[{"related_material":{"record":[{"status":"public","id":"818","relation":"dissertation_contains"}]},"title":"Bacterial responses to antibiotics and their combinations","doi":"10.1111/1758-2229.12190","year":"2014","ec_funded":1,"_id":"2001","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","project":[{"name":"Revealing the fundamental limits of cell growth","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013"},{"grant_number":"303507","name":"Optimality principles in responses to antibiotics","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"quality_controlled":"1","publist_id":"5076","volume":6,"date_updated":"2023-09-07T12:00:25Z","abstract":[{"text":"Antibiotics affect bacterial cell physiology at many levels. Rather than just compensating for the direct cellular defects caused by the drug, bacteria respond to antibiotics by changing their morphology, macromolecular composition, metabolism, gene expression and possibly even their mutation rate. Inevitably, these processes affect each other, resulting in a complex response with changes in the expression of numerous genes. Genome‐wide approaches can thus help in gaining a comprehensive understanding of bacterial responses to antibiotics. In addition, a combination of experimental and theoretical approaches is needed for identifying general principles that underlie these responses. Here, we review recent progress in our understanding of bacterial responses to antibiotics and their combinations, focusing on effects at the levels of growth rate and gene expression. We concentrate on studies performed in controlled laboratory conditions, which combine promising experimental techniques with quantitative data analysis and mathematical modeling. While these basic research approaches are not immediately applicable in the clinic, uncovering the principles and mechanisms underlying bacterial responses to antibiotics may, in the long term, contribute to the development of new treatment strategies to cope with and prevent the rise of resistant pathogenic bacteria.","lang":"eng"}],"author":[{"id":"39B66846-F248-11E8-B48F-1D18A9856A87","full_name":"Mitosch, Karin","last_name":"Mitosch","first_name":"Karin"},{"full_name":"Bollenbach, Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","citation":{"ieee":"K. Mitosch and M. T. Bollenbach, “Bacterial responses to antibiotics and their combinations,” <i>Environmental Microbiology Reports</i>, vol. 6, no. 6. Wiley, pp. 545–557, 2014.","apa":"Mitosch, K., &#38; Bollenbach, M. T. (2014). Bacterial responses to antibiotics and their combinations. <i>Environmental Microbiology Reports</i>. Wiley. <a href=\"https://doi.org/10.1111/1758-2229.12190\">https://doi.org/10.1111/1758-2229.12190</a>","chicago":"Mitosch, Karin, and Mark Tobias Bollenbach. “Bacterial Responses to Antibiotics and Their Combinations.” <i>Environmental Microbiology Reports</i>. Wiley, 2014. <a href=\"https://doi.org/10.1111/1758-2229.12190\">https://doi.org/10.1111/1758-2229.12190</a>.","mla":"Mitosch, Karin, and Mark Tobias Bollenbach. “Bacterial Responses to Antibiotics and Their Combinations.” <i>Environmental Microbiology Reports</i>, vol. 6, no. 6, Wiley, 2014, pp. 545–57, doi:<a href=\"https://doi.org/10.1111/1758-2229.12190\">10.1111/1758-2229.12190</a>.","ama":"Mitosch K, Bollenbach MT. Bacterial responses to antibiotics and their combinations. <i>Environmental Microbiology Reports</i>. 2014;6(6):545-557. doi:<a href=\"https://doi.org/10.1111/1758-2229.12190\">10.1111/1758-2229.12190</a>","short":"K. Mitosch, M.T. Bollenbach, Environmental Microbiology Reports 6 (2014) 545–557.","ista":"Mitosch K, Bollenbach MT. 2014. Bacterial responses to antibiotics and their combinations. Environmental Microbiology Reports. 6(6), 545–557."},"date_created":"2018-12-11T11:55:08Z","department":[{"_id":"ToBo"}],"publisher":"Wiley","scopus_import":1,"language":[{"iso":"eng"}],"month":"06","date_published":"2014-06-22T00:00:00Z","issue":"6","publication":"Environmental Microbiology Reports","page":"545 - 557","intvolume":"         6","status":"public","day":"22","type":"journal_article"},{"project":[{"grant_number":"268548","_id":"25C0F108-B435-11E9-9278-68D0E5697425","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7"}],"oa_version":"Published Version","quality_controlled":"1","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2002","oa":1,"date_updated":"2021-01-12T06:54:39Z","publist_id":"5074","volume":9,"author":[{"id":"394AB1C8-F248-11E8-B48F-1D18A9856A87","full_name":"Kim, Sooyun","last_name":"Kim","first_name":"Sooyun"}],"abstract":[{"text":"Oriens-lacunosum moleculare (O-LM) interneurons in the CA1 region of the hippocampus play a key role in feedback inhibition and in the control of network activity. However, how these cells are efficiently activated in the network remains unclear. To address this question, I performed recordings from CA1 pyramidal neuron axons, the presynaptic fibers that provide feedback innervation of these interneurons. Two forms of axonal action potential (AP) modulation were identified. First, repetitive stimulation resulted in activity-dependent AP broadening. Broadening showed fast onset, with marked changes in AP shape following a single AP. Second, tonic depolarization in CA1 pyramidal neuron somata induced AP broadening in the axon, and depolarization-induced broadening summated with activity-dependent broadening. Outsideout patch recordings from CA1 pyramidal neuron axons revealed a high density of a-dendrotoxin (α-DTX)-sensitive, inactivating K+ channels, suggesting that K+ channel inactivation mechanistically contributes to AP broadening. To examine the functional consequences of axonal AP modulation for synaptic transmission, I performed paired recordings between synaptically connected CA1 pyramidal neurons and O-LM interneurons. CA1 pyramidal neuron-O-LM interneuron excitatory postsynaptic currents (EPSCs) showed facilitation during both repetitive stimulation and tonic depolarization of the presynaptic neuron. Both effects were mimicked and occluded by α-DTX, suggesting that they were mediated by K+ channel inactivation. Therefore, axonal AP modulation can greatly facilitate the activation of O-LM interneurons. In conclusion, modulation of AP shape in CA1 pyramidal neuron axons substantially enhances the efficacy of principal neuron-interneuron synapses, promoting the activation of O-LM interneurons in recurrent inhibitory microcircuits.","lang":"eng"}],"citation":{"ama":"Kim S. Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus. <i>PLoS One</i>. 2014;9(11). doi:<a href=\"https://doi.org/10.1371/journal.pone.0113124\">10.1371/journal.pone.0113124</a>","mla":"Kim, Sooyun. “Action Potential Modulation in CA1 Pyramidal Neuron Axons Facilitates OLM Interneuron Activation in Recurrent Inhibitory Microcircuits of Rat Hippocampus.” <i>PLoS One</i>, vol. 9, no. 11, 0113124, Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pone.0113124\">10.1371/journal.pone.0113124</a>.","ista":"Kim S. 2014. Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus. PLoS One. 9(11), 0113124.","short":"S. Kim, PLoS One 9 (2014).","ieee":"S. Kim, “Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus,” <i>PLoS One</i>, vol. 9, no. 11. Public Library of Science, 2014.","apa":"Kim, S. (2014). Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0113124\">https://doi.org/10.1371/journal.pone.0113124</a>","chicago":"Kim, Sooyun. “Action Potential Modulation in CA1 Pyramidal Neuron Axons Facilitates OLM Interneuron Activation in Recurrent Inhibitory Microcircuits of Rat Hippocampus.” <i>PLoS One</i>. Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pone.0113124\">https://doi.org/10.1371/journal.pone.0113124</a>."},"publication_status":"published","ddc":["570"],"article_number":"0113124","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)"},"title":"Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus","pubrep_id":"434","ec_funded":1,"year":"2014","doi":"10.1371/journal.pone.0113124","file_date_updated":"2020-07-14T12:45:24Z","publication":"PLoS One","issue":"11","status":"public","intvolume":"         9","type":"journal_article","day":"19","date_created":"2018-12-11T11:55:09Z","file":[{"file_size":5179993,"file_name":"IST-2016-434-v1+1_journal.pone.0113124.pdf","checksum":"85e4f4ea144f827272aaf376b2830564","date_created":"2018-12-12T10:14:52Z","access_level":"open_access","date_updated":"2020-07-14T12:45:24Z","relation":"main_file","content_type":"application/pdf","file_id":"5107","creator":"system"}],"department":[{"_id":"PeJo"}],"has_accepted_license":"1","license":"https://creativecommons.org/licenses/by-sa/4.0/","language":[{"iso":"eng"}],"scopus_import":1,"publisher":"Public Library of Science","date_published":"2014-11-19T00:00:00Z","month":"11"},{"year":"2014","doi":"10.1016/j.neuron.2014.06.013","month":"07","date_published":"2014-07-02T00:00:00Z","title":"Learning by example in the hippocampus","scopus_import":1,"publisher":"Elsevier","language":[{"iso":"eng"}],"department":[{"_id":"JoCs"}],"date_created":"2018-12-11T11:55:09Z","citation":{"chicago":"O’Neill, Joseph, and Jozsef L Csicsvari. “Learning by Example in the Hippocampus.” <i>Neuron</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.neuron.2014.06.013\">https://doi.org/10.1016/j.neuron.2014.06.013</a>.","ieee":"J. O’Neill and J. L. Csicsvari, “Learning by example in the hippocampus,” <i>Neuron</i>, vol. 83, no. 1. Elsevier, pp. 8–10, 2014.","apa":"O’Neill, J., &#38; Csicsvari, J. L. (2014). Learning by example in the hippocampus. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2014.06.013\">https://doi.org/10.1016/j.neuron.2014.06.013</a>","ista":"O’Neill J, Csicsvari JL. 2014. Learning by example in the hippocampus. Neuron. 83(1), 8–10.","short":"J. O’Neill, J.L. Csicsvari, Neuron 83 (2014) 8–10.","mla":"O’Neill, Joseph, and Jozsef L. Csicsvari. “Learning by Example in the Hippocampus.” <i>Neuron</i>, vol. 83, no. 1, Elsevier, 2014, pp. 8–10, doi:<a href=\"https://doi.org/10.1016/j.neuron.2014.06.013\">10.1016/j.neuron.2014.06.013</a>.","ama":"O’Neill J, Csicsvari JL. Learning by example in the hippocampus. <i>Neuron</i>. 