[{"volume":5096,"main_file_link":[{"open_access":"0","url":"http://www.kyb.mpg.de/fileadmin/user_upload/files/publications/attachments/DAGM2008-Lampert-Blaschko_5072%5b0%5d.pdf"}],"extern":1,"status":"public","date_updated":"2021-01-12T07:51:41Z","citation":{"mla":"Lampert, Christoph, and Matthew Blaschko. <i>A Multiple Kernel Learning Approach to Joint Multi-Class Object Detection</i>. Vol. 5096, Springer, 2008, pp. 31–40, doi:<a href=\"https://doi.org/10.1007/978-3-540-69321-5_4\">10.1007/978-3-540-69321-5_4</a>.","short":"C. Lampert, M. Blaschko, in:, Springer, 2008, pp. 31–40.","ista":"Lampert C, Blaschko M. 2008. A multiple kernel learning approach to joint multi-class object detection. DAGM: German Association For Pattern Recognition, LNCS, vol. 5096, 31–40.","apa":"Lampert, C., &#38; Blaschko, M. (2008). A multiple kernel learning approach to joint multi-class object detection (Vol. 5096, pp. 31–40). Presented at the DAGM: German Association For Pattern Recognition, Springer. <a href=\"https://doi.org/10.1007/978-3-540-69321-5_4\">https://doi.org/10.1007/978-3-540-69321-5_4</a>","ama":"Lampert C, Blaschko M. A multiple kernel learning approach to joint multi-class object detection. In: Vol 5096. Springer; 2008:31-40. doi:<a href=\"https://doi.org/10.1007/978-3-540-69321-5_4\">10.1007/978-3-540-69321-5_4</a>","chicago":"Lampert, Christoph, and Matthew Blaschko. “A Multiple Kernel Learning Approach to Joint Multi-Class Object Detection,” 5096:31–40. Springer, 2008. <a href=\"https://doi.org/10.1007/978-3-540-69321-5_4\">https://doi.org/10.1007/978-3-540-69321-5_4</a>.","ieee":"C. Lampert and M. Blaschko, “A multiple kernel learning approach to joint multi-class object detection,” presented at the DAGM: German Association For Pattern Recognition, 2008, vol. 5096, pp. 31–40."},"year":"2008","date_published":"2008-07-07T00:00:00Z","type":"conference","doi":"10.1007/978-3-540-69321-5_4","day":"07","abstract":[{"lang":"eng","text":"Most current methods for multi-class object classification and localization work as independent 1-vs-rest classifiers. They decide whether and where an object is visible in an image purely on a per-class basis. Joint learning of more than one object class would generally be preferable, since this would allow the use of contextual information such as co-occurrence between classes. However, this approach is usually not employed because of its computational cost.\n\nIn this paper we propose a method to combine the efficiency of single class localization with a subsequent decision process that works jointly for all given object classes. By following a multiple kernel learning (MKL) approach, we automatically obtain a sparse dependency graph of relevant object classes on which to base the decision. Experiments on the PASCAL VOC 2006 and 2007 datasets show that the subsequent joint decision step clearly improves the accuracy compared to single class detection.\n"}],"publist_id":"2641","page":"31 - 40","quality_controlled":0,"publisher":"Springer","conference":{"name":"DAGM: German Association For Pattern Recognition"},"_id":"3716","author":[{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Christoph Lampert","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph"},{"full_name":"Blaschko,Matthew B","last_name":"Blaschko","first_name":"Matthew"}],"publication_status":"published","date_created":"2018-12-11T12:04:46Z","alternative_title":["LNCS"],"month":"07","title":"A multiple kernel learning approach to joint multi-class object detection","intvolume":"      5096"},{"publisher":"Springer","page":"279 - 311","quality_controlled":0,"publication_status":"published","date_created":"2018-12-11T12:04:50Z","title":"Single-molecule microscopy and force spectroscopy of membrane proteins","month":"01","intvolume":"        12","_id":"3726","publication":"Single Molecules and Nanotechnology","author":[{"full_name":"Engel, Andreas","last_name":"Engel","first_name":"Andreas"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Harald Janovjak","orcid":"0000-0002-8023-9315","last_name":"Janovjak","first_name":"Harald L"},{"full_name":"Fotiadis, Dimtrios","first_name":"Dimtrios","last_name":"Fotiadis"},{"full_name":"Kedrov, Alexej","last_name":"Kedrov","first_name":"Alexej"},{"full_name":"Cisneros, David","last_name":"Cisneros","first_name":"David"},{"full_name":"Mueller, Daniel J","last_name":"Mueller","first_name":"Daniel"}],"volume":12,"extern":1,"status":"public","doi":"10.1007/978-3-540-73924-1_11","day":"08","abstract":[{"lang":"eng","text":"Single-molecule atomic force microscopy (AFM) provides novel ways to characterize the structure-function relationship of native membrane proteins. High-resolution AFM topographs allow observing the structure of single proteins at sub-nanometer resolution as well as their conformational changes, oligomeric state, molecular dynamics and assembly. We will review these feasibilities illustrating examples of membrane proteins in native and reconstituted membranes. Classification of individual topographs of single proteins allows understanding the principles of motions of their extrinsic domains, to learn about their local structural flexibilities and to find the entropy minima of certain conformations. Combined with the visualization of functionally related conformational changes these insights allow understanding why certain flexibilities are required for the protein to function and how structurally flexible regions allow certain conformational changes. Complementary to AFM imaging, single-molecule force spectroscopy (SMFS) experiments detect molecular interactions established within and between membrane proteins. The sensitivity of this method makes it possible to measure interactions that stabilize secondary structures such as transmembrane α-helices, polypeptide loops and segments within. Changes in temperature or protein-protein assembly do not change the locations of stable structural segments, but influence their stability established by collective molecular interactions. Such changes alter the probability of proteins to choose a certain unfolding pathway. Recent examples have elucidated unfolding and refolding pathways of membrane proteins as well as their energy landscapes."}],"publist_id":"2503","date_updated":"2021-01-12T07:51:45Z","year":"2008","citation":{"apa":"Engel, A., Janovjak, H. L., Fotiadis, D., Kedrov, A., Cisneros, D., &#38; Mueller, D. (2008). Single-molecule microscopy and force spectroscopy of membrane proteins. In <i>Single Molecules and Nanotechnology</i> (Vol. 12, pp. 279–311). Springer. <a href=\"https://doi.org/10.1007/978-3-540-73924-1_11\">https://doi.org/10.1007/978-3-540-73924-1_11</a>","ama":"Engel A, Janovjak HL, Fotiadis D, Kedrov A, Cisneros D, Mueller D. Single-molecule microscopy and force spectroscopy of membrane proteins. In: <i>Single Molecules and Nanotechnology</i>. Vol 12. Springer; 2008:279-311. doi:<a href=\"https://doi.org/10.1007/978-3-540-73924-1_11\">10.1007/978-3-540-73924-1_11</a>","chicago":"Engel, Andreas, Harald L Janovjak, Dimtrios Fotiadis, Alexej Kedrov, David Cisneros, and Daniel Mueller. “Single-Molecule Microscopy and Force Spectroscopy of Membrane Proteins.” In <i>Single Molecules and Nanotechnology</i>, 12:279–311. Springer, 2008. <a href=\"https://doi.org/10.1007/978-3-540-73924-1_11\">https://doi.org/10.1007/978-3-540-73924-1_11</a>.","ieee":"A. Engel, H. L. Janovjak, D. Fotiadis, A. Kedrov, D. Cisneros, and D. Mueller, “Single-molecule microscopy and force spectroscopy of membrane proteins,” in <i>Single Molecules and Nanotechnology</i>, vol. 12, Springer, 2008, pp. 279–311.","short":"A. Engel, H.L. Janovjak, D. Fotiadis, A. Kedrov, D. Cisneros, D. Mueller, in:, Single Molecules and Nanotechnology, Springer, 2008, pp. 279–311.","mla":"Engel, Andreas, et al. “Single-Molecule Microscopy and Force Spectroscopy of Membrane Proteins.” <i>Single Molecules and Nanotechnology</i>, vol. 12, Springer, 2008, pp. 279–311, doi:<a href=\"https://doi.org/10.1007/978-3-540-73924-1_11\">10.1007/978-3-540-73924-1_11</a>.","ista":"Engel A, Janovjak HL, Fotiadis D, Kedrov A, Cisneros D, Mueller D. 2008.Single-molecule microscopy and force spectroscopy of membrane proteins. In: Single Molecules and Nanotechnology. vol. 12, 279–311."},"date_published":"2008-01-08T00:00:00Z","type":"book_chapter"},{"issue":"7","author":[{"orcid":"0000-0002-6699-1455","full_name":"Gasper Tkacik","first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gregor, Thomas","first_name":"Thomas","last_name":"Gregor"},{"last_name":"Bialek","first_name":"William","full_name":"Bialek, William S"}],"_id":"3734","publication":"PLoS One","intvolume":"         3","title":"The role of input noise in transcriptional regulation","month":"07","date_created":"2018-12-11T12:04:52Z","publication_status":"published","quality_controlled":0,"publisher":"Public Library of Science","type":"journal_article","date_published":"2008-07-23T00:00:00Z","citation":{"chicago":"Tkačik, Gašper, Thomas Gregor, and William Bialek. “The Role of Input Noise in Transcriptional Regulation.” <i>PLoS One</i>. Public Library of Science, 2008. <a href=\"https://doi.org/10.1371/journal.pone.0002774\">https://doi.org/10.1371/journal.pone.0002774</a>.","ieee":"G. Tkačik, T. Gregor, and W. Bialek, “The role of input noise in transcriptional regulation,” <i>PLoS One</i>, vol. 3, no. 7. Public Library of Science, 2008.","ama":"Tkačik G, Gregor T, Bialek W. The role of input noise in transcriptional regulation. <i>PLoS One</i>. 