[{"department":[{"_id":"MaSe"}],"article_processing_charge":"No","doi":"10.1103/PhysRevB.96.104201","citation":{"mla":"Serbyn, Maksym, et al. “Thouless Energy and Multifractality across the Many-Body Localization Transition.” <i>Physical Review B</i>, vol. 96, no. 10, 104201, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">10.1103/PhysRevB.96.104201</a>.","apa":"Serbyn, M., Zlatko, P., &#38; Abanin, D. (2017). Thouless energy and multifractality across the many-body localization transition. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">https://doi.org/10.1103/PhysRevB.96.104201</a>","short":"M. Serbyn, P. Zlatko, D. Abanin, Physical Review B 96 (2017).","chicago":"Serbyn, Maksym, Papic Zlatko, and Dmitry Abanin. “Thouless Energy and Multifractality across the Many-Body Localization Transition.” <i>Physical Review B</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">https://doi.org/10.1103/PhysRevB.96.104201</a>.","ama":"Serbyn M, Zlatko P, Abanin D. Thouless energy and multifractality across the many-body localization transition. <i>Physical Review B</i>. 2017;96(10). doi:<a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">10.1103/PhysRevB.96.104201</a>","ieee":"M. Serbyn, P. Zlatko, and D. Abanin, “Thouless energy and multifractality across the many-body localization transition,” <i>Physical Review B</i>, vol. 96, no. 10. American Physical Society, 2017.","ista":"Serbyn M, Zlatko P, Abanin D. 2017. Thouless energy and multifractality across the many-body localization transition. Physical Review B. 96(10), 104201."},"abstract":[{"lang":"eng","text":"Thermal and many-body localized phases are separated by a dynamical phase transition of a new kind. We analyze the distribution of off-diagonal matrix elements of local operators across this transition in two different models of disordered spin chains. We show that the behavior of matrix elements can be used to characterize the breakdown of thermalization and to extract the many-body Thouless energy. We find that upon increasing the disorder strength the system enters a critical region around the many-body localization transition. The properties of the system in this region are: (i) the Thouless energy becomes smaller than the level spacing, (ii) the matrix elements show critical dependence on the energy difference, and (iii) the matrix elements, viewed as amplitudes of a fictitious wave function, exhibit strong multifractality. This critical region decreases with the system size, which we interpret as evidence for a diverging correlation length at the many-body localization transition. Our findings show that the correlation length becomes larger than the accessible system sizes in a broad range of disorder strength values and shed light on the critical behavior near the many-body localization transition."}],"publication_identifier":{"issn":["2469-9950"]},"title":"Thouless energy and multifractality across the many-body localization transition","_id":"834","publisher":"American Physical Society","date_updated":"2026-08-12T14:24:27Z","acknowledgement":"We   acknowledge   useful   discussions with V. Kravtsov, T. Grover, and R. Vasseur.  M.S. was supported by Gordon and Betty Moore Foundation’s EPiQS Initiative through Grant GBMF4307.  M.S. and D.A.  acknowledge  hospitality  of  KITP,  where  parts  of this work were completed (supported in part by the National Science Foundation under Grant No. NSF PHY11-25915)","external_id":{"isi":["000409429300004"],"arxiv":["1610.02389"]},"month":"09","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1610.02389","open_access":"1"}],"oa_version":"Submitted Version","article_number":"104201","publist_id":"6814","arxiv":1,"publication_status":"published","fulldoi":"https://doi.org/10.1103/PhysRevB.96.104201","publication":"Physical Review B","date_created":"2018-12-11T11:48:45Z","oa":1,"date_published":"2017-09-06T00:00:00Z","intvolume":"        96","year":"2017","status":"public","issue":"10","type":"journal_article","author":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","last_name":"Serbyn","full_name":"Serbyn, Maksym","first_name":"Maksym"},{"last_name":"Zlatko","full_name":"Zlatko, Papic","first_name":"Papic"},{"full_name":"Abanin, Dmitry","first_name":"Dmitry","last_name":"Abanin"}],"isi":1,"day":"06","volume":96,"quality_controlled":"1"},{"volume":96,"quality_controlled":"1","day":"10","author":[{"first_name":"Daniele","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","last_name":"De Martino"},{"last_name":"Capuani","first_name":"Fabrizio","full_name":"Capuani, Fabrizio"},{"full_name":"De Martino, Andrea","first_name":"Andrea","last_name":"De Martino"}],"isi":1,"das_tickbox":"1","ec_funded":1,"oa":1,"date_published":"2017-07-10T00:00:00Z","date_created":"2018-12-11T11:49:21Z","issue":"1","type":"journal_article","intvolume":"        96","status":"public","year":"2017","publist_id":"6470","publication":"Physical Review E","arxiv":1,"publication_status":"published","fulldoi":"https://doi.org/10.1103/PhysRevE.96.010401","article_number":"010401","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"scopus_import":"1","month":"07","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","main_file_link":[{"url":"https://arxiv.org/abs/1703.00219","open_access":"1"}],"title":"Quantifying the entropic cost of cellular growth control","external_id":{"isi":["000405194200002"],"arxiv":["1703.00219"]},"_id":"947","publisher":"American Physical Society","date_updated":"2026-08-12T14:29:46Z","department":[{"_id":"GaTk"}],"doi":"10.1103/PhysRevE.96.010401","citation":{"apa":"De Martino, D., Capuani, F., &#38; De Martino, A. (2017). Quantifying the entropic cost of cellular growth control. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.96.010401\">https://doi.org/10.1103/PhysRevE.96.010401</a>","mla":"De Martino, Daniele, et al. “Quantifying the Entropic Cost of Cellular Growth Control.” <i>Physical Review E</i>, vol. 96, no. 1, 010401, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.010401\">10.1103/PhysRevE.96.010401</a>.","ista":"De Martino D, Capuani F, De Martino A. 2017. Quantifying the entropic cost of cellular growth control. Physical Review E. 96(1), 010401.","ieee":"D. De Martino, F. Capuani, and A. De Martino, “Quantifying the entropic cost of cellular growth control,” <i>Physical Review E</i>, vol. 96, no. 1. American Physical Society, 2017.","ama":"De Martino D, Capuani F, De Martino A. Quantifying the entropic cost of cellular growth control. <i>Physical Review E</i>. 2017;96(1). doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.010401\">10.1103/PhysRevE.96.010401</a>","chicago":"De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Quantifying the Entropic Cost of Cellular Growth Control.” <i>Physical Review E</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevE.96.010401\">https://doi.org/10.1103/PhysRevE.96.010401</a>.","short":"D. De Martino, F. Capuani, A. De Martino, Physical Review E 96 (2017)."