[{"language":[{"iso":"eng"}],"intvolume":"        14","month":"03","publication_identifier":{"issn":["1439-6092"]},"department":[{"_id":"JiFr"},{"_id":"EvBe"}],"_id":"2227","isi":1,"page":"1 - 10","volume":14,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","citation":{"ieee":"E. Cires Rodriguez, M. Baltisberger, C. Cuesta, P. Vargas, and J. Prieto, “Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences,” <i>Organisms Diversity and Evolution</i>, vol. 14, no. 1. Springer, pp. 1–10, 2014.","ama":"Cires Rodriguez E, Baltisberger M, Cuesta C, Vargas P, Prieto J. Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences. <i>Organisms Diversity and Evolution</i>. 2014;14(1):1-10. doi:<a href=\"https://doi.org/10.1007/s13127-013-0150-6\">10.1007/s13127-013-0150-6</a>","short":"E. Cires Rodriguez, M. Baltisberger, C. Cuesta, P. Vargas, J. Prieto, Organisms Diversity and Evolution 14 (2014) 1–10.","ista":"Cires Rodriguez E, Baltisberger M, Cuesta C, Vargas P, Prieto J. 2014. Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences. Organisms Diversity and Evolution. 14(1), 1–10.","mla":"Cires Rodriguez, Eduardo, et al. “Allopolyploid Origin of the Balkan Endemic Ranunculus Wettsteinii (Ranunculaceae) Inferred from Nuclear and Plastid DNA Sequences.” <i>Organisms Diversity and Evolution</i>, vol. 14, no. 1, Springer, 2014, pp. 1–10, doi:<a href=\"https://doi.org/10.1007/s13127-013-0150-6\">10.1007/s13127-013-0150-6</a>.","apa":"Cires Rodriguez, E., Baltisberger, M., Cuesta, C., Vargas, P., &#38; Prieto, J. (2014). Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences. <i>Organisms Diversity and Evolution</i>. Springer. <a href=\"https://doi.org/10.1007/s13127-013-0150-6\">https://doi.org/10.1007/s13127-013-0150-6</a>","chicago":"Cires Rodriguez, Eduardo, Matthias Baltisberger, Candela Cuesta, Pablo Vargas, and José Prieto. “Allopolyploid Origin of the Balkan Endemic Ranunculus Wettsteinii (Ranunculaceae) Inferred from Nuclear and Plastid DNA Sequences.” <i>Organisms Diversity and Evolution</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s13127-013-0150-6\">https://doi.org/10.1007/s13127-013-0150-6</a>."},"publication":"Organisms Diversity and Evolution","date_created":"2018-12-11T11:56:26Z","quality_controlled":"1","date_updated":"2025-09-29T11:25:37Z","issue":"1","external_id":{"isi":["000332585400001"]},"doi":"10.1007/s13127-013-0150-6","title":"Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences","publist_id":"4734","oa_version":"None","day":"01","article_processing_charge":"No","author":[{"last_name":"Cires Rodriguez","id":"2AD56A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Eduardo","full_name":"Cires Rodriguez, Eduardo"},{"last_name":"Baltisberger","first_name":"Matthias","full_name":"Baltisberger, Matthias"},{"orcid":"0000-0003-1923-2410","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","first_name":"Candela","full_name":"Cuesta, Candela","last_name":"Cuesta"},{"first_name":"Pablo","full_name":"Vargas, Pablo","last_name":"Vargas"},{"full_name":"Prieto, José","first_name":"José","last_name":"Prieto"}],"publisher":"Springer","date_published":"2014-03-01T00:00:00Z","corr_author":"1","status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"The Balkan Peninsula, characterized by high rates of endemism, is recognised as one of the most diverse and species-rich areas of Europe. However, little is known about the origin of Balkan endemics. The present study addresses the phylogenetic position of the Balkan endemic Ranunculus wettsteinii, as well as its taxonomic status and relationship with the widespread R. parnassiifolius, based on nuclear DNA (internal transcribed spacer, ITS) and plastid regions (rpl32-trnL, rps16-trnQ, trnK-matK and ycf6-psbM). Maximum parsimony and Bayesian inference analyses revealed a well-supported clade formed by accessions of R. wettsteinii. Furthermore, our phylogenetic and network analyses supported previous hypotheses of a likely allopolyploid origin for R. wettsteinii between R. montenegrinus and R. parnassiifolius, with the latter as the maternal parent."}],"year":"2014","scopus_import":"1"},{"doi":"10.1038/nn.3678","title":"A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons","publist_id":"4733","oa_version":"Submitted Version","ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286295/"}],"issue":"5","project":[{"grant_number":"268548","call_identifier":"FP7","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","_id":"25C0F108-B435-11E9-9278-68D0E5697425"},{"_id":"25C26B1E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Mechanisms of transmitter release at GABAergic synapses","grant_number":"P24909-B24"}],"external_id":{"isi":["000335016200012"]},"status":"public","corr_author":"1","publication_status":"published","abstract":[{"text":"Fast-spiking, parvalbumin-expressing GABAergic interneurons, a large proportion of which are basket cells (BCs), have a key role in feedforward and feedback inhibition, gamma oscillations and complex information processing. For these functions, fast propagation of action potentials (APs) from the soma to the presynaptic terminals is important. However, the functional properties of interneuron axons remain elusive. We examined interneuron axons by confocally targeted subcellular patch-clamp recording in rat hippocampal slices. APs were initiated in the proximal axon ∼20 μm from the soma and propagated to the distal axon with high reliability and speed. Subcellular mapping revealed a stepwise increase of Na^+ conductance density from the soma to the proximal axon, followed by a further gradual increase in the distal axon. Active cable modeling and experiments with partial channel block revealed that low axonal Na^+ conductance density was sufficient for reliability, but high Na^+ density was necessary for both speed of propagation and fast-spiking AP phenotype. Our results suggest that a supercritical density of Na^+ channels compensates for the morphological properties of interneuron axons (small segmental diameter, extensive branching and high bouton density), ensuring fast AP propagation and high-frequency repetitive firing.","lang":"eng"}],"scopus_import":"1","year":"2014","article_processing_charge":"No","day":"23","publisher":"Nature Publishing Group","author":[{"last_name":"Hu","full_name":"Hu, Hua","first_name":"Hua","id":"4AC0145C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M"}],"date_published":"2014-03-23T00:00:00Z","publication_identifier":{"issn":["1097-6256"]},"isi":1,"_id":"2228","department":[{"_id":"PeJo"}],"page":"686-693","language":[{"iso":"eng"}],"intvolume":"        17","month":"03","type":"journal_article","publication":"Nature Neuroscience","citation":{"apa":"Hu, H., &#38; Jonas, P. M. (2014). A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons. <i>Nature Neuroscience</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nn.3678\">https://doi.org/10.1038/nn.3678</a>","chicago":"Hu, Hua, and Peter M Jonas. “A Supercritical Density of Na^+ Channels Ensures Fast Signaling in GABAergic Interneuron Axons.” <i>Nature Neuroscience</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/nn.3678\">https://doi.org/10.1038/nn.3678</a>.","mla":"Hu, Hua, and Peter M. Jonas. “A Supercritical Density of Na^+ Channels Ensures Fast Signaling in GABAergic Interneuron Axons.” <i>Nature Neuroscience</i>, vol. 17, no. 5, Nature Publishing Group, 2014, pp. 686–93, doi:<a href=\"https://doi.org/10.1038/nn.3678\">10.1038/nn.3678</a>.","ama":"Hu H, Jonas PM. A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons. <i>Nature Neuroscience</i>. 2014;17(5):686-693. doi:<a href=\"https://doi.org/10.1038/nn.3678\">10.1038/nn.3678</a>","short":"H. Hu, P.M. Jonas, Nature Neuroscience 17 (2014) 686–693.","ista":"Hu H, Jonas PM. 2014. A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons. Nature Neuroscience. 17(5), 686–693.","ieee":"H. Hu and P. M. Jonas, “A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons,” <i>Nature Neuroscience</i>, vol. 17, no. 5. Nature Publishing Group, pp. 686–693, 2014."},"date_created":"2018-12-11T11:56:26Z","quality_controlled":"1","date_updated":"2025-09-29T11:25:07Z","oa":1,"volume":17,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"month":"02","intvolume":"       343","language":[{"iso":"eng"}],"page":"665 - 670","department":[{"_id":"PeJo"}],"_id":"2229","isi":1,"publication_identifier":{"issn":["0036-8075"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":343,"oa":1,"date_updated":"2025-09-29T11:24:38Z","quality_controlled":"1","date_created":"2018-12-11T11:56:27Z","citation":{"ama":"Vyleta N, Jonas PM. Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse. <i>Science</i>. 2014;343(6171):665-670. doi:<a href=\"https://doi.org/10.1126/science.1244811\">10.1126/science.1244811</a>","short":"N. Vyleta, P.M. Jonas, Science 343 (2014) 665–670.","ista":"Vyleta N, Jonas PM. 2014. Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse. Science. 343(6171), 665–670.","ieee":"N. Vyleta and P. M. Jonas, “Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse,” <i>Science</i>, vol. 343, no. 6171. American Association for the Advancement of Science, pp. 665–670, 2014.","apa":"Vyleta, N., &#38; Jonas, P. M. (2014). Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1244811\">https://doi.org/10.1126/science.1244811</a>","chicago":"Vyleta, Nicholas, and Peter M Jonas. “Loose Coupling between Ca^2+ Channels and Release Sensors at a Plastic Hippocampal Synapse.” <i>Science</i>. American Association for the Advancement of Science, 2014. <a href=\"https://doi.org/10.1126/science.1244811\">https://doi.org/10.1126/science.1244811</a>.","mla":"Vyleta, Nicholas, and Peter M. Jonas. “Loose Coupling between Ca^2+ Channels and Release Sensors at a Plastic Hippocampal Synapse.” <i>Science</i>, vol. 343, no. 6171, American Association for the Advancement of Science, 2014, pp. 665–70, doi:<a href=\"https://doi.org/10.1126/science.1244811\">10.1126/science.1244811</a>."