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Novak, “Evolutionary proccesses in variable emvironments,” Institute of Science and Technology Austria, 2016.","short":"S. Novak, Evolutionary Proccesses in Variable Emvironments, Institute of Science and Technology Austria, 2016.","mla":"Novak, Sebastian. <i>Evolutionary Proccesses in Variable Emvironments</i>. Institute of Science and Technology Austria, 2016."},"_id":"1125","oa_version":"Published Version","date_updated":"2026-07-29T11:27:43Z","oa":1,"date_published":"2016-07-01T00:00:00Z","article_processing_charge":"No","type":"dissertation","corr_author":"1","ddc":["576"],"abstract":[{"text":"Natural environments are never constant but subject to spatial and temporal change on\r\nall scales, increasingly so due to human activity. Hence, it is crucial to understand the\r\nimpact of environmental variation on evolutionary processes. In this thesis, I present\r\nthree topics that share the common theme of environmental variation, yet illustrate its\r\neffect from different perspectives.\r\nFirst, I show how a temporally fluctuating environment gives rise to second-order\r\nselection on a modifier for stress-induced mutagenesis. Without fluctuations, when\r\npopulations are adapted to their environment, mutation rates are minimized. I argue\r\nthat a stress-induced mutator mechanism may only be maintained if the population is\r\nrepeatedly subjected to diverse environmental challenges, and I outline implications of\r\nthe presented results to antibiotic treatment strategies.\r\nSecond, I discuss my work on the evolution of dispersal. Besides reproducing\r\nknown results about the effect of heterogeneous habitats on dispersal, it identifies\r\nspatial changes in dispersal type frequencies as a source for selection for increased\r\npropensities to disperse. This concept contains effects of relatedness that are known\r\nto promote dispersal, and I explain how it identifies other forces selecting for dispersal\r\nand puts them on a common scale.\r\nThird, I analyse genetic variances of phenotypic traits under multivariate stabilizing\r\nselection. For the case of constant environments, I generalize known formulae of\r\nequilibrium variances to multiple traits and discuss how the genetic variance of a focal\r\ntrait is influenced by selection on background traits. I conclude by presenting ideas and\r\npreliminary work aiming at including environmental fluctuations in the form of moving\r\ntrait optima into the model.","lang":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"year":"2016","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"date_created":"2018-12-11T11:50:17Z","language":[{"iso":"eng"}],"author":[{"first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X","last_name":"Novak"}],"file":[{"file_size":3564901,"content_type":"application/pdf","date_created":"2019-08-13T09:01:00Z","creator":"dernst","checksum":"81dcc838dfcf7aa0b1a27ecf4fe2da4e","relation":"main_file","file_name":"Novak_thesis.pdf","access_level":"closed","file_id":"6811","date_updated":"2019-08-13T09:01:00Z"},{"creator":"dernst","checksum":"30808d2f7ca920e09f63a95cdc49bffd","date_created":"2021-02-22T13:42:47Z","file_size":2814384,"content_type":"application/pdf","success":1,"date_updated":"2021-02-22T13:42:47Z","access_level":"open_access","file_id":"9186","relation":"main_file","file_name":"2016_Novak_Thesis.pdf"}],"page":"124","month":"07","supervisor":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}]},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"01","publist_id":"6232","publication_status":"published","doi_confirm":"1","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","status":"public","_id":"1128","oa_version":"Published Version","citation":{"apa":"Rieckh, G. (2016). <i>Studying the complexities of transcriptional regulation</i>. Institute of Science and Technology Austria.","ama":"Rieckh G. Studying the complexities of transcriptional regulation. 2016.","chicago":"Rieckh, Georg. “Studying the Complexities of Transcriptional Regulation.” Institute of Science and Technology Austria, 2016.","ista":"Rieckh G. 2016. Studying the complexities of transcriptional regulation. Institute of Science and Technology Austria.","ieee":"G. Rieckh, “Studying the complexities of transcriptional regulation,” Institute of Science and Technology Austria, 2016.","mla":"Rieckh, Georg. <i>Studying the Complexities of Transcriptional Regulation</i>. Institute of Science and Technology Austria, 2016.","short":"G. Rieckh, Studying the Complexities of Transcriptional Regulation, Institute of Science and Technology Austria, 2016."},"degree_awarded":"PhD","OA_place":"publisher","file_date_updated":"2020-09-21T11:30:40Z","title":"Studying the complexities of transcriptional regulation","abstract":[{"lang":"eng","text":"The process of gene expression is central to the modern understanding of how cellular systems\r\nfunction. In this process, a special kind of regulatory proteins, called transcription factors,\r\nare important to determine how much protein is produced from a given gene. As biological\r\ninformation is transmitted from transcription factor concentration to mRNA levels to amounts of\r\nprotein, various sources of noise arise and pose limits to the fidelity of intracellular signaling.\r\nThis thesis concerns itself with several aspects of stochastic gene expression: (i) the mathematical\r\ndescription of complex promoters responsible for the stochastic production of biomolecules,\r\n(ii) fundamental limits to information processing the cell faces due to the interference from multiple\r\nfluctuating signals, (iii) how the presence of gene expression noise influences the evolution\r\nof regulatory sequences, (iv) and tools for the experimental study of origins and consequences\r\nof cell-cell heterogeneity, including an application to bacterial stress response systems."}],"corr_author":"1","ddc":["570"],"type":"dissertation","date_published":"2016-08-01T00:00:00Z","article_processing_charge":"No","date_updated":"2026-07-29T11:29:22Z","oa":1,"supervisor":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","full_name":"Tkacik, Gasper"}],"month":"08","file":[{"file_id":"6815","access_level":"closed","date_updated":"2019-08-13T11:46:25Z","file_name":"Thesis_Georg_Rieckh_w_signature_page.pdf","relation":"main_file","date_created":"2019-08-13T11:46:25Z","checksum":"ec453918c3bf8e6f460fd1156ef7b493","creator":"dernst","file_size":2614660,"content_type":"application/pdf"},{"date_updated":"2020-09-21T11:30:40Z","access_level":"open_access","file_id":"8542","relation":"main_file","file_name":"Thesis_Georg_Rieckh.pdf","creator":"dernst","checksum":"51ae398166370d18fd22478b6365c4da","date_created":"2020-09-21T11:30:40Z","file_size":6096178,"content_type":"application/pdf","success":1}],"page":"114","date_created":"2018-12-11T11:50:18Z","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"},{"_id":"GradSch"}],"author":[{"full_name":"Rieckh, Georg","last_name":"Rieckh","first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87"}],"year":"2016","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"]},{"type":"dissertation","corr_author":"1","ddc":["570"],"date_published":"2016-03-01T00:00:00Z","article_processing_charge":"No","date_updated":"2026-07-29T11:26:59Z","oa":1,"supervisor":[{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak","full_name":"Janovjak, Harald L"}],"month":"03","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:50:17Z","department":[{"_id":"HaJa"},{"_id":"GradSch"}],"author":[{"last_name":"Morri","full_name":"Morri, Maurizio","id":"4863116E-F248-11E8-B48F-1D18A9856A87","first_name":"Maurizio"}],"file":[{"file_name":"MORRI_PhD_thesis_FINALPLUSSIGNATURES (2).pdf","relation":"main_file","date_updated":"2019-08-13T10:50:00Z","file_id":"6812","access_level":"closed","content_type":"application/pdf","file_size":4785167,"checksum":"b439803ac0827cdddd56562a54e3b53b","creator":"dernst","date_created":"2019-08-13T10:50:00Z"},{"date_created":"2021-02-22T11:42:06Z","creator":"dernst","checksum":"dd4136247fe472e7d47880ec68ac8de0","content_type":"application/pdf","success":1,"file_size":4495669,"access_level":"open_access","file_id":"9180","date_updated":"2021-02-22T11:42:06Z","relation":"main_file","file_name":"2016_MORRI_Thesis.pdf"}],"page":"129","year":"2016","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"publist_id":"6236","day":"01","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","doi_confirm":"1","status":"public","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","_id":"1124","citation":{"apa":"Morri, M. (2016). <i>Optical functionalization of human class A orphan G-protein coupled receptors</i>. Institute of Science and Technology Austria.","ama":"Morri M. Optical functionalization of human class A orphan G-protein coupled receptors. 2016.","chicago":"Morri, Maurizio. “Optical Functionalization of Human Class A Orphan G-Protein Coupled Receptors.” Institute of Science and Technology Austria, 2016.","ieee":"M. Morri, “Optical functionalization of human class A orphan G-protein coupled receptors,” Institute of Science and Technology Austria, 2016.","ista":"Morri M. 2016. Optical functionalization of human class A orphan G-protein coupled receptors. Institute of Science and Technology Austria.","short":"M. Morri, Optical Functionalization of Human Class A Orphan G-Protein Coupled Receptors, Institute of Science and Technology Austria, 2016.","mla":"Morri, Maurizio. <i>Optical Functionalization of Human Class A Orphan G-Protein Coupled Receptors</i>. Institute of Science and Technology Austria, 2016."