_level":"open_access"},{"date_created":"2018-12-12T10:12:55Z","creator":"system","file_name":"IST-2017-890-v1+2_elife-25100-figures-v1.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"4976","file_size":3428681,"date_updated":"2020-07-14T12:47:48Z","checksum":"ca21530389b720243552678125fdba35"}],"file_date_updated":"2020-07-14T12:47:48Z","quality_controlled":"1","volume":6,"citation":{"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>","short":"M. Steinrück, C.C. Guet, ELife 6 (2017).","ista":"Steinrück M, Guet CC. 2017. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife. 6, e25100.","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>.","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>.","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."},"article_number":"e25100","doi":"10.7554/eLife.25100","scopus_import":"1","ddc":["576"],"has_accepted_license":"1","day":"25","intvolume":"         6","publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"_id":"704","oa_version":"Published Version","publication":"eLife","status":"public","type":"journal_article","date_created":"2018-12-11T11:48:01Z","corr_author":"1","related_material":{"record":[{"relation":"popular_science","id":"5564","status":"public"},{"id":"26","status":"public","relation":"dissertation_contains"}]}},{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2017-06-01T00:00:00Z","publist_id":"7034","author":[{"full_name":"Ukai, Hikari","last_name":"Ukai","first_name":"Hikari"},{"full_name":"Kawahara, Aiko","first_name":"Aiko","last_name":"Kawahara"},{"first_name":"Keiko","last_name":"Hirayama","full_name":"Hirayama, Keiko"},{"last_name":"Case","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Matthew J","full_name":"Case, Matthew J"},{"full_name":"Aino, Shotaro","last_name":"Aino","first_name":"Shotaro"},{"full_name":"Miyabe, Masahiro","last_name":"Miyabe","first_name":"Masahiro"},{"last_name":"Wakita","first_name":"Ken","full_name":"Wakita, Ken"},{"full_name":"Oogi, Ryohei","first_name":"Ryohei","last_name":"Oogi"},{"first_name":"Michiyo","last_name":"Kasayuki","full_name":"Kasayuki, Michiyo"},{"full_name":"Kawashima, Shihomi","first_name":"Shihomi","last_name":"Kawashima"},{"first_name":"Shunichi","last_name":"Sugimoto","full_name":"Sugimoto, Shunichi"},{"last_name":"Chikamatsu","first_name":"Kanako","full_name":"Chikamatsu, Kanako"},{"full_name":"Nitta, Noritaka","last_name":"Nitta","first_name":"Noritaka"},{"full_name":"Koga, Tsuneyuki","last_name":"Koga","first_name":"Tsuneyuki"},{"orcid":"0000-0001-8761-9444","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"},{"full_name":"Takai, Toshiyuki","first_name":"Toshiyuki","last_name":"Takai"},{"full_name":"Ito, Isao","first_name":"Isao","last_name":"Ito"}],"issue":"6","title":"PirB regulates asymmetries in hippocampal circuitry","date_updated":"2026-07-22T22:30:25Z","article_processing_charge":"No","external_id":{"isi":["000402923200125"]},"department":[{"_id":"RySh"}],"publisher":"Public Library of Science","pubrep_id":"897","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."}],"oa":1,"language":[{"iso":"eng"}],"isi":1,"month":"06","year":"2017","type":"journal_article","status":"public","oa_version":"Published Version","publication":"PLoS One","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"51"}]},"date_created":"2018-12-11T11:47:54Z","has_accepted_license":"1","ddc":["571"],"scopus_import":"1","_id":"682","publication_identifier":{"issn":["1932-6203"]},"publication_status":"published","intvolume":"        12","day":"01","article_type":"original","article_number":"e0179377","volume":12,"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>.","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>","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).","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>","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.","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>.","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."},"doi":"10.1371/journal.pone.0179377","file":[{"date_created":"2018-12-12T10:12:16Z","creator":"system","file_name":"IST-2017-897-v1+1_journal.pone.0179377.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"4934","file_size":5798454,"date_updated":"2020-07-14T12:47:40Z","checksum":"24dd19c46fb1c761b0bcbbcd1025a3a8"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","file_date_updated":"2020-07-14T12:47:40Z"},{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation","issue":"10","date_updated":"2026-07-22T22:30:27Z","date_published":"2017-05-15T00:00:00Z","publist_id":"7047","author":[{"full_name":"Krens, Gabriel","last_name":"Krens","orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel"},{"first_name":"Jim","last_name":"Veldhuis","full_name":"Veldhuis, Jim"},{"full_name":"Barone, Vanessa","first_name":"Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","last_name":"Barone","orcid":"0000-0003-2676-3367"},{"full_name":"Capek, Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","orcid":"0000-0001-5199-9940","last_name":"Capek"},{"orcid":"0000-0002-3688-1474","last_name":"Maître","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","first_name":"Jean-Léon","full_name":"Maître, Jean-Léon"},{"full_name":"Brodland, Wayne","first_name":"Wayne","last_name":"Brodland"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"Bio"},{"_id":"CaHe"}],"article_processing_charge":"No","external_id":{"pmid":["28512197"],"isi":["000402275900007"]},"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"}],"publisher":"Company of Biologists","oa":1,"year":"2017","month":"05","page":"1798 - 1806","isi":1,"language":[{"iso":"eng"}],"status":"public","publication":"Development","oa_version":"Published Version","type":"journal_article","date_created":"2018-12-11T11:47:52Z","pmid":1,"corr_author":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"961","status":"public"},{"relation":"dissertation_contains","id":"50","status":"public"}]},"scopus_import":"1","has_accepted_license":"1","ddc":["570"],"publication_status":"published","day":"15","intvolume":"       144","_id":"676","publication_identifier":{"issn":["0950-1991"]},"citation":{"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.","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>","short":"G. Krens, J. Veldhuis, V. Barone, D. Capek, J.