2008;3(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0002774\">10.1371/journal.pone.0002774</a>","apa":"Tkačik, G., Gregor, T., &#38; Bialek, W. (2008). The role of input noise in transcriptional regulation. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0002774\">https://doi.org/10.1371/journal.pone.0002774</a>","ista":"Tkačik G, Gregor T, Bialek W. 2008. The role of input noise in transcriptional regulation. PLoS One. 3(7).","short":"G. Tkačik, T. Gregor, W. Bialek, PLoS One 3 (2008).","mla":"Tkačik, Gašper, et al. “The Role of Input Noise in Transcriptional Regulation.” <i>PLoS One</i>, vol. 3, no. 7, Public Library of Science, 2008, doi:<a href=\"https://doi.org/10.1371/journal.pone.0002774\">10.1371/journal.pone.0002774</a>."},"year":"2008","date_updated":"2021-01-12T07:51:49Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publist_id":"2498","abstract":[{"lang":"eng","text":"Gene expression levels fluctuate even under constant external conditions. Much emphasis has usually been placed on the components of this noise that are due to randomness in transcription and translation. Here we focus on the role of noise associated with the inputs to transcriptional regulation; in particular, we analyze the effects of random arrival times and binding of transcription factors to their target sites along the genome. This contribution to the total noise sets a fundamental physical limit to the reliability of genetic control, and has clear signatures, but we show that these are easily obscured by experimental limitations and even by conventional methods for plotting the variance vs. mean expression level. We argue that simple, universal models of noise dominated by transcription and translation are inconsistent with the embedding of gene expression in a network of regulatory interactions. Analysis of recent experiments on transcriptional control in the early Drosophila embryo shows that these results are quantitatively consistent with the predicted signatures of input noise, and we discuss the experiments needed to test the importance of input noise more generally."}],"day":"23","doi":"10.1371/journal.pone.0002774","status":"public","extern":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2475664"}],"acknowledgement":"NSF Grant PHY-0650617; NIH grants P50 GM071508, R01 GM077599; Burroughs Wellcome Program in Biological Dynamics","volume":3},{"year":"2008","citation":{"ieee":"G. Tkačik, C. Callan, and W. Bialek, “Information capacity of genetic regulatory elements,” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 78, no. 1. American Institute of Physics, 2008.","chicago":"Tkačik, Gašper, Curtis Callan, and William Bialek. “Information Capacity of Genetic Regulatory Elements.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics, 2008. <a href=\"https://doi.org/10.1103/PhysRevE.78.011910\">https://doi.org/10.1103/PhysRevE.78.011910</a>.","apa":"Tkačik, G., Callan, C., &#38; Bialek, W. (2008). Information capacity of genetic regulatory elements. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.78.011910\">https://doi.org/10.1103/PhysRevE.78.011910</a>","ama":"Tkačik G, Callan C, Bialek W. Information capacity of genetic regulatory elements. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. 2008;78(1). doi:<a href=\"https://doi.org/10.1103/PhysRevE.78.011910\">10.1103/PhysRevE.78.011910</a>","ista":"Tkačik G, Callan C, Bialek W. 2008. Information capacity of genetic regulatory elements. Physical Review E Statistical Nonlinear and Soft Matter Physics. 78(1).","mla":"Tkačik, Gašper, et al. “Information Capacity of Genetic Regulatory Elements.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 78, no. 1, American Institute of Physics, 2008, doi:<a href=\"https://doi.org/10.1103/PhysRevE.78.011910\">10.1103/PhysRevE.78.011910</a>.","short":"G. Tkačik, C. Callan, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter Physics 78 (2008)."},"date_updated":"2021-01-12T07:51:51Z","type":"journal_article","date_published":"2008-07-21T00:00:00Z","day":"21","doi":"10.1103/PhysRevE.78.011910","publist_id":"2488","abstract":[{"text":"Changes in a cell's external or internal conditions are usually reflected in the concentrations of the relevant transcription factors. These proteins in turn modulate the expression levels of the genes under their control and sometimes need to perform nontrivial computations that integrate several inputs and affect multiple genes. At the same time, the activities of the regulated genes would fluctuate even if the inputs were held fixed, as a consequence of the intrinsic noise in the system, and such noise must fundamentally limit the reliability of any genetic computation. Here we use information theory to formalize the notion of information transmission in simple genetic regulatory elements in the presence of physically realistic noise sources. The dependence of this &quot;channel capacity&quot; on noise parameters, cooperativity and cost of making signaling molecules is explored systematically. We find that, in the range of parameters probed by recent in vivo measurements, capacities higher than one bit should be achievable. It is of course generally accepted that gene regulatory elements must, in order to function properly, have a capacity of at least one bit. The central point of our analysis is the demonstration that simple physical models of noisy gene transcription, with realistic parameters, can indeed achieve this capacity: it was not self-evident that this should be so. We also demonstrate that capacities significantly greater than one bit are possible, so that transcriptional regulation need not be limited to simple &quot;on-off&quot; components. The question whether real systems actually exploit this richer possibility is beyond the scope of this investigation.","lang":"eng"}],"volume":78,"status":"public","extern":1,"_id":"3739","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","issue":"1","author":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper","full_name":"Gasper Tkacik","orcid":"0000-0002-6699-1455"},{"first_name":"Curtis","last_name":"Callan","full_name":"Callan,Curtis G"},{"last_name":"Bialek","first_name":"William","full_name":"Bialek, William S"}],"date_created":"2018-12-11T12:04:54Z","publication_status":"published","intvolume":"        78","title":"Information capacity of genetic regulatory elements","month":"07","quality_controlled":0,"publisher":"American Institute of Physics"},{"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527900","open_access":"1"}],"volume":105,"acknowledgement":"P50 GM071508/GM/NIGMS NIH HHS/United States; R01 GM077599/GM/NIGMS NIH HHS/United States","status":"public","extern":1,"day":"01","doi":"10.1073/pnas.0806077105","publist_id":"2489","oa":1,"abstract":[{"text":"In the simplest view of transcriptional regulation, the expression of a gene is turned on or off by changes in the concentration of a transcription factor (TF). We use recent data on noise levels in gene expression to show that it should be possible to transmit much more than just one regulatory bit. Realizing this optimal information capacity would require that the dynamic range of TF concentrations used by the cell, the input/output relation of the regulatory module, and the noise in gene expression satisfy certain matching relations, which we derive. These results provide parameter-free, quantitative predictions connecting independently measurable quantities. Although we have considered only the simplified problem of a single gene responding to a single TF, we find that these predictions are in surprisingly good agreement with recent experiments on the Bicoid/Hunchback system in the early Drosophila embryo and that this system achieves approximately 90% of its theoretical maximum information transmission.","lang":"eng"}],"year":"2008","citation":{"chicago":"Tkačik, Gašper, Curtis Callan, and William Bialek. “Information Flow and Optimization in Transcriptional Regulation.” <i>PNAS</i>. National Academy of Sciences, 2008. <a href=\"https://doi.org/10.1073/pnas.0806077105\">https://doi.org/10.1073/pnas.0806077105</a>.","ieee":"G. Tkačik, C. Callan, and W. Bialek, “Information flow and optimization in transcriptional regulation,” <i>PNAS</i>, vol. 105, no. 34. National Academy of Sciences, pp. 12265–12270, 2008.","apa":"Tkačik, G., Callan, C., &#38; Bialek, W. (2008). Information flow and optimization in transcriptional regulation. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0806077105\">https://doi.org/10.1073/pnas.0806077105</a>","ama":"Tkačik G, Callan C, Bialek W. Information flow and optimization in transcriptional regulation. <i>PNAS</i>. 2008;105(34):12265-12270. doi:<a href=\"https://doi.org/10.1073/pnas.0806077105\">10.1073/pnas.0806077105</a>","ista":"Tkačik G, Callan C, Bialek W. 2008. Information flow and optimization in transcriptional regulation. PNAS. 105(34), 12265–12270.","short":"G. Tkačik, C. Callan, W. Bialek, PNAS 105 (2008) 12265–12270.","mla":"Tkačik, Gašper, et al. “Information Flow and Optimization in Transcriptional Regulation.” <i>PNAS</i>, vol. 105, no. 34, National Academy of Sciences, 2008, pp. 12265–70, doi:<a href=\"https://doi.org/10.1073/pnas.0806077105\">10.1073/pnas.0806077105</a>."