[{"page":"83","day":"01","publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"id":"1432","status":"public","relation":"part_of_dissertation"}]},"supervisor":[{"last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"}],"_id":"1396","has_accepted_license":"1","citation":{"apa":"Mishra, R. K. (2016). <i>Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus</i>. Institute of Science and Technology Austria.","ieee":"R. K. Mishra, “Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus,” Institute of Science and Technology Austria, 2016.","chicago":"Mishra, Rajiv Kumar. “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.","ama":"Mishra RK. Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus. 2016."},"date_updated":"2026-04-09T10:52:26Z","language":[{"iso":"eng"}],"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."}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"type":"dissertation","corr_author":"1","date_published":"2016-03-01T00:00:00Z","degree_awarded":"PhD","publication_status":"published","department":[{"_id":"PeJo"}],"date_created":"2018-12-11T11:51:46Z","publist_id":"5811","publication_identifier":{"issn":["2663-337X"]},"author":[{"id":"46CB58F2-F248-11E8-B48F-1D18A9856A87","full_name":"Mishra, Rajiv Kumar","last_name":"Mishra","first_name":"Rajiv Kumar"}],"year":"2016","month":"03","status":"public","alternative_title":["ISTA Thesis"],"title":"Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus","file":[{"file_name":"Thesis_Mishra_Rajiv (Final).pdf","access_level":"closed","date_created":"2019-08-09T12:14:46Z","date_updated":"2020-07-14T12:44:48Z","file_id":"6782","creator":"dernst","content_type":"application/pdf","file_size":2407572,"checksum":"5a010a838faf040f7064f3cfb802f743","relation":"main_file"},{"checksum":"81b26d9ede92c99f1d8cc6fa1d04cbbb","success":1,"file_size":2407572,"creator":"dernst","content_type":"application/pdf","file_id":"9183","date_updated":"2021-02-22T11:48:44Z","date_created":"2021-02-22T11:48:44Z","access_level":"open_access","file_name":"2016_RajivMishra_Thesis.pdf","relation":"main_file"}],"OA_place":"publisher","ddc":["570"],"file_date_updated":"2021-02-22T11:48:44Z","oa_version":"Published Version","article_processing_charge":"No"},{"department":[{"_id":"NiBa"}],"date_published":"2016-02-19T00:00:00Z","year":"2016","status":"public","_id":"5553","month":"02","date_created":"2018-12-12T12:31:30Z","day":"19","publisher":"Institute of Science and Technology Austria","author":[{"first_name":"David","last_name":"Field","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David"},{"orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Ellis"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"1398","status":"public"}]},"file":[{"date_created":"2018-12-12T13:03:02Z","date_updated":"2020-07-14T12:47:01Z","file_name":"IST-2016-37-v1+1_paternity_archive.zip","access_level":"open_access","file_size":132808,"checksum":"4ae751b1fa4897fa216241f975a57313","file_id":"5620","content_type":"application/zip","creator":"system","relation":"main_file"}],"doi":"10.15479/AT:ISTA:37","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).","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>","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.","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>.","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>."},"oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:01Z","ddc":["576"],"tmp":{"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","short":"CC0 (1.0)"},"has_accepted_license":"1","title":"Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012","datarep_id":"37","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","contributor":[{"contributor_type":"project_manager","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"keyword":["paternity assignment","pedigree","matting patterns","assortative mating","Antirrhinum majus","frequency-dependent selection","plant-pollinator interaction"],"article_processing_charge":"No","type":"research_data","date_updated":"2026-04-09T10:52:06Z","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."