},"type":"journal_article","publication":"Science","external_id":{"isi":["000330724000044"]},"project":[{"_id":"25C26B1E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Mechanisms of transmitter release at GABAergic synapses","grant_number":"P24909-B24"},{"grant_number":"268548","call_identifier":"FP7","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","_id":"25C0F108-B435-11E9-9278-68D0E5697425"}],"issue":"6171","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617475/","open_access":"1"}],"ec_funded":1,"oa_version":"Submitted Version","publist_id":"4732","doi":"10.1126/science.1244811","title":"Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse","date_published":"2014-02-01T00:00:00Z","author":[{"full_name":"Vyleta, Nicholas","first_name":"Nicholas","id":"36C4978E-F248-11E8-B48F-1D18A9856A87","last_name":"Vyleta"},{"first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas"}],"publisher":"American Association for the Advancement of Science","day":"01","article_processing_charge":"No","year":"2014","scopus_import":"1","abstract":[{"text":"The distance between Ca^2+ channels and release sensors determines the speed and efficacy of synaptic transmission. Tight &quot;nanodomain&quot; channel-sensor coupling initiates transmitter release at synapses in the mature brain, whereas loose &quot;microdomain&quot; coupling appears restricted to early developmental stages. To probe the coupling configuration at a plastic synapse in the mature central nervous system, we performed paired recordings between mossy fiber terminals and CA3 pyramidal neurons in rat hippocampus. Millimolar concentrations of both the fast Ca^2+ chelator BAPTA [1,2-bis(2-aminophenoxy)ethane- N,N, N′,N′-tetraacetic acid] and the slow chelator EGTA efficiently suppressed transmitter release, indicating loose coupling between Ca^2+ channels and release sensors. Loose coupling enabled the control of initial release probability by fast endogenous Ca^2+ buffers and the generation of facilitation by buffer saturation. Thus, loose coupling provides the molecular framework for presynaptic plasticity.","lang":"eng"}],"publication_status":"published","corr_author":"1","status":"public"},{"title":"Stimfit: Quantifying electrophysiological data with Python","doi":"10.3389/fninf.2014.00016","publist_id":"4731","oa_version":"Published Version","issue":"FEB","external_id":{"isi":["000348105900001"]},"status":"public","publication_status":"published","abstract":[{"text":"Intracellular electrophysiological recordings provide crucial insights into elementary neuronal signals such as action potentials and synaptic currents. Analyzing and interpreting these signals is essential for a quantitative understanding of neuronal information processing, and requires both fast data visualization and ready access to complex analysis routines. To achieve this goal, we have developed Stimfit, a free software package for cellular neurophysiology with a Python scripting interface and a built-in Python shell. The program supports most standard file formats for cellular neurophysiology and other biomedical signals through the Biosig library. To quantify and interpret the activity of single neurons and communication between neurons, the program includes algorithms to characterize the kinetics of presynaptic action potentials and postsynaptic currents, estimate latencies between pre- and postsynaptic events, and detect spontaneously occurring events. We validate and benchmark these algorithms, give estimation errors, and provide sample use cases, showing that Stimfit represents an efficient, accessible and extensible way to accurately analyze and interpret neuronal signals.","lang":"eng"}],"year":"2014","scopus_import":"1","file":[{"date_created":"2018-12-12T10:12:17Z","date_updated":"2020-07-14T12:45:34Z","content_type":"application/pdf","access_level":"open_access","checksum":"eeca00bba7232ff7d27db83321f6ea30","file_id":"4935","file_size":2883372,"relation":"main_file","creator":"system","file_name":"IST-2016-425-v1+1_fninf-08-00016.pdf"}],"day":"21","article_processing_charge":"No","pubrep_id":"425","author":[{"last_name":"Guzmán","first_name":"José","full_name":"Guzmán, José","orcid":"0000-0003-2209-5242","id":"30CC5506-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","first_name":"Alois"},{"last_name":"Schmidt Hieber","first_name":"Christoph","full_name":"Schmidt Hieber, Christoph"}],"publisher":"Frontiers Research Foundation","date_published":"2014-02-21T00:00:00Z","publication_identifier":{"issn":["1662-5196"]},"isi":1,"_id":"2230","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"article_number":"16","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"ddc":["570"],"intvolume":"         8","month":"02","type":"journal_article","citation":{"mla":"Guzmán, José, et al. “Stimfit: Quantifying Electrophysiological Data with Python.” <i>Frontiers in Neuroinformatics</i>, vol. 8, no. FEB, 16, Frontiers Research Foundation, 2014, doi:<a href=\"https://doi.org/10.3389/fninf.2014.00016\">10.3389/fninf.2014.00016</a>.","chicago":"Guzmán, José, Alois Schlögl, and Christoph Schmidt Hieber. “Stimfit: Quantifying Electrophysiological Data with Python.” <i>Frontiers in Neuroinformatics</i>. Frontiers Research Foundation, 2014. <a href=\"https://doi.org/10.3389/fninf.2014.00016\">https://doi.org/10.3389/fninf.2014.00016</a>.","apa":"Guzmán, J., Schlögl, A., &#38; Schmidt Hieber, C. (2014). Stimfit: Quantifying electrophysiological data with Python. <i>Frontiers in Neuroinformatics</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fninf.2014.00016\">https://doi.org/10.3389/fninf.2014.00016</a>","ieee":"J. Guzmán, A. Schlögl, and C. Schmidt Hieber, “Stimfit: Quantifying electrophysiological data with Python,” <i>Frontiers in Neuroinformatics</i>, vol. 8, no. FEB. Frontiers Research Foundation, 2014.","ista":"Guzmán J, Schlögl A, Schmidt Hieber C. 2014. Stimfit: Quantifying electrophysiological data with Python. Frontiers in Neuroinformatics. 8(FEB), 16.","short":"J. Guzmán, A. Schlögl, C. Schmidt Hieber, Frontiers in Neuroinformatics 8 (2014).","ama":"Guzmán J, Schlögl A, Schmidt Hieber C. Stimfit: Quantifying electrophysiological data with Python. <i>Frontiers in Neuroinformatics</i>. 2014;8(FEB). doi:<a href=\"https://doi.org/10.3389/fninf.2014.00016\">10.3389/fninf.2014.00016</a>"},"publication":"Frontiers in Neuroinformatics","date_created":"2018-12-11T11:56:27Z","file_date_updated":"2020-07-14T12:45:34Z","quality_controlled":"1","date_updated":"2025-09-29T11:24:02Z","volume":8,"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"external_id":{"pmid":["24606943"],"isi":["000332501300022"]},"issue":"5","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4026790/"}],"oa_version":"Submitted Version","publist_id":"4730","doi":"10.1016/j.bpj.2014.01.014","title":"Noise and information transmission in promoters with multiple internal states","date_published":"2014-03-04T00:00:00Z","pmid":1,"publisher":"Biophysical Society","author":[{"last_name":"Rieckh","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","full_name":"Rieckh, Georg","first_name":"Georg"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik"}],"day":"04","article_processing_charge":"No","year":"2014","scopus_import":"1","abstract":[{"text":"Based on the measurements of noise in gene expression performed during the past decade, it has become customary to think of gene regulation in terms of a two-state model, where the promoter of a gene can stochastically switch between an ON and an OFF state. As experiments are becoming increasingly precise and the deviations from the two-state model start to be observable, we ask about the experimental signatures of complex multistate promoters, as well as the functional consequences of this additional complexity. In detail, we i), extend the calculations for noise in gene expression to promoters described by state transition diagrams with multiple states, ii), systematically compute the experimentally accessible noise characteristics for these complex promoters, and iii), use information theory to evaluate the channel capacities of complex promoter architectures and compare them with the baseline provided by the two-state model. We find that adding internal states to the promoter generically decreases channel capacity, except in certain cases, three of which (cooperativity, dual-role regulation, promoter cycling) we analyze in detail.","lang":"eng"}],"publication_status":"published","corr_author":"1","status":"public","month":"03","intvolume":"       106","language":[{"iso":"eng"}],"page":"1194 - 1204","isi":1,"_id":"2231","department":[{"_id":"GaTk"}],"publication_identifier":{"issn":["0006-3495"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":106,"oa":1,"date_updated":"2025-09-29T11:23:30Z","quality_controlled":"1","date_created":"2018-12-11T11:56:28Z","publication":"Biophysical Journal","type":"journal_article","citation":{"chicago":"Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in Promoters with Multiple Internal States.” <i>Biophysical Journal</i>. Biophysical Society, 2014. <a href=\"https://doi.org/10.1016/j.bpj.2014.01.014\">https://doi.org/10.1016/j.bpj.2014.01.014</a>.","apa":"Rieckh, G., &#38; Tkačik, G. (2014). Noise and information transmission in promoters with multiple internal states. <i>Biophysical Journal</i>. Biophysical Society. <a href=\"https://doi.org/10.1016/j.bpj.2014.01.014\">https://doi.org/10.1016/j.bpj.2014.01.014</a>","mla":"Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in Promoters with Multiple Internal States.” <i>Biophysical Journal</i>, vol. 106, no. 5, Biophysical Society, 2014, pp. 1194–204, doi:<a href=\"https://doi.org/10.1016/j.bpj.2014.01.014\">10.1016/j.bpj.2014.01.014</a>.","ista":"Rieckh G, Tkačik G. 2014. Noise and information transmission in promoters with multiple internal states. Biophysical Journal. 106(5), 1194–1204.","ama":"Rieckh G, Tkačik G. Noise and information transmission in promoters with multiple internal states. <i>Biophysical Journal</i>. 2014;106(5):1194-1204. doi:<a href=\"https://doi.org/10.1016/j.bpj.2014.01.014\">10.1016/j.bpj.2014.01.014</a>","short":"G. Rieckh, G. Tkačik, Biophysical Journal 106 (2014) 1194–1204.","ieee":"G. Rieckh and G. Tkačik, “Noise and information transmission in promoters with multiple internal states,” <i>Biophysical Journal</i>, vol. 106, no. 5. Biophysical Society, pp. 1194–1204, 2014."}},{"year":"2014","scopus_import":"1","publication_status":"published","abstract":[{"lang":"eng","text":"The purpose of this contribution is to summarize and discuss recent advances regarding the onset of turbulence in shear flows. The absence of a clear-cut instability mechanism, the spatio-temporal intermittent character and extremely long lived transients are some of the major difficulties encountered in these flows and have hindered progress towards understanding the transition process. We will show for the case of pipe flow that concepts from nonlinear dynamics and statistical physics can help to explain the onset of turbulence. In particular, the turbulent structures (puffs) observed close to onset are spatially localized chaotic transients and their lifetimes increase super-exponentially with Reynolds number. At the same time fluctuations of individual turbulent puffs can (although very rarely) lead to the nucleation of new puffs. The competition between these two stochastic processes gives rise to a non-equilibrium phase transition where turbulence changes from a super-transient to a sustained state."}],"corr_author":"1","status":"public","date_published":"2014-02-01T00:00:00Z","arxiv":1,"author":[{"last_name":"Song","first_name":"Baofang","full_name":"Song, Baofang","id":"a79e57f5-e8a5-11ec-9dc9-83fb8c81cf72"},{"last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","first_name":"Björn"}],"publisher":"IOP Publishing","day":"01","article_processing_charge":"No","oa_version":"Submitted Version","publist_id":"4729","doi":"10.1088/1742-5468/2014/02/P02001","title":"Deterministic and stochastic aspects of the transition to turbulence","external_id":{"isi":["000332098100001"],"arxiv":["1403.4516"]},"issue":"2","main_file_link":[{"url":"http://arxiv.org/abs/1403.4516","open_access":"1"}],"date_updated":"2025-09-29T11:22:37Z","quality_controlled":"1","date_created":"2018-12-11T11:56:28Z","citation":{"ista":"Song B, Hof B. 2014. Deterministic and stochastic aspects of the transition to turbulence. Journal of Statistical Mechanics Theory and Experiment. 