2014;83(1):8-10. doi:<a href=\"https://doi.org/10.1016/j.neuron.2014.06.013\">10.1016/j.neuron.2014.06.013</a>"},"day":"02","publication_status":"published","type":"journal_article","intvolume":"        83","abstract":[{"lang":"eng","text":"Learning can be facilitated by previous knowledge when it is organized into relational representations forming schemas. In this issue of Neuron, McKenzie et al. (2014) demonstrate that the hippocampus rapidly forms interrelated, hierarchical memory representations to support schema-based learning."}],"author":[{"last_name":"O'Neill","full_name":"O'Neill, Joseph","first_name":"Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"status":"public","publication":"Neuron","issue":"1","page":"8 - 10","date_updated":"2021-01-12T06:54:39Z","publist_id":"5073","volume":83,"_id":"2003","quality_controlled":"1","oa_version":"None","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"article_number":"e111430","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"related_material":{"record":[{"relation":"research_data","id":"9722","status":"public"}]},"ec_funded":1,"year":"2014","doi":"10.1371/journal.pone.0111430","title":"Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord","pubrep_id":"435","publist_id":"5072","volume":9,"oa":1,"date_updated":"2023-02-23T14:06:14Z","project":[{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"oa_version":"Published Version","quality_controlled":"1","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2004","citation":{"ama":"Lovrics A, Gao Y, Juhász B, et al. Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord. <i>PLoS One</i>. 2014;9(11). doi:<a href=\"https://doi.org/10.1371/journal.pone.0111430\">10.1371/journal.pone.0111430</a>","mla":"Lovrics, Anna, et al. “Boolean Modelling Reveals New Regulatory Connections between Transcription Factors Orchestrating the Development of the Ventral Spinal Cord.” <i>PLoS One</i>, vol. 9, no. 11, e111430, Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pone.0111430\">10.1371/journal.pone.0111430</a>.","ista":"Lovrics A, Gao Y, Juhász B, Bock I, Byrne H, Dinnyés A, Kovács K. 2014. Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord. PLoS One. 9(11), e111430.","short":"A. Lovrics, Y. Gao, B. Juhász, I. Bock, H. Byrne, A. Dinnyés, K. Kovács, PLoS One 9 (2014).","ieee":"A. Lovrics <i>et al.</i>, “Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord,” <i>PLoS One</i>, vol. 9, no. 11. Public Library of Science, 2014.","apa":"Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H., Dinnyés, A., &#38; Kovács, K. (2014). Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0111430\">https://doi.org/10.1371/journal.pone.0111430</a>","chicago":"Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen Byrne, András Dinnyés, and Krisztián Kovács. “Boolean Modelling Reveals New Regulatory Connections between Transcription Factors Orchestrating the Development of the Ventral Spinal Cord.” <i>PLoS One</i>. Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pone.0111430\">https://doi.org/10.1371/journal.pone.0111430</a>."},"publication_status":"published","author":[{"first_name":"Anna","full_name":"Lovrics, Anna","last_name":"Lovrics"},{"first_name":"Yu","last_name":"Gao","full_name":"Gao, Yu"},{"first_name":"Bianka","full_name":"Juhász, Bianka","last_name":"Juhász"},{"first_name":"István","full_name":"Bock, István","last_name":"Bock"},{"first_name":"Helen","last_name":"Byrne","full_name":"Byrne, Helen"},{"first_name":"András","full_name":"Dinnyés, András","last_name":"Dinnyés"},{"id":"2AB5821E-F248-11E8-B48F-1D18A9856A87","last_name":"Kovács","full_name":"Kovács, Krisztián","first_name":"Krisztián"}],"abstract":[{"text":"We have assembled a network of cell-fate determining transcription factors that play a key role in the specification of the ventral neuronal subtypes of the spinal cord on the basis of published transcriptional interactions. Asynchronous Boolean modelling of the network was used to compare simulation results with reported experimental observations. Such comparison highlighted the need to include additional regulatory connections in order to obtain the fixed point attractors of the model associated with the five known progenitor cell types located in the ventral spinal cord. The revised gene regulatory network reproduced previously observed cell state switches between progenitor cells observed in knock-out animal models or in experiments where the transcription factors were overexpressed. Furthermore the network predicted the inhibition of Irx3 by Nkx2.2 and this prediction was tested experimentally. Our results provide evidence for the existence of an as yet undescribed inhibitory connection which could potentially have significance beyond the ventral spinal cord. The work presented in this paper demonstrates the strength of Boolean modelling for identifying gene regulatory networks.","lang":"eng"}],"department":[{"_id":"JoCs"}],"has_accepted_license":"1","file":[{"date_updated":"2020-07-14T12:45:24Z","access_level":"open_access","date_created":"2018-12-12T10:10:58Z","checksum":"a2289b843f7463eb1233f9ce45e6a943","file_name":"IST-2016-435-v1+1_journal.pone.0111430.pdf","file_size":829363,"file_id":"4850","creator":"system","content_type":"application/pdf","relation":"main_file"}],"date_created":"2018-12-11T11:55:09Z","date_published":"2014-11-14T00:00:00Z","month":"11","language":[{"iso":"eng"}],"scopus_import":1,"publisher":"Public Library of Science","file_date_updated":"2020-07-14T12:45:24Z","publication":"PLoS One","issue":"11","type":"journal_article","day":"14","status":"public","intvolume":"         9"},{"date_created":"2018-12-11T11:55:09Z","department":[{"_id":"JoCs"}],"publisher":"Nature Publishing Group","scopus_import":1,"title":"Turning heads to remember places","language":[{"iso":"eng"}],"year":"2014","doi":"10.1038/nn.3700","month":"04","date_published":"2014-04-25T00:00:00Z","_id":"2005","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"None","quality_controlled":"1","issue":"5","publication":"Nature Neuroscience","volume":17,"date_updated":"2021-01-12T06:54:40Z","publist_id":"5071","page":"643 - 644","intvolume":"        17","abstract":[{"lang":"eng","text":"By eliciting a natural exploratory behavior in rats, head scanning, a study reveals that hippocampal place cells form new, stable firing fields in those locations where the behavior has just occurred."}],"status":"public","author":[{"first_name":"David","full_name":"Dupret, David","last_name":"Dupret"},{"orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","day":"25","citation":{"chicago":"Dupret, David, and Jozsef L Csicsvari. “Turning Heads to Remember Places.” <i>Nature Neuroscience</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/nn.3700\">https://doi.org/10.1038/nn.3700</a>.","ieee":"D. Dupret and J. L. Csicsvari, “Turning heads to remember places,” <i>Nature Neuroscience</i>, vol. 17, no. 5. Nature Publishing Group, pp. 643–644, 2014.","apa":"Dupret, D., &#38; Csicsvari, J. L. (2014). Turning heads to remember places. <i>Nature Neuroscience</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nn.3700\">https://doi.org/10.1038/nn.3700</a>","short":"D. Dupret, J.L. Csicsvari, Nature Neuroscience 17 (2014) 643–644.","ista":"Dupret D, Csicsvari JL. 2014. Turning heads to remember places. Nature Neuroscience. 17(5), 643–644.","ama":"Dupret D, Csicsvari JL. Turning heads to remember places. <i>Nature Neuroscience</i>. 2014;17(5):643-644. doi:<a href=\"https://doi.org/10.1038/nn.3700\">10.1038/nn.3700</a>","mla":"Dupret, David, and Jozsef L. Csicsvari. “Turning Heads to Remember Places.” <i>Nature Neuroscience</i>, vol. 17, no. 5, Nature Publishing Group, 2014, pp. 643–44, doi:<a href=\"https://doi.org/10.1038/nn.3700\">10.1038/nn.3700</a>."},"type":"journal_article"},{"citation":{"chicago":"Klimova, Anna, and Tamás Rudas. “GIPFrm: Generalized Iterative Proportional Fitting for Relational Models.” The Comprehensive R Archive Network, 2014.","apa":"Klimova, A., &#38; Rudas, T. (2014). gIPFrm: Generalized iterative proportional fitting for relational models. The Comprehensive R Archive Network.","ieee":"A. Klimova and T. Rudas, “gIPFrm: Generalized iterative proportional fitting for relational models.” The Comprehensive R Archive Network, 2014.","ista":"Klimova A, Rudas T. 2014. gIPFrm: Generalized iterative proportional fitting for relational models, The Comprehensive R Archive Network.","short":"A. Klimova, T. Rudas, (2014).","ama":"Klimova A, Rudas T. gIPFrm: Generalized iterative proportional fitting for relational models. 2014.","mla":"Klimova, Anna, and Tamás Rudas. <i>GIPFrm: Generalized Iterative Proportional Fitting for Relational Models</i>. The Comprehensive R Archive Network, 2014."