},"abstract":[{"lang":"eng","text":"Viewing the ways a living cell can organize its metabolism as the phase space of a physical system, regulation can be seen as the ability to reduce the entropy of that space by selecting specific cellular configurations that are, in some sense, optimal. Here we quantify the amount of regulation required to control a cell's growth rate by a maximum-entropy approach to the space of underlying metabolic phenotypes, where a configuration corresponds to a metabolic flux pattern as described by genome-scale models. We link the mean growth rate achieved by a population of cells to the minimal amount of metabolic regulation needed to achieve it through a phase diagram that highlights how growth suppression can be as costly (in regulatory terms) as growth enhancement. Moreover, we provide an interpretation of the inverse temperature β controlling maximum-entropy distributions based on the underlying growth dynamics. Specifically, we show that the asymptotic value of β for a cell population can be expected to depend on (i) the carrying capacity of the environment, (ii) the initial size of the colony, and (iii) the probability distribution from which the inoculum was sampled. Results obtained for E. coli and human cells are found to be remarkably consistent with empirical evidence."}],"publication_identifier":{"issn":["2470-0045"]},"article_processing_charge":"No"},{"external_id":{"arxiv":["1612.07061"],"isi":["000405367200012"]},"publisher":"American Physical Society","_id":"700","date_updated":"2026-08-12T14:29:59Z","title":"Optomechanical proposal for monitoring microtubule mechanical vibrations","citation":{"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 Physical Society, 2017.","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 Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">https://doi.org/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>","mla":"Barzanjeh, Shabir, et al. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” <i>Physical Review E</i>, vol. 96, no. 1, 012404, American Physical Society, 2017, 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 Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">https://doi.org/10.1103/PhysRevE.96.012404</a>"},"doi":"10.1103/PhysRevE.96.012404","publication_identifier":{"issn":["2470-0045"]},"abstract":[{"lang":"eng","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."}],"article_processing_charge":"No","department":[{"_id":"JoFi"}],"project":[{"grant_number":"707438","call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics"}],"article_number":"012404","oa_version":"Submitted Version","main_file_link":[{"url":"https://arxiv.org/abs/1612.07061","open_access":"1"}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","language":[{"iso":"eng"}],"issue":"1","type":"journal_article","intvolume":"        96","status":"public","year":"2017","oa":1,"date_published":"2017-07-12T00:00:00Z","date_created":"2018-12-11T11:48:00Z","publication":"Physical Review E","arxiv":1,"publication_status":"published","fulldoi":"https://doi.org/10.1103/PhysRevE.96.012404","publist_id":"6997","quality_controlled":"1","volume":96,"das_tickbox":"1","ec_funded":1,"day":"12","author":[{"full_name":"Barzanjeh, Shabir","first_name":"Shabir","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423"},{"full_name":"Salari, Vahid","first_name":"Vahid","last_name":"Salari"},{"first_name":"Jack","full_name":"Tuszynski, Jack","last_name":"Tuszynski"},{"full_name":"Cifra, Michal","first_name":"Michal","last_name":"Cifra"},{"full_name":"Simon, Christoph","first_name":"Christoph","last_name":"Simon"}],"isi":1},{"department":[{"_id":"GaTk"}],"article_processing_charge":"No","publication_identifier":{"issn":["2470-0045"]},"abstract":[{"text":"In this work it is shown that scale-free tails in metabolic flux distributions inferred in stationary models are an artifact due to reactions involved in thermodynamically unfeasible cycles, unbounded by physical constraints and in principle able to perform work without expenditure of free energy. After implementing thermodynamic constraints by removing such loops, metabolic flux distributions scale meaningfully with the physical limiting factors, acquiring in turn a richer multimodal structure potentially leading to symmetry breaking while optimizing for objective functions.","lang":"eng"}],"doi":"10.1103/PhysRevE.95.062419","citation":{"ista":"De Martino D. 2017. Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. Physical Review E. 95(6), 062419.","ieee":"D. De Martino, “Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics,” <i>Physical Review E</i>, vol. 95, no. 6. American Physical Society, p. 062419, 2017.","ama":"De Martino D. Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. <i>Physical Review E</i>. 2017;95(6):062419. doi:<a href=\"https://doi.org/10.1103/PhysRevE.95.062419\">10.1103/PhysRevE.95.062419</a>","chicago":"De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary Metabolic Network Models via Thermodynamics.” <i>Physical Review E</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevE.95.062419\">https://doi.org/10.1103/PhysRevE.95.062419</a>.","short":"D. De Martino, Physical Review E 95 (2017) 062419.","apa":"De Martino, D. (2017). Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.95.062419\">https://doi.org/10.1103/PhysRevE.95.062419</a>","mla":"De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary Metabolic Network Models via Thermodynamics.” <i>Physical Review E</i>, vol. 95, no. 6, American Physical Society, 2017, p. 062419, doi:<a href=\"https://doi.org/10.1103/PhysRevE.95.062419\">10.1103/PhysRevE.95.062419</a>."},"title":"Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics","date_updated":"2026-08-12T14:29:35Z","publisher":"American Physical Society","_id":"959","external_id":{"arxiv":["1703.00853"],"isi":["000404546400004"]},"language":[{"iso":"eng"}],"month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.00853"}],"oa_version":"Submitted Version","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"publist_id":"6446","fulldoi":"https://doi.org/10.1103/PhysRevE.95.062419","publication_status":"published","arxiv":1,"publication":"Physical Review E","date_created":"2018-12-11T11:49:25Z","date_published":"2017-06-28T00:00:00Z","oa":1,"year":"2017","status":"public","intvolume":"        95","type":"journal_article","issue":"6","isi":1,"author":[{"last_name":"De Martino","orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","full_name":"De Martino, Daniele"}],"day":"28","ec_funded":1,"page":"062419","das_tickbox":"1","volume":95,"quality_controlled":"1"},{"volume":14,"file":[{"file_id":"5843","content_type":"application/pdf","success":1,"file_size":1092015,"creator":"dernst","date_created":"2019-01-18T09:14:02Z","access_level":"open_access","file_name":"2017_JRSI_Redondo.pdf","date_updated":"2019-01-18T09:14:02Z","relation":"main_file"}],"quality_controlled":"1","isi":1,"author":[{"id":"409D5C96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5837-2793","last_name":"Fernandes Redondo","full_name":"Fernandes Redondo, Rodrigo A","first_name":"Rodrigo A"},{"orcid":"0000-0002-5985-7653","last_name":"Vladar","id":"2A181218-F248-11E8-B48F-1D18A9856A87","full_name":"Vladar, Harold","first_name":"Harold"},{"last_name":"Włodarski","first_name":"Tomasz","full_name":"Włodarski, Tomasz"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","first_name":"Jonathan P"}],"day":"04","ec_funded":1,"license":"https://creativecommons.org/licenses/by/4.0/","date_created":"2018-12-11T11:50:01Z","date_published":"2017-01-04T00:00:00Z","oa":1,"status":"public","year":"2017","intvolume":"        14","related_material":{"record":[{"relation":"research_data","status":"public","id":"9864"}]},"type":"journal_article","issue":"126","publist_id":"6303","fulldoi":"https://doi.org/10.1098/rsif.2016.0139","publication_status":"published","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"Journal of the Royal Society Interface","article_number":"20160139","project":[{"name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152"},{"grant_number":"648440","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"scopus_import":"1","oa_version":"Published Version","title":"Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","ddc":["570"],"date_updated":"2026-08-27T12:09:33Z","_id":"1077","publisher":"Royal Society","external_id":{"isi":["000393380400001"]},"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"issn":["1742-5689"]},"abstract":[{"text":"Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the fX174 phage family by first reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.","lang":"eng"}],"doi":"10.1098/rsif.2016.0139","file_date_updated":"2019-01-18T09:14:02Z","citation":{"mla":"Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” <i>Journal of the Royal Society Interface</i>, vol. 14, no. 126, 20160139, Royal Society, 2017, doi:<a href=\"https://doi.org/10.1098/rsif.2016.0139\">10.1098/rsif.2016.0139</a>.","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., &#38; Bollback, J. P. (2017). Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. <i>Journal of the Royal Society Interface</i>. Royal Society. <a href=\"https://doi.org/10.1098/rsif.2016.0139\">https://doi.org/10.1098/rsif.2016.0139</a>","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family,” <i>Journal of the Royal Society Interface</i>, vol. 14, no. 126. Royal Society, 2017.","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2017. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 14(126), 20160139.","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal of the Royal Society Interface 14 (2017).","chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” <i>Journal of the Royal Society Interface</i>. Royal Society, 2017. <a href=\"https://doi.org/10.1098/rsif.2016.0139\">https://doi.org/10.1098/rsif.2016.0139</a>.","ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. <i>Journal of the Royal Society Interface</i>. 2017;14(126). doi:<a href=\"https://doi.org/10.1098/rsif.2016.0139\">10.1098/rsif.2016.0139</a>"}},{"department":[{"_id":"ScienComp"}],"has_accepted_license":"1","conference":{"location":"Grundlsee, Austria","end_date":"2017-03-03","name":"AHPC: Austrian HPC Meeting","start_date":"2017-03-01"},"corr_author":"1","publication":"AHPC17 – Austrian HPC Meeting 2017","citation":{"apa":"Schlögl, A., &#38; Kiss, J. (2017). Scientific Computing at IST Austria. In <i>AHPC17 – Austrian HPC Meeting 2017</i> (p. 28). Grundlsee, Austria: FSP Scientific Computing.","mla":"Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.” <i>AHPC17 – Austrian HPC Meeting 2017</i>, FSP Scientific Computing, 2017, p. 28.","ista":"Schlögl A, Kiss J. 2017. Scientific Computing at IST Austria. AHPC17 – Austrian HPC Meeting 2017. AHPC: Austrian HPC Meeting, 28.","ieee":"A. Schlögl and J. Kiss, “Scientific Computing at IST Austria,” in <i>AHPC17 – Austrian HPC Meeting 2017</i>, Grundlsee, Austria, 2017, p. 28.","ama":"Schlögl A, Kiss J. Scientific Computing at IST Austria. In: <i>AHPC17 – Austrian HPC Meeting 2017</i>. FSP Scientific Computing; 2017:28.","chicago":"Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.” In <i>AHPC17 – Austrian HPC Meeting 2017</i>, 28. FSP Scientific Computing, 2017.","short":"A. Schlögl, J. Kiss, in:, AHPC17 – Austrian HPC Meeting 2017, FSP Scientific Computing, 2017, p. 28."},"file_date_updated":"2023-05-16T07:20:50Z","article_processing_charge":"No","publication_status":"published","date_published":"2017-03-03T00:00:00Z","title":"Scientific Computing at IST Austria","oa":1,"date_created":"2023-05-05T12:58:53Z","type":"conference_abstract","year":"2017","date_updated":"2026-10-14T09:39:37Z","status":"public","ddc":["000"],"_id":"12905","publisher":"FSP Scientific Computing","day":"03","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","author":[{"full_name":"Schlögl, Alois","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","last_name":"Schlögl"},{"first_name":"Janos","full_name":"Kiss, Janos","last_name":"Kiss","id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87"}],"page":"28","oa_version":"Published Version","main_file_link":[{"url":"https://asc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc17/BOOKLET_AHPC17.pdf","open_access":"1"}],"file":[{"file_id":"12969","content_type":"application/pdf","success":1,"file_size":1005486,"creator":"dernst","date_created":"2023-05-16T07:20:50Z","access_level":"open_access","file_name":"2017_AHPC_Schloegl.pdf","date_updated":"2023-05-16T07:20:50Z","relation":"main_file","checksum":"7bcc499479d4f4c5ce6c0071c24ca6c6"}]},{"project":[{"_id":"25985A36-B435-11E9-9278-68D0E5697425","name":"The biochemical basis of PAR polarization","call_identifier":"FWF","grant_number":"T00817-B21"},{"call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22"}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451238/","open_access":"1"}],"scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"month":"06","external_id":{"isi":["000402620800008"],"pmid":["28504646"]},"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.","date_updated":"2026-10-23T22:30:15Z","publisher":"American Society for Clinical Investigation","_id":"679","title":"The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection","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."}],"publication_identifier":{"issn":["0021-9738"]},"doi":"10.1172/JCI80631","citation":{"apa":"Ebner, F., Sedlyarov, V., Tasciyan, S., Ivin, M., Kratochvill, F., Gratz, N., … Kovarik, P. (2017). The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. <i>The Journal of Clinical Investigation</i>. American Society for Clinical Investigation. <a href=\"https://doi.org/10.1172/JCI80631\">https://doi.org/10.1172/JCI80631</a>","mla":"Ebner, Florian, et al. “The RNA-Binding Protein Tristetraprolin Schedules Apoptosis of Pathogen-Engaged Neutrophils during Bacterial Infection.” <i>The Journal of Clinical Investigation</i>, vol. 127, no. 6, American Society for Clinical Investigation, 2017, pp. 2051–65, doi:<a href=\"https://doi.org/10.1172/JCI80631\">10.1172/JCI80631</a>.","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.","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.","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>","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>.","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."},"article_processing_charge":"No","department":[{"_id":"MiSi"}],"quality_controlled":"1","pmid":1,"volume":127,"page":"2051 - 2065","day":"01","isi":1,"author":[{"first_name":"Florian","full_name":"Ebner, Florian","last_name":"Ebner"},{"full_name":"Sedlyarov, Vitaly","first_name":"Vitaly","last_name":"Sedlyarov"},{"orcid":"0000-0003-1671-393X","last_name":"Tasciyan","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","full_name":"Tasciyan, Saren","first_name":"Saren"},{"first_name":"Masa","full_name":"Ivin, Masa","last_name":"Ivin"},{"first_name":"Franz","full_name":"Kratochvill, Franz","last_name":"Kratochvill"},{"full_name":"Gratz, Nina","first_name":"Nina","last_name":"Gratz"},{"last_name":"Kenner","full_name":"Kenner, Lukas","first_name":"Lukas"},{"last_name":"Villunger","first_name":"Andreas","full_name":"Villunger, Andreas"},{"orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","first_name":"Michael K"},{"last_name":"Kovarik","first_name":"Pavel","full_name":"Kovarik, Pavel"}],"type":"journal_article","issue":"6","status":"public","year":"2017","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12401"}]},"intvolume":"       127","date_published":"2017-06-01T00:00:00Z","oa":1,"date_created":"2018-12-11T11:47:53Z","publication":"The Journal of Clinical Investigation","fulldoi":"https://doi.org/10.1172/JCI80631","publication_status":"published","publist_id":"7038"},{"date_created":"2018-12-11T11:48:01Z","date_published":"2017-07-25T00:00:00Z","oa":1,"status":"public","year":"2017","intvolume":"         