2014(2), P02001.","ama":"Song B, Hof B. Deterministic and stochastic aspects of the transition to turbulence. <i>Journal of Statistical Mechanics Theory and Experiment</i>. 2014;2014(2). doi:<a href=\"https://doi.org/10.1088/1742-5468/2014/02/P02001\">10.1088/1742-5468/2014/02/P02001</a>","short":"B. Song, B. Hof, Journal of Statistical Mechanics Theory and Experiment 2014 (2014).","ieee":"B. Song and B. Hof, “Deterministic and stochastic aspects of the transition to turbulence,” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2014, no. 2. IOP Publishing, 2014.","chicago":"Song, Baofang, and Björn Hof. “Deterministic and Stochastic Aspects of the Transition to Turbulence.” <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing, 2014. <a href=\"https://doi.org/10.1088/1742-5468/2014/02/P02001\">https://doi.org/10.1088/1742-5468/2014/02/P02001</a>.","apa":"Song, B., &#38; Hof, B. (2014). Deterministic and stochastic aspects of the transition to turbulence. <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1742-5468/2014/02/P02001\">https://doi.org/10.1088/1742-5468/2014/02/P02001</a>","mla":"Song, Baofang, and Björn Hof. “Deterministic and Stochastic Aspects of the Transition to Turbulence.” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2014, no. 2, P02001, IOP Publishing, 2014, doi:<a href=\"https://doi.org/10.1088/1742-5468/2014/02/P02001\">10.1088/1742-5468/2014/02/P02001</a>."},"publication":"Journal of Statistical Mechanics Theory and Experiment","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","volume":2014,"oa":1,"_id":"2232","department":[{"_id":"BjHo"}],"isi":1,"publication_identifier":{"issn":["1742-5468"]},"month":"02","intvolume":"      2014","article_number":"P02001","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"intvolume":"        10","ddc":["000"],"month":"02","publication_identifier":{"issn":["1860-5974"]},"_id":"2233","department":[{"_id":"ToHe"}],"isi":1,"has_accepted_license":"1","oa":1,"volume":10,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Logical Methods in Computer Science","type":"journal_article","citation":{"chicago":"Boker, Udi, and Thomas A Henzinger. “Exact and Approximate Determinization of Discounted-Sum Automata.” <i>Logical Methods in Computer Science</i>. International Federation of Computational Logic, 2014. <a href=\"https://doi.org/10.2168/LMCS-10(1:10)2014\">https://doi.org/10.2168/LMCS-10(1:10)2014</a>.","apa":"Boker, U., &#38; Henzinger, T. A. (2014). Exact and approximate determinization of discounted-sum automata. <i>Logical Methods in Computer Science</i>. International Federation of Computational Logic. <a href=\"https://doi.org/10.2168/LMCS-10(1:10)2014\">https://doi.org/10.2168/LMCS-10(1:10)2014</a>","mla":"Boker, Udi, and Thomas A. Henzinger. “Exact and Approximate Determinization of Discounted-Sum Automata.” <i>Logical Methods in Computer Science</i>, vol. 10, no. 1, International Federation of Computational Logic, 2014, doi:<a href=\"https://doi.org/10.2168/LMCS-10(1:10)2014\">10.2168/LMCS-10(1:10)2014</a>.","ista":"Boker U, Henzinger TA. 2014. Exact and approximate determinization of discounted-sum automata. Logical Methods in Computer Science. 10(1).","short":"U. Boker, T.A. Henzinger, Logical Methods in Computer Science 10 (2014).","ama":"Boker U, Henzinger TA. Exact and approximate determinization of discounted-sum automata. <i>Logical Methods in Computer Science</i>. 2014;10(1). doi:<a href=\"https://doi.org/10.2168/LMCS-10(1:10)2014\">10.2168/LMCS-10(1:10)2014</a>","ieee":"U. Boker and T. A. Henzinger, “Exact and approximate determinization of discounted-sum automata,” <i>Logical Methods in Computer Science</i>, vol. 10, no. 1. International Federation of Computational Logic, 2014."},"date_created":"2018-12-11T11:56:28Z","date_updated":"2025-09-29T11:22:08Z","quality_controlled":"1","file_date_updated":"2020-07-14T12:45:34Z","ec_funded":1,"issue":"1","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000333744700015"]},"doi":"10.2168/LMCS-10(1:10)2014","title":"Exact and approximate determinization of discounted-sum automata","publist_id":"4728","oa_version":"Published Version","file":[{"file_id":"4643","file_size":550936,"access_level":"open_access","checksum":"9f6ea2e2d8d4a32ff0becc29d835bbf8","date_updated":"2020-07-14T12:45:34Z","content_type":"application/pdf","date_created":"2018-12-12T10:07:45Z","file_name":"IST-2015-389-v1+1_1401.3957.pdf","creator":"system","relation":"main_file"}],"article_processing_charge":"No","day":"13","publisher":"International Federation of Computational Logic","author":[{"last_name":"Boker","first_name":"Udi","full_name":"Boker, Udi"},{"last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"pubrep_id":"389","date_published":"2014-02-13T00:00:00Z","status":"public","publication_status":"published","abstract":[{"lang":"eng","text":" A discounted-sum automaton (NDA) is a nondeterministic finite automaton with edge weights, valuing a run by the discounted sum of visited edge weights. More precisely, the weight in the i-th position of the run is divided by λi, where the discount factor λ is a fixed rational number greater than 1. The value of a word is the minimal value of the automaton runs on it. Discounted summation is a common and useful measuring scheme, especially for infinite sequences, reflecting the assumption that earlier weights are more important than later weights. Unfortunately, determinization of NDAs, which is often essential in formal verification, is, in general, not possible. We provide positive news, showing that every NDA with an integral discount factor is determinizable. We complete the picture by proving that the integers characterize exactly the discount factors that guarantee determinizability: for every nonintegral rational discount factor λ, there is a nondeterminizable λ-NDA. We also prove that the class of NDAs with integral discount factors enjoys closure under the algebraic operations min, max, addition, and subtraction, which is not the case for general NDAs nor for deterministic NDAs. For general NDAs, we look into approximate determinization, which is always possible as the influence of a word's suffix decays. We show that the naive approach, of unfolding the automaton computations up to a sufficient level, is doubly exponential in the discount factor. We provide an alternative construction for approximate determinization, which is singly exponential in the discount factor, in the precision, and in the number of states. We also prove matching lower bounds, showing that the exponential dependency on each of these three parameters cannot be avoided. All our results hold equally for automata over finite words and for automata over infinite words. "}],"scopus_import":"1","year":"2014"},{"title":"Markov decision processes with multiple long-run average objectives","doi":"10.2168/LMCS-10(1:13)2014","oa_version":"Published Version","publist_id":"4727","issue":"1","ec_funded":1,"external_id":{"isi":["000333744700001"]},"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"status":"public","scopus_import":"1","year":"2014","abstract":[{"text":"We study Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) functions. We consider two different objectives, namely, expectation and satisfaction objectives. Given an MDP with κ limit-average functions, in the expectation objective the goal is to maximize the expected limit-average value, and in the satisfaction objective the goal is to maximize the probability of runs such that the limit-average value stays above a given vector. We show that under the expectation objective, in contrast to the case of one limit-average function, both randomization and memory are necessary for strategies even for ε-approximation, and that finite-memory randomized strategies are sufficient for achieving Pareto optimal values. Under the satisfaction objective, in contrast to the case of one limit-average function, infinite memory is necessary for strategies achieving a specific value (i.e. randomized finite-memory strategies are not sufficient), whereas memoryless randomized strategies are sufficient for ε-approximation, for all ε &gt; 0. We further prove that the decision problems for both expectation and satisfaction objectives can be solved in polynomial time and the trade-off curve (Pareto curve) can be ε-approximated in time polynomial in the size of the MDP and 1/ε, and exponential in the number of limit-average functions, for all ε &gt; 0. Our analysis also reveals flaws in previous work for MDPs with multiple mean-payoff functions under the expectation objective, corrects the flaws, and allows us to obtain improved results.","lang":"eng"}],"publication_status":"published","article_processing_charge":"No","day":"14","file":[{"date_created":"2018-12-12T10:07:57Z","date_updated":"2020-07-14T12:45:34Z","content_type":"application/pdf","checksum":"803edcc2d8c1acfba44a9ec43a5eb9f0","access_level":"open_access","file_size":375388,"file_id":"4656","relation":"main_file","creator":"system","file_name":"IST-2016-428-v1+1_1104.3489.pdf"}],"date_published":"2014-02-14T00:00:00Z","publisher":"International Federation of Computational Logic","author":[{"last_name":"Brázdil","full_name":"Brázdil, Tomáš","first_name":"Tomáš"},{"last_name":"Brožek","full_name":"Brožek, Václav","first_name":"Václav"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Forejt","full_name":"Forejt, Vojtěch","first_name":"Vojtěch"},{"last_name":"Kučera","full_name":"Kučera, Antonín","first_name":"Antonín"}],"pubrep_id":"428","publication_identifier":{"issn":["1860-5974"]},"has_accepted_license":"1","_id":"2234","department":[{"_id":"KrCh"}],"isi":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"month":"02","intvolume":"        10","ddc":["000"],"citation":{"ama":"Brázdil T, Brožek V, Chatterjee K, Forejt V, Kučera A. Markov decision processes with multiple long-run average objectives. <i>Logical Methods in Computer Science</i>. 2014;10(1). doi:<a href=\"https://doi.org/10.2168/LMCS-10(1:13)2014\">10.2168/LMCS-10(1:13)2014</a>","short":"T. Brázdil, V. Brožek, K. Chatterjee, V. Forejt, A. Kučera, Logical Methods in Computer Science 10 (2014).","ista":"Brázdil T, Brožek V, Chatterjee K, Forejt V, Kučera A. 2014. Markov decision processes with multiple long-run average objectives. Logical Methods in Computer Science. 10(1).","ieee":"T. Brázdil, V. Brožek, K. Chatterjee, V. Forejt, and A. Kučera, “Markov decision processes with multiple long-run average objectives,” <i>Logical Methods in Computer Science</i>, vol. 10, no. 1. International Federation of Computational Logic, 2014.","apa":"Brázdil, T., Brožek, V., Chatterjee, K., Forejt, V., &#38; Kučera, A. (2014). Markov decision processes with multiple long-run average objectives. <i>Logical Methods in Computer Science</i>. International Federation of Computational Logic. <a href=\"https://doi.org/10.2168/LMCS-10(1:13)2014\">https://doi.org/10.2168/LMCS-10(1:13)2014</a>","chicago":"Brázdil, Tomáš, Václav Brožek, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Markov Decision Processes with Multiple Long-Run Average Objectives.” <i>Logical Methods in Computer Science</i>. International Federation of Computational Logic, 2014. <a href=\"https://doi.org/10.2168/LMCS-10(1:13)2014\">https://doi.org/10.2168/LMCS-10(1:13)2014</a>.","mla":"Brázdil, Tomáš, et al. “Markov Decision Processes with Multiple Long-Run Average Objectives.” <i>Logical Methods in Computer Science</i>, vol. 10, no. 1, International Federation of Computational Logic, 2014, doi:<a href=\"https://doi.org/10.2168/LMCS-10(1:13)2014\">10.2168/LMCS-10(1:13)2014</a>."