}]},{"date_published":"2016-02-19T00:00:00Z","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","day":"19","date_created":"2018-12-12T12:31:29Z","related_material":{"record":[{"status":"public","id":"1398","relation":"part_of_dissertation"}]},"author":[{"full_name":"Ellis, Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","last_name":"Ellis","first_name":"Thomas"}],"year":"2016","month":"02","_id":"5551","status":"public","title":"Data on pollinator observations and offpsring phenotypes","tmp":{"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","short":"CC0 (1.0)"},"has_accepted_license":"1","file":[{"relation":"main_file","access_level":"open_access","file_name":"IST-2016-35-v1+1_array_data.zip","date_created":"2018-12-12T13:05:12Z","date_updated":"2020-07-14T12:47:01Z","creator":"system","file_id":"5640","content_type":"application/zip","checksum":"aa3eb85d52b110cd192aa23147c4d4f3","file_size":32775}],"doi":"10.15479/AT:ISTA:35","file_date_updated":"2020-07-14T12:47:01Z","citation":{"short":"T. Ellis, (2016).","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>","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>.","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>.","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>","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>."},"oa_version":"Published Version","date_updated":"2026-04-09T10:52:07Z","abstract":[{"lang":"eng","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."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"datarep_id":"35","article_processing_charge":"No","type":"research_data","contributor":[{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}]},{"abstract":[{"lang":"eng","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."}],"date_updated":"2026-04-09T10:52:07Z","article_processing_charge":"No","type":"research_data","contributor":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","datarep_id":"36","oa":1,"has_accepted_license":"1","title":"Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.","oa_version":"Published Version","citation":{"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>.","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.","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>","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>","short":"T. Ellis, (2016).","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>."},"file_date_updated":"2020-07-14T12:47:01Z","doi":"10.15479/AT:ISTA:36","file":[{"relation":"main_file","access_level":"open_access","file_name":"IST-2016-36-v1+1_tag_assay_archive.zip","date_created":"2018-12-12T13:03:07Z","date_updated":"2020-07-14T12:47:01Z","content_type":"application/zip","file_id":"5625","creator":"system","checksum":"cbc61b523d4d475a04a737d50dc470ef","file_size":44905}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"1398","status":"public"}]},"author":[{"orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","full_name":"Ellis, Thomas","first_name":"Thomas","last_name":"Ellis"}],"publisher":"Institute of Science and Technology Austria","day":"19","date_created":"2018-12-12T12:31:30Z","_id":"5552","month":"02","status":"public","year":"2016","date_published":"2016-02-19T00:00:00Z","department":[{"_id":"NiBa"}]},{"day":"07","publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"relation":"part_of_dissertation","id":"2218","status":"public"},{"id":"2445","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1729"}]},"supervisor":[{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A"}],"_id":"1130","page":"151","date_updated":"2026-04-09T10:54:01Z","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"In this thesis we present a computer-aided programming approach to concurrency. Our approach helps the programmer by automatically fixing concurrency-related bugs, i.e. bugs that occur when the program is executed using an aggressive preemptive scheduler, but not when using a non-preemptive (cooperative) scheduler. Bugs are program behaviours that are incorrect w.r.t. a specification. We consider both user-provided explicit specifications in the form of assertion\r\nstatements in the code as well as an implicit specification. The implicit specification is inferred from the non-preemptive behaviour. Let us consider sequences of calls that the program makes to an external interface. The implicit specification requires that any such sequence produced under a preemptive scheduler should be included in the set of sequences produced under a non-preemptive scheduler. We consider several semantics-preserving fixes that go beyond atomic sections typically explored in the synchronisation synthesis literature. Our synthesis is able to place locks, barriers and wait-signal statements and last, but not least reorder independent statements. The latter may be useful if a thread is released to early, e.g., before some initialisation is completed. We guarantee that our synthesis does not introduce deadlocks and that the synchronisation inserted is optimal w.r.t. a given objective function. We dub our solution trace-based synchronisation synthesis and it is loosely based on counterexample-guided inductive synthesis (CEGIS). The synthesis works by discovering a trace that is incorrect w.r.t. the specification and identifying ordering constraints crucial to