},"day":"20","type":"research_data_reference","abstract":[{"lang":"eng","text":"Maximum likelihood estimation under relational models, with or without the overall effect. For more information see the reference manual"}],"author":[{"id":"31934120-F248-11E8-B48F-1D18A9856A87","last_name":"Klimova","full_name":"Klimova, Anna","first_name":"Anna"},{"first_name":"Tamás","full_name":"Rudas, Tamás","last_name":"Rudas"}],"status":"public","article_processing_charge":"No","date_updated":"2022-08-26T08:12:12Z","oa":1,"publist_id":"5069","_id":"2007","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2014","month":"03","date_published":"2014-03-20T00:00:00Z","title":"gIPFrm: Generalized iterative proportional fitting for relational models","publisher":"The Comprehensive R Archive Network","main_file_link":[{"url":"https://CRAN.R-project.org/package=gIPFrm ","open_access":"1"}],"department":[{"_id":"CaUh"}],"date_created":"2018-12-11T11:55:10Z"},{"language":[{"iso":"eng"}],"title":"Scalable privacy-preserving data sharing methodology for genome-wide association studies","scopus_import":1,"publisher":"Elsevier","date_published":"2014-08-01T00:00:00Z","year":"2014","doi":"10.1016/j.jbi.2014.01.008","month":"08","date_created":"2018-12-11T11:55:12Z","main_file_link":[{"url":"http://arxiv.org/abs/1401.5193","open_access":"1"}],"department":[{"_id":"CaUh"}],"author":[{"last_name":"Yu","full_name":"Yu, Fei","first_name":"Fei"},{"full_name":"Fienberg, Stephen","last_name":"Fienberg","first_name":"Stephen"},{"first_name":"Alexandra","full_name":"Slaković, Alexandra","last_name":"Slaković"},{"first_name":"Caroline","last_name":"Uhler","full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"}],"status":"public","intvolume":"        50","abstract":[{"lang":"eng","text":"The protection of privacy of individual-level information in genome-wide association study (GWAS) databases has been a major concern of researchers following the publication of “an attack” on GWAS data by Homer et al. (2008). Traditional statistical methods for confidentiality and privacy protection of statistical databases do not scale well to deal with GWAS data, especially in terms of guarantees regarding protection from linkage to external information. The more recent concept of differential privacy, introduced by the cryptographic community, is an approach that provides a rigorous definition of privacy with meaningful privacy guarantees in the presence of arbitrary external information, although the guarantees may come at a serious price in terms of data utility. Building on such notions, Uhler et al. (2013) proposed new methods to release aggregate GWAS data without compromising an individual’s privacy. We extend the methods developed in Uhler et al. (2013) for releasing differentially-private χ2χ2-statistics by allowing for arbitrary number of cases and controls, and for releasing differentially-private allelic test statistics. We also provide a new interpretation by assuming the controls’ data are known, which is a realistic assumption because some GWAS use publicly available data as controls. We assess the performance of the proposed methods through a risk-utility analysis on a real data set consisting of DNA samples collected by the Wellcome Trust Case Control Consortium and compare the methods with the differentially-private release mechanism proposed by Johnson and Shmatikov (2013)."}],"type":"journal_article","citation":{"ista":"Yu F, Fienberg S, Slaković A, Uhler C. 2014. Scalable privacy-preserving data sharing methodology for genome-wide association studies. Journal of Biomedical Informatics. 50, 133–141.","short":"F. Yu, S. Fienberg, A. Slaković, C. Uhler, Journal of Biomedical Informatics 50 (2014) 133–141.","mla":"Yu, Fei, et al. “Scalable Privacy-Preserving Data Sharing Methodology for Genome-Wide Association Studies.” <i>Journal of Biomedical Informatics</i>, vol. 50, Elsevier, 2014, pp. 133–41, doi:<a href=\"https://doi.org/10.1016/j.jbi.2014.01.008\">10.1016/j.jbi.2014.01.008</a>.","ama":"Yu F, Fienberg S, Slaković A, Uhler C. Scalable privacy-preserving data sharing methodology for genome-wide association studies. <i>Journal of Biomedical Informatics</i>. 2014;50:133-141. doi:<a href=\"https://doi.org/10.1016/j.jbi.2014.01.008\">10.1016/j.jbi.2014.01.008</a>","chicago":"Yu, Fei, Stephen Fienberg, Alexandra Slaković, and Caroline Uhler. “Scalable Privacy-Preserving Data Sharing Methodology for Genome-Wide Association Studies.” <i>Journal of Biomedical Informatics</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.jbi.2014.01.008\">https://doi.org/10.1016/j.jbi.2014.01.008</a>.","apa":"Yu, F., Fienberg, S., Slaković, A., &#38; Uhler, C. (2014). Scalable privacy-preserving data sharing methodology for genome-wide association studies. <i>Journal of Biomedical Informatics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jbi.2014.01.008\">https://doi.org/10.1016/j.jbi.2014.01.008</a>","ieee":"F. Yu, S. Fienberg, A. Slaković, and C. Uhler, “Scalable privacy-preserving data sharing methodology for genome-wide association studies,” <i>Journal of Biomedical Informatics</i>, vol. 50. Elsevier, pp. 133–141, 2014."},"day":"01","publication_status":"published","quality_controlled":"1","oa_version":"Submitted Version","acknowledgement":"This research was partially supported by NSF Awards EMSW21-RTG and BCS-0941518 to the Department of Statistics at Carnegie Mellon University, and by NSF Grant BCS-0941553 to the Department of Statistics at Pennsylvania State University. This work was also supported in part by the National Center for Research Resources, Grant UL1 RR033184, and is now at the National Center for Advancing Translational Sciences, Grant UL1 TR000127 to Pennsylvania State University. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NSF and NIH.","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2011","page":"133 - 141","date_updated":"2021-01-12T06:54:42Z","publist_id":"5065","oa":1,"volume":50,"publication":"Journal of Biomedical Informatics"},{"doi":"10.48550/arXiv.1401.0468","year":"2014","month":"01","date_published":"2014-01-01T00:00:00Z","title":"Sphere packing with limited overlap","external_id":{"arxiv":["1401.0468"]},"language":[{"iso":"eng"}],"department":[{"_id":"HeEd"},{"_id":"CaUh"}],"main_file_link":[{"url":"http://cccg.ca/proceedings/2014/papers/paper23.pdf","open_access":"1"}],"article_number":"1401.0468","date_created":"2018-12-11T11:55:12Z","publication_status":"submitted","citation":{"apa":"Iglesias Ham, M., Kerber, M., &#38; Uhler, C. (n.d.). Sphere packing with limited overlap. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.1401.0468\">https://doi.org/10.48550/arXiv.1401.0468</a>","ieee":"M. Iglesias Ham, M. Kerber, and C. Uhler, “Sphere packing with limited overlap,” <i>arXiv</i>. .","chicago":"Iglesias Ham, Mabel, Michael Kerber, and Caroline Uhler. “Sphere Packing with Limited Overlap.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.1401.0468\">https://doi.org/10.48550/arXiv.1401.0468</a>.","mla":"Iglesias Ham, Mabel, et al. “Sphere Packing with Limited Overlap.” <i>ArXiv</i>, 1401.0468, doi:<a href=\"https://doi.org/10.48550/arXiv.1401.0468\">10.48550/arXiv.1401.0468</a>.","ama":"Iglesias Ham M, Kerber M, Uhler C. Sphere packing with limited overlap. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.1401.0468\">10.48550/arXiv.1401.0468</a>","short":"M. Iglesias Ham, M. Kerber, C. Uhler, ArXiv (n.d.).","ista":"Iglesias Ham M, Kerber M, Uhler C. Sphere packing with limited overlap. arXiv, 1401.0468."},"day":"01","type":"preprint","abstract":[{"text":"The classical sphere packing problem asks for the best (infinite) arrangement of non-overlapping unit balls which cover as much space as possible. We define a generalized version of the problem, where we allow each ball a limited amount of overlap with other balls. We study two natural choices of overlap measures and obtain the optimal lattice packings in a parameterized family of lattices which contains the FCC, BCC, and integer lattice.","lang":"eng"}],"author":[{"id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","first_name":"Mabel","last_name":"Iglesias Ham","full_name":"Iglesias Ham, Mabel"},{"full_name":"Kerber, Michael","last_name":"Kerber","orcid":"0000-0002-8030-9299","first_name":"Michael"},{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","last_name":"Uhler","full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","first_name":"Caroline"}],"status":"public","arxiv":1,"publication":"arXiv","publist_id":"5064","oa":1,"date_updated":"2023-10-18T08:06:45Z","article_processing_charge":"No","_id":"2012","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank Herbert Edelsbrunner for his valuable discussions and ideas on the topic of this paper.  The second author has been supported by the Max Planck Center for Visual Computing and Communication","oa_version":"Submitted Version"},{"issue":"5","publication":"Foundations of Computational Mathematics","page":"1079 - 1116","day":"10","type":"journal_article","intvolume":"        14","status":"public","department":[{"_id":"CaUh"}],"date_created":"2018-12-11T11:55:12Z","month":"10","date_published":"2014-10-10T00:00:00Z","publisher":"Springer","scopus_import":1,"language":[{"iso":"eng"}],"date_updated":"2021-01-12T06:54:43Z","publist_id":"5063","volume":14,"oa":1,"_id":"2013","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported in part by the US National Science Foundation (DMS-0968882) and the Defense Advanced Research Projects Agency (DARPA) Deep Learning program (FA8650-10-C-7020).","oa_version":"Submitted Version","quality_controlled":"1","publication_status":"published","citation":{"apa":"Lin, S., Uhler, C., Sturmfels, B., &#38; Bühlmann, P. (2014). Hypersurfaces and their singularities in partial correlation testing. <i>Foundations of Computational Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s10208-014-9205-0\">https://doi.org/10.1007/s10208-014-9205-0</a>","ieee":"S. Lin, C. Uhler, B. Sturmfels, and P. Bühlmann, “Hypersurfaces and their singularities in partial correlation testing,” <i>Foundations of Computational Mathematics</i>, vol. 14, no. 5. Springer, pp. 1079–1116, 2014.","chicago":"Lin, Shaowei, Caroline Uhler, Bernd Sturmfels, and Peter Bühlmann. “Hypersurfaces and Their Singularities in Partial Correlation Testing.” <i>Foundations of Computational Mathematics</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s10208-014-9205-0\">https://doi.org/10.1007/s10208-014-9205-0</a>.","ama":"Lin S, Uhler C, Sturmfels B, Bühlmann P. Hypersurfaces and their singularities in partial correlation testing. <i>Foundations of Computational Mathematics</i>. 2014;14(5):1079-1116. doi:<a href=\"https://doi.org/10.1007/s10208-014-9205-0\">10.1007/s10208-014-9205-0</a>","mla":"Lin, Shaowei, et al. “Hypersurfaces and Their Singularities in Partial Correlation Testing.” <i>Foundations of Computational Mathematics</i>, vol. 14, no. 5, Springer, 2014, pp. 1079–116, doi:<a href=\"https://doi.org/10.1007/s10208-014-9205-0\">10.1007/s10208-014-9205-0</a>.","ista":"Lin S, Uhler C, Sturmfels B, Bühlmann P. 2014. Hypersurfaces and their singularities in partial correlation testing. Foundations of Computational Mathematics. 