6","related_material":{"record":[{"id":"5564","relation":"popular_science","status":"public"},{"id":"26","status":"public","relation":"dissertation_contains"}]},"type":"journal_article","publist_id":"6990","fulldoi":"https://doi.org/10.7554/eLife.25100","publication_status":"published","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"eLife","volume":6,"file":[{"file_name":"IST-2017-890-v1+1_elife-25100-v1.pdf","date_created":"2018-12-12T10:12:54Z","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:47:48Z","checksum":"6b908b5db9f61f6820ebd7f8fa815571","file_id":"4975","content_type":"application/pdf","creator":"system","file_size":2092088},{"file_id":"4976","content_type":"application/pdf","creator":"system","file_size":3428681,"file_name":"IST-2017-890-v1+2_elife-25100-figures-v1.pdf","access_level":"open_access","date_created":"2018-12-12T10:12:55Z","checksum":"ca21530389b720243552678125fdba35","date_updated":"2020-07-14T12:47:48Z","relation":"main_file"}],"quality_controlled":"1","isi":1,"author":[{"orcid":"0000-0003-1229-9719","last_name":"Steinrück","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","first_name":"Magdalena","full_name":"Steinrück, Magdalena"},{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C","first_name":"Calin C"}],"day":"25","pubrep_id":"890","title":"Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection","date_updated":"2026-10-23T22:30:19Z","ddc":["576"],"_id":"704","publisher":"eLife Sciences Publications","external_id":{"isi":["000406183700001"]},"corr_author":"1","department":[{"_id":"CaGu"}],"has_accepted_license":"1","article_processing_charge":"No","abstract":[{"lang":"eng","text":"How the organization of genes on a chromosome shapes adaptation is essential for understanding evolutionary paths. Here, we investigate how adaptation to rapidly increasing levels of antibiotic depends on the chromosomal neighborhood of a drug-resistance gene inserted at different positions of the Escherichia coli chromosome. Using a dual-fluorescence reporter that allows us to distinguish gene amplifications from other up-mutations, we track in real-time adaptive changes in expression of the drug-resistance gene. We find that the relative contribution of several mutation types differs systematically between loci due to properties of neighboring genes: essentiality, expression, orientation, termination, and presence of duplicates. These properties determine rate and fitness effects of gene amplification, deletions, and mutations compromising transcriptional termination. Thus, the adaptive potential of a gene under selection is a system-property with a complex genetic basis that is specific for each chromosomal locus, and it can be inferred from detailed functional and genomic data."}],"publication_identifier":{"issn":["2050-084X"]},"file_date_updated":"2020-07-14T12:47:48Z","doi":"10.7554/eLife.25100","citation":{"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.","ista":"Steinrück M, Guet CC. 2017. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife. 6, e25100.","chicago":"Steinrück, Magdalena, and Calin C Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/eLife.25100\">https://doi.org/10.7554/eLife.25100</a>.","short":"M. Steinrück, C.C. Guet, ELife 6 (2017).","ama":"Steinrück M, Guet CC. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/eLife.25100\">10.7554/eLife.25100</a>","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>.","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>"},"article_number":"e25100","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"07","scopus_import":"1","oa_version":"Published Version"},{"_id":"735","publisher":"Cell Press","date_updated":"2026-10-23T22:30:23Z","external_id":{"isi":["000413443700011"]},"title":"An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate","article_processing_charge":"No","doi":"10.1016/j.devcel.2017.09.014","citation":{"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>","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>","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>.","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.","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."},"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"}],"publication_identifier":{"issn":["1534-5807"]},"corr_author":"1","department":[{"_id":"CaHe"},{"_id":"CaGu"},{"_id":"GaTk"}],"project":[{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"I2058","_id":"252DD2A6-B435-11E9-9278-68D0E5697425","name":"Cell segregation in gastrulation: the role of cell fate specification","call_identifier":"FWF"}],"oa_version":"None","language":[{"iso":"eng"}],"month":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"961"},{"status":"public","relation":"dissertation_contains","id":"8350"}]},"intvolume":"        43","year":"2017","status":"public","issue":"2","type":"journal_article","date_created":"2018-12-11T11:48:13Z","date_published":"2017-10-23T00:00:00Z","publication_status":"published","fulldoi":"https://doi.org/10.1016/j.devcel.2017.09.014","publication":"Developmental Cell","publist_id":"6934","quality_controlled":"1","volume":43,"ec_funded":1,"page":"198 - 211","author":[{"orcid":"0000-0003-2676-3367","last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","full_name":"Barone, Vanessa"},{"last_name":"Lang","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","full_name":"Lang, Moritz","first_name":"Moritz"},{"orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens","full_name":"Krens, Gabriel","first_name":"Gabriel"},{"last_name":"Pradhan","first_name":"Saurabh","full_name":"Pradhan, Saurabh"},{"id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour","first_name":"Shayan","full_name":"Shamipour, Shayan"},{"last_name":"Sako","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6453-8075","first_name":"Keisuke","full_name":"Sako, Keisuke"},{"id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","last_name":"Sikora","full_name":"Sikora, Mateusz K","first_name":"Mateusz K"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","full_name":"Guet, Calin C"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J"}],"isi":1,"day":"23"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","language":[{"iso":"eng"}],"scopus_import":"1","oa_version":"Published Version","article_number":"e0174066","has_accepted_license":"1","department":[{"_id":"ToBo"}],"article_processing_charge":"Yes","file_date_updated":"2018-12-12T10:09:47Z","doi":"10.1371/journal.pone.0174066","citation":{"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.","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.","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>.","short":"M. Lukacisin, M. Landon, R. Jajoo, PLoS One 12 (2017).","ama":"Lukacisin M, Landon M, Jajoo R. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. <i>PLoS One</i>. 2017;12(3). doi:<a href=\"https://doi.org/10.1371/journal.pone.0174066\">10.1371/journal.pone.0174066</a>","mla":"Lukacisin, Martin, et al. “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” <i>PLoS One</i>, vol. 12, no. 3, e0174066, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pone.0174066\">10.1371/journal.pone.0174066</a>.","apa":"Lukacisin, M., Landon, M., &#38; Jajoo, R. (2017). Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0174066\">https://doi.org/10.1371/journal.pone.0174066</a>"},"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"}],"publication_identifier":{"issn":["1932-6203"]},"title":"Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast","publisher":"Public Library of Science","_id":"1029","date_updated":"2026-10-23T22:30:35Z","ddc":["570"],"external_id":{"isi":["000396318300121"]},"author":[{"full_name":"Lukacisin, Martin","first_name":"Martin","orcid":"0000-0001-6549-4177","last_name":"Lukacisin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Landon, Matthieu","first_name":"Matthieu","last_name":"Landon"},{"first_name":"Rishi","full_name":"Jajoo, Rishi","last_name":"Jajoo"}],"isi":1,"pubrep_id":"800","day":"16","volume":12,"quality_controlled":"1","file":[{"date_updated":"2018-12-12T10:09:47Z","relation":"main_file","access_level":"open_access","date_created":"2018-12-12T10:09:47Z","file_name":"IST-2017-800-v1+1_journal.pone.0174066.pdf","file_size":3429381,"creator":"system","content_type":"application/pdf","file_id":"4772"}],"publist_id":"6361","publication_status":"published","fulldoi":"https://doi.org/10.1371/journal.pone.0174066","publication":"PLoS One","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2018-12-11T11:49:46Z","oa":1,"date_published":"2017-03-16T00:00:00Z","intvolume":"        12","related_material":{"record":[{"status":"public","relation":"popular_science","id":"5556"},{"status":"public","id":"6392","relation":"dissertation_contains"}]},"status":"public","year":"2017","issue":"3","type":"journal_article"},{"page":"1798 - 1806","day":"15","isi":1,"author":[{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","last_name":"Krens","full_name":"Krens, Gabriel","first_name":"Gabriel"},{"last_name":"Veldhuis","full_name":"Veldhuis, Jim","first_name":"Jim"},{"first_name":"Vanessa","full_name":"Barone, Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","last_name":"Barone","orcid":"0000-0003-2676-3367"},{"last_name":"Capek","orcid":"0000-0001-5199-9940","id":"31C42484-F248-11E8-B48F-1D18A9856A87","full_name":"Capek, Daniel","first_name":"Daniel"},{"orcid":"0000-0002-3688-1474","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","last_name":"Maître","full_name":"Maître, Jean-Léon","first_name":"Jean-Léon"},{"last_name":"Brodland","full_name":"Brodland, Wayne","first_name":"Wayne"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J"}],"file":[{"relation":"main_file","date_updated":"2020-07-14T12:47:39Z","checksum":"bc25125fb664706cdf180e061429f91d","date_created":"2019-09-24T06:56:22Z","access_level":"open_access","file_name":"2017_Development_Krens.pdf","file_size":8194516,"creator":"dernst","file_id":"6905","content_type":"application/pdf"}],"quality_controlled":"1","pmid":1,"article_type":"original","volume":144,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"Development","fulldoi":"https://doi.org/10.1242/dev.144964","publication_status":"published","publist_id":"7047","type":"journal_article","issue":"10","year":"2017","status":"public","intvolume":"       144","related_material":{"record":[{"id":"961","relation":"dissertation_contains","status":"public"},{"relation":"dissertation_contains","id":"50","status":"public"}]},"date_published":"2017-05-15T00:00:00Z","oa":1,"date_created":"2018-12-11T11:47:52Z","oa_version":"Published Version","scopus_import":"1","month":"05","language":[{"iso":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["0950-1991"]},"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"}],"doi":"10.1242/dev.144964","citation":{"apa":"Krens, G., Veldhuis, J., Barone, V., Capek, D., Maître, J.-L., Brodland, W., &#38; Heisenberg, C.-P. J. (2017). Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.144964\">https://doi.org/10.1242/dev.144964</a>","mla":"Krens, Gabriel, et al. “Interstitial Fluid Osmolarity Modulates the Action of Differential Tissue Surface Tension in Progenitor Cell Segregation during Gastrulation.” <i>Development</i>, vol. 144, no. 10, Company of Biologists, 2017, pp. 1798–806, doi:<a href=\"https://doi.org/10.1242/dev.144964\">10.1242/dev.144964</a>.","ista":"Krens G, Veldhuis J, Barone V, Capek D, Maître J-L, Brodland W, Heisenberg C-PJ. 2017. Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. Development. 144(10), 1798–1806.","ieee":"G. Krens <i>et al.</i>, “Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation,” <i>Development</i>, vol. 144, no. 10. Company of Biologists, pp. 1798–1806, 2017.","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>","chicago":"Krens, Gabriel, Jim Veldhuis, Vanessa Barone, Daniel Capek, Jean-Léon Maître, Wayne Brodland, and Carl-Philipp J Heisenberg. “Interstitial Fluid Osmolarity Modulates the Action of Differential Tissue Surface Tension in Progenitor Cell Segregation during Gastrulation.” <i>Development</i>. Company of Biologists, 2017. <a href=\"https://doi.org/10.1242/dev.144964\">https://doi.org/10.1242/dev.144964</a>.","short":"G. Krens, J. Veldhuis, V. Barone, D. Capek, J.-L. Maître, W. Brodland, C.-P.J. Heisenberg, Development 144 (2017) 1798–1806."},"file_date_updated":"2020-07-14T12:47:39Z","article_processing_charge":"No","department":[{"_id":"Bio"},{"_id":"CaHe"}],"has_accepted_license":"1","corr_author":"1","external_id":{"pmid":["28512197"],"isi":["000402275900007"]},"date_updated":"2026-10-23T22:30:40Z","ddc":["570"],"_id":"676","publisher":"Company of Biologists","title":"Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation"},{"department":[{"_id":"CaHe"},{"_id":"BjHo"},{"_id":"Bio"}],"corr_author":"1","abstract":[{"text":"During embryonic development, mechanical forces are essential for cellular rearrangements driving tissue morphogenesis. Here, we show that in the early zebrafish embryo, friction forces are generated at the interface between anterior axial mesoderm (prechordal plate, ppl) progenitors migrating towards the animal pole and neurectoderm progenitors moving in the opposite direction towards the vegetal pole of the embryo. These friction forces lead to global rearrangement of cells within the neurectoderm and determine the position of the neural anlage. Using a combination of experiments and simulations, we show that this process depends on hydrodynamic coupling between neurectoderm and ppl as a result of E-cadherin-mediated adhesion between those tissues. Our data thus establish the emergence of friction forces at the interface between moving tissues as a critical force-generating process shaping the embryo.","lang":"eng"}],"publication_identifier":{"issn":["1465-7392"]},"doi":"10.1038/ncb3492","citation":{"short":"M. Smutny, Z. Ákos, S. Grigolon, S. Shamipour, V. Ruprecht, D. Capek, M. Behrndt, E. Papusheva, M. Tada, B. Hof, T. Vicsek, G. Salbreux, C.-P.J. Heisenberg, Nature Cell Biology 19 (2017) 306–317.","chicago":"Smutny, Michael, Zsuzsa Ákos, Silvia Grigolon, Shayan Shamipour, Verena Ruprecht, Daniel Capek, Martin Behrndt, et al. “Friction Forces Position the Neural Anlage.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncb3492\">https://doi.org/10.1038/ncb3492</a>.","ama":"Smutny M, Ákos Z, Grigolon S, et al. Friction forces position the neural anlage. <i>Nature Cell Biology</i>. 2017;19:306-317. doi:<a href=\"https://doi.org/10.1038/ncb3492\">10.1038/ncb3492</a>","ieee":"M. Smutny <i>et al.</i>, “Friction forces position the neural anlage,” <i>Nature Cell Biology</i>, vol. 19. Nature Publishing Group, pp. 306–317, 2017.","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.","mla":"Smutny, Michael, et al. “Friction Forces Position the Neural Anlage.” <i>Nature Cell Biology</i>, vol. 19, Nature Publishing Group, 2017, pp. 306–17, doi:<a href=\"https://doi.org/10.1038/ncb3492\">10.1038/ncb3492</a>.","apa":"Smutny, M., Ákos, Z., Grigolon, S., Shamipour, S., Ruprecht, V., Capek, D., … Heisenberg, C.-P. J. (2017). Friction forces position the neural anlage. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb3492\">https://doi.org/10.1038/ncb3492</a>"},"article_processing_charge":"No","title":"Friction forces position the neural anlage","external_id":{"isi":["000397917000009"],"pmid":["28346437"]},"date_updated":"2026-10-23T22:30:40Z","_id":"661","publisher":"Nature Publishing Group","scopus_import":"1","month":"03","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Submitted Version","main_file_link":[{"url":"https://europepmc.org/articles/pmc5635970","open_access":"1"}],"project":[{"_id":"25152F3A-B435-11E9-9278-68D0E5697425","name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7","grant_number":"306589"},{"call_identifier":"FWF","_id":"252ABD0A-B435-11E9-9278-68D0E5697425","name":"Control of Epithelial Cell Layer Spreading in Zebrafish","grant_number":"I930-B20"}],"publist_id":"7074","publication":"Nature Cell Biology","fulldoi":"https://doi.org/10.1038/ncb3492","publication_status":"published","date_published":"2017-03-27T00:00:00Z","oa":1,"date_created":"2018-12-11T11:47:46Z","type":"journal_article","year":"2017","status":"public","intvolume":"        19","related_material":{"record":[{"id":"8350","status":"public","relation":"dissertation_contains"},{"id":"50","relation":"dissertation_contains","status":"public"}]},"day":"27","acknowledged_ssus":[{"_id":"SSU"}],"isi":1,"author":[{"full_name":"Smutny, Michael","first_name":"Michael","orcid":"0000-0002-5920-9090","last_name":"Smutny","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ákos, Zsuzsa","first_name":"Zsuzsa","last_name":"Ákos"},{"last_name":"Grigolon","first_name":"Silvia","full_name":"Grigolon, Silvia"},{"full_name":"Shamipour, Shayan","first_name":"Shayan","last_name":"Shamipour","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ruprecht","first_name":"Verena","full_name":"Ruprecht, Verena"},{"id":"31C42484-F248-11E8-B48F-1D18A9856A87","last_name":"Capek","orcid":"0000-0001-5199-9940","first_name":"Daniel","full_name":"Capek, Daniel"},{"id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","last_name":"Behrndt","full_name":"Behrndt, Martin","first_name":"Martin"},{"first_name":"Ekaterina","full_name":"Papusheva, Ekaterina","id":"41DB591E-F248-11E8-B48F-1D18A9856A87","last_name":"Papusheva"},{"last_name":"Tada","full_name":"Tada, Masazumi","first_name":"Masazumi"},{"full_name":"Hof, Björn","first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tamás","full_name":"Vicsek, Tamás","last_name":"Vicsek"},{"first_name":"Guillaume","full_name":"Salbreux, Guillaume","last_name":"Salbreux"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J"}],"page":"306 - 317","ec_funded":1,"volume":19,"quality_controlled":"1","pmid":1},{"publist_id":"7065","fulldoi":"https://doi.org/10.1016/j.immuni.2017.04.006","publication_status":"published","publication":"Immunity","date_created":"2018-12-11T11:47:47Z","date_published":"2017-04-18T00:00:00Z","year":"2017","status":"public","intvolume":"        46","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6947"}]},"type":"journal_article","issue":"4","isi":1,"author":[{"full_name":"Assen, Frank P","first_name":"Frank P","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3470-6119","last_name":"Assen"},{"first_name":"Michael K","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt"}],"day":"18","page":"519 - 520","volume":46,"quality_controlled":"1","corr_author":"1","department":[{"_id":"MiSi"}],"article_processing_charge":"No","publication_identifier":{"issn":["1074-7613"]},"abstract":[{"lang":"eng","text":"Immune cells communicate using cytokine signals, but the quantitative rules of this communication aren't clear. In this issue of Immunity, Oyler-Yaniv et al. (2017) suggest that the distribution of a cytokine within a lymphatic organ is primarily governed by the local density of cells consuming it."}],"doi":"10.1016/j.immuni.2017.04.006","citation":{"short":"F.P. Assen, M.K. Sixt, Immunity 46 (2017) 519–520.","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>.","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>","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.","ista":"Assen FP, Sixt MK. 2017. The dynamic cytokine niche. Immunity. 46(4), 519–520.","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>.","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>"},"title":"The dynamic cytokine niche","date_updated":"2026-10-23T22:30:54Z","publisher":"Cell Press","_id":"664","external_id":{"isi":["000399451100002"]},"month":"04","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"scopus_import":"1","oa_version":"None"},{"date_created":"2018-12-11T11:49:22Z","oa":1,"date_published":"2017-01-01T00:00:00Z","related_material":{"record":[{"status":"public","id":"8934","relation":"dissertation_contains"}]},"intvolume":"     10482","year":"2017","status":"public","type":"conference","conference":{"end_date":"2017-10-06","name":"ATVA: Automated Technology for Verification and Analysis","start_date":"2017-10-03","location":"Pune, India"},"publist_id":"6468","publication_status":"published","fulldoi":"https://doi.org/10.1007/978-3-319-68167-2_4","volume":10482,"editor":[{"first_name":"Deepak","full_name":"D'Souza, Deepak","last_name":"D'Souza"}],"quality_controlled":"1","file":[{"file_id":"4835","content_type":"application/pdf","creator":"system","file_size":948514,"file_name":"IST-2017-845-v1+1_2017_Chatterjee_JTDec.pdf","date_created":"2018-12-12T10:10:45Z","access_level":"open_access","date_updated":"2020-07-14T12:48:16Z","relation":"main_file","checksum":"a0d9f5f94dc594c4e71e78525c9942f1"}],"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Goharshady","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir","full_name":"Goharshady, Amir"},{"last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","first_name":"Andreas"}],"isi":1,"pubrep_id":"845","day":"01","ec_funded":1,"page":"59 - 66","title":"JTDec: A tool for tree decompositions in soot","publisher":"Springer","_id":"949","ddc":["005"],"date_updated":"2026-10-23T22:31:00Z","external_id":{"isi":["000723567800004"]},"alternative_title":["LNCS"],"corr_author":"1","has_accepted_license":"1","department":[{"_id":"KrCh"}],"article_processing_charge":"No","file_date_updated":"2020-07-14T12:48:16Z","doi":"10.1007/978-3-319-68167-2_4","citation":{"ista":"Chatterjee K, Goharshady AK, Pavlogiannis A. 2017. JTDec: A tool for tree decompositions in soot. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 10482, 59–66.","ieee":"K. Chatterjee, A. K. Goharshady, and A. Pavlogiannis, “JTDec: A tool for tree decompositions in soot,” presented at the ATVA: Automated Technology for Verification and Analysis, Pune, India, 2017, vol. 10482, pp. 59–66.","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>","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>.","short":"K. Chatterjee, A.K. Goharshady, A. Pavlogiannis, in:, D. D’Souza (Ed.), Springer, 2017, pp. 59–66.","apa":"Chatterjee, K., Goharshady, A. K., &#38; Pavlogiannis, A. (2017). JTDec: A tool for tree decompositions in soot. In D. D’Souza (Ed.) (Vol. 10482, pp. 59–66). Presented at the ATVA: Automated Technology for Verification and Analysis, Pune, India: Springer. <a href=\"https://doi.org/10.1007/978-3-319-68167-2_4\">https://doi.org/10.1007/978-3-319-68167-2_4</a>","mla":"Chatterjee, Krishnendu, et al. <i>JTDec: A Tool for Tree Decompositions in Soot</i>. Edited by Deepak D’Souza, vol. 10482, Springer, 2017, pp. 59–66, doi:<a href=\"https://doi.org/10.1007/978-3-319-68167-2_4\">10.1007/978-3-319-68167-2_4</a>."},"publication_identifier":{"issn":["0302-9743"]},"abstract":[{"lang":"eng","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."