},"date_updated":"2021-01-12T07:51:52Z","type":"journal_article","date_published":"2008-01-01T00:00:00Z","publisher":"National Academy of Sciences","quality_controlled":0,"page":"12265 - 12270","date_created":"2018-12-11T12:04:54Z","publication_status":"published","intvolume":"       105","month":"01","title":"Information flow and optimization in transcriptional regulation","_id":"3740","publication":"PNAS","issue":"34","author":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Gasper Tkacik"},{"first_name":"Curtis","last_name":"Callan","full_name":"Callan,Curtis G"},{"full_name":"Bialek, William S","first_name":"William","last_name":"Bialek"}]},{"page":"90 - 100","quality_controlled":0,"publisher":"Elsevier","_id":"3744","publication":"Biosystems","author":[{"last_name":"Tkacik","first_name":"Gasper","full_name":"Gasper Tkacik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marcelo","last_name":"Magnasco","full_name":"Magnasco, Marcelo O"}],"issue":"1-2","publication_status":"published","date_created":"2018-12-11T12:04:56Z","month":"07","title":"Decoding spike timing: The differential reverse-correlation method","intvolume":"        93","volume":93,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2792887","open_access":"1"}],"extern":1,"status":"public","date_updated":"2021-01-12T07:51:53Z","citation":{"apa":"Tkačik, G., &#38; Magnasco, M. (2008). Decoding spike timing: The differential reverse-correlation method. <i>Biosystems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.biosystems.2008.04.011\">https://doi.org/10.1016/j.biosystems.2008.04.011</a>","ama":"Tkačik G, Magnasco M. Decoding spike timing: The differential reverse-correlation method. <i>Biosystems</i>. 2008;93(1-2):90-100. doi:<a href=\"https://doi.org/10.1016/j.biosystems.2008.04.011\">10.1016/j.biosystems.2008.04.011</a>","ieee":"G. Tkačik and M. Magnasco, “Decoding spike timing: The differential reverse-correlation method,” <i>Biosystems</i>, vol. 93, no. 1–2. Elsevier, pp. 90–100, 2008.","chicago":"Tkačik, Gašper, and Marcelo Magnasco. “Decoding Spike Timing: The Differential Reverse-Correlation Method.” <i>Biosystems</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.biosystems.2008.04.011\">https://doi.org/10.1016/j.biosystems.2008.04.011</a>.","mla":"Tkačik, Gašper, and Marcelo Magnasco. “Decoding Spike Timing: The Differential Reverse-Correlation Method.” <i>Biosystems</i>, vol. 93, no. 1–2, Elsevier, 2008, pp. 90–100, doi:<a href=\"https://doi.org/10.1016/j.biosystems.2008.04.011\">10.1016/j.biosystems.2008.04.011</a>.","short":"G. Tkačik, M. Magnasco, Biosystems 93 (2008) 90–100.","ista":"Tkačik G, Magnasco M. 2008. Decoding spike timing: The differential reverse-correlation method. Biosystems. 93(1–2), 90–100."},"year":"2008","date_published":"2008-07-01T00:00:00Z","type":"journal_article","doi":"10.1016/j.biosystems.2008.04.011","day":"01","abstract":[{"lang":"eng","text":"It is widely acknowledged that detailed timing of action potentials is used to encode information, for example, in auditory pathways; however, the computational tools required to analyze encoding through timing are still in their infancy. We present a simple example of encoding, based on a recent model of time-frequency analysis, in which units fire action potentials when a certain condition is met, but the timing of the action potential depends also on other features of the stimulus. We show that, as a result, spike-triggered averages are smoothed so much that they do not represent the true features of the encoding. Inspired by this example, we present a simple method, differential reverse correlations, that can separate an analysis of what causes a neuron to spike, and what controls its timing. We analyze with this method the leaky integrate-and-fire neuron and show the method accurately reconstructs the model's kernel."}],"publist_id":"2482","oa":1},{"publist_id":"2477","oa":1,"date_published":"2008-04-30T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/pdf","file_name":"2008_PLOS1_Kinkhabwala.PDF","date_updated":"2020-07-14T12:46:15Z","checksum":"42c26f8337298a9ecadbe34a16139466","file_size":679786,"date_created":"2019-05-10T11:00:36Z","creator":"dernst","file_id":"6400","relation":"main_file","access_level":"open_access"}],"month":"04","article_number":"e2030","oa_version":"Published Version","publication":"PLoS One","has_accepted_license":"1","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Revealing the spectrum of combinatorial regulation of transcription at individual promoters is essential for understanding the complex structure of biological networks. However, the computations represented by the integration of various molecular signals at complex promoters are difficult to decipher in the absence of simple cis regulatory codes. Here we synthetically shuffle the regulatory architecture-operator sequences binding activators and repressors-of a canonical bacterial promoter. The resulting library of complex promoters allows for rapid exploration of promoter encoded logic regulation. Among all possible logic functions, NOR and ANDN promoter encoded logics predominate. A simple transcriptional cis regulatory code determines both logics, establishing a straightforward map between promoter structure and logic phenotype. The regulatory code is determined solely by the type of transcriptional regulation combinations: two repressors generate a NOR: NOT (a OR b) whereas a repressor and an activator generate an ANDN: a AND NOT b. Three-input versions of both logics, having an additional repressor as an input, are also present in the library. The resulting complex promoters cover a wide dynamic range of transcriptional strengths. Synthetic promoter shuffling represents a fast and efficient method for exploring the spectrum of complex regulatory functions that can be encoded by complex promoters. From an engineering point of view, synthetic promoter shuffling enables the experimental testing of the functional properties of complex promoters that cannot necessarily be inferred ab initio from the known properties of the individual genetic components. Synthetic promoter shuffling may provide a useful experimental tool for studying naturally occurring promoter shuffling."}],"doi":"10.1371/journal.pone.0002030","day":"30","external_id":{"pmid":["18446205"]},"date_updated":"2021-01-12T07:51:56Z","citation":{"chicago":"Kinkhabwala, Ali, and Calin C Guet. “Uncovering Cis Regulatory Codes Using Synthetic Promoter Shuffling.” <i>PLoS One</i>. Public Library of Science, 2008. <a href=\"https://doi.org/10.1371/journal.pone.0002030\">https://doi.org/10.1371/journal.pone.0002030</a>.","ieee":"A. Kinkhabwala and C. C. Guet, “Uncovering cis regulatory codes using synthetic promoter shuffling,” <i>PLoS One</i>, vol. 3, no. 4. Public Library of Science, 2008.","ama":"Kinkhabwala A, Guet CC. Uncovering cis regulatory codes using synthetic promoter shuffling. <i>PLoS One</i>. 2008;3(4). doi:<a href=\"https://doi.org/10.1371/journal.pone.0002030\">10.1371/journal.pone.0002030</a>","apa":"Kinkhabwala, A., &#38; Guet, C. C. (2008). Uncovering cis regulatory codes using synthetic promoter shuffling. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0002030\">https://doi.org/10.1371/journal.pone.0002030</a>","ista":"Kinkhabwala A, Guet CC. 2008. Uncovering cis regulatory codes using synthetic promoter shuffling. PLoS One. 3(4), e2030.","short":"A. Kinkhabwala, C.C. Guet, PLoS One 3 (2008).","mla":"Kinkhabwala, Ali, and Calin C. Guet. “Uncovering Cis Regulatory Codes Using Synthetic Promoter Shuffling.” <i>PLoS One</i>, vol. 3, no. 4, e2030, Public Library of Science, 2008, doi:<a href=\"https://doi.org/10.1371/journal.pone.0002030\">10.1371/journal.pone.0002030</a>."},"year":"2008","extern":"1","ddc":["570"],"volume":3,"title":"Uncovering cis regulatory codes using synthetic promoter shuffling","intvolume":"         3","publication_status":"published","date_created":"2018-12-11T12:04:58Z","author":[{"full_name":"Kinkhabwala, Ali","first_name":"Ali","last_name":"Kinkhabwala"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"}],"issue":"4","_id":"3751","pmid":1,"publisher":"Public Library of Science","file_date_updated":"2020-07-14T12:46:15Z","quality_controlled":"1"},{"volume":36,"acknowledgement":"PMCID: PMC2475643 ","extern":1,"status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"date_updated":"2021-01-12T07:51:57Z","citation":{"ista":"Guet CC, Bruneaux L, Min T, Siegal Gaskins D, Figueroa I, Emonet T, Cluzel P. 2008. Minimally invasive determination of mRNA concentration in single living bacteria. Nucleic Acids Research. 36(12).","short":"C.C. Guet, L. Bruneaux, T. Min, D. Siegal Gaskins, I. Figueroa, T. Emonet, P. Cluzel, Nucleic Acids Research 36 (2008).","mla":"Guet, Calin C., et al. “Minimally Invasive Determination of MRNA Concentration in Single Living Bacteria.” <i>Nucleic Acids Research</i>, vol. 36, no. 12, Oxford University Press, 2008, doi:<a href=\"https://doi.org/10.1093/nar/gkn329\">10.1093/nar/gkn329</a>.","chicago":"Guet, Calin C, Luke Bruneaux, Taejin Min, Dan Siegal Gaskins, Israel Figueroa, Thierry Emonet, and Philippe Cluzel. “Minimally Invasive Determination of MRNA Concentration in Single Living Bacteria.” <i>Nucleic Acids Research</i>. Oxford University Press, 2008. <a href=\"https://doi.org/10.1093/nar/gkn329\">https://doi.org/10.1093/nar/gkn329</a>.","ieee":"C. C. Guet <i>et al.</i>, “Minimally invasive determination of mRNA concentration in single living bacteria,” <i>Nucleic Acids Research</i>, vol. 36, no. 12. Oxford University Press, 2008.","apa":"Guet, C. C., Bruneaux, L., Min, T., Siegal Gaskins, D., Figueroa, I., Emonet, T., &#38; Cluzel, P. (2008). Minimally invasive determination of mRNA concentration in single living bacteria. <i>Nucleic Acids Research</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nar/gkn329\">https://doi.org/10.1093/nar/gkn329</a>","ama":"Guet CC, Bruneaux L, Min T, et al. Minimally invasive determination of mRNA concentration in single living bacteria. <i>Nucleic Acids Research</i>. 