trigger the specification violation. Synchronisation may be placed immediately (greedy approach) or delayed until all incorrect traces are found (non-greedy approach). For the non-greedy approach we construct a set of global constraints over synchronisation placements. Each model of the global constraints set corresponds to a correctness-ensuring synchronisation placement. The placement that is optimal w.r.t. the given objective function is chosen as the synchronisation solution. We evaluate our approach on a number of realistic (albeit simplified) Linux device-driver\r\nbenchmarks. The benchmarks are versions of the drivers with known concurrency-related bugs. For the experiments with an explicit specification we added assertions that would detect the bugs in the experiments. Device drivers lend themselves to implicit specification, where the device and the operating system are the external interfaces. Our experiments demonstrate that our synthesis method is precise and efficient. We implemented objective functions for coarse-grained and fine-grained locking and observed that different synchronisation placements are produced for our experiments, favouring e.g. a minimal number of synchronisation operations or maximum concurrency."}],"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"type":"dissertation","has_accepted_license":"1","citation":{"ama":"Tarrach T. Automatic synthesis of synchronisation primitives for concurrent programs. 2016. doi:<a href=\"https://doi.org/10.15479/at:ista:1130\">10.15479/at:ista:1130</a>","short":"T. Tarrach, Automatic Synthesis of Synchronisation Primitives for Concurrent Programs, Institute of Science and Technology Austria, 2016.","mla":"Tarrach, Thorsten. <i>Automatic Synthesis of Synchronisation Primitives for Concurrent Programs</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/at:ista:1130\">10.15479/at:ista:1130</a>.","ista":"Tarrach T. 2016. Automatic synthesis of synchronisation primitives for concurrent programs. Institute of Science and Technology Austria.","ieee":"T. Tarrach, “Automatic synthesis of synchronisation primitives for concurrent programs,” Institute of Science and Technology Austria, 2016.","chicago":"Tarrach, Thorsten. “Automatic Synthesis of Synchronisation Primitives for Concurrent Programs.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/at:ista:1130\">https://doi.org/10.15479/at:ista:1130</a>.","apa":"Tarrach, T. (2016). <i>Automatic synthesis of synchronisation primitives for concurrent programs</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:1130\">https://doi.org/10.15479/at:ista:1130</a>"},"date_created":"2018-12-11T11:50:19Z","publist_id":"6230","publication_identifier":{"issn":["2663-337X"]},"author":[{"last_name":"Tarrach","first_name":"Thorsten","full_name":"Tarrach, Thorsten","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4409-8487"}],"year":"2016","month":"07","status":"public","corr_author":"1","main_file_link":[{"open_access":"1","url":"http://thorstent.github.io/theses/phd_thorsten_tarrach.pdf"}],"date_published":"2016-07-07T00:00:00Z","ec_funded":1,"degree_awarded":"PhD","publication_status":"published","department":[{"_id":"ToHe"},{"_id":"GradSch"}],"article_processing_charge":"No","alternative_title":["ISTA Thesis"],"title":"Automatic synthesis of synchronisation primitives for concurrent programs","file":[{"relation":"main_file","date_created":"2021-02-22T11:39:32Z","date_updated":"2021-02-22T11:39:32Z","access_level":"open_access","file_name":"2016_Tarrach_Thesis.pdf","success":1,"checksum":"319a506831650327e85376db41fc1094","file_size":1523935,"content_type":"application/pdf","creator":"dernst","file_id":"9179"},{"file_size":1306068,"checksum":"39efcd789f0ad859ff15652cb7afc412","content_type":"application/pdf","file_id":"10296","creator":"cchlebak","date_updated":"2021-11-17T13:46:55Z","date_created":"2021-11-16T14:14:38Z","file_name":"2016_Tarrach_Thesispdfa.pdf","access_level":"closed","relation":"main_file"}],"OA_place":"publisher","ddc":["000"],"oa_version":"Published Version","doi":"10.15479/at:ista:1130","file_date_updated":"2021-11-17T13:46:55Z"},{"author":[{"full_name":"Tugrul, Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8523-0758","last_name":"Tugrul","first_name":"Murat"}],"publist_id":"6229","publication_identifier":{"issn":["2663-337X"]},"date_created":"2018-12-11T11:50:19Z","status":"public","month":"07","year":"2016","date_published":"2016-07-01T00:00:00Z","corr_author":"1","department":[{"_id":"NiBa"}],"publication_status":"published","degree_awarded":"PhD","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.","article_processing_charge":"No","title":"Evolution of transcriptional regulatory sequences","alternative_title":["ISTA