14(5), 1079–1116.","short":"S. Lin, C. Uhler, B. Sturmfels, P. Bühlmann, Foundations of Computational Mathematics 14 (2014) 1079–1116."},"abstract":[{"text":"An asymptotic theory is developed for computing volumes of regions in the parameter space of a directed Gaussian graphical model that are obtained by bounding partial correlations. We study these volumes using the method of real log canonical thresholds from algebraic geometry. Our analysis involves the computation of the singular loci of correlation hypersurfaces. Statistical applications include the strong-faithfulness assumption for the PC algorithm and the quantification of confounder bias in causal inference. A detailed analysis is presented for trees, bow ties, tripartite graphs, and complete graphs.\r\n","lang":"eng"}],"author":[{"last_name":"Lin","full_name":"Lin, Shaowei","first_name":"Shaowei"},{"orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline","last_name":"Uhler","first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Bernd","full_name":"Sturmfels, Bernd","last_name":"Sturmfels"},{"first_name":"Peter","last_name":"Bühlmann","full_name":"Bühlmann, Peter"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1209.0285"}],"year":"2014","doi":"10.1007/s10208-014-9205-0","title":"Hypersurfaces and their singularities in partial correlation testing"},{"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1406.4901"}],"date_created":"2018-12-11T11:55:14Z","date_published":"2014-06-18T00:00:00Z","month":"06","year":"2014","title":" Exact formulas for the normalizing constants of Wishart distributions for graphical models","publisher":"ArXiv","publist_id":"5058","oa":1,"date_updated":"2021-01-12T06:54:44Z","publication":"ArXiv","quality_controlled":0,"acknowledgement":"A.L.'s research was supported by Statistics for Innovation sfi2 in Oslo.\nD.R.'s research was partially supported by the U.S. National Science Foun-dation grant DMS-1309808; and by a Romberg Guest Professorship at the Heidelberg University Graduate School for Mathematical and Computational Methods in the Sciences, funded by German Universities Excellence Initiative grant GSC 220/2.","extern":1,"_id":"2017","type":"preprint","citation":{"apa":"Uhler, C., Lenkoski, A., &#38; Richards, D. (2014).  Exact formulas for the normalizing constants of Wishart distributions for graphical models. <i>ArXiv</i>. ArXiv.","ieee":"C. Uhler, A. Lenkoski, and D. Richards, “ Exact formulas for the normalizing constants of Wishart distributions for graphical models,” <i>ArXiv</i>. ArXiv, 2014.","chicago":"Uhler, Caroline, Alex Lenkoski, and Donald Richards. “ Exact Formulas for the Normalizing Constants of Wishart Distributions for Graphical Models.” <i>ArXiv</i>. ArXiv, 2014.","ama":"Uhler C, Lenkoski A, Richards D.  Exact formulas for the normalizing constants of Wishart distributions for graphical models. <i>ArXiv</i>. 2014.","mla":"Uhler, Caroline, et al. “ Exact Formulas for the Normalizing Constants of Wishart Distributions for Graphical Models.” <i>ArXiv</i>, ArXiv, 2014.","short":"C. Uhler, A. Lenkoski, D. Richards, ArXiv (2014).","ista":"Uhler C, Lenkoski A, Richards D. 2014.  Exact formulas for the normalizing constants of Wishart distributions for graphical models. ArXiv, ."},"day":"18","publication_status":"published","status":"public","author":[{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","last_name":"Uhler","full_name":"Caroline Uhler","orcid":"0000-0002-7008-0216","first_name":"Caroline"},{"first_name":"Alex","last_name":"Lenkoski","full_name":"Lenkoski, Alex"},{"first_name":"Donald","full_name":"Richards, Donald","last_name":"Richards"}],"abstract":[{"text":"     Gaussian graphical models have received considerable attention during the past four decades from the statistical and machine learning communities. In Bayesian treatments of this model, the G-Wishart distribution serves as the conjugate prior for inverse covariance matrices satisfying graphical constraints. While it is straightforward to posit the unnormalized densities, the normalizing constants of these distributions have been known only for graphs that are chordal, or decomposable. Up until now, it was unknown whether the normalizing constant for a general graph could be represented explicitly, and a considerable body of computational literature emerged that attempted to avoid this apparent intractability. We close this question by providing an explicit representation of the G-Wishart normalizing constant for general graphs.","lang":"eng"}]},{"intvolume":"        34","status":"public","day":"19","type":"journal_article","issue":"47","publication":"Journal of Neuroscience","file_date_updated":"2022-05-24T08:41:41Z","page":"15779 - 15792","publisher":"Society for Neuroscience","scopus_import":"1","language":[{"iso":"eng"}],"month":"11","date_published":"2014-11-19T00:00:00Z","article_type":"original","file":[{"date_created":"2022-05-24T08:41:41Z","checksum":"6913e9bc26e9fc1c0441a739a4199229","file_name":"2014_JournNeuroscience_Matsukawa.pdf","file_size":3963728,"date_updated":"2022-05-24T08:41:41Z","access_level":"open_access","success":1,"file_id":"11410","creator":"dernst","content_type":"application/pdf","relation":"main_file"}],"date_created":"2018-12-11T11:55:14Z","has_accepted_license":"1","department":[{"_id":"RySh"}],"abstract":[{"lang":"eng","text":"Synaptic cell adhesion molecules are increasingly gaining attention for conferring specific properties to individual synapses. Netrin-G1 and netrin-G2 are trans-synaptic adhesion molecules that distribute on distinct axons, and their presence restricts the expression of their cognate receptors, NGL1 and NGL2, respectively, to specific subdendritic segments of target neurons. However, the neural circuits and functional roles of netrin-G isoform complexes remain unclear. Here, we use netrin-G-KO and NGL-KO mice to reveal that netrin-G1/NGL1 and netrin-G2/NGL2 interactions specify excitatory synapses in independent hippocampal pathways. In the hippocampal CA1 area, netrin-G1/NGL1 and netrin-G2/NGL2 were expressed in the temporoammonic and Schaffer collateral pathways, respectively. The lack of presynaptic netrin-Gs led to the dispersion of NGLs from postsynaptic membranes. In accord, netrin-G mutant synapses displayed opposing phenotypes in long-term and short-term plasticity through discrete biochemical pathways. The plasticity phenotypes in netrin-G-KOs were phenocopied in NGL-KOs, with a corresponding loss of netrin-Gs from presynaptic membranes. Our findings show that netrin-G/NGL interactions differentially control synaptic plasticity in distinct circuits via retrograde signaling mechanisms and explain how synaptic inputs are diversified to control neuronal activity."}],"author":[{"last_name":"Matsukawa","full_name":"Matsukawa, Hiroshi","first_name":"Hiroshi"},{"first_name":"Sachiko","last_name":"Akiyoshi Nishimura","full_name":"Akiyoshi Nishimura, Sachiko"},{"first_name":"Qi","full_name":"Zhang, Qi","last_name":"Zhang"},{"first_name":"Rafael","last_name":"Luján","full_name":"Luján, Rafael"},{"first_name":"Kazuhiko","full_name":"Yamaguchi, Kazuhiko","last_name":"Yamaguchi"},{"full_name":"Goto, Hiromichi","last_name":"Goto","first_name":"Hiromichi"},{"first_name":"Kunio","last_name":"Yaguchi","full_name":"Yaguchi, Kunio"},{"full_name":"Hashikawa, Tsutomu","last_name":"Hashikawa","first_name":"Tsutomu"},{"first_name":"Chie","full_name":"Sano, Chie","last_name":"Sano"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","first_name":"Ryuichi"},{"first_name":"Toshiaki","full_name":"Nakashiba, Toshiaki","last_name":"Nakashiba"},{"full_name":"Itohara, Shigeyoshi","last_name":"Itohara","first_name":"Shigeyoshi"}],"publication_status":"published","citation":{"chicago":"Matsukawa, Hiroshi, Sachiko Akiyoshi Nishimura, Qi Zhang, Rafael Luján, Kazuhiko Yamaguchi, Hiromichi Goto, Kunio Yaguchi, et al. “Netrin-G/NGL Complexes Encode Functional Synaptic Diversification.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2014. <a href=\"https://doi.org/10.1523/JNEUROSCI.1141-14.2014\">https://doi.org/10.1523/JNEUROSCI.1141-14.2014</a>.","ieee":"H. Matsukawa <i>et al.</i>, “Netrin-G/NGL complexes encode functional synaptic diversification,” <i>Journal of Neuroscience</i>, vol. 34, no. 47. Society for Neuroscience, pp. 15779–15792, 2014.","apa":"Matsukawa, H., Akiyoshi Nishimura, S., Zhang, Q., Luján, R., Yamaguchi, K., Goto, H., … Itohara, S. (2014). Netrin-G/NGL complexes encode functional synaptic diversification. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.1141-14.2014\">https://doi.org/10.1523/JNEUROSCI.1141-14.2014</a>","ista":"Matsukawa H, Akiyoshi Nishimura S, Zhang Q, Luján R, Yamaguchi K, Goto H, Yaguchi K, Hashikawa T, Sano C, Shigemoto R, Nakashiba T, Itohara S. 2014. Netrin-G/NGL complexes encode functional synaptic diversification. Journal of Neuroscience. 34(47), 15779–15792.","short":"H. Matsukawa, S. Akiyoshi Nishimura, Q. Zhang, R. Luján, K. Yamaguchi, H. Goto, K. Yaguchi, T. Hashikawa, C. Sano, R. Shigemoto, T. Nakashiba, S. Itohara, Journal of Neuroscience 34 (2014) 15779–15792.","mla":"Matsukawa, Hiroshi, et al. “Netrin-G/NGL Complexes Encode Functional Synaptic Diversification.” <i>Journal of Neuroscience</i>, vol. 34, no. 47, Society for Neuroscience, 2014, pp. 15779–92, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1141-14.2014\">10.1523/JNEUROSCI.1141-14.2014</a>.","ama":"Matsukawa H, Akiyoshi Nishimura S, Zhang Q, et al. Netrin-G/NGL complexes encode functional synaptic diversification. <i>Journal of Neuroscience</i>. 2014;34(47):15779-15792. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1141-14.2014\">10.1523/JNEUROSCI.1141-14.2014</a>"},"_id":"2018","pmid":1,"publication_identifier":{"issn":["0270-6474"],"eissn":["1529-2401"]},"acknowledgement":"This work was supported by “Funding Program for World-Leading Innovative R&D on Science and Technology (FIRST Program)” initiated by the Council for Science and Technology Policy.