},"degree_awarded":"PhD","title":"Optical functionalization of human class A orphan G-protein coupled receptors","OA_place":"publisher","file_date_updated":"2021-02-22T11:42:06Z"},{"article_processing_charge":"No","date_published":"2016-05-13T00:00:00Z","volume":7,"doi":"10.1038/ncomms11552","oa":1,"date_updated":"2026-07-29T11:31:52Z","ec_funded":1,"abstract":[{"text":"CA3–CA3 recurrent excitatory synapses are thought to play a key role in memory storage and pattern completion. Whether the plasticity properties of these synapses are consistent with their proposed network functions remains unclear. Here, we examine the properties of spike timing-dependent plasticity (STDP) at CA3–CA3 synapses. Low-frequency pairing of excitatory postsynaptic potentials (EPSPs) and action potentials (APs) induces long-term potentiation (LTP), independent of temporal order. The STDP curve is symmetric and broad (half-width ~150 ms). Consistent with these STDP induction properties, AP–EPSP sequences lead to supralinear summation of spine [Ca2+] transients. Furthermore, afterdepolarizations (ADPs) following APs efficiently propagate into dendrites of CA3 pyramidal neurons, and EPSPs summate with dendritic ADPs. In autoassociative network models, storage and recall are more robust with symmetric than with asymmetric STDP rules. Thus, a specialized STDP induction rule allows reliable storage and recall of information in the hippocampal CA3 network.","lang":"eng"}],"quality_controlled":"1","scopus_import":"1","type":"journal_article","publication":"Nature Communications","ddc":["570"],"intvolume":"         7","corr_author":"1","pubrep_id":"582","year":"2016","month":"05","author":[{"id":"46CB58F2-F248-11E8-B48F-1D18A9856A87","first_name":"Rajiv Kumar","last_name":"Mishra","full_name":"Mishra, Rajiv Kumar"},{"first_name":"Sooyun","id":"394AB1C8-F248-11E8-B48F-1D18A9856A87","full_name":"Kim, Sooyun","last_name":"Kim"},{"first_name":"José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","full_name":"Guzmán, José","orcid":"0000-0003-2209-5242","last_name":"Guzmán"},{"orcid":"0000-0001-5001-4804","last_name":"Jonas","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"department":[{"_id":"PeJo"}],"date_created":"2018-12-11T11:51:59Z","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","file_size":4510512,"creator":"system","checksum":"7e84d0392348c874d473b62f1042de22","date_created":"2018-12-12T10:18:33Z","relation":"main_file","file_name":"IST-2016-582-v1+1_ncomms11552.pdf","date_updated":"2020-07-14T12:44:53Z","access_level":"open_access","file_id":"5355"}],"external_id":{"isi":["000375938200001"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"isi":1,"status":"public","has_accepted_license":"1","publisher":"Nature Publishing Group","article_number":"11552","publist_id":"5766","acknowledgement":"We thank Jozsef Csicsvari and Nelson Spruston for critically reading the manuscript. We also thank A. Schlögl for programming, F. Marr for technical assistance and E. Kramberger for manuscript editing. ","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"13","publication_status":"published","title":"Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks","file_date_updated":"2020-07-14T12:44:53Z","project":[{"grant_number":"P24909-B24","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Mechanisms of transmitter release at GABAergic synapses"},{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","grant_number":"268548","call_identifier":"FP7","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons"}],"oa_version":"Published Version","_id":"1432","citation":{"apa":"Mishra, R. K., Kim, S., Guzmán, J., &#38; Jonas, P. M. (2016). Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms11552\">https://doi.org/10.1038/ncomms11552</a>","ama":"Mishra RK, Kim S, Guzmán J, Jonas PM. Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms11552\">10.1038/ncomms11552</a>","ieee":"R. K. Mishra, S. Kim, J. Guzmán, and P. M. Jonas, “Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016.","ista":"Mishra RK, Kim S, Guzmán J, Jonas PM. 2016. Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. Nature Communications. 7, 11552.","chicago":"Mishra, Rajiv Kumar, Sooyun Kim, José Guzmán, and Peter M Jonas. “Symmetric Spike Timing-Dependent Plasticity at CA3–CA3 Synapses Optimizes Storage and Recall in Autoassociative Networks.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms11552\">https://doi.org/10.1038/ncomms11552</a>.","mla":"Mishra, Rajiv Kumar, et al. “Symmetric Spike Timing-Dependent Plasticity at CA3–CA3 Synapses Optimizes Storage and Recall in Autoassociative Networks.” <i>Nature Communications</i>, vol. 7, 11552, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms11552\">10.1038/ncomms11552</a>.","short":"R.K. Mishra, S. Kim, J. Guzmán, P.M. Jonas, Nature Communications 7 (2016)."},"related_material":{"record":[{"status":"public","id":"1396","relation":"dissertation_contains"}]}},{"month":"03","supervisor":[{"orcid":"0000-0001-5001-4804","last_name":"Jonas","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"author":[{"full_name":"Mishra, Rajiv Kumar","last_name":"Mishra","first_name":"Rajiv Kumar","id":"46CB58F2-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"PeJo"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:51:46Z","page":"83","file":[{"file_size":2407572,"content_type":"application/pdf","checksum":"5a010a838faf040f7064f3cfb802f743","creator":"dernst","date_created":"2019-08-09T12:14:46Z","file_name":"Thesis_Mishra_Rajiv (Final).pdf","relation":"main_file","date_updated":"2020-07-14T12:44:48Z","file_id":"6782","access_level":"closed"},{"relation":"main_file","file_name":"2016_RajivMishra_Thesis.pdf","access_level":"open_access","file_id":"9183","date_updated":"2021-02-22T11:48:44Z","success":1,"content_type":"application/pdf","file_size":2407572,"date_created":"2021-02-22T11:48:44Z","creator":"dernst","checksum":"81b26d9ede92c99f1d8cc6fa1d04cbbb"}],"year":"2016","alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"abstract":[{"lang":"eng","text":"CA3 pyramidal neurons are thought to pay a key role in memory storage and pattern completion by activity-dependent synaptic plasticity between CA3-CA3 recurrent excitatory synapses. To examine the induction rules of synaptic plasticity at CA3-CA3 synapses, we performed whole-cell patch-clamp recordings in acute hippocampal slices from rats (postnatal 21-24 days) at room temperature. Compound excitatory postsynaptic potentials (ESPSs) were recorded by tract stimulation in stratum oriens in the presence of 10 µM gabazine. High-frequency stimulation (HFS) induced N-methyl-D-aspartate (NMDA) receptor-dependent long-term potentiation (LTP). Although LTP by HFS did not requier postsynaptic spikes, it was blocked by Na+-channel blockers suggesting that local active processes (e.g.) dendritic spikes) may contribute to LTP induction without requirement of a somatic action potential (AP). We next examined the properties of spike timing-dependent plasticity (STDP) at CA3-CA3 synapses. Unexpectedly, low-frequency pairing of EPSPs and backpropagated action potentialy (bAPs) induced LTP, independent of temporal order. The STDP curve was symmetric and broad, with a half-width of ~150 ms. Consistent with these specific STDP induction properties, post-presynaptic sequences led to a supralinear summation of spine [Ca2+] transients. Furthermore, in autoassociative network models, storage and recall was substantially more robust with symmetric than with asymmetric STDP rules. In conclusion, we found associative forms of LTP at CA3-CA3 recurrent collateral synapses with distinct induction rules. LTP induced by HFS may be associated with dendritic spikes. In contrast, low frequency pairing of pre- and postsynaptic activity induced LTP only if EPSP-AP were temporally very close. Together, these induction mechanisms of synaptiic plasticity may contribute to memory storage in the CA3-CA3 microcircuit at different ranges of activity."}],"type":"dissertation","ddc":["570"],"corr_author":"1","article_processing_charge":"No","date_published":"2016-03-01T00:00:00Z","oa":1,"date_updated":"2026-07-29T11:31:52Z","oa_version":"Published Version","_id":"1396","citation":{"chicago":"Mishra, Rajiv Kumar. “Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses in Hippocampus.” Institute of Science and Technology Austria, 2016.","ieee":"R. K. Mishra, “Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus,” Institute of Science and Technology Austria, 2016.","ista":"Mishra RK. 2016. Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus. Institute of Science and Technology Austria.","mla":"Mishra, Rajiv Kumar. <i>Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses in Hippocampus</i>. Institute of Science and Technology Austria, 2016.","short":"R.K. Mishra, Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses in Hippocampus, Institute of Science and Technology Austria, 2016.","apa":"Mishra, R. K. (2016). <i>Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus</i>. Institute of Science and Technology Austria.","ama":"Mishra RK. Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus. 2016."},"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1432"}]},"degree_awarded":"PhD","title":"Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus","file_date_updated":"2021-02-22T11:48:44Z","OA_place":"publisher","publist_id":"5811","day":"01","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","doi_confirm":"1","has_accepted_license":"1","status":"public","publisher":"Institute of Science and Technology Austria"},{"publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"01","acknowledgement":"This PhD thesis may not have been completed without the help and care I received from some peo- ple during my PhD life. I am especially grateful to Tiago Paixao, Gasper Tkacik, Nick Barton, not only for their scientific advices but also for their patience and support. I thank Calin Guet and Jonathan Bollback for allowing me to “play around” in their labs and get some experience on experimental evolution. I thank Magdalena Steinrueck and Fabienne Jesse for collaborating and sharing their experimental data with me. I thank Johannes Jaeger for reviewing my thesis. I thank all members of Barton group (aka bartonians) for their feedback, and all workers of IST Austria for making the best working conditions. Lastly, I thank two special women, Nejla Sag ̆lam and Setenay Dog ̆an, for their continuous support and encouragement. I truly had a great chance of having right people around me.","publist_id":"6229","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","status":"public","doi_confirm":"1","related_material":{"record":[{"relation":"research_data","id":"5554","status":"public"},{"id":"1666","status":"public","relation":"part_of_dissertation"}]},"citation":{"ama":"Tugrul M. Evolution of transcriptional regulatory sequences. 2016.","apa":"Tugrul, M. (2016). <i>Evolution of transcriptional regulatory sequences</i>. Institute of Science and Technology Austria.","short":"M. Tugrul, Evolution of Transcriptional Regulatory Sequences, Institute of Science and Technology Austria, 2016.","mla":"Tugrul, Murat. <i>Evolution of Transcriptional Regulatory Sequences</i>. Institute of Science and Technology Austria, 2016.","ieee":"M. Tugrul, “Evolution of transcriptional regulatory sequences,” Institute of Science and Technology Austria, 2016.","chicago":"Tugrul, Murat. “Evolution of Transcriptional Regulatory Sequences.” Institute of Science and Technology Austria, 2016.","ista":"Tugrul M. 2016. Evolution of transcriptional regulatory sequences. Institute of Science and Technology Austria."},"_id":"1131","oa_version":"Published Version","OA_place":"publisher","file_date_updated":"2021-02-22T11:45:20Z","title":"Evolution of transcriptional regulatory sequences","degree_awarded":"PhD","corr_author":"1","ddc":["576"],"type":"dissertation","abstract":[{"lang":"eng","text":"Evolution of gene regulation is important for phenotypic evolution and diversity. Sequence-specific binding of regulatory proteins is one of the key regulatory mechanisms determining gene expression. Although there has been intense interest in evolution of regulatory binding sites in the last decades, a theoretical understanding is far from being complete. In this thesis, I aim at a better understanding of the evolution of transcriptional regulatory binding sequences by using biophysical and population genetic models.