-L. Maître, W. Brodland, C.-P.J. Heisenberg, Development 144 (2017) 1798–1806.","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>","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>.","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>."},"volume":144,"article_type":"original","doi":"10.1242/dev.144964","file":[{"date_created":"2019-09-24T06:56:22Z","file_name":"2017_Development_Krens.pdf","creator":"dernst","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"6905","date_updated":"2020-07-14T12:47:39Z","file_size":8194516,"checksum":"bc25125fb664706cdf180e061429f91d"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file_date_updated":"2020-07-14T12:47:39Z","quality_controlled":"1"},{"oa":1,"language":[{"iso":"eng"}],"year":"2017","month":"03","page":"1 - 29","publisher":"Springer","pubrep_id":"1019","abstract":[{"lang":"eng","text":"The history of auxin and cytokinin biology including the initial discoveries by father–son duo Charles Darwin and Francis Darwin (1880), and Gottlieb Haberlandt (1919) is a beautiful demonstration of unceasing continuity of research. Novel findings are integrated into existing hypotheses and models and deepen our understanding of biological principles. At the same time new questions are triggered and hand to hand with this new methodologies are developed to address these new challenges."}],"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":[{"id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Andrej","last_name":"Hurny","orcid":"0000-0003-3638-1426","full_name":"Hurny, Andrej"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva"}],"date_published":"2017-03-17T00:00:00Z","publist_id":"6369","date_updated":"2026-07-22T22:30:27Z","title":"Methodological advances in auxin and cytokinin biology","article_processing_charge":"No","department":[{"_id":"EvBe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":840646,"date_updated":"2019-10-15T07:47:05Z","file_id":"5068","content_type":"application/pdf","relation":"main_file","access_level":"open_access","creator":"system","file_name":"IST-2018-1019-v1+1_Hurny_MethodsMolBiol_2017.pdf","date_created":"2018-12-12T10:14:18Z"}],"quality_controlled":"1","file_date_updated":"2019-10-15T07:47:05Z","citation":{"mla":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” <i>Auxins and Cytokinins in Plant Biology</i>, vol. 1569, Springer, 2017, pp. 1–29, doi:<a href=\"https://doi.org/10.1007/978-1-4939-6831-2_1\">10.1007/978-1-4939-6831-2_1</a>.","short":"A. Hurny, E. Benková, Auxins and Cytokinins in Plant Biology 1569 (2017) 1–29.","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>","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>","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>."},"volume":1569,"doi":"10.1007/978-1-4939-6831-2_1","ddc":["575"],"has_accepted_license":"1","scopus_import":"1","publication_identifier":{"issn":["1064-3745"]},"_id":"1024","intvolume":"      1569","day":"17","publication_status":"published","type":"journal_article","alternative_title":["Methods in Molecular Biology"],"publication":"Auxins and Cytokinins in Plant Biology","oa_version":"Submitted Version","status":"public","corr_author":"1","related_material":{"record":[{"status":"public","id":"539","relation":"dissertation_contains"}]},"date_created":"2018-12-11T11:49:45Z"},{"related_material":{"record":[{"relation":"research_data","status":"public","id":"9849"},{"status":"public","id":"9850","relation":"research_data"},{"status":"public","id":"9851","relation":"research_data"},{"status":"public","id":"9852","relation":"research_data"},{"relation":"dissertation_contains","id":"6263","status":"public"}]},"corr_author":"1","date_created":"2018-12-11T11:47:58Z","type":"journal_article","oa_version":"Published Version","status":"public","publication":"PLoS Computational Biology","publication_identifier":{"issn":["1553-734X"]},"_id":"696","day":"18","intvolume":"        13","publication_status":"published","ddc":["576"],"has_accepted_license":"1","scopus_import":"1","doi":"10.1371/journal.pcbi.1005609","article_number":"e1005609","article_type":"original","volume":13,"citation":{"ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” <i>PLoS Computational Biology</i>, vol. 13, no. 7. Public Library of Science, 2017.","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>.","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>","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.","short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).","ama":"Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. 2017;13(7). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>","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>."