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","quality_controlled":"1","oa":1,"publist_id":"5054","volume":34,"date_updated":"2022-05-24T08:54:54Z","article_processing_charge":"No","title":"Netrin-G/NGL complexes encode functional synaptic diversification","external_id":{"pmid":["25411505"]},"year":"2014","doi":"10.1523/JNEUROSCI.1141-14.2014","ddc":["570"]},{"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1407.1552"}],"year":"2014","doi":"10.1007/s11040-014-9164-3","ec_funded":1,"title":"Phase transition in the density of states of quantum spin glasses","publist_id":"5053","date_updated":"2021-01-12T06:54:45Z","volume":17,"oa":1,"_id":"2019","quality_controlled":"1","project":[{"grant_number":"338804","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"oa_version":"Submitted Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"L. Erdös and D. J. Schröder, “Phase transition in the density of states of quantum spin glasses,” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 17, no. 3–4. Springer, pp. 441–464, 2014.","apa":"Erdös, L., &#38; Schröder, D. J. (2014). Phase transition in the density of states of quantum spin glasses. <i>Mathematical Physics, Analysis and Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s11040-014-9164-3\">https://doi.org/10.1007/s11040-014-9164-3</a>","chicago":"Erdös, László, and Dominik J Schröder. “Phase Transition in the Density of States of Quantum Spin Glasses.” <i>Mathematical Physics, Analysis and Geometry</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s11040-014-9164-3\">https://doi.org/10.1007/s11040-014-9164-3</a>.","mla":"Erdös, László, and Dominik J. Schröder. “Phase Transition in the Density of States of Quantum Spin Glasses.” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 17, no. 3–4, Springer, 2014, pp. 441–64, doi:<a href=\"https://doi.org/10.1007/s11040-014-9164-3\">10.1007/s11040-014-9164-3</a>.","ama":"Erdös L, Schröder DJ. Phase transition in the density of states of quantum spin glasses. <i>Mathematical Physics, Analysis and Geometry</i>. 2014;17(3-4):441-464. doi:<a href=\"https://doi.org/10.1007/s11040-014-9164-3\">10.1007/s11040-014-9164-3</a>","ista":"Erdös L, Schröder DJ. 2014. Phase transition in the density of states of quantum spin glasses. Mathematical Physics, Analysis and Geometry. 17(3–4), 441–464.","short":"L. Erdös, D.J. Schröder, Mathematical Physics, Analysis and Geometry 17 (2014) 441–464."},"publication_status":"published","abstract":[{"lang":"eng","text":"We prove that the empirical density of states of quantum spin glasses on arbitrary graphs converges to a normal distribution as long as the maximal degree is negligible compared with the total number of edges. This extends the recent results of Keating et al. (2014) that were proved for graphs with bounded chromatic number and with symmetric coupling distribution. Furthermore, we generalise the result to arbitrary hypergraphs. We test the optimality of our condition on the maximal degree for p-uniform hypergraphs that correspond to p-spin glass Hamiltonians acting on n distinguishable spin- 1/2 particles. At the critical threshold p = n1/2 we find a sharp classical-quantum phase transition between the normal distribution and the Wigner semicircle law. The former is characteristic to classical systems with commuting variables, while the latter is a signature of noncommutative random matrix theory."}],"author":[{"orcid":"0000-0001-5366-9603","last_name":"Erdös","full_name":"Erdös, László","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dominik J","full_name":"Schröder, Dominik J","last_name":"Schröder"}],"department":[{"_id":"LaEr"}],"date_created":"2018-12-11T11:55:15Z","month":"12","date_published":"2014-12-17T00:00:00Z","scopus_import":1,"publisher":"Springer","language":[{"iso":"eng"}],"publication":"Mathematical Physics, Analysis and Geometry","issue":"3-4","page":"441 - 464","day":"17","type":"journal_article","intvolume":"        17","status":"public"},{"language":[{"iso":"eng"}],"title":"Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice","scopus_import":1,"publisher":"National Academy of Sciences","date_published":"2014-06-17T00:00:00Z","doi":"10.1073/pnas.1408233111","year":"2014","month":"06","date_created":"2018-12-11T11:55:15Z","department":[{"_id":"SiHi"}],"status":"public","author":[{"last_name":"Ali","full_name":"Ali, Shah","first_name":"Shah"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","first_name":"Simon"},{"first_name":"Lily","last_name":"Saadat","full_name":"Saadat, Lily"},{"first_name":"Liqun","full_name":"Luo, Liqun","last_name":"Luo"},{"first_name":"Irving","full_name":"Weissman, Irving","last_name":"Weissman"},{"last_name":"Ardehali","full_name":"Ardehali, Reza","first_name":"Reza"}],"intvolume":"       111","abstract":[{"lang":"eng","text":"The mammalian heart has long been considered a postmitotic organ, implying that the total number of cardiomyocytes is set at birth. Analysis of cell division in the mammalian heart is complicated by cardiomyocyte binucleation shortly after birth, which makes it challenging to interpret traditional assays of cell turnover [Laflamme MA, Murray CE (2011) Nature 473(7347):326–335; Bergmann O, et al. (2009) Science 324(5923):98–102]. An elegant multi-isotope imaging-mass spectrometry technique recently calculated the low, discrete rate of cardiomyocyte generation in mice [Senyo SE, et al. (2013) Nature 493(7432):433–436], yet our cellular-level understanding of postnatal cardiomyogenesis remains limited. Herein, we provide a new line of evidence for the differentiated α-myosin heavy chain-expressing cardiomyocyte as the cell of origin of postnatal cardiomyogenesis using the “mosaic analysis with double markers” mouse model. We show limited, life-long, symmetric division of cardiomyocytes as a rare event that is evident in utero but significantly diminishes after the first month of life in mice; daughter cardiomyocytes divide very seldom, which this study is the first to demonstrate, to our knowledge. Furthermore, ligation of the left anterior descending coronary artery, which causes a myocardial infarction in the mosaic analysis with double-marker mice, did not increase the rate of cardiomyocyte division above the basal level for up to 4 wk after the injury. The clonal analysis described here provides direct evidence of postnatal mammalian cardiomyogenesis."}],"type":"journal_article","day":"17","citation":{"ista":"Ali S, Hippenmeyer S, Saadat L, Luo L, Weissman I, Ardehali R. 2014. Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice. PNAS. 111(24), 8850–8855.","short":"S. Ali, S. Hippenmeyer, L. Saadat, L. Luo, I. Weissman, R. Ardehali, PNAS 111 (2014) 8850–8855.","mla":"Ali, Shah, et al. “Existing Cardiomyocytes Generate Cardiomyocytes at a Low Rate after Birth in Mice.” <i>PNAS</i>, vol. 111, no. 24, National Academy of Sciences, 2014, pp. 8850–55, doi:<a href=\"https://doi.org/10.1073/pnas.1408233111\">10.1073/pnas.1408233111</a>.","ama":"Ali S, Hippenmeyer S, Saadat L, Luo L, Weissman I, Ardehali R. Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice. <i>PNAS</i>. 2014;111(24):8850-8855. doi:<a href=\"https://doi.org/10.1073/pnas.1408233111\">10.1073/pnas.1408233111</a>","chicago":"Ali, Shah, Simon Hippenmeyer, Lily Saadat, Liqun Luo, Irving Weissman, and Reza Ardehali. “Existing Cardiomyocytes Generate Cardiomyocytes at a Low Rate after Birth in Mice.” <i>PNAS</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1408233111\">https://doi.org/10.1073/pnas.1408233111</a>.","ieee":"S. Ali, S. Hippenmeyer, L. Saadat, L. Luo, I. Weissman, and R. Ardehali, “Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice,” <i>PNAS</i>, vol. 111, no. 24. National Academy of Sciences, pp. 8850–8855, 2014.","apa":"Ali, S., Hippenmeyer, S., Saadat, L., Luo, L., Weissman, I., &#38; Ardehali, R. (2014). Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1408233111\">https://doi.org/10.1073/pnas.1408233111</a>"},"publication_status":"published","quality_controlled":"1","oa_version":"None","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2020","page":"8850 - 8855","publist_id":"5052","date_updated":"2021-01-12T06:54:46Z","volume":111,"publication":"PNAS","issue":"24"},{"type":"journal_article","publication_status":"published","day":"31","citation":{"chicago":"William, Joo, Simon Hippenmeyer, and Liqun Luo. “Dendrite Morphogenesis Depends on Relative Levels of NT-3/TrkC Signaling.” <i>Science</i>. American Association for the Advancement of Science, 2014. <a href=\"https://doi.org/10.1126/science.1258996\">https://doi.org/10.1126/science.1258996</a>.","ieee":"J. William, S. Hippenmeyer, and L. Luo, “Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling,” <i>Science</i>, vol. 346, no. 6209. American Association for the Advancement of Science, pp. 626–629, 2014.","apa":"William, J., Hippenmeyer, S., &#38; Luo, L. (2014). Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1258996\">https://doi.org/10.1126/science.1258996</a>","ista":"William J, Hippenmeyer S, Luo L. 2014. Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling. Science. 346(6209), 626–629.","short":"J. William, S. Hippenmeyer, L. Luo, Science 346 (2014) 626–629.","mla":"William, Joo, et al. “Dendrite Morphogenesis Depends on Relative Levels of NT-3/TrkC Signaling.” <i>Science</i>, vol. 346, no. 6209, American Association for the Advancement of Science, 2014, pp. 626–29, doi:<a href=\"https://doi.org/10.1126/science.1258996\">10.1126/science.1258996</a>.","ama":"William J, Hippenmeyer S, Luo L. Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling. <i>Science</i>. 