Thesis"],"file_date_updated":"2021-02-22T11:45:20Z","oa_version":"Published Version","ddc":["576"],"OA_place":"publisher","file":[{"file_size":3695257,"checksum":"66cb61a59943e4fb7447c6a86be5ef51","file_id":"6810","creator":"dernst","content_type":"application/pdf","date_created":"2019-08-13T08:53:52Z","date_updated":"2019-08-13T08:53:52Z","file_name":"Tugrul_thesis_w_signature_page.pdf","access_level":"closed","relation":"main_file"},{"relation":"main_file","access_level":"open_access","file_name":"2016_Tugrul_Thesis.pdf","date_created":"2021-02-22T11:45:20Z","date_updated":"2021-02-22T11:45:20Z","file_id":"9182","creator":"dernst","content_type":"application/pdf","checksum":"293e388d70563760f6b24c3e66283dda","success":1,"file_size":3880811}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"5554"},{"status":"public","id":"1666","relation":"part_of_dissertation"}]},"publisher":"Institute of Science and Technology Austria","day":"01","_id":"1131","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"}],"page":"89","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."}],"language":[{"iso":"eng"}],"date_updated":"2026-04-09T10:52:40Z","type":"dissertation","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","citation":{"mla":"Tugrul, Murat. <i>Evolution of Transcriptional Regulatory Sequences</i>. Institute of Science and Technology Austria, 2016.","ama":"Tugrul M. Evolution of transcriptional regulatory sequences. 2016.","short":"M. Tugrul, Evolution of Transcriptional Regulatory Sequences, 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.","apa":"Tugrul, M. (2016). <i>Evolution of transcriptional regulatory sequences</i>. Institute of Science and Technology Austria.","ista":"Tugrul M. 2016. Evolution of transcriptional regulatory sequences. Institute of Science and Technology Austria."}},{"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"date_published":"2016-05-12T00:00:00Z","year":"2016","month":"05","_id":"5554","status":"public","publisher":"Institute of Science and Technology Austria","day":"12","date_created":"2018-12-12T12:31:30Z","related_material":{"record":[{"id":"1131","status":"public","relation":"used_in_publication"}]},"author":[{"orcid":"0000-0002-8523-0758","full_name":"Tugrul, Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","first_name":"Murat","last_name":"Tugrul"}],"file":[{"date_created":"2018-12-12T13:03:08Z","date_updated":"2020-07-14T12:47:01Z","file_name":"IST-2016-43-v1+1_DATA_MTugrul_PhDThesis_Chapter3.zip","access_level":"open_access","file_size":1123495,"checksum":"1fc0a10bb7ce110fcb5e1fbe3cf0c4e2","content_type":"application/zip","file_id":"5626","creator":"system","relation":"main_file"}],"citation":{"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>.","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>","ieee":"M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016.","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>.","short":"M. Tugrul, (2016).","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>","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>."},"file_date_updated":"2020-07-14T12:47:01Z","doi":"10.15479/AT:ISTA:43","oa_version":"Published Version","tmp":{"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","short":"CC0 (1.0)"},"title":"Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"datarep_id":"43","article_processing_charge":"No","type":"research_data","contributor":[{"id":"2C023F40-F248-11E8-B48F-1D18A9856A87","last_name":"Steinrück","contributor_type":"researcher","first_name":"Magdalena"},{"contributor_type":"researcher","first_name":"Fabienne","last_name":"Jesse","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87"}],"keyword":["RNAP binding","de novo promoter evolution","lac promoter"],"date_updated":"2026-04-09T10:52:40Z","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."}]},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"type":"dissertation","date_updated":"2026-04-09T14:25:34Z","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","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."}],"citation":{"chicago":"Novak, Sebastian. “Evolutionary Proccesses in Variable Emvironments.” Institute of Science and Technology Austria, 2016.","ieee":"S. Novak, “Evolutionary proccesses in variable emvironments,” Institute of Science and Technology Austria, 2016.","apa":"Novak, S. (2016). <i>Evolutionary proccesses in variable emvironments</i>. Institute of Science and Technology Austria.","ista":"Novak S. 2016. Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria.","mla":"Novak, Sebastian. <i>Evolutionary Proccesses in Variable Emvironments</i>. Institute of Science and Technology Austria, 2016.","ama":"Novak S. Evolutionary proccesses in variable emvironments. 