2008;36(12). doi:<a href=\"https://doi.org/10.1093/nar/gkn329\">10.1093/nar/gkn329</a>"},"year":"2008","date_published":"2008-01-01T00:00:00Z","type":"journal_article","doi":"10.1093/nar/gkn329","day":"01","abstract":[{"text":"Fluorescence correlation spectroscopy (FCS) has permitted the characterization of high concentrations of noncoding RNAs in a single living bacterium. Here, we extend the use of FCS to low concentrations of coding RNAs in single living cells. We genetically fuse a red fluorescent protein (RFP) gene and two binding sites for an RNA-binding protein, whose translated product is the RFP protein alone. Using this construct, we determine in single cells both the absolute [mRNA] concentration and the associated [RFP] expressed from an inducible plasmid. We find that the FCS method allows us to reliably monitor in real-time [mRNA] down to similar to 40 nM (i.e. approximately two transcripts per volume of detection). To validate these measurements, we show that [mRNA] is proportional to the associated expression of the RFP protein. This FCS-based technique establishes a framework for minimally invasive measurements of mRNA concentration in individual living bacteria.","lang":"eng"}],"publist_id":"2474","quality_controlled":0,"publisher":"Oxford University Press","publication":"Nucleic Acids Research","_id":"3754","author":[{"orcid":"0000-0001-6220-2052","full_name":"Calin Guet","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bruneaux,Luke","last_name":"Bruneaux","first_name":"Luke"},{"full_name":"Min,Taejin L","last_name":"Min","first_name":"Taejin"},{"full_name":"Siegal-Gaskins,Dan","first_name":"Dan","last_name":"Siegal Gaskins"},{"last_name":"Figueroa","first_name":"Israel","full_name":"Figueroa,Israel"},{"full_name":"Emonet,Thierry","first_name":"Thierry","last_name":"Emonet"},{"full_name":"Cluzel,Philippe","first_name":"Philippe","last_name":"Cluzel"}],"issue":"12","publication_status":"published","date_created":"2018-12-11T12:04:59Z","title":"Minimally invasive determination of mRNA concentration in single living bacteria","month":"01","intvolume":"        36"},{"publication_status":"published","oa_version":"None","date_created":"2018-12-11T12:05:01Z","article_processing_charge":"No","title":"Fast viscoelastic behavior with thin features","month":"08","intvolume":"        27","publication":"ACM Transactions on Graphics","_id":"3760","author":[{"first_name":"Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Turk, Greg","first_name":"Greg","last_name":"Turk"}],"issue":"3","publisher":"ACM","language":[{"iso":"eng"}],"doi":"10.1145/1360612.1360646","day":"01","abstract":[{"text":"We introduce a method for efficiently animating a wide range of deformable materials. We combine a high resolution surface mesh with a tetrahedral finite element simulator that makes use of frequent re-meshing. This combination allows for fast and detailed simulations of complex elastic and plastic behavior. We significantly expand the range of physical parameters that can be simulated with a single technique, and the results are free from common artifacts such as volume-loss, smoothing, popping, and the absence of thin features like strands and sheets. Our decision to couple a high resolution surface with low-resolution physics leads to efficient simulation and detailed surface features, and our approach to creating the tetrahedral mesh leads to an order-of-magnitude speedup over previous techniques in the time spent re-meshing. We compute masses, collisions, and surface tension forces on the scale of the fine mesh, which helps avoid visual artifacts due to the differing mesh resolutions. The result is a method that can simulate a large array of different material behaviors with high resolution features in a short amount of time.","lang":"eng"}],"publist_id":"2467","date_updated":"2023-02-23T11:41:29Z","year":"2008","citation":{"chicago":"Wojtan, Chris, and Greg Turk. “Fast Viscoelastic Behavior with Thin Features.” <i>ACM Transactions on Graphics</i>. ACM, 2008. <a href=\"https://doi.org/10.1145/1360612.1360646\">https://doi.org/10.1145/1360612.1360646</a>.","ieee":"C. Wojtan and G. Turk, “Fast viscoelastic behavior with thin features,” <i>ACM Transactions on Graphics</i>, vol. 27, no. 3. ACM, 2008.","apa":"Wojtan, C., &#38; Turk, G. (2008). Fast viscoelastic behavior with thin features. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/1360612.1360646\">https://doi.org/10.1145/1360612.1360646</a>","ama":"Wojtan C, Turk G. Fast viscoelastic behavior with thin features. <i>ACM Transactions on Graphics</i>. 2008;27(3). doi:<a href=\"https://doi.org/10.1145/1360612.1360646\">10.1145/1360612.1360646</a>","ista":"Wojtan C, Turk G. 2008. Fast viscoelastic behavior with thin features. ACM Transactions on Graphics. 27(3).","mla":"Wojtan, Chris, and Greg Turk. “Fast Viscoelastic Behavior with Thin Features.” <i>ACM Transactions on Graphics</i>, vol. 27, no. 3, ACM, 2008, doi:<a href=\"https://doi.org/10.1145/1360612.1360646\">10.1145/1360612.1360646</a>.","short":"C. Wojtan, G. Turk, ACM Transactions on Graphics 27 (2008)."},"date_published":"2008-08-01T00:00:00Z","type":"journal_article","volume":27,"main_file_link":[{"url":"http://www.cc.gatech.edu/~turk/my_papers/fast_goop_2008.pdf"}],"extern":"1","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"abstract":[{"text":"The geometrical representation of the space of phylogenetic trees implies a metric on the space of weighted trees. This metric, the geodesic distance, is the length of the shortest path through that space. We present an exact algorithm to compute this metric. For biologically reasonable trees, the implementation allows fast computations of the geodesic distance, although the running time of the algorithm is worst-case exponential. The algorithm was applied to pairs of 118 gene trees of the metazoa. The results show that a special path in tree space, the cone path, which can be computed in linear time, is a good approximation of the geodesic distance. The program GeoMeTree is a python implementation of the geodesic distance, and it is approximations and is available from www.cibiv.at/software/geometree.","lang":"eng"}],"publist_id":"2458","doi":"4200","day":"01","date_published":"2008-01-01T00:00:00Z","type":"journal_article","date_updated":"2021-01-12T07:52:04Z","citation":{"ama":"Kupczok A, Von Haeseler A, Klaere S. An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees. <i>Journal of Computational Biology</i>. 2008;15(6):577-591. doi:<a href=\"https://doi.org/4200\">4200</a>","apa":"Kupczok, A., Von Haeseler, A., &#38; Klaere, S. (2008). An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees. <i>Journal of Computational Biology</i>. Mary Ann Liebert. <a href=\"https://doi.org/4200\">https://doi.org/4200</a>","ieee":"A. Kupczok, A. Von Haeseler, and S. Klaere, “An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees.,” <i>Journal of Computational Biology</i>, vol. 15, no. 6. Mary Ann Liebert, pp. 577–591, 2008.","chicago":"Kupczok, Anne, Arndt Von Haeseler, and Steffen Klaere. “An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees.” <i>Journal of Computational Biology</i>. Mary Ann Liebert, 2008. <a href=\"https://doi.org/4200\">https://doi.org/4200</a>.","mla":"Kupczok, Anne, et al. “An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees.” <i>Journal of Computational Biology</i>, vol. 15, no. 6, Mary Ann Liebert, 2008, pp. 577–91, doi:<a href=\"https://doi.org/4200\">4200</a>.","short":"A. Kupczok, A. Von Haeseler, S. Klaere, Journal of Computational Biology 15 (2008) 577–591.","ista":"Kupczok A, Von Haeseler A, Klaere S. 2008. An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees. Journal of Computational Biology. 15(6), 577–591."},"year":"2008","extern":1,"status":"public","volume":15,"acknowledgement":"10.1089/cmb.2008.0068","month":"01","title":"An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees.","intvolume":"        15","publication_status":"published","date_created":"2018-12-11T12:05:04Z","author":[{"id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Anne Kupczok","last_name":"Kupczok","first_name":"Anne"},{"last_name":"Von Haeseler","first_name":"Arndt","full_name":"von Haeseler,Arndt"},{"full_name":"Klaere,Steffen","first_name":"Steffen","last_name":"Klaere"}],"issue":"6","publication":"Journal of Computational Biology","_id":"3769","publisher":"Mary Ann Liebert","page":"577 - 591","quality_controlled":0},{"oa":1,"publist_id":"2387","abstract":[{"text":"Dentate gyrus granule cells transmit action potentials (APs) along their unmyelinated mossy fibre axons to the CA3 region. Although the initiation and propagation of APs are fundamental steps during neural computation, little is known about the site of AP initiation and the speed of propagation in mossy fibre axons. To address these questions, we performed simultaneous somatic and axonal whole-cell recordings from granule cells in acute hippocampal slices of adult mice at approximately 23 degrees C. Injection of short current pulses or synaptic stimulation evoked axonal and somatic APs with similar amplitudes. By contrast, the time course was significantly different, as axonal APs had a higher maximal rate of rise (464 +/- 30 V s(-1) in the axon versus 297 +/- 12 V s(-1) in the soma, mean +/- s.e.m.). Furthermore, analysis of latencies between the axonal and somatic signals showed that APs were initiated in the proximal axon at approximately 20-30 mum