2014;346(6209):626-629. doi:<a href=\"https://doi.org/10.1126/science.1258996\">10.1126/science.1258996</a>"},"status":"public","author":[{"first_name":"Joo","last_name":"William","full_name":"William, Joo"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","first_name":"Simon"},{"last_name":"Luo","full_name":"Luo, Liqun","first_name":"Liqun"}],"intvolume":"       346","abstract":[{"lang":"eng","text":"Neurotrophins regulate diverse aspects of neuronal development and plasticity, but their precise in vivo functions during neural circuit assembly in the central brain remain unclear. We show that the neurotrophin receptor tropomyosin-related kinase C (TrkC) is required for dendritic growth and branching of mouse cerebellar Purkinje cells. Sparse TrkC knockout reduced dendrite complexity, but global Purkinje cell knockout had no effect. Removal of the TrkC ligand neurotrophin-3 (NT-3) from cerebellar granule cells, which provide major afferent input to developing Purkinje cell dendrites, rescued the dendrite defects caused by sparse TrkC disruption in Purkinje cells. Our data demonstrate that NT-3 from presynaptic neurons (granule cells) is required for TrkC-dependent competitive dendrite morphogenesis in postsynaptic neurons (Purkinje cells)—a previously unknown mechanism of neural circuit development."}],"publist_id":"5051","date_updated":"2021-01-12T06:54:47Z","oa":1,"volume":346,"page":"626 - 629","issue":"6209","publication":"Science","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","quality_controlled":"1","_id":"2021","date_published":"2014-10-31T00:00:00Z","year":"2014","month":"10","doi":"10.1126/science.1258996","language":[{"iso":"eng"}],"publisher":"American Association for the Advancement of Science","title":"Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling","scopus_import":1,"department":[{"_id":"SiHi"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631524/","open_access":"1"}],"date_created":"2018-12-11T11:55:15Z"},{"ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"title":"Deterministic progenitor behavior and unitary production of neurons in the neocortex","pubrep_id":"423","ec_funded":1,"doi":"10.1016/j.cell.2014.10.027","year":"2014","project":[{"call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development","_id":"25D61E48-B435-11E9-9278-68D0E5697425","grant_number":"618444"},{"grant_number":"RGP0053/2014","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","_id":"25D7962E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa_version":"Published Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2022","publist_id":"5050","volume":159,"oa":1,"date_updated":"2021-01-12T06:54:47Z","author":[{"first_name":"Peng","last_name":"Gao","full_name":"Gao, Peng"},{"last_name":"Postiglione","full_name":"Postiglione, Maria P","first_name":"Maria P","id":"2C67902A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Teresa","last_name":"Krieger","full_name":"Krieger, Teresa"},{"first_name":"Luisirene","full_name":"Hernandez, Luisirene","last_name":"Hernandez"},{"first_name":"Chao","full_name":"Wang, Chao","last_name":"Wang"},{"first_name":"Zhi","full_name":"Han, Zhi","last_name":"Han"},{"first_name":"Carmen","last_name":"Streicher","full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"id":"41DB591E-F248-11E8-B48F-1D18A9856A87","first_name":"Ekaterina","full_name":"Papusheva, Ekaterina","last_name":"Papusheva"},{"last_name":"Insolera","full_name":"Insolera, Ryan","first_name":"Ryan"},{"first_name":"Kritika","full_name":"Chugh, Kritika","last_name":"Chugh"},{"full_name":"Kodish, Oren","last_name":"Kodish","first_name":"Oren"},{"full_name":"Huang, Kun","last_name":"Huang","first_name":"Kun"},{"full_name":"Simons, Benjamin","last_name":"Simons","first_name":"Benjamin"},{"first_name":"Liqun","full_name":"Luo, Liqun","last_name":"Luo"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","first_name":"Simon"},{"full_name":"Shi, Song","last_name":"Shi","first_name":"Song"}],"abstract":[{"text":"Radial glial progenitors (RGPs) are responsible for producing nearly all neocortical neurons. To gain insight into the patterns of RGP division and neuron production, we quantitatively analyzed excitatory neuron genesis in the mouse neocortex using Mosaic Analysis with Double Markers, which provides single-cell resolution of progenitor division patterns and potential in vivo. We found that RGPs progress through a coherent program in which their proliferative potential diminishes in a predictable manner. Upon entry into the neurogenic phase, individual RGPs produce ∼8–9 neurons distributed in both deep and superficial layers, indicating a unitary output in neuronal production. Removal of OTX1, a transcription factor transiently expressed in RGPs, results in both deep- and superficial-layer neuron loss and a reduction in neuronal unit size. Moreover, ∼1/6 of neurogenic RGPs proceed to produce glia. These results suggest that progenitor behavior and histogenesis in the mammalian neocortex conform to a remarkably orderly and deterministic program.","lang":"eng"}],"citation":{"ieee":"P. Gao <i>et al.</i>, “Deterministic progenitor behavior and unitary production of neurons in the neocortex,” <i>Cell</i>, vol. 159, no. 4. Cell Press, pp. 775–788, 2014.","apa":"Gao, P., Postiglione, M. P., Krieger, T., Hernandez, L., Wang, C., Han, Z., … Shi, S. (2014). Deterministic progenitor behavior and unitary production of neurons in the neocortex. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2014.10.027\">https://doi.org/10.1016/j.cell.2014.10.027</a>","chicago":"Gao, Peng, Maria P Postiglione, Teresa Krieger, Luisirene Hernandez, Chao Wang, Zhi Han, Carmen Streicher, et al. “Deterministic Progenitor Behavior and Unitary Production of Neurons in the Neocortex.” <i>Cell</i>. Cell Press, 2014. <a href=\"https://doi.org/10.1016/j.cell.2014.10.027\">https://doi.org/10.1016/j.cell.2014.10.027</a>.","mla":"Gao, Peng, et al. “Deterministic Progenitor Behavior and Unitary Production of Neurons in the Neocortex.” <i>Cell</i>, vol. 159, no. 4, Cell Press, 2014, pp. 775–88, doi:<a href=\"https://doi.org/10.1016/j.cell.2014.10.027\">10.1016/j.cell.2014.10.027</a>.","ama":"Gao P, Postiglione MP, Krieger T, et al. Deterministic progenitor behavior and unitary production of neurons in the neocortex. <i>Cell</i>. 2014;159(4):775-788. doi:<a href=\"https://doi.org/10.1016/j.cell.2014.10.027\">10.1016/j.cell.2014.10.027</a>","ista":"Gao P, Postiglione MP, Krieger T, Hernandez L, Wang C, Han Z, Streicher C, Papusheva E, Insolera R, Chugh K, Kodish O, Huang K, Simons B, Luo L, Hippenmeyer S, Shi S. 2014. Deterministic progenitor behavior and unitary production of neurons in the neocortex. Cell. 159(4), 775–788.","short":"P. Gao, M.P. Postiglione, T. Krieger, L. Hernandez, C. Wang, Z. Han, C. Streicher, E. Papusheva, R. Insolera, K. Chugh, O. Kodish, K. Huang, B. Simons, L. Luo, S. Hippenmeyer, S. Shi, Cell 159 (2014) 775–788."},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","creator":"system","file_id":"4709","date_updated":"2020-07-14T12:45:25Z","access_level":"open_access","file_name":"IST-2016-423-v1+1_1-s2.0-S0092867414013154-main.pdf","file_size":4435787,"date_created":"2018-12-12T10:08:47Z","checksum":"6c5de8329bb2ffa71cba9fda750f14ce"}],"date_created":"2018-12-11T11:55:16Z","department":[{"_id":"SiHi"},{"_id":"Bio"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"scopus_import":1,"publisher":"Cell Press","date_published":"2014-11-06T00:00:00Z","month":"11","page":"775 - 788","file_date_updated":"2020-07-14T12:45:25Z","publication":"Cell","issue":"4","status":"public","intvolume":"       159","type":"journal_article","day":"06"},{"language":[{"iso":"eng"}],"publisher":"Wiley-Blackwell","scopus_import":1,"date_published":"2014-11-27T00:00:00Z","month":"11","date_created":"2018-12-11T11:55:16Z","file":[{"file_name":"IST-2016-462-v1+1_Novak-2014-Ecology_and_Evolution.pdf","file_size":118813,"date_created":"2018-12-12T10:12:28Z","checksum":"9ab43db1b0fede7bfe560ed77e177b76","date_updated":"2020-07-14T12:45:25Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"4946","creator":"system"}],"department":[{"_id":"NiBa"}],"has_accepted_license":"1","status":"public","intvolume":"         4","type":"journal_article","day":"27","file_date_updated":"2020-07-14T12:45:25Z","page":"4589 - 4597","issue":"24","publication":"Ecology and Evolution","pubrep_id":"462","title":"Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution","ec_funded":1,"doi":"10.1002/ece3.1289","year":"2014","ddc":["570"],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1125"}]},"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"author":[{"full_name":"Novak, Sebastian","last_name":"Novak","orcid":"0000-0002-2519-824X","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"text":"Understanding the evolution of dispersal is essential for understanding and predicting the dynamics of natural populations. Two main factors are known to influence dispersal evolution: spatio-temporal variation in the environment and relatedness between individuals. However, the relation between these factors is still poorly understood, and they are usually treated separately. In this article, I present a theoretical framework that contains and connects effects of both environmental variation and relatedness, and reproduces and extends their known features. Spatial habitat variation selects for balanced dispersal strategies, whereby the population is kept at an ideal free distribution. Within this class of dispersal strategies, I explain how increased dispersal is promoted by perturbations to the dispersal type frequencies. An explicit formula shows the magnitude of the selective advantage of increased dispersal in terms of the spatial variability in the frequencies of the different dispersal strategies present. These variances are capable of capturing various sources of stochasticity and hence establish a common scale for their effects on the evolution of dispersal. The results furthermore indicate an alternative approach to identifying effects of relatedness on dispersal evolution.","lang":"eng"}],"publication_status":"published","citation":{"ama":"Novak S. Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. <i>Ecology and Evolution</i>. 2014;4(24):4589-4597. doi:<a href=\"https://doi.org/10.1002/ece3.1289\">10.1002/ece3.1289</a>","mla":"Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances as Driving Forces of Dispersal Evolution.” <i>Ecology and Evolution</i>, vol. 4, no. 24, Wiley-Blackwell, 2014, pp. 4589–97, doi:<a href=\"https://doi.org/10.1002/ece3.1289\">10.1002/ece3.1289</a>.","ista":"Novak S. 2014. Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. Ecology and Evolution. 4(24), 4589–4597.","short":"S. Novak, Ecology and Evolution 4 (2014) 4589–4597.","apa":"Novak, S. (2014). Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. <i>Ecology and Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/ece3.1289\">https://doi.org/10.1002/ece3.1289</a>","ieee":"S. Novak, “Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution,” <i>Ecology and Evolution</i>, vol. 4, no. 24. Wiley-Blackwell, pp. 4589–4597, 2014.","chicago":"Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances as Driving Forces of Dispersal Evolution.” <i>Ecology and Evolution</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1002/ece3.1289\">https://doi.org/10.1002/ece3.1289</a>."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","oa_version":"Published Version","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"_id":"2023","date_updated":"2023-09-07T11:55:53Z","publist_id":"5049","oa":1,"volume":4},{"scopus_import":1,"publisher":"Nature Publishing Group","language":[{"iso":"eng"}],"month":"03","date_published":"2014-03-25T00:00:00Z","file":[{"creator":"system","file_id":"4864","content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:45:25Z","access_level":"open_access","date_created":"2018-12-12T10:11:11Z","checksum":"614fb6579c86d1f95bdd95eeb9ab01b0","file_name":"IST-2016-616-v1+1_DaSi_Bifurcation_Postprint.pdf","file_size":4803515}],"date_created":"2018-12-11T11:55:16Z","has_accepted_license":"1","department":[{"_id":"DaSi"}],"intvolume":"         5","status":"public","day":"25","type":"journal_article","publication":"Nature Communications","file_date_updated":"2020-07-14T12:45:25Z","title":"Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole","pubrep_id":"616","year":"2014","doi":"10.1038/ncomms4498","ddc":["570"],"article_number":"3498","abstract":[{"lang":"eng","text":"The yeast Rab5 homologue, Vps21p, is known to be involved both in the vacuolar protein sorting (VPS) pathway from the trans-Golgi network to the vacuole, and in the endocytic pathway from the plasma membrane to the vacuole. However, the intracellular location at which these two pathways converge remains unclear. In addition, the endocytic pathway is not completely blocked in yeast cells lacking all Rab5 genes, suggesting the existence of an unidentified route that bypasses the Rab5-dependent endocytic pathway. Here we show that convergence of the endocytic and VPS pathways occurs upstream of the requirement for Vps21p in these pathways. We also identify a previously unidentified endocytic pathway mediated by the AP-3 complex. Importantly, the AP-3-mediated pathway appears mostly intact in Rab5-disrupted cells, and thus works as an alternative route to the vacuole/lysosome. We propose that the endocytic traffic branches into two routes to reach the vacuole: a Rab5-dependent VPS pathway and a Rab5-independent AP-3-mediated pathway."}],"author":[{"first_name":"Junko","last_name":"Toshima","full_name":"Toshima, Junko"},{"full_name":"Nishinoaki, Show","last_name":"Nishinoaki","first_name":"Show"},{"first_name":"Yoshifumi","last_name":"Sato","full_name":"Sato, Yoshifumi"},{"last_name":"Yamamoto","full_name":"Yamamoto, Wataru","first_name":"Wataru"},{"full_name":"Furukawa, Daiki","last_name":"Furukawa","first_name":"Daiki"},{"orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","last_name":"Siekhaus","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Akira","last_name":"Sawaguchi","full_name":"Sawaguchi, Akira"},{"full_name":"Toshima, Jiro","last_name":"Toshima","first_name":"Jiro"}],"citation":{"ista":"Toshima J, Nishinoaki S, Sato Y, Yamamoto W, Furukawa D, Siekhaus DE, Sawaguchi A, Toshima J. 2014. Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole. Nature Communications. 5, 3498.","short":"J. Toshima, S. Nishinoaki, Y. Sato, W. Yamamoto, D. Furukawa, D.E. Siekhaus, A. Sawaguchi, J. Toshima, Nature Communications 5 (2014).","ama":"Toshima J, Nishinoaki S, Sato Y, et al. Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole. <i>Nature Communications</i>. 2014;5. doi:<a href=\"https://doi.org/10.1038/ncomms4498\">10.1038/ncomms4498</a>","mla":"Toshima, Junko, et al. “Bifurcation of the Endocytic Pathway into Rab5-Dependent and -Independent Transport to the Vacuole.” <i>Nature Communications</i>, vol. 5, 3498, Nature Publishing Group, 2014, doi:<a href=\"https://doi.org/10.1038/ncomms4498\">10.1038/ncomms4498</a>.","chicago":"Toshima, Junko, Show Nishinoaki, Yoshifumi Sato, Wataru Yamamoto, Daiki Furukawa, Daria E Siekhaus, Akira Sawaguchi, and Jiro Toshima. “Bifurcation of the Endocytic Pathway into Rab5-Dependent and -Independent Transport to the Vacuole.” <i>Nature Communications</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/ncomms4498\">https://doi.org/10.1038/ncomms4498</a>.","apa":"Toshima, J., Nishinoaki, S., Sato, Y., Yamamoto, W., Furukawa, D., Siekhaus, D. E., … Toshima, J. (2014). Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms4498\">https://doi.org/10.1038/ncomms4498</a>","ieee":"J. Toshima <i>et al.</i>, “Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole,” <i>Nature Communications</i>, vol. 5. Nature Publishing Group, 2014."},"publication_status":"published","_id":"2024","quality_controlled":"1","oa_version":"Submitted Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","volume":5,"date_updated":"2021-01-12T06:54:48Z","publist_id":"5048","oa":1},{"alternative_title":["LNCS"],"ec_funded":1,"doi":"10.1007/978-3-319-11936-6_17","year":"2014","title":"Rabinizer 3: Safraless translation of ltl to small deterministic automata","publist_id":"5045","date_updated":"2021-01-12T06:54:49Z","volume":8837,"editor":[{"last_name":"Cassez","full_name":"Cassez, Franck","first_name":"Franck"},{"last_name":"Raskin","full_name":"Raskin, Jean-François","first_name":"Jean-François"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Sponsor: P202/12/G061; GACR; Czech Science Foundation\r\n\r\n","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms"}],"oa_version":"None","quality_controlled":"1","_id":"2026","publication_status":"published","citation":{"chicago":"Komárková, Zuzana, and Jan Kretinsky. “Rabinizer 3: Safraless Translation of Ltl to Small Deterministic Automata.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Franck Cassez and Jean-François Raskin, 8837:235–41. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-11936-6_17\">https://doi.org/10.1007/978-3-319-11936-6_17</a>.","apa":"Komárková, Z., &#38; Kretinsky, J. (2014). Rabinizer 3: Safraless translation of ltl to small deterministic automata. In F. Cassez &#38; J.-F. Raskin (Eds.), <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 8837, pp. 235–241). Sydney, Australia: Springer. <a href=\"https://doi.org/10.1007/978-3-319-11936-6_17\">https://doi.org/10.1007/978-3-319-11936-6_17</a>","ieee":"Z. Komárková and J. Kretinsky, “Rabinizer 3: Safraless translation of ltl to small deterministic automata,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Sydney, Australia, 2014, vol. 8837, pp. 235–241.","short":"Z. Komárková, J. Kretinsky, in:, F. Cassez, J.-F. Raskin (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 235–241.","ista":"Komárková Z, Kretinsky J. 2014. Rabinizer 3: Safraless translation of ltl to small deterministic automata. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 8837, 235–241.","mla":"Komárková, Zuzana, and Jan Kretinsky. “Rabinizer 3: Safraless Translation of Ltl to Small Deterministic Automata.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Franck Cassez and Jean-François Raskin, vol. 8837, Springer, 2014, pp. 235–41, doi:<a href=\"https://doi.org/10.1007/978-3-319-11936-6_17\">10.1007/978-3-319-11936-6_17</a>.","ama":"Komárková Z, Kretinsky J. Rabinizer 3: Safraless translation of ltl to small deterministic automata. In: Cassez F, Raskin J-F, eds. <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 8837. Springer; 2014:235-241. doi:<a href=\"https://doi.org/10.1007/978-3-319-11936-6_17\">10.1007/978-3-319-11936-6_17</a>"},"author":[{"full_name":"Komárková, Zuzana","last_name":"Komárková","first_name":"Zuzana"},{"orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","last_name":"Kretinsky","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"We present a tool for translating LTL formulae into deterministic ω-automata. It is the first tool that covers the whole LTL that does not use Safra’s determinization or any of its variants. This leads to smaller automata. There are several outputs of the tool: firstly, deterministic Rabin automata, which are the standard input for probabilistic model checking, e.g. for the probabilistic model-checker PRISM; secondly, deterministic generalized Rabin automata, which can also be used for probabilistic model checking and are sometimes by orders of magnitude smaller. We also link our tool to PRISM and show that this leads to a significant speed-up of probabilistic LTL model checking, especially with the generalized Rabin automata."