2016.","short":"S. Novak, Evolutionary Proccesses in Variable Emvironments, Institute of Science and Technology Austria, 2016."},"has_accepted_license":"1","supervisor":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"}],"_id":"1125","day":"01","publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"status":"public","id":"2023","relation":"part_of_dissertation"}]},"page":"124","article_processing_charge":"No","file":[{"date_created":"2019-08-13T09:01:00Z","date_updated":"2019-08-13T09:01:00Z","access_level":"closed","file_name":"Novak_thesis.pdf","checksum":"81dcc838dfcf7aa0b1a27ecf4fe2da4e","file_size":3564901,"creator":"dernst","file_id":"6811","content_type":"application/pdf","relation":"main_file"},{"creator":"dernst","content_type":"application/pdf","file_id":"9186","checksum":"30808d2f7ca920e09f63a95cdc49bffd","success":1,"file_size":2814384,"access_level":"open_access","file_name":"2016_Novak_Thesis.pdf","date_created":"2021-02-22T13:42:47Z","date_updated":"2021-02-22T13:42:47Z","relation":"main_file"}],"OA_place":"publisher","ddc":["576"],"file_date_updated":"2021-02-22T13:42:47Z","oa_version":"Published Version","alternative_title":["ISTA Thesis"],"title":"Evolutionary proccesses in variable emvironments","year":"2016","month":"07","status":"public","date_created":"2018-12-11T11:50:17Z","publication_identifier":{"issn":["2663-337X"]},"publist_id":"6235","author":[{"first_name":"Sebastian","last_name":"Novak","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"}],"degree_awarded":"PhD","publication_status":"published","department":[{"_id":"NiBa"}],"corr_author":"1","date_published":"2016-07-01T00:00:00Z"},{"page":"674 - 703","day":"10","publisher":"Academic Press","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1399"}]},"_id":"1662","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","citation":{"ama":"Edelsbrunner H, Pausinger F. Approximation and convergence of the intrinsic volume. <i>Advances in Mathematics</i>. 2016;287:674-703. doi:<a href=\"https://doi.org/10.1016/j.aim.2015.10.004\">10.1016/j.aim.2015.10.004</a>","short":"H. Edelsbrunner, F. Pausinger, Advances in Mathematics 287 (2016) 674–703.","mla":"Edelsbrunner, Herbert, and Florian Pausinger. “Approximation and Convergence of the Intrinsic Volume.” <i>Advances in Mathematics</i>, vol. 287, Academic Press, 2016, pp. 674–703, doi:<a href=\"https://doi.org/10.1016/j.aim.2015.10.004\">10.1016/j.aim.2015.10.004</a>.","ista":"Edelsbrunner H, Pausinger F. 2016. Approximation and convergence of the intrinsic volume. Advances in Mathematics. 287, 674–703.","chicago":"Edelsbrunner, Herbert, and Florian Pausinger. “Approximation and Convergence of the Intrinsic Volume.” <i>Advances in Mathematics</i>. Academic Press, 2016. <a href=\"https://doi.org/10.1016/j.aim.2015.10.004\">https://doi.org/10.1016/j.aim.2015.10.004</a>.","ieee":"H. Edelsbrunner and F. Pausinger, “Approximation and convergence of the intrinsic volume,” <i>Advances in Mathematics</i>, vol. 287. Academic Press, pp. 674–703, 2016.","apa":"Edelsbrunner, H., &#38; Pausinger, F. (2016). Approximation and convergence of the intrinsic volume. <i>Advances in Mathematics</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.aim.2015.10.004\">https://doi.org/10.1016/j.aim.2015.10.004</a>"},"date_updated":"2026-04-09T14:26:05Z","language":[{"iso":"eng"}],"abstract":[{"text":"We introduce a modification of the classic notion of intrinsic volume using persistence moments of height functions. Evaluating the modified first intrinsic volume on digital approximations of a compact body with smoothly embedded boundary in Rn, we prove convergence to the first intrinsic volume of the body as the resolution of the approximation improves. We have weaker results for the other modified intrinsic volumes, proving they converge to the corresponding intrinsic volumes of the n-dimensional unit ball.","lang":"eng"}],"project":[{"grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Topological Complex Systems"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"type":"journal_article","volume":287,"corr_author":"1","date_published":"2016-01-10T00:00:00Z","ec_funded":1,"publication_status":"published","department":[{"_id":"HeEd"}],"pubrep_id":"774","date_created":"2018-12-11T11:53:20Z","isi":1,"intvolume":"       287","publist_id":"5488","author":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert"},{"first_name":"Florian","last_name":"Pausinger","orcid":"0000-0002-8379-3768","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","full_name":"Pausinger, Florian"}],"year":"2016","month":"01","status":"public","scopus_import":"1","quality_controlled":"1","title":"Approximation and convergence of the intrinsic volume","file":[{"file_name":"IST-2017-774-v1+1_2016-J-03-FirstIntVolume.