\r\nIn the first part of the thesis, I discuss how to formulate the evolutionary dynamics of binding se- quences in a single isolated binding site and in promoter/enhancer regions. I develop a theoretical framework bridging between a thermodynamical model for transcription and a mutation-selection-drift model for monomorphic populations. I mainly address the typical evolutionary rates, and how they de- pend on biophysical parameters (e.g. binding length and specificity) and population genetic parameters (e.g. population size and selection strength).\r\nIn the second part of the thesis, I analyse empirical data for a better evolutionary and biophysical understanding of sequence-specific binding of bacterial RNA polymerase. First, I infer selection on regulatory and non-regulatory binding sites of RNA polymerase in the E. coli K12 genome. Second, I infer the chemical potential of RNA polymerase, an important but unknown physical parameter defining the threshold energy for strong binding. Furthermore, I try to understand the relation between the lac promoter sequence diversity and the LacZ activity variation among 20 bacterial isolates by constructing a simple but biophysically motivated gene expression model. Lastly, I lay out a statistical framework to predict adaptive point mutations in de novo promoter evolution in a selection experiment."}],"date_updated":"2026-07-29T11:31:14Z","oa":1,"date_published":"2016-07-01T00:00:00Z","article_processing_charge":"No","file":[{"file_size":3695257,"content_type":"application/pdf","checksum":"66cb61a59943e4fb7447c6a86be5ef51","creator":"dernst","date_created":"2019-08-13T08:53:52Z","file_name":"Tugrul_thesis_w_signature_page.pdf","relation":"main_file","date_updated":"2019-08-13T08:53:52Z","file_id":"6810","access_level":"closed"},{"content_type":"application/pdf","success":1,"file_size":3880811,"creator":"dernst","checksum":"293e388d70563760f6b24c3e66283dda","date_created":"2021-02-22T11:45:20Z","relation":"main_file","file_name":"2016_Tugrul_Thesis.pdf","date_updated":"2021-02-22T11:45:20Z","access_level":"open_access","file_id":"9182"}],"page":"89","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:50:19Z","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"author":[{"orcid":"0000-0002-8523-0758","last_name":"Tugrul","full_name":"Tugrul, Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","first_name":"Murat"}],"supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"month":"07","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"year":"2016"},{"article_processing_charge":"No","date_published":"2016-05-12T00:00:00Z","tmp":{"short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"publisher":"Institute of Science and Technology Austria","oa":1,"date_updated":"2026-07-29T11:31:13Z","doi":"10.15479/AT:ISTA:43","has_accepted_license":"1","status":"public","day":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The data stored here is used in Murat Tugrul's PhD thesis (Chapter 3), which is related to the evolution of bacterial RNA polymerase binding.\r\nMagdalena Steinrueck (PhD Student in Calin Guet's group at IST Austria) performed the experiments and created the data on de novo promoter evolution. Fabienne Jesse (PhD Student in Jon Bollback's group at IST Austria) performed the experiments and created the data on lac promoter evolution."}],"type":"research_data","year":"2016","file_date_updated":"2020-07-14T12:47:01Z","contributor":[{"id":"2C023F40-F248-11E8-B48F-1D18A9856A87","first_name":"Magdalena","last_name":"Steinrück","contributor_type":"researcher"},{"contributor_type":"researcher","last_name":"Jesse","first_name":"Fabienne","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87"}],"title":"Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase","_id":"5554","oa_version":"Published Version","keyword":["RNAP binding","de novo promoter evolution","lac promoter"],"month":"05","datarep_id":"43","file":[{"file_size":1123495,"content_type":"application/zip","date_created":"2018-12-12T13:03:08Z","creator":"system","checksum":"1fc0a10bb7ce110fcb5e1fbe3cf0c4e2","relation":"main_file","file_name":"IST-2016-43-v1+1_DATA_MTugrul_PhDThesis_Chapter3.zip","access_level":"open_access","file_id":"5626","date_updated":"2020-07-14T12:47:01Z"}],"citation":{"ama":"Tugrul M. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:43\">10.15479/AT:ISTA:43</a>","apa":"Tugrul, M. (2016). Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:43\">https://doi.org/10.15479/AT:ISTA:43</a>","mla":"Tugrul, Murat. <i>Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:43\">10.15479/AT:ISTA:43</a>.","short":"M. Tugrul, (2016).","ista":"Tugrul M. 2016. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:43\">10.15479/AT:ISTA:43</a>.","chicago":"Tugrul, Murat. “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:43\">https://doi.org/10.15479/AT:ISTA:43</a>.","ieee":"M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016."},"author":[{"id":"37C323C6-F248-11E8-B48F-1D18A9856A87","first_name":"Murat","orcid":"0000-0002-8523-0758","last_name":"Tugrul","full_name":"Tugrul, Murat"}],"related_material":{"record":[{"status":"public","id":"1131","relation":"used_in_publication"}]},"date_created":"2018-12-12T12:31:30Z","department":[{"_id":"NiBa"},{"_id":"JoBo"}]},{"article_number":"104","publisher":"ACM","has_accepted_license":"1","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"isi":1,"external_id":{"isi":["000380112400074"]},"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","publist_id":"5880","file_date_updated":"2020-07-14T12:44:46Z","title":"Fast approximations for boundary element based brittle fracture simulation","related_material":{"record":[{"id":"839","status":"public","relation":"dissertation_contains"}]},"citation":{"chicago":"Hahn, David, and Chris Wojtan. “Fast Approximations for Boundary Element Based Brittle Fracture Simulation,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2897824.2925902\">https://doi.org/10.1145/2897824.2925902</a>.","ieee":"D. Hahn and C. Wojtan, “Fast approximations for boundary element based brittle fracture simulation,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4.","ista":"Hahn D, Wojtan C. 2016. Fast approximations for boundary element based brittle fracture simulation. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 104.","short":"D. Hahn, C. Wojtan, in:, ACM, 2016.","mla":"Hahn, David, and Chris Wojtan. <i>Fast Approximations for Boundary Element Based Brittle Fracture Simulation</i>. Vol. 35, no. 4, 104, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2897824.2925902\">10.1145/2897824.2925902</a>.","apa":"Hahn, D., &#38; Wojtan, C. (2016). Fast approximations for boundary element based brittle fracture simulation (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2897824.2925902\">https://doi.org/10.1145/2897824.2925902</a>","ama":"Hahn D, Wojtan C. Fast approximations for boundary element based brittle fracture simulation. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2897824.2925902\">10.1145/2897824.2925902</a>"},"oa_version":"Published Version","_id":"1362","project":[{"call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"date_updated":"2026-07-29T13:27:24Z","oa":1,"volume":35,"doi":"10.1145/2897824.2925902","date_published":"2016-07-01T00:00:00Z","article_processing_charge":"No","corr_author":"1","intvolume":"        35","ddc":["000"],"type":"conference","scopus_import":"1","conference":{"end_date":"2016-07-28","name":"ACM SIGGRAPH","start_date":"2016-07-24","location":"Anaheim, CA, USA"},"quality_controlled":"1","ec_funded":1,"abstract":[{"lang":"eng","text":"We present a boundary element based method for fast simulation of brittle fracture. By introducing simplifying assumptions that allow us to quickly estimate stress intensities and opening displacements during crack propagation, we build a fracture algorithm where the cost of each time step scales linearly with the length of the crackfront. The transition from a full boundary element method to our faster variant is possible at the beginning of any time step. This allows us to build a hybrid method, which uses the expensive but more accurate BEM while the number of degrees of freedom is low, and uses the fast method once that number exceeds a given threshold as the crack geometry becomes more complicated. Furthermore, we integrate this fracture simulation with a standard rigid-body solver. Our rigid-body coupling solves a Neumann boundary value problem by carefully separating translational, rotational and deformational components of the collision forces and then applying a Tikhonov regularizer to the resulting linear system. We show that our method produces physically reasonable results in standard test cases and is capable of dealing with complex scenes faster than previous finite- or boundary element approaches."}],"alternative_title":["ACM Transactions on Graphics"],"year":"2016","pubrep_id":"632","file":[{"file_name":"IST-2016-632-v1+2_a104-hahn.pdf","relation":"main_file","date_updated":"2020-07-14T12:44:46Z","file_id":"5121","access_level":"open_access","file_size":12453704,"content_type":"application/pdf","checksum":"943712d9c9dc8bb5048d4adc561d7d38","creator":"system","date_created":"2018-12-12T10:15:04Z"}],"date_created":"2018-12-11T11:51:35Z","department":[{"_id":"ChWo"}],"language":[{"iso":"eng"}],"author":[{"full_name":"Hahn, David","last_name":"Hahn","first_name":"David","id":"357A6A66-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6646-5546","last_name":"Wojtan","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"}],"issue":"4","month":"07"},{"publisher":"Springer","has_accepted_license":"1","status":"public","isi":1,"external_id":{"isi":["000386324500016"]},"publication_status":"published","day":"09","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"Research  supported  by  the  European  Research  Council,  ERC  starting  grant (259668-PSPC) and ERC consolidator grant (682815 - TOCNeT).","publist_id":"6105","file_date_updated":"2020-07-14T12:44:39Z","title":"Offline witness encryption","related_material":{"record":[{"status":"public","id":"83","relation":"dissertation_contains"}]},"citation":{"ama":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. Offline witness encryption. In: Vol 9696. Springer; 2016:285-303. doi:<a href=\"https://doi.org/10.1007/978-3-319-39555-5_16\">10.1007/978-3-319-39555-5_16</a>","apa":"Abusalah, H. M., Fuchsbauer, G., &#38; Pietrzak, K. Z. (2016). Offline witness encryption (Vol. 9696, pp. 285–303). Presented at the ACNS: Applied Cryptography and Network Security, Guildford, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-319-39555-5_16\">https://doi.org/10.1007/978-3-319-39555-5_16</a>","short":"H.M. Abusalah, G. Fuchsbauer, K.Z. Pietrzak, in:, Springer, 2016, pp. 285–303.","mla":"Abusalah, Hamza M., et al. <i>Offline Witness Encryption</i>. Vol. 9696, Springer, 2016, pp. 285–303, doi:<a href=\"https://doi.org/10.1007/978-3-319-39555-5_16\">10.1007/978-3-319-39555-5_16</a>.","ista":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. 