},"quality_controlled":"1","file_date_updated":"2020-07-14T12:47:46Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"access_level":"open_access","file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","creator":"system","date_created":"2018-12-12T10:15:01Z","checksum":"9143c290fa6458ed2563bff4b295554a","date_updated":"2020-07-14T12:47:46Z","file_size":3775716,"file_id":"5117","relation":"main_file","content_type":"application/pdf"}],"ec_funded":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"isi":["000406619800014"]},"article_processing_charge":"No","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"author":[{"last_name":"Lukacisinova","orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87","first_name":"Marta","full_name":"Lukacisinova, Marta"},{"full_name":"Novak, Sebastian","last_name":"Novak","orcid":"0000-0002-2519-824X","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2361-3953","last_name":"Paixao","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"}],"publist_id":"7004","date_published":"2017-07-18T00:00:00Z","title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","issue":"7","date_updated":"2026-07-22T22:30:28Z","project":[{"grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"pubrep_id":"894","publisher":"Public Library of Science","abstract":[{"text":"Mutator strains are expected to evolve when the availability and effect of beneficial mutations are high enough to counteract the disadvantage from deleterious mutations that will inevitably accumulate. As the population becomes more adapted to its environment, both availability and effect of beneficial mutations necessarily decrease and mutation rates are predicted to decrease. It has been shown that certain molecular mechanisms can lead to increased mutation rates when the organism finds itself in a stressful environment. While this may be a correlated response to other functions, it could also be an adaptive mechanism, raising mutation rates only when it is most advantageous. Here, we use a mathematical model to investigate the plausibility of the adaptive hypothesis. We show that such a mechanism can be mantained if the population is subjected to diverse stresses. By simulating various antibiotic treatment schemes, we find that combination treatments can reduce the effectiveness of second-order selection on stress-induced mutagenesis. We discuss the implications of our results to strategies of antibiotic therapy.","lang":"eng"}],"isi":1,"language":[{"iso":"eng"}],"month":"07","year":"2017","oa":1},{"oa":1,"isi":1,"language":[{"iso":"eng"}],"year":"2017","page":"90 - 97","month":"08","publisher":"Elsevier","pubrep_id":"801","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."}],"project":[{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions"},{"_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"303507","name":"Optimality principles in responses to antibiotics"},{"name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"}],"publist_id":"6364","date_published":"2017-08-01T00:00:00Z","author":[{"full_name":"Lukacisinova, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","first_name":"Marta","orcid":"0000-0002-2519-8004","last_name":"Lukacisinova"},{"full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach"}],"date_updated":"2026-07-22T22:30:28Z","title":"Toward a quantitative understanding of antibiotic resistance evolution","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000408077400015"]},"department":[{"_id":"ToBo"}],"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"ec_funded":1,"file":[{"file_id":"5846","content_type":"application/pdf","relation":"main_file","file_size":858338,"date_updated":"2019-01-18T09:57:57Z","creator":"dernst","file_name":"2017_CurrentOpinion_Lukaciinova.pdf","date_created":"2019-01-18T09:57:57Z","success":1,"access_level":"open_access"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","file_date_updated":"2019-01-18T09:57:57Z","article_type":"original","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","citation":{"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>.","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>","ista":"Lukacisinova M, Bollenbach MT. 2017. Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. 46, 90–97.","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>","short":"M. Lukacisinova, M.T. Bollenbach, Current Opinion in Biotechnology 46 (2017) 90–97.","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>.","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."},"volume":46,"doi":"10.1016/j.copbio.2017.02.013","has_accepted_license":"1","ddc":["570"],"scopus_import":"1","_id":"1027","publication_status":"published","intvolume":"        46","day":"01","type":"journal_article","status":"public","oa_version":"Published Version","publication":"Current Opinion in Biotechnology","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6263"}]},"corr_author":"1","date_created":"2018-12-11T11:49:45Z"},{"scopus_import":"1","has_accepted_license":"1","ddc":["570"],"publication_status":"published","intvolume":"        12","day":"16","_id":"1029","publication_identifier":{"issn":["1932-6203"]},"publication":"PLoS One","status":"public","oa_version":"Published Version","type":"journal_article","date_created":"2018-12-11T11:49:46Z","related_material":{"record":[{"relation":"popular_science","status":"public","id":"5556"},{"relation":"dissertation_contains","status":"public","id":"6392"}]},"file":[{"file_name":"IST-2017-800-v1+1_journal.pone.0174066.pdf","creator":"system","date_created":"2018-12-12T10:09:47Z","access_level":"open_access","file_id":"4772","relation":"main_file","content_type":"application/pdf","date_updated":"2018-12-12T10:09:47Z","file_size":3429381}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2018-12-12T10:09:47Z","quality_controlled":"1","citation":{"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>","short":"M. Lukacisin, M. Landon, R. Jajoo, PLoS One 12 (2017).","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.","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>","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>.","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.","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>."