},"type":"journal_article","publication":"Logical Methods in Computer Science","quality_controlled":"1","date_updated":"2025-09-29T11:21:40Z","file_date_updated":"2020-07-14T12:45:34Z","date_created":"2018-12-11T11:56:29Z","oa":1,"volume":10,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"doi":"10.1038/nature12977","title":"Disease associations between honeybees and bumblebees as a threat to wild pollinators","publist_id":"4726","oa_version":"Submitted Version","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985068/","open_access":"1"}],"issue":"7488","external_id":{"isi":["000331477800040"]},"status":"public","corr_author":"1","abstract":[{"text":"Emerging infectious diseases (EIDs) pose a risk to human welfare, both directly and indirectly, by affecting managed livestock and wildlife that provide valuable resources and ecosystem services, such as the pollination of crops. Honeybees (Apis mellifera), the prevailing managed insect crop pollinator, suffer from a range of emerging and exotic high-impact pathogens, and population maintenance requires active management by beekeepers to control them. Wild pollinators such as bumblebees (Bombus spp.) are in global decline, one cause of which may be pathogen spillover from managed pollinators like honeybees or commercial colonies of bumblebees. Here we use a combination of infection experiments and landscape-scale field data to show that honeybee EIDs are indeed widespread infectious agents within the pollinator assemblage. The prevalence of deformed wing virus (DWV) and the exotic parasite Nosema ceranae in honeybees and bumblebees is linked; as honeybees have higher DWV prevalence, and sympatric bumblebees and honeybees are infected by the same DWV strains, Apis is the likely source of at least one major EID in wild pollinators. Lessons learned from vertebrates highlight the need for increased pathogen control in managed bee species to maintain wild pollinators, as declines in native pollinators may be caused by interspecies pathogen transmission originating from managed pollinators.","lang":"eng"}],"publication_status":"published","scopus_import":"1","year":"2014","article_processing_charge":"No","day":"20","author":[{"last_name":"Fürst","orcid":"0000-0002-3712-925X","id":"393B1196-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","full_name":"Fürst, Matthias"},{"full_name":"Mcmahon, Dino","first_name":"Dino","last_name":"Mcmahon"},{"first_name":"Juliet","full_name":"Osborne, Juliet","last_name":"Osborne"},{"last_name":"Paxton","full_name":"Paxton, Robert","first_name":"Robert"},{"last_name":"Brown","first_name":"Mark","full_name":"Brown, Mark"}],"publisher":"Nature Publishing Group","date_published":"2014-02-20T00:00:00Z","publication_identifier":{"issn":["0028-0836"]},"isi":1,"_id":"2235","department":[{"_id":"SyCr"}],"page":"364 - 366","language":[{"iso":"eng"}],"intvolume":"       506","month":"02","citation":{"apa":"Fürst, M., Mcmahon, D., Osborne, J., Paxton, R., &#38; Brown, M. (2014). Disease associations between honeybees and bumblebees as a threat to wild pollinators. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature12977\">https://doi.org/10.1038/nature12977</a>","chicago":"Fürst, Matthias, Dino Mcmahon, Juliet Osborne, Robert Paxton, and Mark Brown. “Disease Associations between Honeybees and Bumblebees as a Threat to Wild Pollinators.” <i>Nature</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/nature12977\">https://doi.org/10.1038/nature12977</a>.","mla":"Fürst, Matthias, et al. “Disease Associations between Honeybees and Bumblebees as a Threat to Wild Pollinators.” <i>Nature</i>, vol. 506, no. 7488, Nature Publishing Group, 2014, pp. 364–66, doi:<a href=\"https://doi.org/10.1038/nature12977\">10.1038/nature12977</a>.","short":"M. Fürst, D. Mcmahon, J. Osborne, R. Paxton, M. Brown, Nature 506 (2014) 364–366.","ama":"Fürst M, Mcmahon D, Osborne J, Paxton R, Brown M. Disease associations between honeybees and bumblebees as a threat to wild pollinators. <i>Nature</i>. 2014;506(7488):364-366. doi:<a href=\"https://doi.org/10.1038/nature12977\">10.1038/nature12977</a>","ista":"Fürst M, Mcmahon D, Osborne J, Paxton R, Brown M. 2014. Disease associations between honeybees and bumblebees as a threat to wild pollinators. Nature. 506(7488), 364–366.","ieee":"M. Fürst, D. Mcmahon, J. Osborne, R. Paxton, and M. Brown, “Disease associations between honeybees and bumblebees as a threat to wild pollinators,” <i>Nature</i>, vol. 506, no. 7488. Nature Publishing Group, pp. 364–366, 2014."},"type":"journal_article","publication":"Nature","date_created":"2018-12-11T11:56:29Z","date_updated":"2025-09-29T11:21:06Z","quality_controlled":"1","oa":1,"volume":506,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:45:34Z","date_created":"2018-12-12T10:17:21Z","file_id":"5275","file_size":313528,"access_level":"open_access","checksum":"42960325c29dcd8d832edadcc3ce0045","creator":"system","relation":"main_file","file_name":"IST-2016-681-v1+1_869_1_.pdf"}],"day":"01","article_processing_charge":"No","pubrep_id":"681","publisher":"Springer","author":[{"first_name":"Dimitar","full_name":"Jetchev, Dimitar","last_name":"Jetchev"},{"last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z"}],"date_published":"2014-02-01T00:00:00Z","corr_author":"1","status":"public","abstract":[{"text":"Consider a joint distribution (X,A) on a set. We show that for any family of distinguishers, there exists a simulator such that 1 no function in can distinguish (X,A) from (X,h(X)) with advantage ε, 2 h is only O(2 3ℓ ε -2) times less efficient than the functions in. For the most interesting settings of the parameters (in particular, the cryptographic case where X has superlogarithmic min-entropy, ε &gt; 0 is negligible and consists of circuits of polynomial size), we can make the simulator h deterministic. As an illustrative application of our theorem, we give a new security proof for the leakage-resilient stream-cipher from Eurocrypt'09. Our proof is simpler and quantitatively much better than the original proof using the dense model theorem, giving meaningful security guarantees if instantiated with a standard blockcipher like AES. Subsequent to this work, Chung, Lui and Pass gave an interactive variant of our main theorem, and used it to investigate weak notions of Zero-Knowledge. Vadhan and Zheng give a more constructive version of our theorem using their new uniform min-max theorem.","lang":"eng"}],"publication_status":"published","year":"2014","scopus_import":"1","ec_funded":1,"project":[{"grant_number":"259668","call_identifier":"FP7","name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"title":"How to fake auxiliary input","doi":"10.1007/978-3-642-54242-8_24","publist_id":"4725","oa_version":"Submitted Version","volume":8349,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Jetchev, Dimitar, and Krzysztof Z Pietrzak. “How to Fake Auxiliary Input.” edited by Yehuda Lindell, 8349:566–90. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-642-54242-8_24\">https://doi.org/10.1007/978-3-642-54242-8_24</a>.","apa":"Jetchev, D., &#38; Pietrzak, K. Z. (2014). How to fake auxiliary input. In Y. Lindell (Ed.) (Vol. 8349, pp. 566–590). Presented at the TCC: Theory of Cryptography Conference, San Diego, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-642-54242-8_24\">https://doi.org/10.1007/978-3-642-54242-8_24</a>","mla":"Jetchev, Dimitar, and Krzysztof Z. Pietrzak. <i>How to Fake Auxiliary Input</i>. Edited by Yehuda Lindell, vol. 8349, Springer, 2014, pp. 566–90, doi:<a href=\"https://doi.org/10.1007/978-3-642-54242-8_24\">10.1007/978-3-642-54242-8_24</a>.","ista":"Jetchev D, Pietrzak KZ. 2014. How to fake auxiliary input. TCC: Theory of Cryptography Conference, LNCS, vol. 8349, 566–590.","ama":"Jetchev D, Pietrzak KZ. How to fake auxiliary input. In: Lindell Y, ed. Vol 8349. Springer; 2014:566-590. doi:<a href=\"https://doi.org/10.1007/978-3-642-54242-8_24\">10.1007/978-3-642-54242-8_24</a>","short":"D. Jetchev, K.Z. Pietrzak, in:, Y. Lindell (Ed.), Springer, 2014, pp. 566–590.","ieee":"D. Jetchev and K. Z. Pietrzak, “How to fake auxiliary input,” presented at the TCC: Theory of Cryptography Conference, San Diego, USA, 2014, vol. 8349, pp. 566–590."},"type":"conference","date_created":"2018-12-11T11:56:29Z","file_date_updated":"2020-07-14T12:45:34Z","date_updated":"2025-06-11T08:02:25Z","quality_controlled":"1","language":[{"iso":"eng"}],"ddc":["004"],"intvolume":"      8349","month":"02","editor":[{"last_name":"Lindell","full_name":"Lindell, Yehuda","first_name":"Yehuda"}],"publication_identifier":{"isbn":["978-364254241-1"]},"conference":{"location":"San Diego, USA","end_date":"2014-02-26","name":"TCC: Theory of Cryptography Conference","start_date":"2014-02-24"},"department":[{"_id":"KrPi"}],"_id":"2236","has_accepted_license":"1","page":"566 - 590","alternative_title":["LNCS"]},{"volume":49,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"conference","citation":{"ista":"Boker U, Henzinger TA, Radhakrishna A. 2014. Battery transition systems. POPL: Principles of Programming Languages vol. 49, 595–606.","ama":"Boker U, Henzinger TA, Radhakrishna A. Battery transition systems. In: Vol 49. ACM; 2014:595-606. doi:<a href=\"https://doi.org/10.1145/2535838.2535875\">10.1145/2535838.2535875</a>","short":"U. Boker, T.A. Henzinger, A. Radhakrishna, in:, ACM, 2014, pp. 595–606.","ieee":"U. Boker, T. A. Henzinger, and A. Radhakrishna, “Battery transition systems,” presented at the POPL: Principles of Programming Languages, San Diego, USA, 2014, vol. 49, no. 1, pp. 595–606.","chicago":"Boker, Udi, Thomas A Henzinger, and Arjun Radhakrishna. “Battery Transition Systems,” 49:595–606. ACM, 2014. <a href=\"https://doi.org/10.1145/2535838.2535875\">https://doi.org/10.1145/2535838.2535875</a>.","apa":"Boker, U., Henzinger, T. A., &#38; Radhakrishna, A. (2014). Battery transition systems (Vol. 49, pp. 595–606). Presented at the POPL: Principles of Programming Languages, San Diego, USA: ACM. <a href=\"https://doi.org/10.1145/2535838.2535875\">https://doi.org/10.1145/2535838.2535875</a>","mla":"Boker, Udi, et al. <i>Battery Transition Systems</i>. Vol. 49, no. 1, ACM, 2014, pp. 595–606, doi:<a href=\"https://doi.org/10.1145/2535838.2535875\">10.1145/2535838.2535875</a>."