2016. Offline witness encryption. ACNS: Applied Cryptography and Network Security, LNCS, vol. 9696, 285–303.","chicago":"Abusalah, Hamza M, Georg Fuchsbauer, and Krzysztof Z Pietrzak. “Offline Witness Encryption,” 9696:285–303. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-39555-5_16\">https://doi.org/10.1007/978-3-319-39555-5_16</a>.","ieee":"H. M. Abusalah, G. Fuchsbauer, and K. Z. Pietrzak, “Offline witness encryption,” presented at the ACNS: Applied Cryptography and Network Security, Guildford, UK, 2016, vol. 9696, pp. 285–303."},"_id":"1229","oa_version":"Submitted Version","project":[{"name":"Provable Security for Physical Cryptography","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668"},{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"date_updated":"2026-07-29T13:38:08Z","oa":1,"volume":9696,"doi":"10.1007/978-3-319-39555-5_16","date_published":"2016-06-09T00:00:00Z","article_processing_charge":"No","intvolume":"      9696","ddc":["005","600"],"scopus_import":"1","type":"conference","conference":{"location":"Guildford, UK","start_date":"2016-06-19","name":"ACNS: Applied Cryptography and Network Security","end_date":"2016-06-22"},"quality_controlled":"1","abstract":[{"lang":"eng","text":"Witness encryption (WE) was introduced by Garg et al. [GGSW13]. A WE scheme is defined for some NP language L and lets a sender encrypt messages relative to instances x. A ciphertext for x can be decrypted using w witnessing x ∈ L, but hides the message if x ∈ L. Garg et al. construct WE from multilinear maps and give another construction [GGH+13b] using indistinguishability obfuscation (iO) for circuits. Due to the reliance on such heavy tools, WE can cur- rently hardly be implemented on powerful hardware and will unlikely be realizable on constrained devices like smart cards any time soon. We construct a WE scheme where encryption is done by simply computing a Naor-Yung ciphertext (two CPA encryptions and a NIZK proof). To achieve this, our scheme has a setup phase, which outputs public parameters containing an obfuscated circuit (only required for decryption), two encryption keys and a common reference string (used for encryption). This setup need only be run once, and the parame- ters can be used for arbitrary many encryptions. Our scheme can also be turned into a functional WE scheme, where a message is encrypted w.r.t. a statement and a function f, and decryption with a witness w yields f (m, w). Our construction is inspired by the functional encryption scheme by Garg et al. and we prove (selective) security assuming iO and statistically simulation-sound NIZK. We give a construction of the latter in bilinear groups and combining it with ElGamal encryption, our ciphertexts are of size 1.3 kB at a 128-bit security level and can be computed on a smart card."}],"ec_funded":1,"alternative_title":["LNCS"],"year":"2016","pubrep_id":"765","file":[{"date_updated":"2020-07-14T12:44:39Z","file_id":"5273","access_level":"open_access","file_name":"IST-2017-765-v1+1_838.pdf","relation":"main_file","checksum":"34fa9ce681da845a1ba945ba3dc57867","creator":"system","date_created":"2018-12-12T10:17:20Z","content_type":"application/pdf","file_size":515000}],"page":"285 - 303","department":[{"_id":"KrPi"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:50:50Z","author":[{"full_name":"Abusalah, Hamza M","last_name":"Abusalah","first_name":"Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87"},{"id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","last_name":"Fuchsbauer","full_name":"Fuchsbauer, Georg"},{"last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}],"month":"06"},{"conference":{"location":"San Francisco, CA, USA","start_date":"2016-02-29","name":"CT-RSA: Topics in Cryptology","end_date":"2016-03-04"},"quality_controlled":"1","abstract":[{"lang":"eng","text":"A constrained pseudorandom function F: K × X → Y for a family T ⊆ 2X of subsets of X is a function where for any key k ∈ K and set S ∈ T one can efficiently compute a constrained key kS which allows to evaluate F (k, ·) on all inputs x ∈ S, while even given this key, the outputs on all inputs x ∉ S look random. At Asiacrypt’13 Boneh and Waters gave a construction which supports the most general set family so far. Its keys kc are defined for sets decided by boolean circuits C and enable evaluation of the PRF on any x ∈ X where C(x) = 1. In their construction the PRF input length and the size of the circuits C for which constrained keys can be computed must be fixed beforehand during key generation. We construct a constrained PRF that has an unbounded input length and whose constrained keys can be defined for any set recognized by a Turing machine. The only a priori bound we make is on the description size of the machines. We prove our construction secure assuming publiccoin differing-input obfuscation. As applications of our constrained PRF we build a broadcast encryption scheme where the number of potential receivers need not be fixed at setup (in particular, the length of the keys is independent of the number of parties) and the first identity-based non-interactive key exchange protocol with no bound on the number of parties that can agree on a shared key."}],"ec_funded":1,"intvolume":"      9610","ddc":["005","600"],"scopus_import":"1","type":"conference","date_published":"2016-02-02T00:00:00Z","article_processing_charge":"No","date_updated":"2026-07-29T13:38:07Z","oa":1,"volume":9610,"doi":"10.1007/978-3-319-29485-8_24","month":"02","file":[{"access_level":"open_access","file_id":"4664","date_updated":"2020-07-14T12:44:41Z","relation":"main_file","file_name":"IST-2017-764-v1+1_279.pdf","date_created":"2018-12-12T10:08:05Z","creator":"system","checksum":"3851cee49933ae13b1272e516f213e13","file_size":495176,"content_type":"application/pdf"}],"page":"413 - 428","date_created":"2018-12-11T11:50:52Z","language":[{"iso":"eng"}],"department":[{"_id":"KrPi"}],"author":[{"first_name":"Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87","full_name":"Abusalah, Hamza M","last_name":"Abusalah"},{"id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","last_name":"Fuchsbauer","full_name":"Fuchsbauer, Georg"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"}],"year":"2016","pubrep_id":"764","alternative_title":["LNCS"],"day":"02","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"Supported by the European Research Council, ERC Starting Grant (259668-PSPC).","publist_id":"6097","publication_status":"published","isi":1,"external_id":{"isi":["000374102500024"]},"publisher":"Springer","has_accepted_license":"1","status":"public","oa_version":"Submitted Version","_id":"1236","project":[{"name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","call_identifier":"FP7"}],"related_material":{"record":[{"id":"83","status":"public","relation":"dissertation_contains"}]},"citation":{"ama":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. Constrained PRFs for unbounded inputs. In: Vol 9610. Springer; 2016:413-428. doi:<a href=\"https://doi.org/10.1007/978-3-319-29485-8_24\">10.1007/978-3-319-29485-8_24</a>","apa":"Abusalah, H. M., Fuchsbauer, G., &#38; Pietrzak, K. Z. (2016). Constrained PRFs for unbounded inputs (Vol. 9610, pp. 413–428). Presented at the CT-RSA: Topics in Cryptology, San Francisco, CA, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-319-29485-8_24\">https://doi.org/10.1007/978-3-319-29485-8_24</a>","mla":"Abusalah, Hamza M., et al. <i>Constrained PRFs for Unbounded Inputs</i>. Vol. 9610, Springer, 2016, pp. 413–28, doi:<a href=\"https://doi.org/10.1007/978-3-319-29485-8_24\">10.1007/978-3-319-29485-8_24</a>.","short":"H.M. Abusalah, G. Fuchsbauer, K.Z. Pietrzak, in:, Springer, 2016, pp. 413–428.","ista":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. 2016. Constrained PRFs for unbounded inputs. CT-RSA: Topics in Cryptology, LNCS, vol. 9610, 413–428.","ieee":"H. M. Abusalah, G. Fuchsbauer, and K. Z. Pietrzak, “Constrained PRFs for unbounded inputs,” presented at the CT-RSA: Topics in Cryptology, San Francisco, CA, USA, 2016, vol. 9610, pp. 413–428.","chicago":"Abusalah, Hamza M, Georg Fuchsbauer, and Krzysztof Z Pietrzak. “Constrained PRFs for Unbounded Inputs,” 9610:413–28. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-29485-8_24\">https://doi.org/10.1007/978-3-319-29485-8_24</a>."},"file_date_updated":"2020-07-14T12:44:41Z","title":"Constrained PRFs for unbounded inputs"},{"date_updated":"2026-07-29T13:38:07Z","oa":1,"volume":9696,"doi":"10.1007/978-3-319-39555-5_24","date_published":"2016-01-01T00:00:00Z","article_processing_charge":"No","intvolume":"      9696","type":"conference","scopus_import":"1","conference":{"end_date":"2016-06-22","name":"ACNS: Applied Cryptography and Network Security","start_date":"2016-06-19","location":"Guildford, UK"},"quality_controlled":"1","abstract":[{"lang":"eng","text":"A constrained pseudorandom function (CPRF) F: K×X → Y for a family T of subsets of χ is a function where for any key k ∈ K and set S ∈ T one can efficiently compute a short constrained key kS, which allows to evaluate F(k, ·) on all inputs x ∈ S, while the outputs on all inputs x /∈ S look random even given kS. Abusalah et al. recently constructed the first constrained PRF for inputs of arbitrary length whose sets S are decided by Turing machines. They use their CPRF to build broadcast encryption and the first ID-based non-interactive key exchange for an unbounded number of users. Their constrained keys are obfuscated circuits and are therefore large. In this work we drastically reduce the key size and define a constrained key for a Turing machine M as a short signature on M. For this, we introduce a new signature primitive with constrained signing keys that let one only sign certain messages, while forging a signature on others is hard even when knowing the coins for key generation."}],"ec_funded":1,"alternative_title":["LNCS"],"year":"2016","page":"445 - 463","date_created":"2018-12-11T11:50:52Z","department":[{"_id":"KrPi"}],"language":[{"iso":"eng"}],"author":[{"id":"40297222-F248-11E8-B48F-1D18A9856A87","first_name":"Hamza M","last_name":"Abusalah","full_name":"Abusalah, Hamza M"},{"id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","last_name":"Fuchsbauer","full_name":"Fuchsbauer, Georg"}],"month":"01","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/279.pdf"}],"publisher":"Springer","status":"public","isi":1,"external_id":{"isi":["000386324500024"]},"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","acknowledgement":"H. Abusalah—Research supported by the European Research Council, ERC starting grant (259668-PSPC) and ERC consolidator grant (682815 - TOCNeT).","publist_id":"6098","title":"Constrained PRFs for unbounded inputs with short keys","related_material":{"record":[{"relation":"dissertation_contains","id":"83","status":"public"}]},"citation":{"apa":"Abusalah, H. M., &#38; Fuchsbauer, G. (2016). Constrained PRFs for unbounded inputs with short keys (Vol. 9696, pp. 445–463). Presented at the ACNS: Applied Cryptography and Network Security, Guildford, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-319-39555-5_24\">https://doi.org/10.1007/978-3-319-39555-5_24</a>","ama":"Abusalah HM, Fuchsbauer G. Constrained PRFs for unbounded inputs with short keys. In: Vol 9696. Springer; 2016:445-463. doi:<a href=\"https://doi.org/10.1007/978-3-319-39555-5_24\">10.1007/978-3-319-39555-5_24</a>","chicago":"Abusalah, Hamza M, and Georg Fuchsbauer. “Constrained PRFs for Unbounded Inputs with Short Keys,” 9696:445–63. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-39555-5_24\">https://doi.org/10.1007/978-3-319-39555-5_24</a>.","ieee":"H. M. Abusalah and G. Fuchsbauer, “Constrained PRFs for unbounded inputs with short keys,” presented at the ACNS: Applied Cryptography and Network Security, Guildford, UK, 2016, vol. 9696, pp. 445–463.","ista":"Abusalah HM, Fuchsbauer G. 2016. Constrained PRFs for unbounded inputs with short keys. ACNS: Applied Cryptography and Network Security, LNCS, vol. 9696, 445–463.","short":"H.M. Abusalah, G. Fuchsbauer, in:, Springer, 2016, pp. 445–463.","mla":"Abusalah, Hamza M., and Georg Fuchsbauer. <i>Constrained PRFs for Unbounded Inputs with Short Keys</i>. Vol. 9696, Springer, 2016, pp. 445–63, doi:<a href=\"https://doi.org/10.1007/978-3-319-39555-5_24\">10.1007/978-3-319-39555-5_24</a>."},"_id":"1235","oa_version":"Submitted Version","project":[{"name":"Provable Security for Physical Cryptography","call_identifier":"FP7","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425"},{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}]},{"doi_confirm":"1","status":"public","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","publist_id":"5809","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"18","acknowledgement":"I am indebted to many people for their support during my PhD, but I particularly wish to thank Nick Barton for his guidance and intuition, and for encouraging me to take the time to look beyond the immediate topic of my PhD to understand the broader context. I am also especially grateful to David Field his bottomless patience, invaluable advice on experimental design, analysis and scientific writing, and for tireless work on the population surveys and genomic work without most of my thesis could not have happened. \r\n\r\nIt has been a pleasure to work with the combined strengths of the groups at The John Innes Centre, University of Toulouse and IST Austria. Thanks to Enrico Coen and his group for hosting me in Norwich in 2011 and especially for setting up the tag experiment. \r\n\r\nI thank David Field, Desmond Bradley and Maria Clara Melo-Hurtado for organising field collections, as well as Monique Burrus and Christophe Andalo and a large number of volunteers for their e ff orts helping with the field work. Furthermore I thank Coline Jaworski for providing seeds and for her input into the design of the experimental arrays, and Matthew Couchman for maintaining the database of. \r\n\r\nIn addition to those mentioned above, I am grateful to Melinda Pickup, Spencer Barrett, and four anonymous reviewers for their insightful comments on sections of this manuscript. I also thank Jana Porsche for her e ff orts in tracking down the more obscure references for chapter 5, and Jon Bollback for his advice about the analysis. \r\n\r\nI am indebted to Jon Ågren for his patience whilst I finished this thesis, and to Sylvia Cremer and Magnus Nordborg for taking the time to read and evaluate the thesis given a shorter deadline than was fair. \r\n\r\nA very positive aspect of my PhD has been the supportive atmosphere of IST. In particular, I have come to appreciate the enormous support from our group assistants Nicole Hotzy, Julia Asimakis, Christine Ostermann and Jerneja Beslagic. I also thank Christian Chaloupka and Stefan Hipfinger for their enthusiasm and readiness to help where possible in setting up our greenhouse and experiments. ","publication_status":"published","degree_awarded":"PhD","title":"The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone","OA_place":"publisher","file_date_updated":"2025-07-03T06:24:39Z","_id":"1398","oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"5553","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"5551","status":"public"},{"status":"public","id":"5552","relation":"part_of_dissertation"}]},"citation":{"ama":"Ellis T. The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">10.15479/AT:ISTA:TH_526 </a>","apa":"Ellis, T. (2016). <i>The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">https://doi.org/10.15479/AT:ISTA:TH_526 </a>","short":"T. Ellis, The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone, Institute of Science and Technology Austria, 2016.","mla":"Ellis, Thomas. <i>The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">10.15479/AT:ISTA:TH_526 </a>.","chicago":"Ellis, Thomas. “The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">https://doi.org/10.15479/AT:ISTA:TH_526 </a>.","ieee":"T. Ellis, “The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone,” Institute of Science and Technology Austria, 2016.","ista":"Ellis T. 2016. The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute of Science and Technology Austria."},"date_published":"2016-02-18T00:00:00Z","article_processing_charge":"No","doi":"10.15479/AT:ISTA:TH_526 ","date_updated":"2026-07-30T14:56:14Z","oa":1,"abstract":[{"text":"Hybrid zones represent evolutionary laboratories, where recombination brings together alleles in combinations which have not previously been tested by selection. This provides an excellent opportunity to test the effect of molecular variation on fitness, and how this variation is able to spread through populations in a natural context. The snapdragon Antirrhinum majus is polymorphic in the wild for two loci controlling the distribution of yellow and magenta floral pigments. Where the yellow A. m. striatum and the magenta A. m. pseudomajus meet along a valley in the Spanish Pyrenees they form a stable hybrid zone Alleles at these loci recombine to give striking transgressive variation for flower colour. The sharp transition in phenotype over ~1km implies strong selection maintaining the hybrid zone. An indirect assay of pollinator visitation in the field found that pollinators forage in a positive-frequency dependent manner on Antirrhinum, matching previous data on fruit set. Experimental arrays and paternity analysis of wild-pollinated seeds demonstrated assortative mating for pigmentation alleles, and that pollinator behaviour alone is sufficient to explain this pattern. Selection by pollinators should be sufficiently strong to maintain the hybrid zone, although other mechanisms may be at work. At a broader scale I examined evolutionary transitions between yellow and anthocyanin pigmentation in the tribe Antirrhinae, and found that selection has acted strate that pollinators are a major determinant of reproductive success and mating patterns in wild Antirrhinum.","lang":"eng"}],"type":"dissertation","corr_author":"1","ddc":["576"],"pubrep_id":"526","year":"2016","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"month":"02","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:51:47Z","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"author":[{"last_name":"Ellis","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"}],"file":[{"access_level":"open_access","file_id":"19957","date_updated":"2025-07-03T06:24:17Z","relation":"main_file","file_name":"2016_Thesis_Ellis_noSignatures.pdf","date_created":"2025-07-03T06:24:17Z","creator":"dernst","checksum":"f0f7c260e19ec1416824b165afe2d5fd","file_size":7590862,"content_type":"application/pdf"},{"relation":"main_file","file_name":"IST-2016-526-v1+1_Ellis_signed_thesis.pdf","access_level":"closed","file_id":"5106","date_updated":"2025-07-03T06:24:39Z","file_size":11928241,"content_type":"application/pdf","date_created":"2018-12-12T10:14:51Z","creator":"system","checksum":"a89b17ff27cf92c9a15f6b3d46bd7e53"}],"page":"130"},{"date_published":"2016-02-19T00:00:00Z","tmp":{"short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"article_processing_charge":"No","date_updated":"2026-07-30T14:56:13Z","publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","status":"public","doi":"10.15479/AT:ISTA:37","day":"19","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Genotypic, phenotypic and demographic data for 2128 wild snapdragons and 1127 open-pollinated progeny from a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted) February 2016).\r\n\r\nTissue samples were sent to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been removed from this dataset.\r\n\r\nOther data were retreived from an online database of this population at www.antspec.org."}],"ddc":["576"],"type":"research_data","year":"2016","file_date_updated":"2020-07-14T12:47:01Z","title":"Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012","contributor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","contributor_type":"project_manager"}],"oa_version":"Published Version","_id":"5553","keyword":["paternity assignment","pedigree","matting patterns","assortative mating","Antirrhinum majus","frequency-dependent selection","plant-pollinator interaction"],"month":"02","file":[{"creator":"system","checksum":"4ae751b1fa4897fa216241f975a57313","date_created":"2018-12-12T13:03:02Z","content_type":"application/zip","file_size":132808,"date_updated":"2020-07-14T12:47:01Z","access_level":"open_access","file_id":"5620","relation":"main_file","file_name":"IST-2016-37-v1+1_paternity_archive.zip"}],"datarep_id":"37","date_created":"2018-12-12T12:31:30Z","department":[{"_id":"NiBa"}],"related_material":{"record":[{"id":"1398","status":"public","relation":"dissertation_contains"}]},"author":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","orcid":"0000-0002-4014-8478","last_name":"Field","full_name":"Field, David"},{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Ellis","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas"}],"citation":{"mla":"Field, David, and Thomas Ellis. <i>Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>.","short":"D. Field, T. Ellis, (2016).","chicago":"Field, David, and Thomas Ellis. “Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:37\">https://doi.org/10.15479/AT:ISTA:37</a>.","ieee":"D. Field and T. Ellis, “Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012.” Institute of Science and Technology Austria, 2016.","ista":"Field D, Ellis T. 2016. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>.","ama":"Field D, Ellis T. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>","apa":"Field, D., &#38; Ellis, T. (2016). Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:37\">https://doi.org/10.15479/AT:ISTA:37</a>"}},{"month":"02","oa_version":"Published Version","_id":"5551","related_material":{"record":[{"status":"public","id":"1398","relation":"dissertation_contains"}]},"date_created":"2018-12-12T12:31:29Z","department":[{"_id":"NiBa"}],"citation":{"ieee":"T. Ellis, “Data on pollinator observations and offpsring phenotypes.” Institute of Science and Technology Austria, 2016.","chicago":"Ellis, Thomas. “Data on Pollinator Observations and Offpsring Phenotypes.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:35\">https://doi.org/10.15479/AT:ISTA:35</a>.","ista":"Ellis T. 2016. Data on pollinator observations and offpsring phenotypes, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:35\">10.15479/AT:ISTA:35</a>.","short":"T. Ellis, (2016).","mla":"Ellis, Thomas. <i>Data on Pollinator Observations and Offpsring Phenotypes</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:35\">10.15479/AT:ISTA:35</a>.","apa":"Ellis, T. (2016). Data on pollinator observations and offpsring phenotypes. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:35\">https://doi.org/10.15479/AT:ISTA:35</a>","ama":"Ellis T. Data on pollinator observations and offpsring phenotypes. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:35\">10.15479/AT:ISTA:35</a>"},"author":[{"first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","full_name":"Ellis, Thomas","last_name":"Ellis","orcid":"0000-0002-8511-0254"}],"file":[{"access_level":"open_access","file_id":"5640","date_updated":"2020-07-14T12:47:01Z","relation":"main_file","file_name":"IST-2016-35-v1+1_array_data.zip","date_created":"2018-12-12T13:05:12Z","creator":"system","checksum":"aa3eb85d52b110cd192aa23147c4d4f3","file_size":32775,"content_type":"application/zip"}],"datarep_id":"35","year":"2016","title":"Data on pollinator observations and offpsring phenotypes","contributor":[{"last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"file_date_updated":"2020-07-14T12:47:01Z","abstract":[{"text":"Data from array experiments investigating pollinator behaviour on snapdragons in controlled conditions, and their effect on plant mating. Data were collected as part of Tom Ellis' PhD thesis , submitted February 2016.\r\n\r\nWe placed a total of 36 plants in a grid inside a closed organza tent, with a single hive of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus, at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6.\r\n\r\nAfter 24 hours to learn how to deal with snapdragons, I observed pollinators foraging on plants, and recorded the transitions between plants. Thereafter seeds on plants were allowed to develops. A sample of these were grown to maturity when their flower colour could be determined, and they were scored as yellow, magenta, or hybrid.","lang":"eng"}],"day":"19","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data","tmp":{"short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"date_published":"2016-02-19T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","status":"public","doi":"10.15479/AT:ISTA:35","date_updated":"2026-07-30T14:56:13Z","oa":1,"publisher":"Institute of Science and Technology Austria"},{"year":"2016","file_date_updated":"2020-07-14T12:47:01Z","contributor":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"title":"Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.","_id":"5552","oa_version":"Published Version","month":"02","datarep_id":"36","file":[{"date_updated":"2020-07-14T12:47:01Z","access_level":"open_access","file_id":"5625","relation":"main_file","file_name":"IST-2016-36-v1+1_tag_assay_archive.zip","creator":"system","checksum":"cbc61b523d4d475a04a737d50dc470ef","date_created":"2018-12-12T13:03:07Z","file_size":44905,"content_type":"application/zip"}],"citation":{"ama":"Ellis T. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:36\">10.15479/AT:ISTA:36</a>","apa":"Ellis, T. (2016). Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:36\">https://doi.org/10.15479/AT:ISTA:36</a>","mla":"Ellis, Thomas. <i>Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data.</i> Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:36\">10.15479/AT:ISTA:36</a>.","short":"T. Ellis, (2016).","chicago":"Ellis, Thomas. “Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:36\">https://doi.org/10.15479/AT:ISTA:36</a>.","ieee":"T. Ellis, “Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.” Institute of Science and Technology Austria, 2016.","ista":"Ellis T. 2016. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data., Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:36\">10.15479/AT:ISTA:36</a>."},"author":[{"full_name":"Ellis, Thomas","last_name":"Ellis","orcid":"0000-0002-8511-0254","first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"1398","status":"public","relation":"dissertation_contains"}]},"department":[{"_id":"NiBa"}],"date_created":"2018-12-12T12:31:30Z","article_processing_charge":"No","date_published":"2016-02-19T00:00:00Z","publisher":"Institute of Science and Technology Austria","oa":1,"date_updated":"2026-07-30T14:56:13Z","status":"public","doi":"10.15479/AT:ISTA:36","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"19","abstract":[{"text":"Data on pollinator visitation to wild snapdragons in a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted February 2016).\r\n\r\nSnapdragon flowers have a mouth-like structure which pollinators must open to access nectar. We placed 5mm cellophane tags in these mouths, which are held in place by the pressure of the flower until a pollinator visits. When she opens the flower, the tag drops out, and one can infer a visit. We surveyed plants over multiple days in 2010, 2011 and 2012.\r\n\r\nAlso included are data on phenotypic and demographic variables which may be explanatory variables for pollinator visitation.","lang":"eng"}],"type":"research_data"},{"pubrep_id":"754","year":"2016","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:50:08Z","department":[{"_id":"CaHe"},{"_id":"HaJa"}],"author":[{"orcid":"0000-0002-6453-8075","last_name":"Sako","full_name":"Sako, Keisuke","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","first_name":"Keisuke"},{"first_name":"Saurabh","last_name":"Pradhan","full_name":"Pradhan, Saurabh"},{"first_name":"Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","full_name":"Barone, Vanessa","last_name":"Barone","orcid":"0000-0003-2676-3367"},{"orcid":"0000-0002-5409-8571","last_name":"Inglés Prieto","full_name":"Inglés Prieto, Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","first_name":"Álvaro"},{"first_name":"Patrick","last_name":"Mueller","full_name":"Mueller, Patrick"},{"full_name":"Ruprecht, Verena","orcid":"0000-0003-4088-8633","last_name":"Ruprecht","first_name":"Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Capek, Daniel","last_name":"Capek","orcid":"0000-0001-5199-9940","first_name":"Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sanjeev","full_name":"Galande, Sanjeev","last_name":"Galande"},{"full_name":"Janovjak, Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"file":[{"file_size":3921947,"content_type":"application/pdf","creator":"system","date_created":"2018-12-12T10:11:04Z","relation":"main_file","file_name":"IST-2017-754-v1+1_1-s2.0-S2211124716307768-main.pdf","date_updated":"2018-12-12T10:11:04Z","access_level":"open_access","file_id":"4857"}],"page":"866 - 877","month":"07","issue":"3","doi":"10.1016/j.celrep.2016.06.036","volume":16,"date_updated":"2026-07-30T22:30:42Z","oa":1,"date_published":"2016-07-19T00:00:00Z","article_processing_charge":"No","scopus_import":"1","type":"journal_article","intvolume":"        16","publication":"Cell Reports","ddc":["570","576"],"quality_controlled":"1","ec_funded":1,"abstract":[{"lang":"eng","text":"During metazoan development, the temporal pattern of morphogen signaling is critical for organizing cell fates in space and time. Yet, tools for temporally controlling morphogen signaling within the embryo are still scarce. Here, we developed a photoactivatable Nodal receptor to determine how the temporal pattern of Nodal signaling affects cell fate specification during zebrafish gastrulation. By using this receptor to manipulate the duration of Nodal signaling in vivo by light, we show that extended Nodal signaling within the organizer promotes prechordal plate specification and suppresses endoderm differentiation. Endoderm differentiation is suppressed by extended Nodal signaling inducing expression of the transcriptional repressor goosecoid (gsc) in prechordal plate progenitors, which in turn restrains Nodal signaling from upregulating the endoderm differentiation gene sox17 within these cells. Thus, optogenetic manipulation of Nodal signaling identifies a critical role of Nodal signaling duration for organizer cell fate specification during gastrulation."}],"title":"Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation","file_date_updated":"2018-12-12T10:11:04Z","acknowledged_ssus":[{"_id":"SSU"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"961","status":"public"},{"relation":"dissertation_contains","status":"public","id":"50"}]},"citation":{"mla":"Sako, Keisuke, et al. “Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.” <i>Cell Reports</i>, vol. 16, no. 3, Cell Press, 2016, pp. 866–77, doi:<a href=\"https://doi.org/10.1016/j.celrep.2016.06.036\">10.1016/j.celrep.2016.06.036</a>.","short":"K. Sako, S. Pradhan, V. Barone, Á. Inglés Prieto, P. Mueller, V. Ruprecht, D. Capek, S. Galande, H.L. Janovjak, C.-P.J. Heisenberg, Cell Reports 16 (2016) 866–877.","ista":"Sako K, Pradhan S, Barone V, Inglés Prieto Á, Mueller P, Ruprecht V, Capek D, Galande S, Janovjak HL, Heisenberg C-PJ. 2016. Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. Cell Reports. 16(3), 866–877.","chicago":"Sako, Keisuke, Saurabh Pradhan, Vanessa Barone, Álvaro Inglés Prieto, Patrick Mueller, Verena Ruprecht, Daniel Capek, Sanjeev Galande, Harald L Janovjak, and Carl-Philipp J Heisenberg. “Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.” <i>Cell Reports</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.celrep.2016.06.036\">https://doi.org/10.1016/j.celrep.2016.06.036</a>.","ieee":"K. Sako <i>et al.</i>, “Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation,” <i>Cell Reports</i>, vol. 16, no. 3. Cell Press, pp. 866–877, 2016.","ama":"Sako K, Pradhan S, Barone V, et al. Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. <i>Cell Reports</i>. 2016;16(3):866-877. doi:<a href=\"https://doi.org/10.1016/j.celrep.2016.06.036\">10.1016/j.celrep.2016.06.036</a>","apa":"Sako, K., Pradhan, S., Barone, V., Inglés Prieto, Á., Mueller, P., Ruprecht, V., … Heisenberg, C.-P. J. (2016). Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2016.06.036\">https://doi.org/10.1016/j.celrep.2016.06.036</a>"},"project":[{"grant_number":"T 560-B17","_id":"2529486C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation"},{"name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","call_identifier":"FWF","grant_number":"I812-B12","_id":"2527D5CC-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"303564","_id":"25548C20-B435-11E9-9278-68D0E5697425","name":"Microbial Ion Channels for Synthetic Neurobiology"}],"_id":"1100","oa_version":"Published Version","has_accepted_license":"1","status":"public","publisher":"Cell Press","external_id":{"isi":["000380264200024"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"isi":1,"publication_status":"published","publist_id":"6275","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"19","acknowledgement":"We are grateful to members of the C.