},"volume":12,"article_number":"e0174066","doi":"10.1371/journal.pone.0174066","issue":"3","date_updated":"2026-07-22T22:30:28Z","title":"Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast","date_published":"2017-03-16T00:00:00Z","publist_id":"6361","author":[{"orcid":"0000-0001-6549-4177","last_name":"Lukacisin","first_name":"Martin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisin, Martin"},{"full_name":"Landon, Matthieu","last_name":"Landon","first_name":"Matthieu"},{"last_name":"Jajoo","first_name":"Rishi","full_name":"Jajoo, Rishi"}],"department":[{"_id":"ToBo"}],"article_processing_charge":"Yes","external_id":{"isi":["000396318300121"]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"month":"03","year":"2017","language":[{"iso":"eng"}],"isi":1,"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"}],"pubrep_id":"800","publisher":"Public Library of Science"},{"department":[{"_id":"CaHe"},{"_id":"BjHo"},{"_id":"Bio"}],"external_id":{"isi":["000397917000009"],"pmid":["28346437"]},"article_processing_charge":"No","title":"Friction forces position the neural anlage","date_updated":"2026-07-22T22:30:48Z","author":[{"full_name":"Smutny, Michael","last_name":"Smutny","orcid":"0000-0002-5920-9090","first_name":"Michael","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ákos, Zsuzsa","last_name":"Ákos","first_name":"Zsuzsa"},{"full_name":"Grigolon, Silvia","first_name":"Silvia","last_name":"Grigolon"},{"full_name":"Shamipour, Shayan","last_name":"Shamipour","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ruprecht, Verena","first_name":"Verena","last_name":"Ruprecht"},{"full_name":"Capek, Daniel","last_name":"Capek","orcid":"0000-0001-5199-9940","first_name":"Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Behrndt, Martin","first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","last_name":"Behrndt"},{"full_name":"Papusheva, Ekaterina","last_name":"Papusheva","id":"41DB591E-F248-11E8-B48F-1D18A9856A87","first_name":"Ekaterina"},{"last_name":"Tada","first_name":"Masazumi","full_name":"Tada, Masazumi"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"},{"first_name":"Tamás","last_name":"Vicsek","full_name":"Vicsek, Tamás"},{"full_name":"Salbreux, Guillaume","last_name":"Salbreux","first_name":"Guillaume"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566"}],"main_file_link":[{"url":"https://europepmc.org/articles/pmc5635970","open_access":"1"}],"publist_id":"7074","date_published":"2017-03-27T00:00:00Z","ec_funded":1,"year":"2017","month":"03","page":"306 - 317","isi":1,"language":[{"iso":"eng"}],"oa":1,"project":[{"_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Decoding the complexity of turbulence at its origin","grant_number":"306589"},{"name":"Control of Epithelial Cell Layer Spreading in Zebrafish","grant_number":"I930-B20","call_identifier":"FWF","_id":"252ABD0A-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"During embryonic development, mechanical forces are essential for cellular rearrangements driving tissue morphogenesis. Here, we show that in the early zebrafish embryo, friction forces are generated at the interface between anterior axial mesoderm (prechordal plate, ppl) progenitors migrating towards the animal pole and neurectoderm progenitors moving in the opposite direction towards the vegetal pole of the embryo. These friction forces lead to global rearrangement of cells within the neurectoderm and determine the position of the neural anlage. Using a combination of experiments and simulations, we show that this process depends on hydrodynamic coupling between neurectoderm and ppl as a result of E-cadherin-mediated adhesion between those tissues. Our data thus establish the emergence of friction forces at the interface between moving tissues as a critical force-generating process shaping the embryo."}],"publisher":"Nature Publishing Group","day":"27","intvolume":"        19","publication_status":"published","publication_identifier":{"issn":["1465-7392"]},"_id":"661","scopus_import":"1","date_created":"2018-12-11T11:47:46Z","related_material":{"record":[{"relation":"dissertation_contains","id":"50","status":"public"},{"id":"8350","status":"public","relation":"dissertation_contains"}]},"corr_author":"1","pmid":1,"status":"public","publication":"Nature Cell Biology","oa_version":"Submitted Version","type":"journal_article","acknowledged_ssus":[{"_id":"SSU"}],"quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1038/ncb3492","volume":19,"citation":{"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.","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.","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>.","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."}},{"ec_funded":1,"article_processing_charge":"No","external_id":{"isi":["000413443700011"]},"department":[{"_id":"CaHe"},{"_id":"CaGu"},{"_id":"GaTk"}],"publist_id":"6934","date_published":"2017-10-23T00:00:00Z","author":[{"full_name":"Barone, Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","last_name":"Barone","orcid":"0000-0003-2676-3367"},{"full_name":"Lang, Moritz","last_name":"Lang","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","first_name":"Moritz"},{"full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","last_name":"Krens","first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pradhan, Saurabh","last_name":"Pradhan","first_name":"Saurabh"},{"full_name":"Shamipour, Shayan","last_name":"Shamipour","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan"},{"full_name":"Sako, Keisuke","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","first_name":"Keisuke","last_name":"Sako","orcid":"0000-0002-6453-8075"},{"full_name":"Sikora, Mateusz