},"date_created":"2018-12-11T11:56:30Z","quality_controlled":"1","date_updated":"2021-01-12T06:56:13Z","language":[{"iso":"eng"}],"intvolume":"        49","month":"01","publication_identifier":{"isbn":["978-145032544-8"]},"conference":{"location":"San Diego, USA","start_date":"2014-01-22","end_date":"2014-01-24","name":"POPL: Principles of Programming Languages"},"_id":"2239","department":[{"_id":"ToHe"}],"page":"595 - 606","day":"13","author":[{"full_name":"Boker, Udi","first_name":"Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","last_name":"Boker"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"last_name":"Radhakrishna","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun","full_name":"Radhakrishna, Arjun"}],"publisher":"ACM","date_published":"2014-01-13T00:00:00Z","status":"public","abstract":[{"text":"The analysis of the energy consumption of software is an important goal for quantitative formal methods. Current methods, using weighted transition systems or energy games, model the energy source as an ideal resource whose status is characterized by one number, namely the amount of remaining energy. Real batteries, however, exhibit behaviors that can deviate substantially from an ideal energy resource. Based on a discretization of a standard continuous battery model, we introduce battery transition systems. In this model, a battery is viewed as consisting of two parts-the available-charge tank and the bound-charge tank. Any charge or discharge is applied to the available-charge tank. Over time, the energy from each tank diffuses to the other tank. Battery transition systems are infinite state systems that, being not well-structured, fall into no decidable class that is known to us. Nonetheless, we are able to prove that the !-regular modelchecking problem is decidable for battery transition systems. We also present a case study on the verification of control programs for energy-constrained semi-autonomous robots.","lang":"eng"}],"publication_status":"published","year":"2014","scopus_import":1,"ec_funded":1,"issue":"1","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"doi":"10.1145/2535838.2535875","title":"Battery transition systems","publist_id":"4722","oa_version":"None"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":156,"quality_controlled":"1","date_updated":"2025-09-29T11:20:21Z","date_created":"2018-12-11T11:56:31Z","publication":"Cell","type":"journal_article","citation":{"ieee":"A. Gadeyne <i>et al.</i>, “The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants,” <i>Cell</i>, vol. 156, no. 4. Cell Press, pp. 691–704, 2014.","ama":"Gadeyne A, Sánchez Rodríguez C, Vanneste S, et al. The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants. <i>Cell</i>. 2014;156(4):691-704. doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.039\">10.1016/j.cell.2014.01.039</a>","short":"A. Gadeyne, C. Sánchez Rodríguez, S. Vanneste, S. Di Rubbo, H. Zauber, K. Vanneste, J. Van Leene, N. De Winne, D. Eeckhout, G. Persiau, E. Van De Slijke, B. Cannoot, L. Vercruysse, J. Mayers, M. Adamowski, U. Kania, M. Ehrlich, A. Schweighofer, T. Ketelaar, S. Maere, S. Bednarek, J. Friml, K. Gevaert, E. Witters, E. Russinova, S. Persson, G. De Jaeger, D. Van Damme, Cell 156 (2014) 691–704.","ista":"Gadeyne A, Sánchez Rodríguez C, Vanneste S, Di Rubbo S, Zauber H, Vanneste K, Van Leene J, De Winne N, Eeckhout D, Persiau G, Van De Slijke E, Cannoot B, Vercruysse L, Mayers J, Adamowski M, Kania U, Ehrlich M, Schweighofer A, Ketelaar T, Maere S, Bednarek S, Friml J, Gevaert K, Witters E, Russinova E, Persson S, De Jaeger G, Van Damme D. 2014. The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants. Cell. 156(4), 691–704.","mla":"Gadeyne, Astrid, et al. “The TPLATE Adaptor Complex Drives Clathrin-Mediated Endocytosis in Plants.” <i>Cell</i>, vol. 156, no. 4, Cell Press, 2014, pp. 691–704, doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.039\">10.1016/j.cell.2014.01.039</a>.","apa":"Gadeyne, A., Sánchez Rodríguez, C., Vanneste, S., Di Rubbo, S., Zauber, H., Vanneste, K., … Van Damme, D. (2014). The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2014.01.039\">https://doi.org/10.1016/j.cell.2014.01.039</a>","chicago":"Gadeyne, Astrid, Clara Sánchez Rodríguez, Steffen Vanneste, Simone Di Rubbo, Henrik Zauber, Kevin Vanneste, Jelle Van Leene, et al. “The TPLATE Adaptor Complex Drives Clathrin-Mediated Endocytosis in Plants.” <i>Cell</i>. Cell Press, 2014. <a href=\"https://doi.org/10.1016/j.cell.2014.01.039\">https://doi.org/10.1016/j.cell.2014.01.039</a>."},"month":"02","intvolume":"       156","language":[{"iso":"eng"}],"page":"691 - 704","isi":1,"_id":"2240","department":[{"_id":"JiFr"}],"publication_identifier":{"issn":["0092-8674"]},"date_published":"2014-02-13T00:00:00Z","publisher":"Cell Press","author":[{"full_name":"Gadeyne, Astrid","first_name":"Astrid","last_name":"Gadeyne"},{"first_name":"Clara","full_name":"Sánchez Rodríguez, Clara","last_name":"Sánchez Rodríguez"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"last_name":"Di Rubbo","first_name":"Simone","full_name":"Di Rubbo, Simone"},{"full_name":"Zauber, Henrik","first_name":"Henrik","last_name":"Zauber"},{"first_name":"Kevin","full_name":"Vanneste, Kevin","last_name":"Vanneste"},{"full_name":"Van Leene, Jelle","first_name":"Jelle","last_name":"Van Leene"},{"full_name":"De Winne, Nancy","first_name":"Nancy","last_name":"De Winne"},{"first_name":"Dominique","full_name":"Eeckhout, Dominique","last_name":"Eeckhout"},{"last_name":"Persiau","first_name":"Geert","full_name":"Persiau, Geert"},{"last_name":"Van De Slijke","full_name":"Van De Slijke, Eveline","first_name":"Eveline"},{"first_name":"Bernard","full_name":"Cannoot, Bernard","last_name":"Cannoot"},{"last_name":"Vercruysse","full_name":"Vercruysse, Leen","first_name":"Leen"},{"first_name":"Jonathan","full_name":"Mayers, Jonathan","last_name":"Mayers"},{"orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek","full_name":"Adamowski, Maciek","last_name":"Adamowski"},{"last_name":"Kania","full_name":"Kania, Urszula","first_name":"Urszula","id":"4AE5C486-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matthias","full_name":"Ehrlich, Matthias","last_name":"Ehrlich"},{"first_name":"Alois","full_name":"Schweighofer, Alois","last_name":"Schweighofer"},{"full_name":"Ketelaar, Tijs","first_name":"Tijs","last_name":"Ketelaar"},{"last_name":"Maere","first_name":"Steven","full_name":"Maere, Steven"},{"full_name":"Bednarek, Sebastian","first_name":"Sebastian","last_name":"Bednarek"},{"full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"full_name":"Gevaert, Kris","first_name":"Kris","last_name":"Gevaert"},{"first_name":"Erwin","full_name":"Witters, Erwin","last_name":"Witters"},{"first_name":"Eugenia","full_name":"Russinova, Eugenia","last_name":"Russinova"},{"full_name":"Persson, Staffan","first_name":"Staffan","last_name":"Persson"},{"first_name":"Geert","full_name":"De Jaeger, Geert","last_name":"De Jaeger"},{"last_name":"Van Damme","full_name":"Van Damme, Daniël","first_name":"Daniël"}],"day":"13","article_processing_charge":"No","year":"2014","scopus_import":"1","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis is the major mechanism for eukaryotic plasma membrane-based proteome turn-over. In plants, clathrin-mediated endocytosis is essential for physiology and development, but the identification and organization of the machinery operating this process remains largely obscure. Here, we identified an eight-core-component protein complex, the TPLATE complex, essential for plant growth via its role as major adaptor module for clathrin-mediated endocytosis. This complex consists of evolutionarily unique proteins that associate closely with core endocytic elements. The TPLATE complex is recruited as dynamic foci at the plasma membrane preceding recruitment of adaptor protein complex 2, clathrin, and dynamin-related proteins. Reduced function of different complex components severely impaired internalization of assorted endocytic cargoes, demonstrating its pivotal role in clathrin-mediated endocytosis. Taken together, the TPLATE complex is an early endocytic module representing a unique evolutionary plant adaptation of the canonical eukaryotic pathway for clathrin-mediated endocytosis."}],"publication_status":"published","status":"public","external_id":{"isi":["000331379800009"]},"issue":"4","oa_version":"None","publist_id":"4721","doi":"10.1016/j.cell.2014.01.039","title":"The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants"},{"abstract":[{"text":"MicroRNAs (miRNAs) are small RNAs that play important regulatory roles in many cellular pathways. MiRNAs associate with members of the Argonaute protein family and bind to partially complementary sequences on mRNAs and induce translational repression or mRNA decay. Using deep sequencing and Northern blotting, we characterized miRNA expression in wild type and miR-155-deficient dendritic cells (DCs) and macrophages. Analysis of different stimuli (LPS, LDL, eLDL, oxLDL) reveals a direct influence of miR-155 on the expression levels of other miRNAs. For example, miR-455 is negatively regulated in miR-155-deficient cells possibly due to inhibition of the transcription factor C/EBPbeta by miR-155. Based on our comprehensive data sets, we propose a model of hierarchical miRNA expression dominated by miR-155 in DCs and macrophages.","lang":"eng"}],"publication_status":"published","year":"2014","scopus_import":"1","status":"public","publisher":"Elsevier","author":[{"last_name":"Dueck","first_name":"Anne","full_name":"Dueck, Anne"},{"last_name":"Eichner","full_name":"Eichner, Alexander","first_name":"Alexander","id":"4DFA52AE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K"},{"first_name":"Gunter","full_name":"Meister, Gunter","last_name":"Meister"}],"date_published":"2014-02-14T00:00:00Z","day":"14","article_processing_charge":"No","publist_id":"4714","oa_version":"None","title":"A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation","doi":"10.1016/j.febslet.2014.01.009","external_id":{"isi":["000331115700016"]},"issue":"4","date_created":"2018-12-11T11:56:31Z","quality_controlled":"1","date_updated":"2025-09-29T11:19:23Z","publication":"FEBS Letters","citation":{"ieee":"A. Dueck, A. Eichner, M. K. Sixt, and G. Meister, “A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation,” <i>FEBS Letters</i>, vol. 588, no. 4. Elsevier, pp. 632–640, 2014.","short":"A. Dueck, A. Eichner, M.K. Sixt, G. Meister, FEBS Letters 588 (2014) 632–640.","ama":"Dueck A, Eichner A, Sixt MK, Meister G. A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation. <i>FEBS Letters</i>. 2014;588(4):632-640. doi:<a href=\"https://doi.org/10.1016/j.febslet.2014.01.009\">10.1016/j.febslet.2014.01.009</a>","ista":"Dueck A, Eichner A, Sixt MK, Meister G. 2014. A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation. FEBS Letters. 588(4), 632–640.","mla":"Dueck, Anne, et al. “A MiR-155-Dependent MicroRNA Hierarchy in Dendritic Cell Maturation and Macrophage Activation.” <i>FEBS Letters</i>, vol. 588, no. 4, Elsevier, 2014, pp. 632–40, doi:<a href=\"https://doi.org/10.1016/j.febslet.2014.01.009\">10.1016/j.febslet.2014.01.009</a>.","apa":"Dueck, A., Eichner, A., Sixt, M. K., &#38; Meister, G. (2014). A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation. <i>FEBS Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.febslet.2014.01.009\">https://doi.org/10.1016/j.febslet.2014.01.009</a>","chicago":"Dueck, Anne, Alexander Eichner, Michael K Sixt, and Gunter Meister. “A MiR-155-Dependent MicroRNA Hierarchy in Dendritic Cell Maturation and Macrophage Activation.” <i>FEBS Letters</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.febslet.2014.01.009\">https://doi.org/10.1016/j.febslet.2014.01.009</a>."