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:10Z","date_created":"2018-12-12T10:12:10Z","file_id":"4928","content_type":"application/pdf","creator":"system","file_size":248985,"checksum":"f8869ec110c35c852ef6a37425374af7","relation":"main_file"}],"ddc":["004"],"doi":"10.1016/j.aim.2015.10.004","file_date_updated":"2020-07-14T12:45:10Z","external_id":{"isi":["000375634100016"]},"oa_version":"Published Version","acknowledgement":"This research is partially supported by the Toposys project FP7-ICT-318493-STREP, and by ESF under the ACAT Research Network Programme.\r\nBoth authors thank Anne Marie Svane for her comments on an early version of this paper. The second author wishes to thank Eva B. Vedel Jensen and Markus Kiderlen from Aarhus University for enlightening discussions and their kind hospitality during a visit of their department in 2014.","publication":"Advances in Mathematics","article_processing_charge":"No"},{"acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989\r\n(QUAREM), the Austrian Science Fund (FWF) under grants project S11402-N23 (RiSE and SHiNE)\r\nand Z211-N23 (Wittgenstein Award), by the Czech Science Foundation Grant No. P202/12/G061, and\r\nby the SNSF Advanced Postdoc. Mobility Fellowship – grant number P300P2_161067.","ddc":["004"],"oa_version":"Published Version","file_date_updated":"2018-12-12T10:11:39Z","doi":"10.4230/LIPIcs.CONCUR.2016.20","file":[{"file_id":"4895","creator":"system","content_type":"application/pdf","file_size":501827,"access_level":"open_access","file_name":"IST-2017-794-v1+1_LIPIcs-CONCUR-2016-20.pdf","date_updated":"2018-12-12T10:11:39Z","date_created":"2018-12-12T10:11:39Z","relation":"main_file"}],"quality_controlled":"1","title":"Linear distances between Markov chains","alternative_title":["LIPIcs"],"scopus_import":1,"month":"08","status":"public","year":"2016","publist_id":"6283","intvolume":"        59","author":[{"last_name":"Daca","first_name":"Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","full_name":"Daca, Przemyslaw"},{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","full_name":"Kretinsky, Jan","first_name":"Jan","last_name":"Kretinsky"},{"orcid":"0000-0002-9041-0905","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrov, Tatjana","first_name":"Tatjana","last_name":"Petrov"}],"date_created":"2018-12-11T11:50:06Z","department":[{"_id":"ToHe"},{"_id":"KrCh"},{"_id":"CaGu"}],"pubrep_id":"794","publication_status":"published","date_published":"2016-08-01T00:00:00Z","ec_funded":1,"volume":59,"type":"conference","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"oa":1,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We introduce a general class of distances (metrics) between Markov chains, which are based on linear behaviour. This class encompasses distances given topologically (such as the total variation distance or trace distance) as well as by temporal logics or automata. We investigate which of the distances can be approximated by observing the systems, i.e. by black-box testing or simulation, and we provide both negative and positive results. "}],"date_updated":"2026-04-15T10:02:12Z","citation":{"short":"P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","ama":"Daca P, Henzinger TA, Kretinsky J, Petrov T. Linear distances between Markov chains. In: Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.20\">10.4230/LIPIcs.CONCUR.2016.20</a>","mla":"Daca, Przemyslaw, et al. <i>Linear Distances between Markov Chains</i>. Vol. 59, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.20\">10.4230/LIPIcs.CONCUR.2016.20</a>.","ista":"Daca P, Henzinger TA, Kretinsky J, Petrov T. 2016. Linear distances between Markov chains. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 20.","apa":"Daca, P., Henzinger, T. A., Kretinsky, J., &#38; Petrov, T. (2016). Linear distances between Markov chains (Vol. 59). Presented at the CONCUR: Concurrency Theory, Quebec City; Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.20\">https://doi.org/10.4230/LIPIcs.CONCUR.2016.20</a>","chicago":"Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Linear Distances between Markov Chains,” Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.20\">https://doi.org/10.4230/LIPIcs.CONCUR.2016.20</a>.","ieee":"P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Linear distances between Markov chains,” presented at the CONCUR: Concurrency Theory, Quebec City; Canada, 2016, vol. 59."