K","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","last_name":"Sikora"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"title":"An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate","date_updated":"2026-07-22T22:30:48Z","issue":"2","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"252DD2A6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I2058","name":"Cell segregation in gastrulation: the role of cell fate specification"}],"publisher":"Cell Press","abstract":[{"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.","lang":"eng"}],"language":[{"iso":"eng"}],"isi":1,"year":"2017","page":"198 - 211","month":"10","corr_author":"1","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"961"},{"relation":"dissertation_contains","id":"8350","status":"public"}]},"date_created":"2018-12-11T11:48:13Z","type":"journal_article","oa_version":"None","status":"public","publication":"Developmental Cell","_id":"735","publication_identifier":{"issn":["1534-5807"]},"publication_status":"published","day":"23","intvolume":"        43","scopus_import":"1","doi":"10.1016/j.devcel.2017.09.014","volume":43,"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>.","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.","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."},"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"pubrep_id":"845","publisher":"Springer","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"}],"project":[{"grant_number":"S11407","name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"oa":1,"isi":1,"language":[{"iso":"eng"}],"page":"59 - 66","month":"01","year":"2017","ec_funded":1,"publist_id":"6468","date_published":"2017-01-01T00:00:00Z","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Amir","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir"},{"last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas"}],"title":"JTDec: A tool for tree decompositions in soot","date_updated":"2026-07-22T22:30:55Z","article_processing_charge":"No","external_id":{"isi":["000723567800004"]},"department":[{"_id":"KrCh"}],"volume":10482,"citation":{"apa":"Chatterjee, K., Goharshady, A. K., &#38; Pavlogiannis, A. (2017). JTDec: A tool for tree decompositions in soot. In D. D’Souza (Ed.) (Vol. 10482, pp. 59–66). Presented at the ATVA: Automated Technology for Verification and Analysis, Pune, India: Springer. <a href=\"https://doi.org/10.1007/978-3-319-68167-2_4\">https://doi.org/10.1007/978-3-319-68167-2_4</a>","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.","short":"K. Chatterjee, A.K. Goharshady, A. Pavlogiannis, in:, D. D’Souza (Ed.), Springer, 2017, pp. 59–66.","ama":"Chatterjee K, Goharshady AK, Pavlogiannis A. JTDec: A tool for tree decompositions in soot. In: D’Souza D, ed. Vol 10482. Springer; 2017:59-66. doi:<a href=\"https://doi.org/10.1007/978-3-319-68167-2_4\">10.1007/978-3-319-68167-2_4</a>","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>.","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>."},"doi":"10.1007/978-3-319-68167-2_4","file":[{"date_updated":"2020-07-14T12:48:16Z","file_size":948514,"checksum":"a0d9f5f94dc594c4e71e78525c9942f1","relation":"main_file","content_type":"application/pdf","file_id":"4835","access_level":"open_access","date_created":"2018-12-12T10:10:45Z","file_name":"IST-2017-845-v1+1_2017_Chatterjee_JTDec.pdf","creator":"system"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","quality_controlled":"1","file_date_updated":"2020-07-14T12:48:16Z","alternative_title":["LNCS"],"type":"conference","conference":{"end_date":"2017-10-06","location":"Pune, India","name":"ATVA: Automated Technology for Verification and Analysis","start_date":"2017-10-03"},"oa_version":"Submitted Version","status":"public","corr_author":"1","related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"date_created":"2018-12-11T11:49:22Z","has_accepted_license":"1","editor":[{"first_name":"Deepak","last_name":"D'Souza","full_name":"D'Souza, Deepak"}],"ddc":["005"],"scopus_import":"1","_id":"949","publication_identifier":{"issn":["0302-9743"]},"publication_status":"published","day":"01","intvolume":"     10482"},{"arxiv":1,"date_created":"2018-12-11T11:47:39Z","related_material":{"record":[{"status":"public","id":"7014","relation":"later_version"},{"relation":"dissertation_contains","id":"8934","status":"public"}]},"status":"public","oa_version":"Submitted Version","type":"conference","alternative_title":["LNCS"],"conference":{"location":"Heidelberg, Germany","start_date":"2017-07-24","name":"CAV: Computer Aided Verification","end_date":"2017-07-28"},"publication_status":"published","day":"01","intvolume":"     10427","_id":"639","publication_identifier":{"isbn":["978-331963389-3"]},"scopus_import":"1","editor":[{"full_name":"Majumdar, Rupak","first_name":"Rupak","last_name":"Majumdar"},{"last_name":"Kunčak","first_name":"Viktor","full_name":"Kunčak, Viktor"}],"doi":"10.1007/978-3-319-63390-9_3","citation":{"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>.","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>.","apa":"Chatterjee, K., Fu, H., &#38; Goharshady, A. K. (2017). Non-polynomial worst case analysis of recursive programs. In R. Majumdar &#38; V. Kunčak (Eds.) (Vol. 10427, pp. 41–63). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. <a href=\"https://doi.org/10.1007/978-3-319-63390-9_3\">https://doi.org/10.1007/978-3-319-63390-9_3</a>","short":"K. Chatterjee, H. Fu, A.K. Goharshady, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 41–63.","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.","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>"},"volume":10427,"quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"department":[{"_id":"KrCh"}],"article_processing_charge":"No","external_id":{"isi":["000431900900003"],"arxiv":["1705.00317"]},"title":"Non-polynomial worst case analysis of recursive programs","date_updated":"2026-07-22T22:30:55Z","publist_id":"7149","date_published":"2017-01-01T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1705.00317","open_access":"1"}],"author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei"},{"last_name":"Goharshady","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir","full_name":"Goharshady, Amir"}],"project":[{"grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"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."}],"publisher":"Springer","page":"41 - 63","year":"2017","month":"01","language":[{"iso":"eng"}],"isi":1,"oa":1},{"scopus_import":"1","publication_status":"published","intvolume":"        46","day":"18","_id":"664","publication_identifier":{"issn":["1074-7613"]},"publication":"Immunity","status":"public","oa_version":"None","type":"journal_article","date_created":"2018-12-11T11:47:47Z","corr_author":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"6947","status":"public"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","volume":46,"citation":{"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.","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>","short":"F.P. Assen, M.K. Sixt, Immunity 46 (2017) 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>","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>."},"doi":"10.1016/j.immuni.2017.04.006","issue":"4","title":"The dynamic cytokine niche","date_updated":"2026-07-22T22:30:57Z","publist_id":"7065","date_published":"2017-04-18T00:00:00Z","author":[{"full_name":"Assen, Frank P","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","first_name":"Frank P","orcid":"0000-0003-3470-6119","last_name":"Assen"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"department":[{"_id":"MiSi"}],"article_processing_charge":"No","external_id":{"isi":["000399451100002"]},"page":"519 - 520","month":"04","year":"2017","language":[{"iso":"eng"}],"isi":1,"abstract":[{"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.","lang":"eng"}],"publisher":"Cell Press"},{"external_id":{"isi":["000404486700001"]},"article_processing_charge":"Yes","department":[{"_id":"SiHi"},{"_id":"MaLo"}],"author":[{"first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","last_name":"Hansen","full_name":"Hansen, Andi H"},{"last_name":"Düllberg","orcid":"0000-0001-6335-9748","id":"459064DC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian F","full_name":"Düllberg, Christian F"},{"full_name":"Mieck, Christine","orcid":"0000-0003-1919-7416","last_name":"Mieck","first_name":"Christine","id":"34CAE85C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Loose, Martin","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","orcid":"0000-0001-7309-9724"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}],"publist_id":"6445","date_published":"2017-06-28T00:00:00Z","title":"Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks","date_updated":"2026-07-22T22:31:02Z","ec_funded":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"isi":1,"language":[{"iso":"eng"}],"year":"2017","month":"06","oa":1,"project":[{"_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development","grant_number":"618444"},{"_id":"25D7962E-B435-11E9-9278-68D0E5697425","grant_number":"RGP0053/2014","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"grant_number":"T00817-B21","name":"The biochemical basis of PAR polarization","_id":"25985A36-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"pubrep_id":"830","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"}],"publication_identifier":{"issn":["1662-5102"]},"_id":"960","day":"28","intvolume":"        11","publication_status":"published","ddc":["570"],"has_accepted_license":"1","scopus_import":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"9962","status":"public"}]},"date_created":"2018-12-11T11:49:25Z","type":"journal_article","publication":"Frontiers in Cellular Neuroscience","status":"public","oa_version":"Published Version","quality_controlled":"1","file_date_updated":"2020-07-14T12:48:16Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","creator":"system","file_name":"IST-2017-830-v1+1_2017_Hansen_CellPolarity.pdf","date_created":"2018-12-12T10:09:40Z","checksum":"dc1f5a475b918d09a0f9f587400b1626","file_size":2153858,"date_updated":"2020-07-14T12:48:16Z","file_id":"4764","content_type":"application/pdf","relation":"main_file"}],"doi":"10.3389/fncel.2017.00176","article_number":"176","citation":{"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.","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>.","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>.","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.","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>","short":"A.H. Hansen, C.F. Düllberg, C. Mieck, M. Loose, S. Hippenmeyer, Frontiers in Cellular Neuroscience 11 (2017).","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>"},"volume":11},{"issue":"16","date_updated":"2026-07-22T22:31:08Z","title":"Green-light-induced inactivation of receptor signaling using cobalamin-binding