}],"project":[{"name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"language":[{"iso":"eng"}],"month":"01","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","scopus_import":"1","oa_version":"Submitted Version"},{"oa":1,"date_published":"2017-01-01T00:00:00Z","date_created":"2018-12-11T11:47:39Z","type":"conference","related_material":{"record":[{"status":"public","id":"7014","relation":"later_version"},{"status":"public","relation":"dissertation_contains","id":"8934"}]},"intvolume":"     10427","status":"public","year":"2017","conference":{"start_date":"2017-07-24","end_date":"2017-07-28","name":"CAV: Computer Aided Verification","location":"Heidelberg, Germany"},"publist_id":"7149","publication_status":"published","arxiv":1,"fulldoi":"https://doi.org/10.1007/978-3-319-63390-9_3","editor":[{"last_name":"Majumdar","first_name":"Rupak","full_name":"Majumdar, Rupak"},{"first_name":"Viktor","full_name":"Kunčak, Viktor","last_name":"Kunčak"}],"volume":10427,"quality_controlled":"1","day":"01","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"last_name":"Fu","first_name":"Hongfei","full_name":"Fu, Hongfei"},{"first_name":"Amir","full_name":"Goharshady, Amir","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","last_name":"Goharshady"}],"isi":1,"page":"41 - 63","ec_funded":1,"title":"Non-polynomial worst case analysis of recursive programs","external_id":{"isi":["000431900900003"],"arxiv":["1705.00317"]},"publisher":"Springer","_id":"639","date_updated":"2026-10-23T22:30:59Z","department":[{"_id":"KrCh"}],"alternative_title":["LNCS"],"citation":{"ista":"Chatterjee K, Fu H, Goharshady AK. 2017. Non-polynomial worst case analysis of recursive programs. CAV: Computer Aided Verification, LNCS, vol. 10427, 41–63.","ieee":"K. Chatterjee, H. Fu, and A. K. Goharshady, “Non-polynomial worst case analysis of recursive programs,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10427, pp. 41–63.","ama":"Chatterjee K, Fu H, Goharshady AK. Non-polynomial worst case analysis of recursive programs. In: Majumdar R, Kunčak V, eds. Vol 10427. Springer; 2017:41-63. doi:<a href=\"https://doi.org/10.1007/978-3-319-63390-9_3\">10.1007/978-3-319-63390-9_3</a>","short":"K. Chatterjee, H. Fu, A.K. Goharshady, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, 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>.","apa":"Chatterjee, K., Fu, H., &#38; Goharshady, A. K. (2017). Non-polynomial worst case analysis of recursive programs. In R. Majumdar &#38; V. Kunčak (Eds.) (Vol. 10427, pp. 41–63). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. <a href=\"https://doi.org/10.1007/978-3-319-63390-9_3\">https://doi.org/10.1007/978-3-319-63390-9_3</a>","mla":"Chatterjee, Krishnendu, et al. <i>Non-Polynomial Worst Case Analysis of Recursive Programs</i>. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10427, Springer, 2017, pp. 41–63, doi:<a href=\"https://doi.org/10.1007/978-3-319-63390-9_3\">10.1007/978-3-319-63390-9_3</a>."},"doi":"10.1007/978-3-319-63390-9_3","publication_identifier":{"isbn":["978-331963389-3"]},"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."}],"article_processing_charge":"No","project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF","grant_number":"S11407"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"scopus_import":"1","month":"01","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.00317"}]},{"article_number":"176","project":[{"grant_number":"618444","call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Cerebral Cortex Development"},{"grant_number":"RGP0053/2014","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","_id":"25D7962E-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"T00817-B21","call_identifier":"FWF","_id":"25985A36-B435-11E9-9278-68D0E5697425","name":"The biochemical basis of PAR polarization"}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"month":"06","oa_version":"Published Version","title":"Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks","external_id":{"isi":["000404486700001"]},"publisher":"Frontiers Research Foundation","_id":"960","date_updated":"2026-10-23T22:31:01Z","ddc":["570"],"has_accepted_license":"1","department":[{"_id":"SiHi"},{"_id":"MaLo"}],"doi":"10.3389/fncel.2017.00176","file_date_updated":"2020-07-14T12:48:16Z","citation":{"mla":"Hansen, Andi H., et al. “Cell Polarity in Cerebral Cortex Development - Cellular Architecture Shaped by Biochemical Networks.” <i>Frontiers in Cellular Neuroscience</i>, vol. 11, 176, Frontiers Research Foundation, 2017, doi:<a href=\"https://doi.org/10.3389/fncel.2017.00176\">10.3389/fncel.2017.00176</a>.","apa":"Hansen, A. H., Düllberg, C. F., Mieck, C., Loose, M., &#38; Hippenmeyer, S. (2017). Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. <i>Frontiers in Cellular Neuroscience</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fncel.2017.00176\">https://doi.org/10.3389/fncel.2017.00176</a>","short":"A.H. Hansen, C.F. Düllberg, C. Mieck, M. Loose, S. Hippenmeyer, Frontiers in Cellular Neuroscience 11 (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>.","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>","ieee":"A. H. Hansen, C. F. Düllberg, C. Mieck, M. Loose, and S. Hippenmeyer, “Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks,” <i>Frontiers in Cellular Neuroscience</i>, vol. 11. Frontiers Research Foundation, 2017.","ista":"Hansen AH, Düllberg CF, Mieck C, Loose M, Hippenmeyer S. 2017. Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. 11, 176."},"publication_identifier":{"issn":["1662-5102"]},"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"}],"article_processing_charge":"Yes","volume":11,"quality_controlled":"1","file":[{"file_id":"4764","content_type":"application/pdf","creator":"system","file_size":2153858,"file_name":"IST-2017-830-v1+1_2017_Hansen_CellPolarity.pdf","date_created":"2018-12-12T10:09:40Z","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:48:16Z","checksum":"dc1f5a475b918d09a0f9f587400b1626"}],"pubrep_id":"830","day":"28","author":[{"last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87","full_name":"Hansen, Andi H","first_name":"Andi H"},{"first_name":"Christian F","full_name":"Düllberg, Christian F","last_name":"Düllberg","id":"459064DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6335-9748"},{"orcid":"0000-0003-1919-7416","last_name":"Mieck","id":"34CAE85C-F248-11E8-B48F-1D18A9856A87","first_name":"Christine","full_name":"Mieck, Christine"},{"orcid":"0000-0001-7309-9724","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","first_name":"Martin"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","first_name":"Simon","full_name":"Hippenmeyer, Simon"}],"isi":1,"ec_funded":1,"oa":1,"date_published":"2017-06-28T00:00:00Z","date_created":"2018-12-11T11:49:25Z","type":"journal_article","intvolume":"        11","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"9962"}]},"status":"public","year":"2017","publist_id":"6445","publication":"Frontiers in Cellular Neuroscience","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"published","fulldoi":"https://doi.org/10.3389/fncel.2017.00176"},{"oa_version":"Published