},"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":588,"_id":"2242","isi":1,"department":[{"_id":"MiSi"}],"page":"632 - 640","publication_identifier":{"issn":["0014-5793"]},"intvolume":"       588","month":"02","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"series_title":"Methods in Molecular Biology","intvolume":"      1056","month":"01","editor":[{"last_name":"Hicks","first_name":"Glenn","full_name":"Hicks, Glenn"},{"last_name":"Robert","full_name":"Robert, Stéphanie","first_name":"Stéphanie"}],"publication_identifier":{"issn":["1064-3745"]},"_id":"2245","department":[{"_id":"JiFr"}],"page":"255 - 264","alternative_title":["Methods in Molecular Biology"],"volume":1056,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Plant Chemical Genomics","type":"book_chapter","citation":{"ama":"Simon S, Skůpa P, Dobrev P, Petrášek J, Zažímalová E, Friml J. Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters. In: Hicks G, Robert S, eds. <i>Plant Chemical Genomics</i>. Vol 1056. Methods in Molecular Biology. Springer; 2014:255-264. doi:<a href=\"https://doi.org/10.1007/978-1-62703-592-7_23\">10.1007/978-1-62703-592-7_23</a>","short":"S. Simon, P. Skůpa, P. Dobrev, J. Petrášek, E. Zažímalová, J. Friml, in:, G. Hicks, S. Robert (Eds.), Plant Chemical Genomics, Springer, 2014, pp. 255–264.","ista":"Simon S, Skůpa P, Dobrev P, Petrášek J, Zažímalová E, Friml J. 2014.Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters. In: Plant Chemical Genomics. Methods in Molecular Biology, vol. 1056, 255–264.","ieee":"S. Simon, P. Skůpa, P. Dobrev, J. Petrášek, E. Zažímalová, and J. Friml, “Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters,” in <i>Plant Chemical Genomics</i>, vol. 1056, G. Hicks and S. Robert, Eds. Springer, 2014, pp. 255–264.","apa":"Simon, S., Skůpa, P., Dobrev, P., Petrášek, J., Zažímalová, E., &#38; Friml, J. (2014). Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters. In G. Hicks &#38; S. Robert (Eds.), <i>Plant Chemical Genomics</i> (Vol. 1056, pp. 255–264). Springer. <a href=\"https://doi.org/10.1007/978-1-62703-592-7_23\">https://doi.org/10.1007/978-1-62703-592-7_23</a>","chicago":"Simon, Sibu, Petr Skůpa, Petre Dobrev, Jan Petrášek, Eva Zažímalová, and Jiří Friml. “Analyzing the in Vivo Status of Exogenously Applied Auxins: A HPLC-Based Method to Characterize the Intracellularly Localized Auxin Transporters.” In <i>Plant Chemical Genomics</i>, edited by Glenn Hicks and Stéphanie Robert, 1056:255–64. Methods in Molecular Biology. Springer, 2014. <a href=\"https://doi.org/10.1007/978-1-62703-592-7_23\">https://doi.org/10.1007/978-1-62703-592-7_23</a>.","mla":"Simon, Sibu, et al. “Analyzing the in Vivo Status of Exogenously Applied Auxins: A HPLC-Based Method to Characterize the Intracellularly Localized Auxin Transporters.” <i>Plant Chemical Genomics</i>, edited by Glenn Hicks and Stéphanie Robert, vol. 1056, Springer, 2014, pp. 255–64, doi:<a href=\"https://doi.org/10.1007/978-1-62703-592-7_23\">10.1007/978-1-62703-592-7_23</a>."},"date_created":"2018-12-11T11:56:32Z","quality_controlled":"1","date_updated":"2025-07-10T11:52:16Z","doi":"10.1007/978-1-62703-592-7_23","title":"Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters","publist_id":"4704","oa_version":"None","day":"01","article_processing_charge":"No","author":[{"last_name":"Simon","first_name":"Sibu","full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Skůpa, Petr","first_name":"Petr","last_name":"Skůpa"},{"last_name":"Dobrev","full_name":"Dobrev, Petre","first_name":"Petre"},{"last_name":"Petrášek","full_name":"Petrášek, Jan","first_name":"Jan"},{"full_name":"Zažímalová, Eva","first_name":"Eva","last_name":"Zažímalová"},{"last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Springer","date_published":"2014-01-01T00:00:00Z","status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"Exogenous application of biologically important molecules for plant growth promotion and/or regulation is very common both in plant research and horticulture. Plant hormones such as auxins and cytokinins are classes of compounds which are often applied exogenously. Nevertheless, plants possess a well-established machinery to regulate the active pool of exogenously applied compounds by converting them to metabolites and conjugates. Consequently, it is often very useful to know the in vivo status of applied compounds to connect them with some of the regulatory events in plant developmental processes. The in vivo status of applied compounds can be measured by incubating plants with radiolabeled compounds, followed by extraction, purification, and HPLC metabolic profiling of plant extracts. Recently we have used this method to characterize the intracellularly localized PIN protein, PIN5. Here we explain the method in detail, with a focus on general application. "}],"year":"2014","scopus_import":"1"},{"day":"01","article_processing_charge":"No","author":[{"first_name":"Daniel","full_name":"Capek, Daniel","orcid":"0000-0001-5199-9940","id":"31C42484-F248-11E8-B48F-1D18A9856A87","last_name":"Capek"},{"first_name":"Brian","full_name":"Metscher, Brian","last_name":"Metscher"},{"full_name":"Müller, Gerd","first_name":"Gerd","last_name":"Müller"}],"publisher":"Wiley-Blackwell","date_published":"2014-01-01T00:00:00Z","status":"public","abstract":[{"text":"Avian forelimb digit homology remains one of the standard themes in comparative biology and EvoDevo research. In order to resolve the apparent contradictions between embryological and paleontological evidence a variety of hypotheses have been presented in recent years. The proposals range from excluding birds from the dinosaur clade, to assignments of homology by different criteria, or even assuming a hexadactyl tetrapod limb ground state. At present two approaches prevail: the frame shift hypothesis and the pyramid reduction hypothesis. While the former postulates a homeotic shift of digit identities, the latter argues for a gradual bilateral reduction of phalanges and digits. Here we present a new model that integrates elements from both hypotheses with the existing experimental and fossil evidence. We start from the main feature common to both earlier concepts, the initiating ontogenetic event: reduction and loss of the anterior-most digit. It is proposed that a concerted mechanism of molecular regulation and developmental mechanics is capable of shifting the boundaries of hoxD expression in embryonic forelimb buds as well as changing the digit phenotypes. Based on a distinction between positional (topological) and compositional (phenotypic) homology criteria, we argue that the identity of the avian digits is II, III, IV, despite a partially altered phenotype. Finally, we introduce an alternative digit reduction scheme that reconciles the current fossil evidence with the presented molecular-morphogenetic model. Our approach identifies specific experiments that allow to test whether gene expression can be shifted and digit phenotypes can be altered by induced digit loss or digit gain.","lang":"eng"}],"publication_status":"published","year":"2014","scopus_import":"1","issue":"1","external_id":{"isi":["000335377400001"]},"title":"Thumbs down: A molecular-morphogenetic approach to avian digit homology","doi":"10.1002/jez.b.22545","publist_id":"4701","oa_version":"None","volume":322,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Journal of Experimental Zoology Part B: Molecular and Developmental Evolution","type":"journal_article","citation":{"apa":"Capek, D., Metscher, B., &#38; Müller, G. (2014). Thumbs down: A molecular-morphogenetic approach to avian digit homology. <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/jez.b.22545\">https://doi.org/10.1002/jez.b.22545</a>","chicago":"Capek, Daniel, Brian Metscher, and Gerd Müller. “Thumbs down: A Molecular-Morphogenetic Approach to Avian Digit Homology.” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1002/jez.b.22545\">https://doi.org/10.1002/jez.b.22545</a>.","mla":"Capek, Daniel, et al. “Thumbs down: A Molecular-Morphogenetic Approach to Avian Digit Homology.” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>, vol. 322, no. 1, Wiley-Blackwell, 2014, pp. 1–12, doi:<a href=\"https://doi.org/10.1002/jez.b.22545\">10.1002/jez.b.22545</a>.","short":"D. Capek, B. Metscher, G. Müller, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 322 (2014) 1–12.","ama":"Capek D, Metscher B, Müller G. Thumbs down: A molecular-morphogenetic approach to avian digit homology. <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. 2014;322(1):1-12. doi:<a href=\"https://doi.org/10.1002/jez.b.22545\">10.1002/jez.b.22545</a>","ista":"Capek D, Metscher B, Müller G. 2014. Thumbs down: A molecular-morphogenetic approach to avian digit homology. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 322(1), 1–12.","ieee":"D. Capek, B. Metscher, and G. Müller, “Thumbs down: A molecular-morphogenetic approach to avian digit homology,” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>, vol. 322, no. 1. Wiley-Blackwell, pp. 1–12, 2014."},"date_created":"2018-12-11T11:56:33Z","quality_controlled":"1","date_updated":"2025-09-29T11:18:02Z","language":[{"iso":"eng"}],"intvolume":"       322","month":"01","publication_identifier":{"issn":["1552-5007"]},"_id":"2248","department":[{"_id":"CaHe"}],"isi":1,"page":"1 - 12"},{"_id":"2250","isi":1,"department":[{"_id":"MD"}],"page":"10 - 20","has_accepted_license":"1","publication_identifier":{"issn":["0022-538X"]},"intvolume":"        88","ddc":["570"],"month":"01","language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:56:34Z","quality_controlled":"1","date_updated":"2025-09-29T11:17:05Z","file_date_updated":"2020-07-14T12:45:34Z","citation":{"ama":"Kuchibhatla D, Sherman W, Chung B, et al. Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently “orphan” viral proteins. <i>Journal of Virology</i>. 2014;88(1):10-20. doi:<a href=\"https://doi.org/10.1128/JVI.02595-13\">10.1128/JVI.02595-13</a>","short":"D. Kuchibhatla, W. Sherman, B. Chung, S. Cook, G. Schneider, B. Eisenhaber, D. Karlin, Journal of Virology 88 (2014) 10–20.","ista":"Kuchibhatla D, Sherman W, Chung B, Cook S, Schneider G, Eisenhaber B, Karlin D. 2014. Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently ‘orphan’ viral proteins. Journal of Virology. 88(1), 10–20.","ieee":"D. Kuchibhatla <i>et al.</i>, “Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently ‘orphan’ viral proteins,” <i>Journal of Virology</i>, vol. 88, no. 1. ASM, pp. 10–20, 2014.","apa":"Kuchibhatla, D., Sherman, W., Chung, B., Cook, S., Schneider, G., Eisenhaber, B., &#38; Karlin, D. (2014). Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently “orphan” viral proteins. <i>Journal of Virology</i>. ASM. <a href=\"https://doi.org/10.1128/JVI.02595-13\">https://doi.org/10.1128/JVI.02595-13</a>","chicago":"Kuchibhatla, Durga, Westley Sherman, Betty Chung, Shelley Cook, Georg Schneider, Birgit Eisenhaber, and David Karlin. “Powerful Sequence Similarity Search Methods and In-Depth Manual Analyses Can Identify Remote Homologs in Many Apparently ‘Orphan’ Viral Proteins.” <i>Journal of Virology</i>. ASM, 2014. <a href=\"https://doi.org/10.1128/JVI.02595-13\">https://doi.org/10.1128/JVI.02595-13</a>.","mla":"Kuchibhatla, Durga, et al. “Powerful Sequence Similarity Search Methods and In-Depth Manual Analyses Can Identify Remote Homologs in Many Apparently ‘Orphan’ Viral Proteins.” <i>Journal of Virology</i>, vol. 88, no. 1, ASM, 2014, pp. 10–20, doi:<a href=\"https://doi.org/10.1128/JVI.02595-13\">10.1128/JVI.02595-13</a>."},"type":"journal_article","publication":"Journal of Virology","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"volume":88,"publist_id":"4698","oa_version":"Published Version","title":"Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently \"orphan\" viral proteins","doi":"10.1128/JVI.02595-13","external_id":{"isi":["000329194600002"]},"issue":"1","abstract":[{"lang":"eng","text":"The genome sequences of new viruses often contain many &quot;orphan&quot; or &quot;taxon-specific&quot; proteins apparently lacking homologs. However, because viral proteins evolve very fast, commonly used sequence similarity detection methods such as BLAST may overlook homologs. We analyzed a data set of proteins from RNA viruses characterized as &quot;genus specific&quot; by BLAST. More powerful methods developed recently, such as HHblits or HHpred (available through web-based, user-friendly interfaces), could detect distant homologs of a quarter of these proteins, suggesting that these methods should be used to annotate viral genomes. In-depth manual analyses of a subset of the remaining sequences, guided by contextual information such as taxonomy, gene order, or domain cooccurrence, identified distant homologs of another third. Thus, a combination of powerful automated methods and manual analyses can uncover distant homologs of many proteins thought to be orphans. We expect these methodological results to be also applicable to cellular organisms, since they generally evolve much more slowly than RNA viruses. As an application, we reanalyzed the genome of a bee pathogen, Chronic bee paralysis virus (CBPV). We could identify homologs of most of its proteins thought to be orphans; in each case, identifying homologs provided functional clues. We discovered that CBPV encodes a domain homologous to the Alphavirus methyltransferase-guanylyltransferase; a putative membrane protein, SP24, with homologs in unrelated insect viruses and insect-transmitted plant viruses having different morphologies (cileviruses, higreviruses, blunerviruses, negeviruses); and a putative virion glycoprotein, ORF2, also found in negeviruses. SP24 and ORF2 are probably major structural components of the virionsd."}],"publication_status":"published","scopus_import":"1","year":"2014","status":"public","author":[{"first_name":"Durga","full_name":"Kuchibhatla, Durga","last_name":"Kuchibhatla"},{"first_name":"Westley","full_name":"Sherman, Westley","last_name":"Sherman"},{"full_name":"Chung, Betty","first_name":"Betty","last_name":"Chung"},{"last_name":"Cook","full_name":"Cook, Shelley","first_name":"Shelley"},{"id":"329095A0-F248-11E8-B48F-1D18A9856A87","full_name":"Schneider, Georg","first_name":"Georg","last_name":"Schneider"},{"full_name":"Eisenhaber, Birgit","first_name":"Birgit","last_name":"Eisenhaber"},{"last_name":"Karlin","full_name":"Karlin, David","first_name":"David"}],"publisher":"ASM","pubrep_id":"417","date_published":"2014-01-01T00:00:00Z","file":[{"file_name":"IST-2016-417-v1+1_J._Virol.-2014-Kuchibhatla-10-20.pdf","relation":"main_file","creator":"system","access_level":"open_access","checksum":"2c121b5e884992dfec5605bdf4e659da","file_id":"5029","file_size":825756,"date_created":"2018-12-12T10:13:43Z","date_updated":"2020-07-14T12:45:34Z","content_type":"application/pdf"}],"article_processing_charge":"No","day":"01"},{"external_id":{"pmid":["24366138"],"isi":["000332465300014"]},"issue":"1635","publist_id":"4697","oa_version":"Published Version","acknowledgement":"CC BY 3.0","doi":"10.1098/rstb.2012.0528","title":"Sharp wave/ripple network oscillations and learning-associated hippocampal maps","pubrep_id":"527","publisher":"Royal Society, The","author":[{"last_name":"Csicsvari","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L"},{"last_name":"Dupret","first_name":"David","full_name":"Dupret, David"}],"pmid":1,"date_published":"2014-02-05T00:00:00Z","file":[{"file_name":"IST-2016-527-v1+1_20120528.full.pdf","relation":"main_file","creator":"system","access_level":"open_access","checksum":"51beb33de71c9c19e0c205a20d206f9a","file_id":"5006","file_size":771896,"date_created":"2018-12-12T10:13:24Z","date_updated":"2020-07-14T12:45:34Z","content_type":"application/pdf"}],"day":"05","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Sharp wave/ripple (SWR, 150–250 Hz) hippocampal events have long been postulated to be involved in memory consolidation. However, more recent work has investigated SWRs that occur during active waking behaviour: findings that suggest that SWRs may also play a role in cell assembly strengthening or spatial working memory. Do such theories of SWR function apply to animal learning? This review discusses how general theories linking SWRs to memory-related function may explain circuit mechanisms related to rodent spatial learning and to the associated stabilization of new cognitive maps."}],"publication_status":"published","year":"2014","scopus_import":"1","corr_author":"1","status":"public","ddc":["570"],"intvolume":"       369","month":"02","language":[{"iso":"eng"}],"article_number":"20120528","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"isi":1,"_id":"2251","department":[{"_id":"JoCs"}],"has_accepted_license":"1","publication_identifier":{"issn":["09628436"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":369,"oa":1,"date_created":"2018-12-11T11:56:34Z","file_date_updated":"2020-07-14T12:45:34Z","date_updated":"2025-09-29T11:16:35Z","quality_controlled":"1","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","type":"journal_article","citation":{"mla":"Csicsvari, Jozsef L., and David Dupret. “Sharp Wave/Ripple Network Oscillations and Learning-Associated Hippocampal Maps.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 369, no. 1635, 20120528, Royal Society, The, 2014, doi:<a href=\"https://doi.org/10.1098/rstb.2012.0528\">10.1098/rstb.2012.0528</a>.","chicago":"Csicsvari, Jozsef L, and David Dupret. “Sharp Wave/Ripple Network Oscillations and Learning-Associated Hippocampal Maps.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, The, 2014. <a href=\"https://doi.org/10.1098/rstb.2012.0528\">https://doi.org/10.1098/rstb.2012.0528</a>.","apa":"Csicsvari, J. L., &#38; Dupret, D. (2014). Sharp wave/ripple network oscillations and learning-associated hippocampal maps. <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rstb.2012.0528\">https://doi.org/10.1098/rstb.2012.0528</a>","ieee":"J. L. Csicsvari and D. Dupret, “Sharp wave/ripple network oscillations and learning-associated hippocampal maps,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 369, no. 1635. Royal Society, The, 2014.","ista":"Csicsvari JL, Dupret D. 2014. Sharp wave/ripple network oscillations and learning-associated hippocampal maps. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 369(1635), 20120528.","ama":"Csicsvari JL, Dupret D. Sharp wave/ripple network oscillations and learning-associated hippocampal maps. <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2014;369(1635). doi:<a href=\"https://doi.org/10.1098/rstb.2012.0528\">10.1098/rstb.2012.0528</a>","short":"J.L. Csicsvari, D. Dupret, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 369 (2014)."}},{"publication_identifier":{"issn":["0022-1503"]},"department":[{"_id":"NiBa"}],"_id":"2252","isi":1,"page":"130 - 135","language":[{"iso":"eng"}],"intvolume":"       105","month":"01","citation":{"ista":"Phadke S, Paixao T, Pham T, Pham S, Zufall R. 2014. Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal of Heredity. 105(1), 130–135.","short":"S. Phadke, T. Paixao, T. Pham, S. Pham, R. Zufall, Journal of Heredity 105 (2014) 130–135.","ama":"Phadke S, Paixao T, Pham T, Pham S, Zufall R. Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. <i>Journal of Heredity</i>. 2014;105(1):130-135. doi:<a href=\"https://doi.org/10.1093/jhered/est063\">10.1093/jhered/est063</a>","ieee":"S. Phadke, T. Paixao, T. Pham, S. Pham, and R. Zufall, “Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila,” <i>Journal of Heredity</i>, vol. 105, no. 1. Oxford University Press, pp. 130–135, 2014.","chicago":"Phadke, Sujal, Tiago Paixao, Tuan Pham, Stephanie Pham, and Rebecca Zufall. “Genetic Background Alters Dominance Relationships between Mat Alleles in the Ciliate Tetrahymena Thermophila.” <i>Journal of Heredity</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/jhered/est063\">https://doi.org/10.1093/jhered/est063</a>.","apa":"Phadke, S., Paixao, T., Pham, T., Pham, S., &#38; Zufall, R. (2014). Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. <i>Journal of Heredity</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jhered/est063\">https://doi.org/10.1093/jhered/est063</a>","mla":"Phadke, Sujal, et al. “Genetic Background Alters Dominance Relationships between Mat Alleles in the Ciliate Tetrahymena Thermophila.” <i>Journal of Heredity</i>, vol. 105, no. 1, Oxford University Press, 2014, pp. 130–35, doi:<a href=\"https://doi.org/10.1093/jhered/est063\">10.1093/jhered/est063</a>."