distance from the soma, and propagated orthodromically with a velocity of 0.24 m s(-1). Qualitatively similar results were obtained at a recording temperature of approximately 34 degrees C. Modelling of AP propagation in detailed cable models of granule cells suggested that a approximately 4 times higher Na(+) channel density ( approximately 1000 pS mum(-2)) in the axon might account for both the higher rate of rise of axonal APs and the robust AP initiation in the proximal mossy fibre axon. This may be of critical importance to separate dendritic integration of thousands of synaptic inputs from the generation and transmission of a common AP output.","lang":"eng"}],"day":"01","doi":"10.1113/jphysiol.2007.150151 ","type":"journal_article","date_published":"2008-01-01T00:00:00Z","citation":{"ieee":"C. Schmidt Hieber, P. M. Jonas, and J. Bischofberger, “Action potential initiation and propagation in hippocampal mossy fibre axons,” <i>Journal of Physiology</i>, vol. 586, no. 7. Wiley-Blackwell, pp. 1849–57, 2008.","chicago":"Schmidt Hieber, Christoph, Peter M Jonas, and Josef Bischofberger. “Action Potential Initiation and Propagation in Hippocampal Mossy Fibre Axons.” <i>Journal of Physiology</i>. Wiley-Blackwell, 2008. <a href=\"https://doi.org/10.1113/jphysiol.2007.150151 \">https://doi.org/10.1113/jphysiol.2007.150151 </a>.","ama":"Schmidt Hieber C, Jonas PM, Bischofberger J. Action potential initiation and propagation in hippocampal mossy fibre axons. <i>Journal of Physiology</i>. 2008;586(7):1849-1857. doi:<a href=\"https://doi.org/10.1113/jphysiol.2007.150151 \">10.1113/jphysiol.2007.150151 </a>","apa":"Schmidt Hieber, C., Jonas, P. M., &#38; Bischofberger, J. (2008). Action potential initiation and propagation in hippocampal mossy fibre axons. <i>Journal of Physiology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1113/jphysiol.2007.150151 \">https://doi.org/10.1113/jphysiol.2007.150151 </a>","ista":"Schmidt Hieber C, Jonas PM, Bischofberger J. 2008. Action potential initiation and propagation in hippocampal mossy fibre axons. Journal of Physiology. 586(7), 1849–57.","short":"C. Schmidt Hieber, P.M. Jonas, J. Bischofberger, Journal of Physiology 586 (2008) 1849–57.","mla":"Schmidt Hieber, Christoph, et al. “Action Potential Initiation and Propagation in Hippocampal Mossy Fibre Axons.” <i>Journal of Physiology</i>, vol. 586, no. 7, Wiley-Blackwell, 2008, pp. 1849–57, doi:<a href=\"https://doi.org/10.1113/jphysiol.2007.150151 \">10.1113/jphysiol.2007.150151 </a>."},"year":"2008","date_updated":"2021-01-12T07:52:27Z","status":"public","extern":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375716/"}],"volume":586,"intvolume":"       586","month":"01","title":"Action potential initiation and propagation in hippocampal mossy fibre axons","date_created":"2018-12-11T12:05:21Z","publication_status":"published","issue":"7","author":[{"first_name":"Christoph","last_name":"Schmidt Hieber","full_name":"Schmidt-Hieber, Christoph"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Peter Jonas"},{"full_name":"Bischofberger, Josef","last_name":"Bischofberger","first_name":"Josef"}],"_id":"3822","publication":"Journal of Physiology","publisher":"Wiley-Blackwell","quality_controlled":0,"page":"1849 - 57"},{"publisher":"Elsevier","quality_controlled":0,"page":"5 - 7","date_created":"2018-12-11T12:05:22Z","publication_status":"published","intvolume":"        57","title":"The two sides of hippocampal mossy fiber plasticity (Review)","month":"01","publication":"Neuron","_id":"3823","issue":"1","author":[{"full_name":"Kerr, Angharad M","last_name":"Kerr","first_name":"Angharad"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Peter Jonas"}],"volume":57,"status":"public","extern":1,"day":"10","doi":"10.1016/j.neuron.2007.12.015","publist_id":"2388","abstract":[{"text":"Two studies in this issue of Neuron (Kwon and Castillo and Rebola et al.) show that the mossy fiber-CA3 pyramidal neuron synapse, a hippocampal synapse well known for its presynaptic plasticity, exhibits a novel form of long-term potentiation of NMDAR-mediated currents, which is induced and expressed postsynaptically.","lang":"eng"}],"citation":{"ista":"Kerr A, Jonas PM. 2008. The two sides of hippocampal mossy fiber plasticity (Review). Neuron. 57(1), 5–7.","short":"A. Kerr, P.M. Jonas, Neuron 57 (2008) 5–7.","mla":"Kerr, Angharad, and Peter M. Jonas. “The Two Sides of Hippocampal Mossy Fiber Plasticity (Review).” <i>Neuron</i>, vol. 57, no. 1, Elsevier, 2008, pp. 5–7, doi:<a href=\"https://doi.org/10.1016/j.neuron.2007.12.015\">10.1016/j.neuron.2007.12.015</a>.","chicago":"Kerr, Angharad, and Peter M Jonas. “The Two Sides of Hippocampal Mossy Fiber Plasticity (Review).” <i>Neuron</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.neuron.2007.12.015\">https://doi.org/10.1016/j.neuron.2007.12.015</a>.","ieee":"A. Kerr and P. M. Jonas, “The two sides of hippocampal mossy fiber plasticity (Review),” <i>Neuron</i>, vol. 57, no. 1. Elsevier, pp. 5–7, 2008.","ama":"Kerr A, Jonas PM. The two sides of hippocampal mossy fiber plasticity (Review). <i>Neuron</i>. 2008;57(1):5-7. doi:<a href=\"https://doi.org/10.1016/j.neuron.2007.12.015\">10.1016/j.neuron.2007.12.015</a>","apa":"Kerr, A., &#38; Jonas, P. M. (2008). The two sides of hippocampal mossy fiber plasticity (Review). <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2007.12.015\">https://doi.org/10.1016/j.neuron.2007.12.015</a>"},"year":"2008","date_updated":"2021-01-12T07:52:27Z","type":"journal_article","date_published":"2008-01-10T00:00:00Z"},{"type":"journal_article","date_published":"2008-01-01T00:00:00Z","citation":{"ama":"Bucurenciu I, Kulik Á, Schwaller B, Frotscher M, Jonas PM. Nanodomain coupling between Ca(2+) channels and Ca2+ sensors promotes fast and efficient transmitter release at a cortical GABAergic synapse. <i>Neuron</i>. 2008;57(4):536-545. doi:<a href=\"https://doi.org/10.1016/j.neuron.2007.12.026\">10.1016/j.neuron.2007.12.026</a>","apa":"Bucurenciu, I., Kulik, Á., Schwaller, B., Frotscher, M., &#38; Jonas, P. M. (2008). Nanodomain coupling between Ca(2+) channels and Ca2+ sensors promotes fast and efficient transmitter release at a cortical GABAergic synapse. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2007.12.026\">https://doi.org/10.1016/j.neuron.2007.12.026</a>","ieee":"I. Bucurenciu, Á. Kulik, B. Schwaller, M. Frotscher, and P. M. Jonas, “Nanodomain coupling between Ca(2+) channels and Ca2+ sensors promotes fast and efficient transmitter release at a cortical GABAergic synapse,” <i>Neuron</i>, vol. 57, no. 4. Elsevier, pp. 536–45, 2008.","chicago":"Bucurenciu, Iancu, Ákos Kulik, Beat Schwaller, Michael Frotscher, and Peter M Jonas. “Nanodomain Coupling between Ca(2+) Channels and Ca2+ Sensors Promotes Fast and Efficient Transmitter Release at a Cortical GABAergic Synapse.” <i>Neuron</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.neuron.2007.12.026\">https://doi.org/10.1016/j.neuron.2007.12.026</a>.","mla":"Bucurenciu, Iancu, et al. “Nanodomain Coupling between Ca(2+) Channels and Ca2+ Sensors Promotes Fast and Efficient Transmitter Release at a Cortical GABAergic Synapse.” <i>Neuron</i>, vol. 57, no. 4, Elsevier, 2008, pp. 536–45, doi:<a href=\"https://doi.org/10.1016/j.neuron.2007.12.026\">10.1016/j.neuron.2007.12.026</a>.","short":"I. Bucurenciu, Á. Kulik, B. Schwaller, M. Frotscher, P.M. Jonas, Neuron 57 (2008) 536–45.","ista":"Bucurenciu I, Kulik Á, Schwaller B, Frotscher M, Jonas PM. 2008. Nanodomain coupling between Ca(2+) channels and Ca2+ sensors promotes fast and efficient transmitter release at a cortical GABAergic synapse. Neuron. 57(4), 536–45."},"year":"2008","date_updated":"2021-01-12T07:52:27Z","publist_id":"2385","abstract":[{"text":"It is generally thought that transmitter release at mammalian central synapses is triggered by Ca2+ microdomains, implying loose coupling between presynaptic Ca2+ channels and Ca2+ sensors of exocytosis. Here we show that Ca2+ channel subunit immunoreactivity is highly concentrated in the active zone of GABAergic presynaptic terminals of putative parvalbumin-containing basket cells in the hippocampus. Paired recording combined with presynaptic patch pipette perfusion revealed that GABA release at basket cell-granule cell synapses is sensitive to millimolar concentrations of the fast Ca2+ chelator BAPTA but insensitive to the slow Ca2+ chelator EGTA. These results show that Ca2+ source and Ca2+ sensor are tightly coupled at this synapse, with distances in the range of 10-20 nm. Models of Ca2+ inflow-exocytosis coupling further reveal that the tightness of coupling increases efficacy, speed, and temporal precision of transmitter release. Thus, tight coupling contributes to fast feedforward and feedback inhibition in the hippocampal network.","lang":"eng"}],"day":"01","doi":"10.1016/j.neuron.2007.12.026","status":"public","extern":1,"volume":57,"issue":"4","author":[{"first_name":"Iancu","last_name":"Bucurenciu","full_name":"Bucurenciu, Iancu"},{"last_name":"Kulik","first_name":"Ákos","full_name":"Kulik, Ákos"},{"full_name":"Schwaller, Beat","last_name":"Schwaller","first_name":"Beat"},{"first_name":"Michael","last_name":"Frotscher","full_name":"Frotscher, Michael"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Peter Jonas","first_name":"Peter M","last_name":"Jonas"}],"_id":"3824","publication":"Neuron","intvolume":"        57","month":"01","title":"Nanodomain coupling between Ca(2+) channels and Ca2+ sensors promotes fast and efficient transmitter release at a cortical GABAergic synapse","date_created":"2018-12-11T12:05:22Z","publication_status":"published","quality_controlled":0,"page":"536 - 45","publisher":"Elsevier"},{"page":"2061 - 75","quality_controlled":0,"publisher":"Wiley-Blackwell","author":[{"first_name":"Yexica","last_name":"Aponte","full_name":"Aponte, Yexica"},{"full_name":"Bischofberger, Josef","last_name":"Bischofberger","first_name":"Josef"},{"full_name":"Peter Jonas","orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"issue":"8","publication":"Journal of Physiology","_id":"3825","title":"Efficient Ca(2+) buffering in fast-spiking basket cells of rat hippocampus","month":"01","intvolume":"       586","publication_status":"published","date_created":"2018-12-11T12:05:22Z","extern":1,"status":"public","volume":586,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2465201/","open_access":"1"}],"date_published":"2008-01-01T00:00:00Z","type":"journal_article","date_updated":"2021-01-12T07:52:28Z","citation":{"apa":"Aponte, Y., Bischofberger, J., &#38; Jonas, P. M. (2008). Efficient Ca(2+) buffering in fast-spiking basket cells of rat hippocampus. <i>Journal of Physiology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1113/jphysiol.2007.147298\">https://doi.org/10.1113/jphysiol.2007.147298</a>","ama":"Aponte Y, Bischofberger J, Jonas PM. Efficient Ca(2+) buffering in fast-spiking basket cells of rat hippocampus. <i>Journal of Physiology</i>. 