-P.H. and H.J. labs for discussions, R. Hauschild and the different Scientific Service Units at IST Austria for technical help, M. Dravecka for performing initial experiments, A. Schier for reading an earlier version of the manuscript, K.W. Rogers for technical help, and C. Hill, A. Bruce, and L. Solnica-Krezel for sending plasmids. This work was supported by grants from the Austrian Science Foundation (FWF): (T560-B17) and (I 812-B12) to V.R. and C.-P.H., and from the European Union (EU FP7): (6275) to H.J. A.I.-P. is supported by a Ramon Areces fellowship."},{"issue":"6","month":"12","page":"1481 - 1494","file":[{"content_type":"application/pdf","file_size":73907957,"date_created":"2018-12-12T10:13:44Z","creator":"system","checksum":"7fe01ab12a6610d3db421e0136db2f77","relation":"main_file","file_name":"IST-2017-771-v1+1_Tarlungeanu_et_al._Final_edited.pdf","access_level":"open_access","file_id":"5030","date_updated":"2020-07-14T12:44:37Z"}],"author":[{"id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","first_name":"Dora-Clara","last_name":"Tarlungeanu","full_name":"Tarlungeanu, Dora-Clara"},{"orcid":"0000-0002-7370-5293","last_name":"Deliu","full_name":"Deliu, Elena","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","first_name":"Elena"},{"first_name":"Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","full_name":"Dotter, Christoph","last_name":"Dotter","orcid":"0000-0002-9033-9096"},{"first_name":"Majdi","last_name":"Kara","full_name":"Kara, Majdi"},{"last_name":"Janiesch","full_name":"Janiesch, Philipp","first_name":"Philipp"},{"first_name":"Mariafrancesca","last_name":"Scalise","full_name":"Scalise, Mariafrancesca"},{"first_name":"Michele","last_name":"Galluccio","full_name":"Galluccio, Michele"},{"first_name":"Mateja","last_name":"Tesulov","full_name":"Tesulov, Mateja"},{"full_name":"Morelli, Emanuela","last_name":"Morelli","first_name":"Emanuela","id":"3F4D1282-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sönmez","full_name":"Sönmez, Fatma","first_name":"Fatma"},{"first_name":"Kaya","full_name":"Bilgüvar, Kaya","last_name":"Bilgüvar"},{"first_name":"Ryuichi","last_name":"Ohgaki","full_name":"Ohgaki, Ryuichi"},{"first_name":"Yoshikatsu","full_name":"Kanai, Yoshikatsu","last_name":"Kanai"},{"first_name":"Anide","full_name":"Johansen, Anide","last_name":"Johansen"},{"first_name":"Seham","full_name":"Esharif, Seham","last_name":"Esharif"},{"last_name":"Ben Omran","full_name":"Ben Omran, Tawfeg","first_name":"Tawfeg"},{"first_name":"Meral","last_name":"Topcu","full_name":"Topcu, Meral"},{"first_name":"Avner","last_name":"Schlessinger","full_name":"Schlessinger, Avner"},{"first_name":"Cesare","last_name":"Indiveri","full_name":"Indiveri, Cesare"},{"last_name":"Duncan","full_name":"Duncan, Kent","first_name":"Kent"},{"full_name":"Caglayan, Ahmet","last_name":"Caglayan","first_name":"Ahmet"},{"full_name":"Günel, Murat","last_name":"Günel","first_name":"Murat"},{"first_name":"Joseph","full_name":"Gleeson, Joseph","last_name":"Gleeson"},{"orcid":"0000-0002-7673-7178","last_name":"Novarino","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"}],"date_created":"2018-12-11T11:50:35Z","department":[{"_id":"GaNo"}],"language":[{"iso":"eng"}],"year":"2016","pubrep_id":"771","article_type":"original","abstract":[{"text":"Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. We previously described abnormalities in the branched-chain amino acid (BCAA) catabolic pathway as a cause of ASD. Here, we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation, and severe neurological abnormalities. Furthermore, we identified several patients with autistic traits and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. Finally, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for the BCAA in human brain function.","lang":"eng"}],"quality_controlled":"1","publication":"Cell","ddc":["576","616"],"intvolume":"       167","scopus_import":"1","type":"journal_article","article_processing_charge":"No","date_published":"2016-12-01T00:00:00Z","oa":1,"date_updated":"2026-07-30T22:30:52Z","doi":"10.1016/j.cell.2016.11.013","volume":167,"_id":"1183","oa_version":"Submitted Version","project":[{"name":"Transmembrane Transporters in Health and Disease","call_identifier":"FWF","_id":"25473368-B435-11E9-9278-68D0E5697425","grant_number":"F03523"}],"citation":{"ama":"Tarlungeanu D-C, Deliu E, Dotter C, et al. Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. <i>Cell</i>. 2016;167(6):1481-1494. doi:<a href=\"https://doi.org/10.1016/j.cell.2016.11.013\">10.1016/j.cell.2016.11.013</a>","apa":"Tarlungeanu, D.-C., Deliu, E., Dotter, C., Kara, M., Janiesch, P., Scalise, M., … Novarino, G. (2016). Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2016.11.013\">https://doi.org/10.1016/j.cell.2016.11.013</a>","mla":"Tarlungeanu, Dora-Clara, et al. “Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.” <i>Cell</i>, vol. 167, no. 6, Cell Press, 2016, pp. 1481–94, doi:<a href=\"https://doi.org/10.1016/j.cell.2016.11.013\">10.1016/j.cell.2016.11.013</a>.","short":"D.-C. Tarlungeanu, E. Deliu, C. Dotter, M. Kara, P. Janiesch, M. Scalise, M. Galluccio, M. Tesulov, E. Morelli, F. Sönmez, K. Bilgüvar, R. Ohgaki, Y. Kanai, A. Johansen, S. Esharif, T. Ben Omran, M. Topcu, A. Schlessinger, C. Indiveri, K. Duncan, A. Caglayan, M. Günel, J. Gleeson, G. Novarino, Cell 167 (2016) 1481–1494.","ieee":"D.-C. Tarlungeanu <i>et al.</i>, “Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder,” <i>Cell</i>, vol. 167, no. 6. Cell Press, pp. 1481–1494, 2016.","ista":"Tarlungeanu D-C, Deliu E, Dotter C, Kara M, Janiesch P, Scalise M, Galluccio M, Tesulov M, Morelli E, Sönmez F, Bilgüvar K, Ohgaki R, Kanai Y, Johansen A, Esharif S, Ben Omran T, Topcu M, Schlessinger A, Indiveri C, Duncan K, Caglayan A, Günel M, Gleeson J, Novarino G. 2016. Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. Cell. 167(6), 1481–1494.","chicago":"Tarlungeanu, Dora-Clara, Elena Deliu, Christoph Dotter, Majdi Kara, Philipp Janiesch, Mariafrancesca Scalise, Michele Galluccio, et al. “Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.” <i>Cell</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.cell.2016.11.013\">https://doi.org/10.1016/j.cell.2016.11.013</a>."},"related_material":{"record":[{"id":"395","status":"public","relation":"dissertation_contains"}]},"file_date_updated":"2020-07-14T12:44:37Z","title":"Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder","acknowledgement":"This work was supported by NICHD (P01HD070494) and SFARI (grant 275275) to J.G.G., and FWF (SFB35_3523) to G.N.\r\nWe thank A.C. Manzano, Mike Liu, and F. Marr for technical assistance, and R. Shigemoto and the IST Austria Electron Microscopy (EM) Facility for assistance. We acknowledge support from CIDR for genome-wide SNP analysis (X01HG008823) and Broad Institute Center for Mendelian Disorders (UM1HG008900 to D. MacArthur), the Yale Center for Mendelian Disorders (U54HG006504 to M.G.), the Gregory M. Kiez and Mehmet Kutman Foundation (M.G.), Italian Ministry of Instruction University and Research (PON01_00937 to C.I.), and NIH (R01-GM108911 to A.S.). This work was supported by NICHD (P01HD070494) and SFARI (grant 275275) to J.G.G., and FWF (SFB35_3523) to G.N.\r\n\r\n#EMFacility","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","publist_id":"6170","publication_status":"published","isi":1,"external_id":{"isi":["000389470500012"]},"publisher":"Cell Press","has_accepted_license":"1","status":"public"},{"title":"Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes","file_date_updated":"2020-07-14T12:44:43Z","acknowledged_ssus":[{"_id":"SSU"}],"related_material":{"record":[{"status":"public","id":"323","relation":"dissertation_contains"}]},"citation":{"chicago":"Leithner, Alexander F, Alexander Eichner, Jan Müller, Anne Reversat, Markus Brown, Jan Schwarz, Jack Merrin, et al. “Diversified Actin Protrusions Promote Environmental Exploration but Are Dispensable for Locomotion of Leukocytes.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncb3426\">https://doi.org/10.1038/ncb3426</a>.","ieee":"A. F. Leithner <i>et al.</i>, “Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes,” <i>Nature Cell Biology</i>, vol. 18. Nature Publishing Group, pp. 1253–1259, 2016.","ista":"Leithner AF, Eichner A, Müller J, Reversat A, Brown M, Schwarz J, Merrin J, De Gorter D, Schur FK, Bayerl J, de Vries I, Wieser S, Hauschild R, Lai F, Moser M, Kerjaschki D, Rottner K, Small V, Stradal T, Sixt MK. 2016. Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. Nature Cell Biology. 18, 1253–1259.","mla":"Leithner, Alexander F., et al. “Diversified Actin Protrusions Promote Environmental Exploration but Are Dispensable for Locomotion of Leukocytes.” <i>Nature Cell Biology</i>, vol. 18, Nature Publishing Group, 2016, pp. 1253–59, doi:<a href=\"https://doi.org/10.1038/ncb3426\">10.1038/ncb3426</a>.","short":"A.F. Leithner, A. Eichner, J. Müller, A. Reversat, M. Brown, J. Schwarz, J. Merrin, D. De Gorter, F.K. Schur, J. Bayerl, I. de Vries, S. Wieser, R. Hauschild, F. Lai, M. Moser, D. Kerjaschki, K. Rottner, V. Small, T. Stradal, M.K. Sixt, Nature Cell Biology 18 (2016) 1253–1259.","apa":"Leithner, A. F., Eichner, A., Müller, J., Reversat, A., Brown, M., Schwarz, J., … Sixt, M. K. (2016). Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb3426\">https://doi.org/10.1038/ncb3426</a>","ama":"Leithner AF, Eichner A, Müller J, et al. Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. <i>Nature Cell Biology</i>. 2016;18:1253-1259. doi:<a href=\"https://doi.org/10.1038/ncb3426\">10.1038/ncb3426</a>"},"project":[{"call_identifier":"FP7","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes"}],"oa_version":"Submitted Version","_id":"1321","has_accepted_license":"1","status":"public","publisher":"Nature Publishing Group","external_id":{"isi":["000387165600018"]},"tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"isi":1,"publication_status":"published","publist_id":"5949","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"24","acknowledgement":"This work was supported by the German Research Foundation (DFG) Priority Program SP 1464 to T.E.B.S. and M.S., and European Research Council (ERC GA 281556) and Human Frontiers Program grants to M.S.