domains","author":[{"full_name":"Kainrath, Stephanie","orcid":"0000-0002-6709-2195","last_name":"Kainrath","first_name":"Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stadler, Manuela","first_name":"Manuela","last_name":"Stadler"},{"full_name":"Gschaider-Reichhart, Eva","orcid":"0000-0002-7218-7738","last_name":"Gschaider-Reichhart","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"full_name":"Distel, Martin","first_name":"Martin","last_name":"Distel"},{"first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"}],"date_published":"2017-03-20T00:00:00Z","publist_id":"6362","department":[{"_id":"CaGu"},{"_id":"HaJa"}],"external_id":{"isi":["000398154000038"]},"article_processing_charge":"No","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"das_tickbox":"1","ec_funded":1,"oa":1,"month":"03","year":"2017","page":"4608-4611","language":[{"iso":"eng"}],"isi":1,"abstract":[{"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.","lang":"eng"}],"publisher":"Wiley-Blackwell","project":[{"_id":"25548C20-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"scopus_import":"1","ddc":["540"],"has_accepted_license":"1","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)","day":"20","intvolume":"        56","publication_status":"published","publication_identifier":{"issn":["1433-7851"]},"_id":"1028","status":"public","publication":"Angewandte Chemie International Edition","oa_version":"Published Version","type":"journal_article","date_created":"2018-12-11T11:49:46Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"418"},{"status":"public","id":"7680","relation":"part_of_dissertation"}]},"corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2019-01-18T09:39:55Z","success":1,"file_name":"2017_communications_Kainrath.pdf","creator":"dernst","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5845","date_updated":"2019-01-18T09:39:55Z","file_size":2614942}],"file_date_updated":"2019-01-18T09:39:55Z","quality_controlled":"1","citation":{"short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie International Edition 56 (2017) 4608–4611.","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>","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>","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>.","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.","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>."},"volume":56,"doi":"10.1002/anie.201611998"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","volume":29,"citation":{"ieee":"M. J. Chalk, O. Marre, and G. Tkačik, “Relevant sparse codes with variational information bottleneck,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 1965–1973.","chicago":"Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Relevant Sparse Codes with Variational Information Bottleneck,” 29:1965–73. Neural Information Processing Systems Foundation, 2016.","mla":"Chalk, Matthew J., et al. <i>Relevant Sparse Codes with Variational Information Bottleneck</i>. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 1965–73.","short":"M.J. Chalk, O. Marre, G. Tkačik, in:, Neural Information Processing Systems Foundation, 2016, pp. 1965–1973.","apa":"Chalk, M. J., Marre, O., &#38; Tkačik, G. (2016). Relevant sparse codes with variational information bottleneck (Vol. 29, pp. 1965–1973). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information Processing Systems Foundation.","ista":"Chalk MJ, Marre O, Tkačik G. 2016. Relevant sparse codes with variational information bottleneck. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 1965–1973.","ama":"Chalk MJ, Marre O, Tkačik G. Relevant sparse codes with variational information bottleneck. In: Vol 29. Neural Information Processing Systems Foundation; 2016:1965-1973."},"scopus_import":"1","_id":"1082","publication_status":"published","day":"01","intvolume":"        29","alternative_title":["Advances in Neural Information Processing Systems"],"type":"conference","conference":{"end_date":"2016-12-10","location":"Barcelona, Spain","start_date":"2016-12-05","name":"NIPS: Neural Information Processing Systems"},"status":"public","oa_version":"Preprint","related_material":{"link":[{"url":"https://papers.nips.cc/paper/6101-relevant-sparse-codes-with-variational-information-bottleneck","relation":"other"}]},"date_created":"2018-12-11T11:50:03Z","arxiv":1,"oa":1,"language":[{"iso":"eng"}],"year":"2016","month":"12","page":"1965-1973","publisher":"Neural Information Processing Systems Foundation","abstract":[{"text":"In many applications, it is desirable to extract only the relevant aspects of data. A principled way to do this is the information bottleneck (IB) method, where one seeks a code that maximises information about a relevance variable, Y, while constraining the information encoded about the original data, X. Unfortunately however, the IB method is computationally demanding when data are high-dimensional and/or non-gaussian. Here we propose an approximate variational scheme for maximising a lower bound on the IB objective, analogous to variational EM. Using this method, we derive an IB algorithm to recover features that are both relevant and sparse. Finally, we demonstrate how kernelised versions of the algorithm can be used to address a broad range of problems with non-linear relation between X and Y.","lang":"eng"}],"date_published":"2016-12-01T00:00:00Z","publist_id":"6298","main_file_link":[{"url":"https://arxiv.org/abs/1605.07332","open_access":"1"}],"author":[{"full_name":"Chalk, Matthew J","first_name":"Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7782-4436","last_name":"Chalk"},{"full_name":"Marre, Olivier","first_name":"Olivier","last_name":"Marre"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"title":"Relevant sparse codes with variational information bottleneck","date_updated":"2025-06-03T11:33:51Z","article_processing_charge":"No","external_id":{"arxiv":["1605.07332"]},"department":[{"_id":"GaTk"}]},{"doi":"10.1093/cercor/bhw090","volume":27,"citation":{"ieee":"S. Booker <i>et al.