2008;586(8):2061-2075. doi:<a href=\"https://doi.org/10.1113/jphysiol.2007.147298\">10.1113/jphysiol.2007.147298</a>","ieee":"Y. Aponte, J. Bischofberger, and P. M. Jonas, “Efficient Ca(2+) buffering in fast-spiking basket cells of rat hippocampus,” <i>Journal of Physiology</i>, vol. 586, no. 8. Wiley-Blackwell, pp. 2061–75, 2008.","chicago":"Aponte, Yexica, Josef Bischofberger, and Peter M Jonas. “Efficient Ca(2+) Buffering in Fast-Spiking Basket Cells of Rat Hippocampus.” <i>Journal of Physiology</i>. Wiley-Blackwell, 2008. <a href=\"https://doi.org/10.1113/jphysiol.2007.147298\">https://doi.org/10.1113/jphysiol.2007.147298</a>.","short":"Y. Aponte, J. Bischofberger, P.M. Jonas, Journal of Physiology 586 (2008) 2061–75.","mla":"Aponte, Yexica, et al. “Efficient Ca(2+) Buffering in Fast-Spiking Basket Cells of Rat Hippocampus.” <i>Journal of Physiology</i>, vol. 586, no. 8, Wiley-Blackwell, 2008, pp. 2061–75, doi:<a href=\"https://doi.org/10.1113/jphysiol.2007.147298\">10.1113/jphysiol.2007.147298</a>.","ista":"Aponte Y, Bischofberger J, Jonas PM. 2008. Efficient Ca(2+) buffering in fast-spiking basket cells of rat hippocampus. Journal of Physiology. 586(8), 2061–75."},"year":"2008","abstract":[{"lang":"eng","text":"Fast-spiking parvalbumin-expressing basket cells (BCs) represent a major type of inhibitory interneuron in the hippocampus. These cells inhibit principal cells in a temporally precise manner and are involved in the generation of network oscillations. Although BCs show a unique expression profile of Ca(2+)-permeable receptors, Ca(2+)-binding proteins and Ca(2+)-dependent signalling molecules, physiological Ca(2+) signalling in these interneurons has not been investigated. To study action potential (AP)-induced dendritic Ca(2+) influx and buffering, we combined whole-cell patch-clamp recordings with ratiometric Ca(2+) imaging from the proximal apical dendrites of rigorously identified BCs in acute slices, using the high-affinity Ca(2+) indicator fura-2 or the low-affinity dye fura-FF. Single APs evoked dendritic Ca(2+) transients with small amplitude. Bursts of APs evoked Ca(2+) transients with amplitudes that increased linearly with AP number. Analysis of Ca(2+) transients under steady-state conditions with different fura-2 concentrations and during loading with 200 microm fura-2 indicated that the endogenous Ca(2+)-binding ratio was approximately 200 (kappa(S) = 202 +/- 26 for the loading experiments). The peak amplitude of the Ca(2+) transients measured directly with 100 microm fura-FF was 39 nm AP(-1). At approximately 23 degrees C, the decay time constant of the Ca(2+) transients was 390 ms, corresponding to an extrusion rate of approximately 600 s(-1). At 34 degrees C, the decay time constant was 203 ms and the corresponding extrusion rate was approximately 1100 s(-1). At both temperatures, continuous theta-burst activity with three to five APs per theta cycle, as occurs in vivo during exploration, led to a moderate increase in the global Ca(2+) concentration that was proportional to AP number, whereas more intense stimulation was required to reach micromolar Ca(2+) concentrations and to shift Ca(2+) signalling into a non-linear regime. In conclusion, dentate gyrus BCs show a high endogenous Ca(2+)-binding ratio, a small AP-induced dendritic Ca(2+) influx, and a relatively slow Ca(2+) extrusion. These specific buffering properties of BCs will sharpen the time course of local Ca(2+) signals, while prolonging the decay of global Ca(2+) signals."}],"publist_id":"2386","oa":1,"doi":"10.1113/jphysiol.2007.147298","day":"01"},{"extern":1,"status":"public","volume":28,"abstract":[{"text":"Gamma frequency (30-100 Hz) oscillations in the mature cortex underlie higher cognitive functions. Fast signaling in GABAergic interneuron networks plays a key role in the generation of these oscillations. During development of the rodent brain, gamma activity appears at the end of the first postnatal week, but frequency and synchrony reach adult levels only by the fourth week. However, the mechanisms underlying the maturation of gamma activity are unclear. Here we demonstrate that hippocampal basket cells (BCs), the proposed cellular substrate of gamma oscillations, undergo marked changes in their morphological, intrinsic, and synaptic properties between postnatal day 6 (P6) and P25. During maturation, action potential duration, propagation time, duration of the release period, and decay time constant of IPSCs decreases by approximately 30-60%. Thus, postnatal development converts BCs from slow into fast signaling devices. Computational analysis reveals that BC networks with young intrinsic and synaptic properties as well as reduced connectivity generate oscillations with moderate coherence in the lower gamma frequency range. In contrast, BC networks with mature properties and increased connectivity generate highly coherent activity in the upper gamma frequency band. Thus, late postnatal maturation of BCs enhances coherence in neuronal networks and will thereby contribute to the development of cognitive brain functions.","lang":"eng"}],"publist_id":"2383","doi":"10.1523/JNEUROSCI.2890-08.2008","day":"01","date_published":"2008-01-01T00:00:00Z","type":"journal_article","date_updated":"2021-01-12T07:52:28Z","year":"2008","citation":{"short":"D. Doischer, J. Hosp, Y. Yanagawa, K. Obata, P.M. Jonas, I. Vida, M. Bartos, Journal of Neuroscience 28 (2008) 12956–68.","mla":"Doischer, Daniel, et al. “Postnatal Differentiation of Basket Cells from Slow to Fast Signaling Devices.” <i>Journal of Neuroscience</i>, vol. 28, no. 48, Society for Neuroscience, 2008, pp. 12956–68, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.2890-08.2008\">10.1523/JNEUROSCI.2890-08.2008</a>.","ista":"Doischer D, Hosp J, Yanagawa Y, Obata K, Jonas PM, Vida I, Bartos M. 2008. Postnatal differentiation of basket cells from slow to fast signaling devices. Journal of Neuroscience. 28(48), 12956–68.","ama":"Doischer D, Hosp J, Yanagawa Y, et al. Postnatal differentiation of basket cells from slow to fast signaling devices. <i>Journal of Neuroscience</i>. 2008;28(48):12956-12968. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.2890-08.2008\">10.1523/JNEUROSCI.2890-08.2008</a>","apa":"Doischer, D., Hosp, J., Yanagawa, Y., Obata, K., Jonas, P. M., Vida, I., &#38; Bartos, M. (2008). Postnatal differentiation of basket cells from slow to fast signaling devices. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.2890-08.2008\">https://doi.org/10.1523/JNEUROSCI.2890-08.2008</a>","ieee":"D. Doischer <i>et al.</i>, “Postnatal differentiation of basket cells from slow to fast signaling devices,” <i>Journal of Neuroscience</i>, vol. 28, no. 48. Society for Neuroscience, pp. 12956–68, 2008.","chicago":"Doischer, Daniel, Jonas Hosp, Yuchio Yanagawa, Kunihiko Obata, Peter M Jonas, Imre Vida, and Marlene Bartos. “Postnatal Differentiation of Basket Cells from Slow to Fast Signaling Devices.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2008. <a href=\"https://doi.org/10.1523/JNEUROSCI.2890-08.2008\">https://doi.org/10.1523/JNEUROSCI.2890-08.2008</a>."},"publisher":"Society for Neuroscience","page":"12956 - 68","quality_controlled":0,"month":"01","title":"Postnatal differentiation of basket cells from slow to fast signaling devices","intvolume":"        28","publication_status":"published","date_created":"2018-12-11T12:05:23Z","author":[{"first_name":"Daniel","last_name":"Doischer","full_name":"Doischer, Daniel"},{"full_name":"Hosp, Jonas Aurel","first_name":"Jonas","last_name":"Hosp"},{"last_name":"Yanagawa","first_name":"Yuchio","full_name":"Yanagawa, Yuchio"},{"last_name":"Obata","first_name":"Kunihiko","full_name":"Obata, Kunihiko"},{"full_name":"Peter Jonas","orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vida, Imre","last_name":"Vida","first_name":"Imre"},{"first_name":"Marlene","last_name":"Bartos","full_name":"Bartos, Marlene"}],"issue":"48","publication":"Journal of Neuroscience","_id":"3826"},{"date_published":"2008-01-01T00:00:00Z","type":"journal_article","date_updated":"2021-01-12T07:52:29Z","citation":{"apa":"Kerr, A., Reisinger, E., &#38; Jonas, P. M. (2008). Differential dependence of phasic transmitter release on synaptotagmin 1 at GABAergic and glutamatergic hippocampal synapses. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0800621105\">https://doi.org/10.1073/pnas.0800621105</a>","ama":"Kerr A, Reisinger E, Jonas PM. Differential dependence of phasic transmitter release on synaptotagmin 1 at GABAergic and glutamatergic hippocampal synapses. <i>PNAS</i>. 2008;105(40):15581-15586. doi:<a href=\"https://doi.org/10.1073/pnas.0800621105\">10.1073/pnas.0800621105</a>","ieee":"A. Kerr, E. Reisinger, and P. M. Jonas, “Differential dependence of phasic transmitter release on synaptotagmin 1 at GABAergic and glutamatergic hippocampal synapses,” <i>PNAS</i>, vol. 105, no. 40. National Academy of Sciences, pp. 15581–6, 2008.","chicago":"Kerr, Angharad, Ellen Reisinger, and Peter M Jonas. “Differential Dependence of Phasic Transmitter Release on Synaptotagmin 1 at GABAergic and Glutamatergic Hippocampal Synapses.” <i>PNAS</i>. National Academy of Sciences, 2008. <a href=\"https://doi.org/10.1073/pnas.0800621105\">https://doi.org/10.1073/pnas.0800621105</a>.","short":"A. Kerr, E. Reisinger, P.M. Jonas, PNAS 105 (2008) 15581–6.","mla":"Kerr, Angharad, et al. “Differential Dependence of Phasic Transmitter Release on Synaptotagmin 1 at GABAergic and Glutamatergic Hippocampal Synapses.” <i>PNAS</i>, vol. 105, no. 40, National Academy of Sciences, 2008, pp. 15581–86, doi:<a href=\"https://doi.org/10.1073/pnas.0800621105\">10.1073/pnas.0800621105</a>.","ista":"Kerr A, Reisinger E, Jonas PM. 2008. Differential dependence of phasic transmitter release on synaptotagmin 1 at GABAergic and glutamatergic hippocampal synapses. PNAS. 105(40), 15581–6."},"year":"2008","abstract":[{"text":"Previous studies revealed that synaptotagmin 1 is the major Ca(2+) sensor for fast synchronous transmitter release at excitatory synapses. However, the molecular identity of the Ca(2+) sensor at hippocampal inhibitory synapses has not been determined. To address the functional role of synaptotagmin 1 at identified inhibitory terminals, we made paired recordings from synaptically connected basket cells (BCs) and granule cells (GCs) in the dentate gyrus in organotypic slice cultures from wild-type and synaptotagmin 1-deficient mice. As expected, genetic elimination of synaptotagmin 1 abolished synchronous transmitter release at excitatory GC-BC synapses. However, synchronous release at inhibitory BC-GC synapses was maintained. Quantitative analysis revealed that elimination of synaptotagmin 1 reduced release probability and depression but maintained the synchrony of transmitter release at BC-GC synapses. Elimination of synaptotagmin 1 also increased the frequency of both miniature excitatory postsynaptic currents (measured in BCs) and miniature inhibitory postsynaptic currents (recorded in GCs), consistent with a clamping function of synaptotagmin 1 at both excitatory and inhibitory terminals. Single-cell reverse-transcription quantitative PCR analysis revealed that single BCs coexpressed multiple synaptotagmin isoforms, including synaptotagmin 1-5, 7, and 11-13. Our results indicate that, in contrast to excitatory synapses, synaptotagmin 1 is not absolutely required for synchronous release at inhibitory BC-GC synapses. Thus, alternative fast Ca(2+) sensors contribute to synchronous release of the inhibitory transmitter GABA in cortical circuits.","lang":"eng"}],"publist_id":"2384","doi":"10.1073/pnas.0800621105","day":"01","extern":1,"status":"public","volume":105,"author":[{"first_name":"Angharad","last_name":"Kerr","full_name":"Kerr, Angharad M"},{"full_name":"Reisinger, Ellen","first_name":"Ellen","last_name":"Reisinger"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Peter Jonas"}],"issue":"40","publication":"PNAS","_id":"3827","title":"Differential dependence of phasic transmitter release on synaptotagmin 1 at GABAergic and glutamatergic hippocampal synapses","month":"01","intvolume":"       105","publication_status":"published","date_created":"2018-12-11T12:05:23Z","page":"15581 - 6","quality_controlled":0,"publisher":"National Academy of Sciences"},{"publication_status":"published","date_created":"2018-12-11T12:05:38Z","alternative_title":["LNCS"],"title":"Value iteration","month":"01","intvolume":"      5000","publication":"25 Years in Model Checking","_id":"3872","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Krishnendu Chatterjee","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724"}],"publisher":"Springer","page":"107 - 138","quality_controlled":0,"doi":"10.1007/978-3-540-69850-0_7","day":"01","abstract":[{"text":"We survey value iteration algorithms on graphs. Such algorithms can be used for determining the existence of certain paths (model checking), the existence of certain strategies (game solving), and the probabilities of certain events (performance analysis). We classify the algorithms according to the value domain (boolean, probabilistic, or quantitative); according to the graph structure (nondeterministic, probabilistic, or multi-player); according to the desired property of paths (Borel level 1, 2, or 3); and according to the alternation depth and convergence rate of fixpoint computations.","lang":"eng"}],"publist_id":"2299","date_updated":"2021-01-12T07:52:51Z","year":"2008","citation":{"ieee":"K. Chatterjee and T. A. Henzinger, “Value iteration,” in <i>25 Years in Model Checking</i>, vol. 5000, Springer, 2008, pp. 107–138.","chicago":"Chatterjee, Krishnendu, and Thomas A Henzinger. “Value Iteration.” In <i>25 Years in Model Checking</i>, 5000:107–38. Springer, 2008. <a href=\"https://doi.org/10.1007/978-3-540-69850-0_7\">https://doi.org/10.1007/978-3-540-69850-0_7</a>.","apa":"Chatterjee, K., &#38; Henzinger, T. A. (2008). Value iteration. In <i>25 Years in Model Checking</i> (Vol. 5000, pp. 107–138). Springer. <a href=\"https://doi.org/10.1007/978-3-540-69850-0_7\">https://doi.org/10.1007/978-3-540-69850-0_7</a>","ama":"Chatterjee K, Henzinger TA. Value iteration. In: <i>25 Years in Model Checking</i>. Vol 5000. Springer; 2008:107-138. doi:<a href=\"https://doi.org/10.1007/978-3-540-69850-0_7\">10.1007/978-3-540-69850-0_7</a>","ista":"Chatterjee K, Henzinger TA. 2008.Value iteration. In: 25 Years in Model Checking. LNCS, vol. 5000, 107–138.","short":"K. Chatterjee, T.A. Henzinger, in:, 25 Years in Model Checking, Springer, 2008, pp. 107–138.","mla":"Chatterjee, Krishnendu, and Thomas A. Henzinger. “Value Iteration.” <i>25 Years in Model Checking</i>, vol. 5000, Springer, 2008, pp. 107–38, doi:<a href=\"https://doi.org/10.1007/978-3-540-69850-0_7\">10.1007/978-3-540-69850-0_7</a>."},"date_published":"2008-01-01T00:00:00Z","type":"book_chapter","acknowledgement":"This research was supported in part by the Swiss National Science Foundation and by the NSF grants CCR-0225610 and CCR-0234690.","volume":5000,"extern":1,"status":"public"},{"year":"2008","citation":{"ama":"Chatterjee K, Majumdar R, Henzinger TA. Controller synthesis with budget constraints. In: Vol 4981. Springer; 2008:72-86. doi:<a href=\"https://doi.org/DOI: 10.1007/978-3-540-78929-1_6\">DOI: 10.1007/978-3-540-78929-1_6</a>","apa":"Chatterjee, K., Majumdar, R., &#38; Henzinger, T. A. (2008). Controller synthesis with budget constraints (Vol. 4981, pp. 72–86). Presented at the HSCC: Hybrid Systems - Computation and Control, Springer. <a href=\"https://doi.org/DOI: 10.1007/978-3-540-78929-1_6\">https://doi.org/DOI: 10.1007/978-3-540-78929-1_6</a>","ieee":"K. Chatterjee, R. Majumdar, and T. A. Henzinger, “Controller synthesis with budget constraints,” presented at the HSCC: Hybrid Systems - Computation and Control, 2008, vol. 4981, pp. 72–86.","chicago":"Chatterjee, Krishnendu, Ritankar Majumdar, and Thomas A Henzinger. “Controller Synthesis with Budget Constraints,” 4981:72–86. Springer, 2008. <a href=\"https://doi.org/DOI: 10.1007/978-3-540-78929-1_6\">https://doi.org/DOI: 10.1007/978-3-540-78929-1_6</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Controller Synthesis with Budget Constraints</i>. Vol. 4981, Springer, 2008, pp. 72–86, doi:<a href=\"https://doi.org/DOI: 10.1007/978-3-540-78929-1_6\">DOI: 10.1007/978-3-540-78929-1_6</a>.","short":"K. Chatterjee, R. Majumdar, T.A. Henzinger, in:, Springer, 2008, pp. 72–86.","ista":"Chatterjee K, Majumdar R, Henzinger TA. 2008. Controller synthesis with budget constraints. HSCC: Hybrid Systems - Computation and Control, LNCS, vol. 4981, 72–86."},"date_updated":"2021-01-12T07:52:51Z","type":"conference","date_published":"2008-04-03T00:00:00Z","day":"03","doi":"DOI: 10.1007/978-3-540-78929-1_6","publist_id":"2296","abstract":[{"lang":"eng","text":"We study the controller synthesis problem under budget constraints. In this problem, there is a cost associated with making an observation, and a controller can make only a limited number of observations in each round so that the total cost of the observations does not exceed a given fixed budget. The controller must ensure some omega-regular requirement subject to the budget constraint. Budget constraints arise in designing and implementing controllers for resource-constrained embedded systems, where a controller may not have enough power, time, or bandwidth to obtain data from all sensors in each round. They lead to games of imperfect information, where the unknown information is not fixed a priori, but can vary from round to round, based on the choices made by the controller how to allocate its budget. We show that the budget-constrained synthesis problem for W-regular objectives is complete for exponential time. In addition to studying synthesis under a fixed budget constraint, we study the budget optimization problem, where given a plant, an objective, and observation costs, we have to find a controller that achieves the objective with minimal average accumulated cost (or minimal peak cost). We show that this problem is reducible to a game of imperfect information where the winning objective is a conjunction of an omega-regular condition and a long-run average condition (or a least max-cost condition), and this again leads to an exponential-time algorithm. Finally, we extend our results to games over infinite state spaces, and show that the budget-constrained synthesis problem is decidable for infinite state games with stable quotients of finite index. Consequently, the discrete time budget-constrained synthesis problem is decidable for rectangular hybrid automata."