Version","scopus_import":"1","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"07","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"618091"}],"article_number":"e1005609","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.","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).","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>.","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>.","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>"},"file_date_updated":"2020-07-14T12:47:46Z","doi":"10.1371/journal.pcbi.1005609","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"}],"publication_identifier":{"issn":["1553-734X"]},"article_processing_charge":"No","has_accepted_license":"1","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"corr_author":"1","external_id":{"isi":["000406619800014"]},"_id":"696","publisher":"Public Library of Science","ddc":["576"],"date_updated":"2026-10-23T22:31:03Z","title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","ec_funded":1,"pubrep_id":"894","day":"18","author":[{"first_name":"Marta","full_name":"Lukacisinova, Marta","last_name":"Lukacisinova","id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004"},{"first_name":"Sebastian","full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","orcid":"0000-0002-2519-824X"},{"full_name":"Paixao, Tiago","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","last_name":"Paixao"}],"isi":1,"quality_controlled":"1","file":[{"creator":"system","file_size":3775716,"content_type":"application/pdf","file_id":"5117","checksum":"9143c290fa6458ed2563bff4b295554a","relation":"main_file","date_updated":"2020-07-14T12:47:46Z","file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","access_level":"open_access","date_created":"2018-12-12T10:15:01Z"}],"article_type":"original","volume":13,"publication":"PLoS Computational Biology","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"published","fulldoi":"https://doi.org/10.1371/journal.pcbi.1005609","publist_id":"7004","issue":"7","type":"journal_article","intvolume":"        13","related_material":{"record":[{"relation":"research_data","id":"9849","status":"public"},{"relation":"research_data","status":"public","id":"9850"},{"status":"public","id":"9851","relation":"research_data"},{"relation":"research_data","status":"public","id":"9852"},{"relation":"dissertation_contains","id":"6263","status":"public"}]},"status":"public","year":"2017","oa":1,"date_published":"2017-07-18T00:00:00Z","date_created":"2018-12-11T11:47:58Z"},{"fulldoi":"https://doi.org/10.1016/j.copbio.2017.02.013","publication_status":"published","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"publication":"Current Opinion in Biotechnology","publist_id":"6364","year":"2017","status":"public","related_material":{"record":[{"status":"public","id":"6263","relation":"dissertation_contains"}]},"intvolume":"        46","type":"journal_article","date_created":"2018-12-11T11:49:45Z","date_published":"2017-08-01T00:00:00Z","oa":1,"ec_funded":1,"page":"90 - 97","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","isi":1,"author":[{"full_name":"Lukacisinova, Marta","first_name":"Marta","orcid":"0000-0002-2519-8004","last_name":"Lukacisinova","id":"4342E402-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bollenbach","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias"}],"day":"01","pubrep_id":"801","article_type":"original","file":[{"file_name":"2017_CurrentOpinion_Lukaciinova.pdf","access_level":"open_access","date_created":"2019-01-18T09:57:57Z","relation":"main_file","date_updated":"2019-01-18T09:57:57Z","success":1,"content_type":"application/pdf","file_id":"5846","creator":"dernst","file_size":858338}],"quality_controlled":"1","volume":46,"article_processing_charge":"Yes (in subscription journal)","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."}],"file_date_updated":"2019-01-18T09:57:57Z","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>.","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>","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.","ista":"Lukacisinova M, Bollenbach MT. 2017. Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. 46, 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>.","short":"M. Lukacisinova, M.T. Bollenbach, Current Opinion in Biotechnology 46 (2017) 90–97.","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>"},"doi":"10.1016/j.copbio.2017.02.013","corr_author":"1","department":[{"_id":"ToBo"}],"has_accepted_license":"1","date_updated":"2026-10-23T22:31:03Z","ddc":["570"],"_id":"1027","publisher":"Elsevier","external_id":{"isi":["000408077400015"]},"title":"Toward a quantitative understanding of antibiotic resistance evolution","oa_version":"Published Version","language":[{"iso":"eng"}],"month":"08","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","project":[{"grant_number":"P27201-B22","call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions"},{"_id":"25E83C2C-B435-11E9-9278-68D0E5697425","name":"Optimality principles in responses to antibiotics","call_identifier":"FP7","grant_number":"303507"},{"name":"Revealing the fundamental limits of cell growth","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013"}]},{"publication_identifier":{"issn":["1932-6203"]},"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."}],"citation":{"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.","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.","short":"H. Ukai, A. Kawahara, K. Hirayama, M.J. Case, S. Aino, M. Miyabe, K. Wakita, R. Oogi, M. Kasayuki, S. Kawashima, S. Sugimoto, K. Chikamatsu, N. Nitta, T. Koga, R. Shigemoto, T. Takai, I. Ito, PLoS One 12 (2017).","chicago":"Ukai, Hikari, Aiko Kawahara, Keiko Hirayama, Matthew J Case, Shotaro Aino, Masahiro Miyabe, Ken Wakita, et al. “PirB Regulates Asymmetries in Hippocampal Circuitry.” <i>PLoS One</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pone.0179377\">https://doi.org/10.1371/journal.pone.0179377</a>.","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>","mla":"Ukai, Hikari, et al. “PirB Regulates Asymmetries in Hippocampal Circuitry.” <i>PLoS One</i>, vol. 12, no. 6, e0179377, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pone.0179377\">10.1371/journal.pone.0179377</a>.","apa":"Ukai, H., Kawahara, A., Hirayama, K., Case, M. J., Aino, S., Miyabe, M., … Ito, I. (2017). PirB regulates asymmetries in hippocampal circuitry. <i>PLoS One</i>. 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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."}],"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>.","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>","short":"A. Hurny, E. Benková, Auxins and Cytokinins in Plant Biology 1569 (2017) 1–29.","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>.","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.","ista":"Hurny A, Benková E. 2017. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 1569, 1–29."},"file_date_updated":"2019-10-15T07:47:05Z","doi":"10.1007/978-1-4939-6831-2_1","volume":1569,"file":[{"content_type":"application/pdf","file_id":"5068","creator":"system","file_size":840646,"file_name":"IST-2018-1019-v1+1_Hurny_MethodsMolBiol_2017.pdf","date_created":"2018-12-12T10:14:18Z","access_level":"open_access","date_updated":"2019-10-15T07:47:05Z","relation":"main_file"}],"quality_controlled":"1","author":[{"full_name":"Hurny, Andrej","first_name":"Andrej","orcid":"0000-0003-3638-1426","last_name":"Hurny","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Eva","full_name":"Benková, Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"day":"17","pubrep_id":"1019","page":"1 - 29","date_created":"2018-12-11T11:49:45Z","date_published":"2017-03-17T00:00:00Z","oa":1,"status":"public","year":"2017","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"539"}]},"intvolume":"      1569","type":"journal_article","publist_id":"6369","fulldoi":"https://doi.org/10.1007/978-1-4939-6831-2_1","publication_status":"published","publication":"Auxins and Cytokinins in Plant Biology"}]