\r\nService Units of IST Austria for excellent technical support.","year":"2016","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:51:21Z","author":[{"id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F","orcid":"0000-0002-1073-744X","last_name":"Leithner","full_name":"Leithner, Alexander F"},{"full_name":"Eichner, Alexander","last_name":"Eichner","first_name":"Alexander","id":"4DFA52AE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Müller","full_name":"Müller, Jan","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","first_name":"Jan"},{"id":"35B76592-F248-11E8-B48F-1D18A9856A87","first_name":"Anne","orcid":"0000-0003-0666-8928","last_name":"Reversat","full_name":"Reversat, Anne"},{"first_name":"Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Markus","last_name":"Brown"},{"id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Schwarz","full_name":"Schwarz, Jan"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin","full_name":"Merrin, Jack"},{"full_name":"De Gorter, David","last_name":"De Gorter","first_name":"David"},{"full_name":"Schur, Florian","orcid":"0000-0003-4790-8078","last_name":"Schur","first_name":"Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jonathan","last_name":"Bayerl","full_name":"Bayerl, Jonathan"},{"first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","full_name":"De Vries, Ingrid","last_name":"De Vries"},{"id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","last_name":"Wieser","orcid":"0000-0002-2670-2217","full_name":"Wieser, Stefan"},{"orcid":"0000-0001-9843-3522","last_name":"Hauschild","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"first_name":"Frank","full_name":"Lai, Frank","last_name":"Lai"},{"first_name":"Markus","full_name":"Moser, Markus","last_name":"Moser"},{"full_name":"Kerjaschki, Dontscho","last_name":"Kerjaschki","first_name":"Dontscho"},{"first_name":"Klemens","last_name":"Rottner","full_name":"Rottner, Klemens"},{"first_name":"Victor","last_name":"Small","full_name":"Small, Victor"},{"last_name":"Stradal","full_name":"Stradal, Theresia","first_name":"Theresia"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"file":[{"file_size":4433280,"content_type":"application/pdf","date_created":"2020-05-14T16:33:46Z","creator":"dernst","checksum":"e1411cb7c99a2d9089c178a6abef25e7","relation":"main_file","file_name":"2018_NatureCell_Leithner.pdf","access_level":"open_access","file_id":"7844","date_updated":"2020-07-14T12:44:43Z"}],"page":"1253 - 1259","month":"10","volume":18,"doi":"10.1038/ncb3426","date_updated":"2026-07-30T22:30:54Z","oa":1,"date_published":"2016-10-24T00:00:00Z","article_processing_charge":"No","scopus_import":"1","type":"journal_article","intvolume":"        18","corr_author":"1","publication":"Nature Cell Biology","ddc":["570"],"quality_controlled":"1","abstract":[{"lang":"eng","text":"Most migrating cells extrude their front by the force of actin polymerization. Polymerization requires an initial nucleation step, which is mediated by factors establishing either parallel filaments in the case of filopodia or branched filaments that form the branched lamellipodial network. Branches are considered essential for regular cell motility and are initiated by the Arp2/3 complex, which in turn is activated by nucleation-promoting factors of the WASP and WAVE families. Here we employed rapid amoeboid crawling leukocytes and found that deletion of the WAVE complex eliminated actin branching and thus lamellipodia formation. The cells were left with parallel filaments at the leading edge, which translated, depending on the differentiation status of the cell, into a unipolar pointed cell shape or cells with multiple filopodia. Remarkably, unipolar cells migrated with increased speed and enormous directional persistence, while they were unable to turn towards chemotactic gradients. Cells with multiple filopodia retained chemotactic activity but their migration was progressively impaired with increasing geometrical complexity of the extracellular environment. These findings establish that diversified leading edge protrusions serve as explorative structures while they slow down actual locomotion."}],"ec_funded":1,"article_type":"original"},{"title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","related_material":{"record":[{"status":"public","id":"5441","relation":"earlier_version"},{"id":"5442","status":"public","relation":"earlier_version"},{"relation":"later_version","status":"public","id":"6009"},{"relation":"dissertation_contains","id":"821","status":"public"},{"id":"8934","status":"public","relation":"dissertation_contains"}]},"citation":{"apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2016). Algorithms for algebraic path properties in concurrent systems of constant treewidth components (Vol. 20–22, pp. 733–747). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. <a href=\"https://doi.org/10.1145/2837614.2837624\">https://doi.org/10.1145/2837614.2837624</a>","ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. In: Vol 20-22. ACM; 2016:733-747. doi:<a href=\"https://doi.org/10.1145/2837614.2837624\">10.1145/2837614.2837624</a>","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components,” 20–22:733–47. ACM, 2016. <a href=\"https://doi.org/10.1145/2837614.2837624\">https://doi.org/10.1145/2837614.2837624</a>.","ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2016. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. POPL: Principles of Programming Languages, POPL, vol. 20–22, 733–747.","ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Algorithms for algebraic path properties in concurrent systems of constant treewidth components,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 733–747.","short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, ACM, 2016, pp. 733–747.","mla":"Chatterjee, Krishnendu, et al. <i>Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components</i>. Vol. 20–22, ACM, 2016, pp. 733–47, doi:<a href=\"https://doi.org/10.1145/2837614.2837624\">10.1145/2837614.2837624</a>."},"oa_version":"Preprint","_id":"1437","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"publisher":"ACM","status":"public","external_id":{"arxiv":["1510.07565"]},"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"11","publist_id":"5761","alternative_title":["POPL"],"year":"2016","page":"733 - 747","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"date_created":"2018-12-11T11:52:01Z","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir","orcid":"0000-0003-1702-6584","last_name":"Goharshady","full_name":"Goharshady, Amir"},{"first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389"},{"last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"}],"month":"01","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1510.07565"}],"date_updated":"2026-07-30T22:31:01Z","oa":1,"volume":"20-22","doi":"10.1145/2837614.2837624","date_published":"2016-01-11T00:00:00Z","corr_author":"1","type":"conference","scopus_import":1,"arxiv":1,"conference":{"location":"St. Petersburg, FL, USA","start_date":"2016-01-20","name":"POPL: Principles of Programming Languages","end_date":"2016-01-22"},"quality_controlled":"1","ec_funded":1,"abstract":[{"text":"We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time. Our main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks.","lang":"eng"}]},{"corr_author":"1","intvolume":"      9779","scopus_import":"1","type":"conference","arxiv":1,"conference":{"start_date":"2016-07-17","location":"Toronto, Canada","end_date":"2016-07-23","name":"CAV: Computer Aided Verification"},"ec_funded":1,"abstract":[{"text":"We consider nondeterministic probabilistic programs with the most basic liveness property of termination. We present efficient methods for termination analysis of nondeterministic probabilistic programs with polynomial guards and assignments. Our approach is through synthesis of polynomial ranking supermartingales, that on one hand significantly generalizes linear ranking supermartingales and on the other hand is a counterpart of polynomial ranking-functions for proving termination of nonprobabilistic programs. The approach synthesizes polynomial ranking-supermartingales through Positivstellensatz's, yielding an efficient method which is not only sound, but also semi-complete over a large subclass of programs. We show experimental results to demonstrate that our approach can handle several classical programs with complex polynomial guards and assignments, and can synthesize efficient quadratic ranking-supermartingales when a linear one does not exist even for simple affine programs.","lang":"eng"}],"quality_controlled":"1","oa":1,"date_updated":"2026-07-30T22:31:01Z","doi":"10.1007/978-3-319-41528-4_1","volume":9779,"article_processing_charge":"No","date_published":"2016-07-01T00:00:00Z","page":"3 - 22","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Fu","full_name":"Fu, Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongfei"},{"first_name":"Amir","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir","last_name":"Goharshady","orcid":"0000-0003-1702-6584"}],"date_created":"2018-12-11T11:51:43Z","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1604.07169"}],"month":"07","alternative_title":["LNCS"],"year":"2016","publication_status":"published","day":"01","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"5824","publisher":"Springer","status":"public","isi":1,"external_id":{"arxiv":["1604.07169"],"isi":["000387731200001"]},"citation":{"apa":"Chatterjee, K., Fu, H., &#38; Goharshady, A. K. (2016). Termination analysis of probabilistic programs through Positivstellensatz’s (Vol. 9779, pp. 3–22). Presented at the CAV: Computer Aided Verification, Toronto, Canada: Springer. <a href=\"https://doi.org/10.1007/978-3-319-41528-4_1\">https://doi.org/10.1007/978-3-319-41528-4_1</a>","ama":"Chatterjee K, Fu H, Goharshady AK. Termination analysis of probabilistic programs through Positivstellensatz’s. In: Vol 9779. Springer; 2016:3-22. doi:<a href=\"https://doi.org/10.1007/978-3-319-41528-4_1\">10.1007/978-3-319-41528-4_1</a>","ieee":"K. Chatterjee, H. Fu, and A. K. Goharshady, “Termination analysis of probabilistic programs through Positivstellensatz’s,” presented at the CAV: Computer Aided Verification, Toronto, Canada, 2016, vol. 9779, pp. 3–22.","chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Termination Analysis of Probabilistic Programs through Positivstellensatz’s,” 9779:3–22. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-41528-4_1\">https://doi.org/10.1007/978-3-319-41528-4_1</a>.","ista":"Chatterjee K, Fu H, Goharshady AK. 2016. Termination analysis of probabilistic programs through Positivstellensatz’s. CAV: Computer Aided Verification, LNCS, vol. 9779, 3–22.","short":"K. Chatterjee, H. Fu, A.K. Goharshady, in:, Springer, 2016, pp. 3–22.","mla":"Chatterjee, Krishnendu, et al. <i>Termination Analysis of Probabilistic Programs through Positivstellensatz’s</i>. Vol. 9779, Springer, 2016, pp. 3–22, doi:<a href=\"https://doi.org/10.1007/978-3-319-41528-4_1\">10.1007/978-3-319-41528-4_1</a>."},"related_material":{"record":[{"relation":"dissertation_contains","id":"8934","status":"public"}]},"oa_version":"Preprint","_id":"1386","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"}],"title":"Termination analysis of probabilistic programs through Positivstellensatz's"}]