}],"department":[{"_id":"ToHe"}],"date_created":"2018-12-11T11:55:17Z","conference":{"end_date":"2014-11-07","location":"Sydney, Australia","name":"ATVA: Automated Technology for Verification and Analysis","start_date":"2014-11-03"},"date_published":"2014-01-01T00:00:00Z","month":"01","language":[{"iso":"eng"}],"publisher":"Springer","page":"235 - 241","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","type":"conference","day":"01","status":"public","intvolume":"      8837"},{"intvolume":"      8837","status":"public","day":"01","type":"conference","publication":" Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","page":"98 - 114","publisher":"Society of Industrial and Applied Mathematics","language":[{"iso":"eng"}],"month":"11","date_published":"2014-11-01T00:00:00Z","conference":{"location":"Sydney, Australia","name":"ALENEX: Algorithm Engineering and Experiments","end_date":"2014-11-07","start_date":"2014-11-03"},"date_created":"2018-12-11T11:55:17Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"abstract":[{"lang":"eng","text":"We present a general framework for applying machine-learning algorithms to the verification of Markov decision processes (MDPs). The primary goal of these techniques is to improve performance by avoiding an exhaustive exploration of the state space. Our framework focuses on probabilistic reachability, which is a core property for verification, and is illustrated through two distinct instantiations. The first assumes that full knowledge of the MDP is available, and performs a heuristic-driven partial exploration of the model, yielding precise lower and upper bounds on the required probability. The second tackles the case where we may only sample the MDP, and yields probabilistic guarantees, again in terms of both the lower and upper bounds, which provides efficient stopping criteria for the approximation. The latter is the first extension of statistical model checking for unbounded properties inMDPs. In contrast with other related techniques, our approach is not restricted to time-bounded (finite-horizon) or discounted properties, nor does it assume any particular properties of the MDP. We also show how our methods extend to LTL objectives. We present experimental results showing the performance of our framework on several examples."}],"author":[{"full_name":"Brázdil, Tomáš","last_name":"Brázdil","first_name":"Tomáš"},{"first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin","last_name":"Chmelik","first_name":"Martin"},{"first_name":"Vojtěch","last_name":"Forejt","full_name":"Forejt, Vojtěch"},{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","last_name":"Kretinsky","full_name":"Kretinsky, Jan","first_name":"Jan"},{"first_name":"Marta","last_name":"Kwiatkowska","full_name":"Kwiatkowska, Marta"},{"last_name":"Parker","full_name":"Parker, David","first_name":"David"},{"first_name":"Mateusz","full_name":"Ujma, Mateusz","last_name":"Ujma"}],"citation":{"chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Vojtěch Forejt, Jan Kretinsky, Marta Kwiatkowska, David Parker, and Mateusz Ujma. “Verification of Markov Decision Processes Using Learning Algorithms.” In <i> Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Franck Cassez and Jean-François Raskin, 8837:98–114. Society of Industrial and Applied Mathematics, 2014. <a href=\"https://doi.org/10.1007/978-3-319-11936-6_8\">https://doi.org/10.1007/978-3-319-11936-6_8</a>.","ieee":"T. Brázdil <i>et al.</i>, “Verification of markov decision processes using learning algorithms,” in <i> Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Sydney, Australia, 2014, vol. 8837, pp. 98–114.","apa":"Brázdil, T., Chatterjee, K., Chmelik, M., Forejt, V., Kretinsky, J., Kwiatkowska, M., … Ujma, M. (2014). Verification of markov decision processes using learning algorithms. In F. Cassez &#38; J.-F. Raskin (Eds.), <i> Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 8837, pp. 98–114). Sydney, Australia: Society of Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1007/978-3-319-11936-6_8\">https://doi.org/10.1007/978-3-319-11936-6_8</a>","short":"T. Brázdil, K. Chatterjee, M. Chmelik, V. Forejt, J. Kretinsky, M. Kwiatkowska, D. Parker, M. Ujma, in:, F. Cassez, J.-F. Raskin (Eds.),  Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Society of Industrial and Applied Mathematics, 2014, pp. 98–114.","ista":"Brázdil T, Chatterjee K, Chmelik M, Forejt V, Kretinsky J, Kwiatkowska M, Parker D, Ujma M. 2014. Verification of markov decision processes using learning algorithms.  Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). ALENEX: Algorithm Engineering and Experiments, LNCS, vol. 8837, 98–114.","ama":"Brázdil T, Chatterjee K, Chmelik M, et al. Verification of markov decision processes using learning algorithms. In: Cassez F, Raskin J-F, eds. <i> Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 8837. Society of Industrial and Applied Mathematics; 2014:98-114. doi:<a href=\"https://doi.org/10.1007/978-3-319-11936-6_8\">10.1007/978-3-319-11936-6_8</a>","mla":"Brázdil, Tomáš, et al. “Verification of Markov Decision Processes Using Learning Algorithms.” <i> Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Franck Cassez and Jean-François Raskin, vol. 8837, Society of Industrial and Applied Mathematics, 2014, pp. 98–114, doi:<a href=\"https://doi.org/10.1007/978-3-319-11936-6_8\">10.1007/978-3-319-11936-6_8</a>."},"publication_status":"published","_id":"2027","quality_controlled":"1","project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"24696","_id":"26241A12-B435-11E9-9278-68D0E5697425","name":"LIGHT-REGULATED LIGAND TRAPS FOR SPATIO-TEMPORAL INHIBITION OF CELL SIGNALING"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"S11402-N23","call_identifier":"FWF","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"oa_version":"Submitted Version","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 246967 (VERIWARE), by the EU FP7 project HIERATIC, by the Czech Science Foundation grant No P202/12/P612, by EPSRC project EP/K038575/1.","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","editor":[{"full_name":"Cassez, Franck","last_name":"Cassez","first_name":"Franck"},{"last_name":"Raskin","full_name":"Raskin, Jean-François","first_name":"Jean-François"}],"oa":1,"publist_id":"5046","volume":8837,"date_updated":"2021-01-12T06:54:49Z","title":"Verification of markov decision processes using learning algorithms","year":"2014","doi":"10.1007/978-3-319-11936-6_8","ec_funded":1,"alternative_title":["LNCS"],"main_file_link":[{"url":"http://arxiv.org/abs/1402.2967","open_access":"1"}]},{"publisher":"Academic Press","scopus_import":"1","language":[{"iso":"eng"}],"month":"10","date_published":"2014-10-12T00:00:00Z","file":[{"access_level":"open_access","date_updated":"2020-07-14T12:45:25Z","file_size":2679222,"file_name":"IST-2016-444-v1+1_1-s2.0-S0022519314005888-main.pdf","checksum":"a9dbae18d3233b3dab6944fd3f2cd49e","date_created":"2018-12-12T10:17:58Z","relation":"main_file","content_type":"application/pdf","file_id":"5316","creator":"system"}],"date_created":"2018-12-11T11:55:18Z","has_accepted_license":"1","department":[{"_id":"GaTk"}],"intvolume":"       365","status":"public","day":"12","type":"journal_article","publication":" Journal of Theoretical Biology","page":"40 - 54","file_date_updated":"2020-07-14T12:45:25Z","pubrep_id":"444","title":"Characterizing spiking in noisy type II neurons","doi":"10.1016/j.jtbi.2014.09.041","year":"2014","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1016/j.jtbi.2015.03.013"}]},"ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"abstract":[{"lang":"eng","text":"Understanding the dynamics of noisy neurons remains an important challenge in neuroscience. Here, we describe a simple probabilistic model that accurately describes the firing behavior in a large class (type II) of neurons. To demonstrate the usefulness of this model, we show how it accurately predicts the interspike interval (ISI) distributions, bursting patterns and mean firing rates found by: (1) simulations of the classic Hodgkin-Huxley model with channel noise, (2) experimental data from squid giant axon with a noisy input current and (3) experimental data on noisy firing from a neuron within the suprachiasmatic nucleus (SCN). This simple model has 6 parameters, however, in some cases, two of these parameters are coupled and only 5 parameters account for much of the known behavior. From these parameters, many properties of spiking can be found through simple calculation. Thus, we show how the complex effects of noise can be understood through a simple and general probabilistic model."}],"author":[{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina","orcid":"0000-0002-7214-0171","full_name":"Bodova, Katarina","last_name":"Bodova"},{"full_name":"Paydarfar, David","last_name":"Paydarfar","first_name":"David"},{"last_name":"Forger","full_name":"Forger, Daniel","first_name":"Daniel"}],"publication_status":"published","citation":{"chicago":"Bodova, Katarina, David Paydarfar, and Daniel Forger. “Characterizing Spiking in Noisy Type II Neurons.” <i> Journal of Theoretical Biology</i>. Academic Press, 2014. <a href=\"https://doi.org/10.1016/j.jtbi.2014.09.041\">https://doi.org/10.1016/j.jtbi.2014.09.041</a>.","apa":"Bodova, K., Paydarfar, D., &#38; Forger, D. (2014). Characterizing spiking in noisy type II neurons. <i> Journal of Theoretical Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jtbi.2014.09.041\">https://doi.org/10.1016/j.jtbi.2014.09.041</a>","ieee":"K. Bodova, D. Paydarfar, and D. Forger, “Characterizing spiking in noisy type II neurons,” <i> Journal of Theoretical Biology</i>, vol. 365. Academic Press, pp. 40–54, 2014.","short":"K. Bodova, D. Paydarfar, D. Forger,  Journal of Theoretical Biology 365 (2014) 40–54.","ista":"Bodova K, Paydarfar D, Forger D. 2014. Characterizing spiking in noisy type II neurons.  Journal of Theoretical Biology. 365, 40–54.","mla":"Bodova, Katarina, et al. “Characterizing Spiking in Noisy Type II Neurons.” <i> Journal of Theoretical Biology</i>, vol. 365, Academic Press, 2014, pp. 40–54, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2014.09.041\">10.1016/j.jtbi.2014.09.041</a>.","ama":"Bodova K, Paydarfar D, Forger D. Characterizing spiking in noisy type II neurons. <i> Journal of Theoretical Biology</i>. 2014;365:40-54. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2014.09.041\">10.1016/j.jtbi.2014.09.041</a>"},"_id":"2028","acknowledgement":"This work is supported by AFOSR grant FA 9550-11-1-0165, program grant RPG 24/2012 from the Human Frontiers of Science (DBF) and travel support from the European Commission Marie Curie International Reintegration Grant PIRG04-GA-2008-239429 (KB). DP was supported by NIHR01 GM104987 and the Wyss Institute of Biologically Inspired Engineering. ","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","quality_controlled":"1","volume":365,"publist_id":"5043","date_updated":"2022-08-25T14:00:47Z","oa":1,"article_processing_charge":"No"}]