</i>, “KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons,” <i>Cerebral Cortex</i>, vol. 27, no. 3. Oxford University Press, pp. 2318–2334, 2016.","chicago":"Booker, Sam, Daniel Althof, Anna Gross, Desiree Loreth, Johanna Müller, Andreas Unger, Bernd Fakler, et al. “KCTD12 Auxiliary Proteins Modulate Kinetics of GABAB Receptor-Mediated Inhibition in Cholecystokinin-Containing Interneurons.” <i>Cerebral Cortex</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/cercor/bhw090\">https://doi.org/10.1093/cercor/bhw090</a>.","mla":"Booker, Sam, et al. “KCTD12 Auxiliary Proteins Modulate Kinetics of GABAB Receptor-Mediated Inhibition in Cholecystokinin-Containing Interneurons.” <i>Cerebral Cortex</i>, vol. 27, no. 3, Oxford University Press, 2016, pp. 2318–34, doi:<a href=\"https://doi.org/10.1093/cercor/bhw090\">10.1093/cercor/bhw090</a>.","ista":"Booker S, Althof D, Gross A, Loreth D, Müller J, Unger A, Fakler B, Varro A, Watanabe M, Gassmann M, Bettler B, Shigemoto R, Vida I, Kulik Á. 2016. KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons. Cerebral Cortex. 27(3), 2318–2334.","apa":"Booker, S., Althof, D., Gross, A., Loreth, D., Müller, J., Unger, A., … Kulik, Á. (2016). KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons. <i>Cerebral Cortex</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/cercor/bhw090\">https://doi.org/10.1093/cercor/bhw090</a>","short":"S. Booker, D. Althof, A. Gross, D. Loreth, J. Müller, A. Unger, B. Fakler, A. Varro, M. Watanabe, M. Gassmann, B. Bettler, R. Shigemoto, I. Vida, Á. Kulik, Cerebral Cortex 27 (2016) 2318–2334.","ama":"Booker S, Althof D, Gross A, et al. KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons. <i>Cerebral Cortex</i>. 2016;27(3):2318-2334. doi:<a href=\"https://doi.org/10.1093/cercor/bhw090\">10.1093/cercor/bhw090</a>"},"quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:50:03Z","publication":"Cerebral Cortex","status":"public","oa_version":"None","type":"journal_article","day":"12","intvolume":"        27","publication_status":"published","_id":"1083","scopus_import":"1","acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft (DFG SFB 780 A2, A.K.; SFB TR3 I.V. and EXC 257, I.V.; FOR 2143, A.K. and I.V.), Spemann Graduate School (D.A.), BIOSS-2 (A6, A.K.), the Swiss National Science Foundation (3100A0-117816, B.B.), The McNaught Bequest (S.A.B. and I.V.), and Tenovus Scotland (I.V.).\r\n\r\n\r\nWe thank Cheryl Hutton and Chinmaya Sadangi for their contributions to neuronal reconstruction as well as Natalie Wernet, Sigrun Nestel, Anikó Schneider, Ina Wolter, and Ulrich Noeller for their excellent technical support. VGAT-Venus transgenic rats were generated by Drs Y. Yanagawa, M. Hirabayashi, and Y. Kawaguchi in National Institute for Physiological Sciences, Okazaki, Japan, using pCS2-Venus provided by Dr A. Miyawaki. The monoclonal mouse CCK antibody was generously provided by Dr G.V. Ohning, CURE Center, UCLA, CA. ","abstract":[{"text":" Cholecystokinin-expressing interneurons (CCK-INs) mediate behavior state-dependent inhibition in cortical circuits and themselves receive strong GABAergic input. However, it remains unclear to what extent GABABreceptors (GABABRs) contribute to their inhibitory control. Using immunoelectron microscopy, we found that CCK-INs in the rat hippocampus possessed high levels of dendritic GABABRs and KCTD12 auxiliary proteins, whereas postsynaptic effector Kir3 channels were present at lower levels. Consistently, whole-cell recordings revealed slow GABABR-mediated inhibitory postsynaptic currents (IPSCs) in most CCK-INs. In spite of the higher surface density of GABABRs in CCK-INs than in CA1 principal cells, the amplitudes of IPSCs were comparable, suggesting that the expression of Kir3 channels is the limiting factor for the GABABR currents in these INs. Morphological analysis showed that CCK-INs were diverse, comprising perisomatic-targeting basket cells (BCs), as well as dendrite-targeting (DT) interneurons, including a previously undescribed DT type. GABABR-mediated IPSCs in CCK-INs were large in BCs, but small in DT subtypes. In response to prolonged activation, GABABR-mediated currents displayed strong desensitization, which was absent in KCTD12-deficient mice. This study highlights that GABABRs differentially control CCK-IN subtypes, and the kinetics and desensitization of GABABR-mediated currents are modulated by KCTD12 proteins. ","lang":"eng"}],"publisher":"Oxford University Press","year":"2016","page":"2318 - 2334","month":"04","language":[{"iso":"eng"}],"isi":1,"department":[{"_id":"RySh"}],"external_id":{"isi":["000397636600048"]},"article_processing_charge":"No","issue":"3","date_updated":"2025-09-22T14:19:11Z","title":"KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons","author":[{"first_name":"Sam","last_name":"Booker","full_name":"Booker, Sam"},{"full_name":"Althof, Daniel","last_name":"Althof","first_name":"Daniel"},{"first_name":"Anna","last_name":"Gross","full_name":"Gross, Anna"},{"full_name":"Loreth, Desiree","last_name":"Loreth","first_name":"Desiree"},{"first_name":"Johanna","last_name":"Müller","full_name":"Müller, Johanna"},{"last_name":"Unger","first_name":"Andreas","full_name":"Unger, Andreas"},{"last_name":"Fakler","first_name":"Bernd","full_name":"Fakler, Bernd"},{"last_name":"Varro","first_name":"Andrea","full_name":"Varro, Andrea"},{"full_name":"Watanabe, Masahiko","last_name":"Watanabe","first_name":"Masahiko"},{"full_name":"Gassmann, Martin","last_name":"Gassmann","first_name":"Martin"},{"last_name":"Bettler","first_name":"Bernhard","full_name":"Bettler, Bernhard"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto"},{"full_name":"Vida, Imre","first_name":"Imre","last_name":"Vida"},{"full_name":"Kulik, Ákos","first_name":"Ákos","last_name":"Kulik"}],"publist_id":"6297","date_published":"2016-04-12T00:00:00Z"}]