},"publication":"Journal of Heredity","type":"journal_article","date_created":"2018-12-11T11:56:35Z","date_updated":"2025-09-29T11:16:03Z","quality_controlled":"1","volume":105,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1093/jhered/est063","title":"Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila","publist_id":"4695","oa_version":"None","issue":"1","external_id":{"isi":["000328427800013"]},"corr_author":"1","status":"public","publication_status":"published","abstract":[{"text":"The pattern of inheritance and mechanism of sex determination can have important evolutionary consequences. We studied probabilistic sex determination in the ciliate Tetrahymena thermophila, which was previously shown to cause evolution of skewed sex ratios. We find that the genetic background alters the sex determination patterns of mat alleles in heterozygotes and that allelic interaction can differentially influence the expression probability of the 7 sexes. We quantify the dominance relationships between several mat alleles and find that A-type alleles, which specify sex I, are indeed recessive to B-type alleles, which are unable to specify that sex. Our results provide additional support for the presence of modifier loci and raise implications for the dynamics of sex ratios in populations of T. thermophila.","lang":"eng"}],"year":"2014","scopus_import":"1","day":"01","article_processing_charge":"No","author":[{"last_name":"Phadke","full_name":"Phadke, Sujal","first_name":"Sujal"},{"orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","full_name":"Paixao, Tiago","last_name":"Paixao"},{"last_name":"Pham","first_name":"Tuan","full_name":"Pham, Tuan"},{"last_name":"Pham","full_name":"Pham, Stephanie","first_name":"Stephanie"},{"last_name":"Zufall","full_name":"Zufall, Rebecca","first_name":"Rebecca"}],"publisher":"Oxford University Press","date_published":"2014-01-01T00:00:00Z"},{"oa_version":"Published Version","acknowledgement":"This work was funded by NSF grant IIS-0613435, NSF grant PHY-0957573, NSF grant CCF-0939370, NIH grant R01 EY14196, NIH grant P50 GM071508, the Fannie and John Hertz Foundation, the Swartz Foundation, the WM Keck Foundation, ANR Optima and the French State program “Investissements d'Avenir” [LIFESENSES: ANR-10-LABX-65], and the Austrian Research Foundation FWF P25651.","publist_id":"4689","title":"Searching for collective behavior in a large network of sensory neurons","doi":"10.1371/journal.pcbi.1003408","external_id":{"isi":["000337948500010"]},"issue":"1","year":"2014","scopus_import":"1","publication_status":"published","abstract":[{"text":"Maximum entropy models are the least structured probability distributions that exactly reproduce a chosen set of statistics measured in an interacting network. Here we use this principle to construct probabilistic models which describe the correlated spiking activity of populations of up to 120 neurons in the salamander retina as it responds to natural movies. Already in groups as small as 10 neurons, interactions between spikes can no longer be regarded as small perturbations in an otherwise independent system; for 40 or more neurons pairwise interactions need to be supplemented by a global interaction that controls the distribution of synchrony in the population. Here we show that such “K-pairwise” models—being systematic extensions of the previously used pairwise Ising models—provide an excellent account of the data. We explore the properties of the neural vocabulary by: 1) estimating its entropy, which constrains the population's capacity to represent visual information; 2) classifying activity patterns into a small set of metastable collective modes; 3) showing that the neural codeword ensembles are extremely inhomogenous; 4) demonstrating that the state of individual neurons is highly predictable from the rest of the population, allowing the capacity for error correction.","lang":"eng"}],"corr_author":"1","status":"public","date_published":"2014-01-02T00:00:00Z","pubrep_id":"436","author":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik"},{"last_name":"Marre","first_name":"Olivier","full_name":"Marre, Olivier"},{"last_name":"Amodei","first_name":"Dario","full_name":"Amodei, Dario"},{"full_name":"Schneidman, Elad","first_name":"Elad","last_name":"Schneidman"},{"last_name":"Bialek","full_name":"Bialek, William","first_name":"William"},{"first_name":"Michael","full_name":"Berry, Michael","last_name":"Berry"}],"publisher":"Public Library of Science","day":"02","article_processing_charge":"No","file":[{"date_created":"2018-12-12T10:12:46Z","date_updated":"2020-07-14T12:45:35Z","content_type":"application/pdf","access_level":"open_access","checksum":"c720222c5e924a4acb17f23b9381a6ca","file_id":"4965","file_size":2194790,"relation":"main_file","creator":"system","file_name":"IST-2016-436-v1+1_journal.pcbi.1003408.pdf"}],"has_accepted_license":"1","_id":"2257","isi":1,"department":[{"_id":"GaTk"}],"publication_identifier":{"issn":["1553-734X"]},"month":"01","ddc":["570"],"intvolume":"        10","article_number":"e1003408","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:35Z","quality_controlled":"1","date_updated":"2025-09-29T11:14:06Z","date_created":"2018-12-11T11:56:36Z","citation":{"apa":"Tkačik, G., Marre, O., Amodei, D., Schneidman, E., Bialek, W., &#38; Berry, M. (2014). Searching for collective behavior in a large network of sensory neurons. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1003408\">https://doi.org/10.1371/journal.pcbi.1003408</a>","chicago":"Tkačik, Gašper, Olivier Marre, Dario Amodei, Elad Schneidman, William Bialek, and Michael Berry. “Searching for Collective Behavior in a Large Network of Sensory Neurons.” <i>PLoS Computational Biology</i>. Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pcbi.1003408\">https://doi.org/10.1371/journal.pcbi.1003408</a>.","mla":"Tkačik, Gašper, et al. “Searching for Collective Behavior in a Large Network of Sensory Neurons.” <i>PLoS Computational Biology</i>, vol. 10, no. 1, e1003408, Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003408\">10.1371/journal.pcbi.1003408</a>.","ama":"Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry M. Searching for collective behavior in a large network of sensory neurons. <i>PLoS Computational Biology</i>. 2014;10(1). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003408\">10.1371/journal.pcbi.1003408</a>","short":"G. Tkačik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, M. Berry, PLoS Computational Biology 10 (2014).","ista":"Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry M. 2014. Searching for collective behavior in a large network of sensory neurons. PLoS Computational Biology. 10(1), e1003408.","ieee":"G. Tkačik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, “Searching for collective behavior in a large network of sensory neurons,” <i>PLoS Computational Biology</i>, vol. 10, no. 1. Public Library of Science, 2014."},"type":"journal_article","publication":"PLoS Computational Biology","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","related_material":{"record":[{"status":"public","relation":"research_data","id":"5562"}]},"volume":10,"oa":1},{"scopus_import":"1","year":"2014","publication_status":"published","abstract":[{"lang":"eng","text":"To reveal the full potential of human pluripotent stem cells, new methods for rapid, site-specific genomic engineering are needed. Here, we describe a system for precise genetic modification of human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). We identified a novel human locus, H11, located in a safe, intergenic, transcriptionally active region of chromosome 22, as the recipient site, to provide robust, ubiquitous expression of inserted genes. Recipient cell lines were established by site-specific placement of a ‘landing pad’ cassette carrying attP sites for phiC31 and Bxb1 integrases at the H11 locus by spontaneous or TALEN-assisted homologous recombination. Dual integrase cassette exchange (DICE) mediated by phiC31 and Bxb1 integrases was used to insert genes of interest flanked by phiC31 and Bxb1 attB sites at the H11 locus, replacing the landing pad. This system provided complete control over content, direction and copy number of inserted genes, with a specificity of 100%. A series of genes, including mCherry and various combinations of the neural transcription factors LMX1a, FOXA2 and OTX2, were inserted in recipient cell lines derived from H9 ESC, as well as iPSC lines derived from a Parkinson’s disease patient and a normal sibling control. The DICE system offers rapid, efficient and precise gene insertion in ESC and iPSC and is particularly well suited for repeated modifications of the same locus."}],"status":"public","date_published":"2014-03-05T00:00:00Z","publisher":"Oxford University Press","author":[{"full_name":"Zhu, Fangfang","first_name":"Fangfang","last_name":"Zhu"},{"last_name":"Gamboa","full_name":"Gamboa, Matthew","first_name":"Matthew"},{"last_name":"Farruggio","full_name":"Farruggio, Alfonso","first_name":"Alfonso"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"},{"last_name":"Tasic","first_name":"Bosiljka","full_name":"Tasic, Bosiljka"},{"last_name":"Schüle","first_name":"Birgitt","full_name":"Schüle, Birgitt"},{"full_name":"Chen Tsai, Yanru","first_name":"Yanru","last_name":"Chen Tsai"},{"first_name":"Michele","full_name":"Calos, Michele","last_name":"Calos"}],"pubrep_id":"961","article_processing_charge":"No","day":"05","file":[{"file_id":"4738","file_size":11044478,"access_level":"open_access","checksum":"e9268f5f96a820f04d7ebbf85927c3cb","content_type":"application/pdf","date_updated":"2020-07-14T12:45:35Z","date_created":"2018-12-12T10:09:15Z","file_name":"IST-2018-961-v1+1_2014_Hippenmeyer_DICE.pdf","creator":"system","relation":"main_file"}],"acknowledgement":"California Institute for Regenerative Medicine [RT2-01880 and TR2-01756]. Funding for open access charge: California Institute for Regenerative Medicine [RT2-01880 and TR2-01756]\r\nCC BY 3,0","oa_version":"Preprint","publist_id":"4684","title":"DICE, an efficient system for iterative genomic editing in human pluripotent stem cells","doi":"10.1093/nar/gkt1290","external_id":{"isi":["000333093600005"]},"issue":"5","quality_controlled":"1","date_updated":"2025-09-29T11:13:18Z","file_date_updated":"2020-07-14T12:45:35Z","date_created":"2018-12-11T11:56:38Z","publication":"Nucleic Acids Research","type":"journal_article","citation":{"mla":"Zhu, Fangfang, et al. “DICE, an Efficient System for Iterative Genomic Editing in Human Pluripotent Stem Cells.” <i>Nucleic Acids Research</i>, vol. 42, no. 5, e34, Oxford University Press, 2014, doi:<a href=\"https://doi.org/10.1093/nar/gkt1290\">10.1093/nar/gkt1290</a>.","chicago":"Zhu, Fangfang, Matthew Gamboa, Alfonso Farruggio, Simon Hippenmeyer, Bosiljka Tasic, Birgitt Schüle, Yanru Chen Tsai, and Michele Calos. “DICE, an Efficient System for Iterative Genomic Editing in Human Pluripotent Stem Cells.” <i>Nucleic Acids Research</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/nar/gkt1290\">https://doi.org/10.1093/nar/gkt1290</a>.","apa":"Zhu, F., Gamboa, M., Farruggio, A., Hippenmeyer, S., Tasic, B., Schüle, B., … Calos, M. (2014). DICE, an efficient system for iterative genomic editing in human pluripotent stem cells. <i>Nucleic Acids Research</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nar/gkt1290\">https://doi.org/10.1093/nar/gkt1290</a>","ieee":"F. Zhu <i>et al.</i>, “DICE, an efficient system for iterative genomic editing in human pluripotent stem cells,” <i>Nucleic Acids Research</i>, vol. 42, no. 5. Oxford University Press, 2014.","ista":"Zhu F, Gamboa M, Farruggio A, Hippenmeyer S, Tasic B, Schüle B, Chen Tsai Y, Calos M. 2014. DICE, an efficient system for iterative genomic editing in human pluripotent stem cells. Nucleic Acids Research. 42(5), e34.","ama":"Zhu F, Gamboa M, Farruggio A, et al. DICE, an efficient system for iterative genomic editing in human pluripotent stem cells. <i>Nucleic Acids Research</i>. 2014;42(5). doi:<a href=\"https://doi.org/10.1093/nar/gkt1290\">10.1093/nar/gkt1290</a>","short":"F. Zhu, M. Gamboa, A. Farruggio, S. Hippenmeyer, B. Tasic, B. Schüle, Y. Chen Tsai, M. Calos, Nucleic Acids Research 42 (2014)."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"volume":42,"has_accepted_license":"1","isi":1,"_id":"2261","department":[{"_id":"SiHi"}],"month":"03","intvolume":"        42","ddc":["571","610"],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"article_number":"e34","language":[{"iso":"eng"}]}]