}],"volume":4981,"status":"public","extern":1,"_id":"3873","author":[{"orcid":"0000-0002-4561-241X","full_name":"Krishnendu Chatterjee","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Majumdar, Ritankar S","first_name":"Ritankar","last_name":"Majumdar"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","first_name":"Thomas A","last_name":"Henzinger"}],"date_created":"2018-12-11T12:05:38Z","publication_status":"published","intvolume":"      4981","title":"Controller synthesis with budget constraints","alternative_title":["LNCS"],"month":"04","quality_controlled":0,"page":"72 - 86","publisher":"Springer","conference":{"name":"HSCC: Hybrid Systems - Computation and Control"}},{"publisher":"Springer","conference":{"name":"HSCC: Hybrid Systems - Computation and Control"},"page":"87 - 100","quality_controlled":0,"publication_status":"published","date_created":"2018-12-11T12:05:38Z","month":"04","title":"Trading infinite memory for uniform randomness in timed games","alternative_title":["LNCS"],"intvolume":"      4981","_id":"3874","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Krishnendu Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Prabhu, Vinayak S","first_name":"Vinayak","last_name":"Prabhu"}],"acknowledgement":"This research was supported in part by the NSF grants CCR-0208875, CCR-0225610, CCR-0234690, by the Swiss National Science Foundation, and by the Artist2 European Network of Excellence.","volume":4981,"extern":1,"status":"public","doi":"10.1007/978-3-540-78929-1_7","day":"03","abstract":[{"text":"We consider concurrent two-player timed automaton games with omega-regular objectives specified as parity conditions. These games offer an appropriate model for the synthesis of real-time controllers. Earlier works on timed games focused on pure strategies for each player. We study, for the first time, the use of randomized strategies in such games. While pure (i.e., nonrandomized) strategies in timed games require infinite memory for winning even with respect to reachability objectives, we show that randomized strategies can win with finite memory with respect to all parity objectives. Also, the synthesized randomized real-time controllers are much simpler in structure than the corresponding pure controllers, and therefore easier to implement. For safety objectives we prove the existence of pure finite-memory winning strategies. Finally, while randomization helps in simplifying the strategies required for winning timed parity games, we prove that randomization does not help in winning at more states.","lang":"eng"}],"publist_id":"2297","date_updated":"2021-01-12T07:52:51Z","year":"2008","citation":{"mla":"Chatterjee, Krishnendu, et al. <i>Trading Infinite Memory for Uniform Randomness in Timed Games</i>. Vol. 4981, Springer, 2008, pp. 87–100, doi:<a href=\"https://doi.org/10.1007/978-3-540-78929-1_7\">10.1007/978-3-540-78929-1_7</a>.","short":"K. Chatterjee, T.A. Henzinger, V. Prabhu, in:, Springer, 2008, pp. 87–100.","ista":"Chatterjee K, Henzinger TA, Prabhu V. 2008. Trading infinite memory for uniform randomness in timed games. HSCC: Hybrid Systems - Computation and Control, LNCS, vol. 4981, 87–100.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Prabhu, V. (2008). Trading infinite memory for uniform randomness in timed games (Vol. 4981, pp. 87–100). Presented at the HSCC: Hybrid Systems - Computation and Control, Springer. <a href=\"https://doi.org/10.1007/978-3-540-78929-1_7\">https://doi.org/10.1007/978-3-540-78929-1_7</a>","ama":"Chatterjee K, Henzinger TA, Prabhu V. Trading infinite memory for uniform randomness in timed games. In: Vol 4981. Springer; 2008:87-100. doi:<a href=\"https://doi.org/10.1007/978-3-540-78929-1_7\">10.1007/978-3-540-78929-1_7</a>","ieee":"K. Chatterjee, T. A. Henzinger, and V. Prabhu, “Trading infinite memory for uniform randomness in timed games,” presented at the HSCC: Hybrid Systems - Computation and Control, 2008, vol. 4981, pp. 87–100.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Vinayak Prabhu. “Trading Infinite Memory for Uniform Randomness in Timed Games,” 4981:87–100. Springer, 2008. <a href=\"https://doi.org/10.1007/978-3-540-78929-1_7\">https://doi.org/10.1007/978-3-540-78929-1_7</a>."},"date_published":"2008-04-03T00:00:00Z","type":"conference"},{"intvolume":"      4962","alternative_title":["LNCS"],"title":"Model-checking omega-regular properties of interval Markov chains","month":"03","date_created":"2018-12-11T12:05:39Z","publication_status":"published","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Krishnendu Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sen","first_name":"Koushik","full_name":"Sen, Koushik"}],"_id":"3875","conference":{"name":"FoSSaCS: Foundations of Software Science and Computation Structures"},"publisher":"Springer","quality_controlled":0,"page":"302 - 317","publist_id":"2298","abstract":[{"lang":"eng","text":"We study the problem of model checking Interval-valued Discrete-time Markov Chains (IDTMC). IDTMCs are discrete-time finite Markov Chains for which the exact transition probabilities are riot known. Instead in IDTMCs, each transition is associated with an interval in which the actual transition probability must lie. We consider two semantic interpretations for the uncertainty in the transition probabilities of an IDTMC. In the first interpretation, we think of an IDTMC as representing a (possibly uncountable) family of (classical) discrete-time Markov Chains, where each member of the family is a Markov Chain whose transition probabilities lie within the interval range given in the IDTMC. We call this semantic interpretation Uncertain Markov Chains (UMC). In the second semantics for an IDTMC, which we call Interval Markov Decision Process (IMDP), we view the uncertainty as being resolved through non-determinism. In other words, each time a state is visited, we adversarially pick a transition distribution that respects the interval constraints, and take a probabilistic step according to the chosen distribution. We introduce a logic omega-PCTL that can express liveness, strong fairness, and omega-regular properties (such properties cannot be expressed in PCTL). We show that the omega-PCTL model checking problem for Uncertain Markov Chain semantics is decidable in PSPACE (same as the best known upper bound for PCTL) and for Interval Markov Decision Process semantics is decidable in coNP (improving the previous known PSPACE bound for PCTL). We also show that the qualitative fragment of the logic can lie solved in coNP for the UMC interpretation, and can be solved in polynomial time for a sub-class of UMCs. We also prove lower bounds for these model checking problems. We show that the model checking problem of IDTMCs with LTL formulas can be solved for both UMC and IMDP semantics by reduction to the model checking problem of IDTMC with omega-PcTL formulas."}],"day":"01","doi":"10.1007/978-3-540-78499-9_22","type":"conference","date_published":"2008-03-01T00:00:00Z","citation":{"ista":"Chatterjee K, Henzinger TA, Sen K. 2008. Model-checking omega-regular properties of interval Markov chains. FoSSaCS: Foundations of Software Science and Computation Structures, LNCS, vol. 4962, 302–317.","short":"K. Chatterjee, T.A. Henzinger, K. Sen, in:, Springer, 2008, pp. 302–317.","mla":"Chatterjee, Krishnendu, et al. <i>Model-Checking Omega-Regular Properties of Interval Markov Chains</i>. Vol. 4962, Springer, 2008, pp. 302–17, doi:<a href=\"https://doi.org/10.1007/978-3-540-78499-9_22\">10.1007/978-3-540-78499-9_22</a>.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Koushik Sen. “Model-Checking Omega-Regular Properties of Interval Markov Chains,” 4962:302–17. Springer, 2008. <a href=\"https://doi.org/10.1007/978-3-540-78499-9_22\">https://doi.org/10.1007/978-3-540-78499-9_22</a>.","ieee":"K. Chatterjee, T. A. Henzinger, and K. Sen, “Model-checking omega-regular properties of interval Markov chains,” presented at the FoSSaCS: Foundations of Software Science and Computation Structures, 2008, vol. 4962, pp. 302–317.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Sen, K. (2008). Model-checking omega-regular properties of interval Markov chains (Vol. 4962, pp. 302–317). Presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Springer. <a href=\"https://doi.org/10.1007/978-3-540-78499-9_22\">https://doi.org/10.1007/978-3-540-78499-9_22</a>","ama":"Chatterjee K, Henzinger TA, Sen K. Model-checking omega-regular properties of interval Markov chains. In: Vol 4962. Springer; 2008:302-317. doi:<a href=\"https://doi.org/10.1007/978-3-540-78499-9_22\">10.1007/978-3-540-78499-9_22</a>"},"year":"2008","date_updated":"2021-01-12T07:52:52Z","status":"public","extern":1,"volume":4962}]