},"has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"20","conference":{"location":"Quebec City; Canada","name":"CONCUR: Concurrency Theory","end_date":"2016-08-26","start_date":"2016-08-23"},"_id":"1093","related_material":{"record":[{"id":"1155","status":"public","relation":"dissertation_contains"}]},"day":"01","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik"},{"_id":"1234","publisher":"Springer","day":"01","related_material":{"record":[{"id":"471","status":"public","relation":"later_version"},{"relation":"dissertation_contains","status":"public","id":"1155"}]},"page":"112 - 129","oa":1,"project":[{"call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"conference","volume":9636,"date_updated":"2026-04-15T10:02:12Z","abstract":[{"lang":"eng","text":"We present a new algorithm for the statistical model checking of Markov chains with respect to unbounded temporal properties, including full linear temporal logic. The main idea is that we monitor each simulation run on the fly, in order to detect quickly if a bottom strongly connected component is entered with high probability, in which case the simulation run can be terminated early. As a result, our simulation runs are often much shorter than required by termination bounds that are computed a priori for a desired level of confidence on a large state space. In comparison to previous algorithms for statistical model checking our method is not only faster in many cases but also requires less information about the system, namely, only the minimum transition probability that occurs in the Markov chain. In addition, our method can be generalised to unbounded quantitative properties such as mean-payoff bounds."}],"language":[{"iso":"eng"}],"citation":{"ieee":"P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Faster statistical model checking for unbounded temporal properties,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Eindhoven, The Netherlands, 2016, vol. 9636, pp. 112–129.","chicago":"Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Faster Statistical Model Checking for Unbounded Temporal Properties,” 9636:112–29. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-49674-9_7\">https://doi.org/10.1007/978-3-662-49674-9_7</a>.","apa":"Daca, P., Henzinger, T. A., Kretinsky, J., &#38; Petrov, T. (2016). Faster statistical model checking for unbounded temporal properties (Vol. 9636, pp. 112–129). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Eindhoven, The Netherlands: Springer. <a href=\"https://doi.org/10.1007/978-3-662-49674-9_7\">https://doi.org/10.1007/978-3-662-49674-9_7</a>","ista":"Daca P, Henzinger TA, Kretinsky J, Petrov T. 2016. Faster statistical model checking for unbounded temporal properties. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 9636, 112–129.","mla":"Daca, Przemyslaw, et al. <i>Faster Statistical Model Checking for Unbounded Temporal Properties</i>. Vol. 9636, Springer, 2016, pp. 112–29, doi:<a href=\"https://doi.org/10.1007/978-3-662-49674-9_7\">10.1007/978-3-662-49674-9_7</a>.","ama":"Daca P, Henzinger TA, Kretinsky J, Petrov T. Faster statistical model checking for unbounded temporal properties. In: Vol 9636. Springer; 2016:112-129. doi:<a href=\"https://doi.org/10.1007/978-3-662-49674-9_7\">10.1007/978-3-662-49674-9_7</a>","short":"P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Springer, 2016, pp. 112–129."},"conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2016-04-08","location":"Eindhoven, The Netherlands","start_date":"2016-04-02"},"year":"2016","status":"public","month":"01","isi":1,"date_created":"2018-12-11T11:50:51Z","arxiv":1,"author":[{"full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","first_name":"Przemyslaw","last_name":"Daca"},{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Kretinsky"},{"id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905","last_name":"Petrov","first_name":"Tatjana"}],"publist_id":"6099","intvolume":"      9636","publication_status":"published","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"ec_funded":1,"date_published":"2016-01-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.05739"}],"article_processing_charge":"No","acknowledgement":"This research was funded in part by the European Research Council (ERC) under\r\ngrant  agreement  267989  (QUAREM),  the  Austrian  Science  Fund  (FWF)  under\r\ngrants project S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), the Peo-\r\nple Programme (Marie Curie Actions) of the European Union’s Seventh Framework\r\nProgramme (FP7/2007-2013) REA Grant No 291734, the SNSF Advanced Postdoc.\r\nMobility Fellowship – grant number P300P2\r\n161067, and the Czech Science Foun-\r\ndation under grant agreement P202/12/G061.","oa_version":"Preprint","doi":"10.1007/978-3-662-49674-9_7","external_id":{"isi":["000406428000007"],"arxiv":["1504.05739"]},"scopus_import":"1","alternative_title":["LNCS"],"title":"Faster statistical model checking for unbounded temporal properties","quality_controlled":"1"},{"article_processing_charge":"No","external_id":{"isi":["000387731400013"],"arxiv":["1603.06850"]},"doi":"10.1007/978-3-319-41540-6_13","oa_version":"Preprint","alternative_title":["LNCS"],"scopus_import":"1","quality_controlled":"1","title":"Array folds logic","year":"2016","month":"07","status":"public","arxiv":1,"isi":1,"date_created":"2018-12-11T11:51:45Z","intvolume":"      9780","publist_id":"5818","author":[{"id":"49351290-F248-11E8-B48F-1D18A9856A87","full_name":"Daca, Przemyslaw","first_name":"Przemyslaw","last_name":"Daca"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Kupriyanov, Andrey","id":"2C311BF8-F248-11E8-B48F-1D18A9856A87","last_name":"Kupriyanov","first_name":"Andrey"}],"publication_status":"published","department":[{"_id":"ToHe"}],"corr_author":"1","date_published":"2016-07-13T00:00:00Z","main_file_link":[{"url":"http://arxiv.org/abs/1603.06850","open_access":"1"}],"ec_funded":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF"}],"oa":1,"type":"conference","volume":9780,"date_updated":"2026-04-15T10:02:12Z","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We present an extension to the quantifier-free theory of integer arrays which allows us to express counting. The properties expressible in Array Folds Logic (AFL) include statements such as &quot;the first array cell contains the array length,&quot; and &quot;the array contains equally many minimal and maximal elements.&quot; These properties cannot be expressed in quantified fragments of the theory of arrays, nor in the theory of concatenation. Using reduction to counter machines, we show that the satisfiability problem of AFL is PSPACE-complete, and with a natural restriction the complexity decreases to NP. We also show that adding either universal quantifiers or concatenation leads to undecidability.\r\nAFL contains terms that fold a function over an array. We demonstrate that folding, a well-known concept from functional languages, allows us to concisely summarize loops that count over arrays, which occurs frequently in real-life programs. We provide a tool that can discharge proof obligations in AFL, and we demonstrate on practical examples that our decision procedure can solve a broad range of problems in symbolic testing and program verification."}],"citation":{"chicago":"Daca, Przemyslaw, Thomas A Henzinger, and Andrey Kupriyanov. “Array Folds Logic,” 9780:230–48. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-41540-6_13\">https://doi.org/10.1007/978-3-319-41540-6_13</a>.","ieee":"P. Daca, T. A. Henzinger, and A. Kupriyanov, “Array folds logic,” presented at the CAV: Computer Aided Verification, Toronto, Canada, 2016, vol. 9780, pp. 230–248.","apa":"Daca, P., Henzinger, T. A., &#38; Kupriyanov, A. (2016). Array folds logic (Vol. 9780, pp. 230–248). Presented at the CAV: Computer Aided Verification, Toronto, Canada: Springer. <a href=\"https://doi.org/10.1007/978-3-319-41540-6_13\">https://doi.org/10.1007/978-3-319-41540-6_13</a>","ista":"Daca P, Henzinger TA, Kupriyanov A. 2016. Array folds logic. CAV: Computer Aided Verification, LNCS, vol. 9780, 230–248.","mla":"Daca, Przemyslaw, et al. <i>Array Folds Logic</i>. Vol. 9780, Springer, 2016, pp. 230–48, doi:<a href=\"https://doi.org/10.1007/978-3-319-41540-6_13\">10.1007/978-3-319-41540-6_13</a>.","ama":"Daca P, Henzinger TA, Kupriyanov A. Array folds logic. In: Vol 9780. Springer; 2016:230-248. doi:<a href=\"https://doi.org/10.1007/978-3-319-41540-6_13\">10.1007/978-3-319-41540-6_13</a>","short":"P. Daca, T.A. Henzinger, A. Kupriyanov, in:, Springer, 2016, pp. 230–248."},"conference":{"start_date":"2016-07-17","location":"Toronto, Canada","name":"CAV: Computer Aided Verification","end_date":"2016-07-23"},"_id":"1391","day":"13","publisher":"Springer","related_material":{"record":[{"id":"1155","status":"public","relation":"dissertation_contains"}]},"page":"230 - 248"},{"page":"328 - 347","publisher":"Springer","day":"01","related_material":{"record":[{"status":"public","id":"1155","relation":"dissertation_contains"}]},"_id":"1230","conference":{"name":"VMCAI: Verification, Model Checking and Abstract Interpretation","end_date":"2016-01-19","location":"St. Petersburg, FL, USA","start_date":"2016-01-17"},"citation":{"short":"P. Daca, A. Gupta, T.A. Henzinger, in:, Springer, 2016, pp. 328–347.","ama":"Daca P, Gupta A, Henzinger TA. Abstraction-driven concolic testing. In: Vol 9583. Springer; 2016:328-347. doi:<a href=\"https://doi.org/10.1007/978-3-662-49122-5_16\">10.1007/978-3-662-49122-5_16</a>","mla":"Daca, Przemyslaw, et al. <i>Abstraction-Driven Concolic Testing</i>. Vol. 9583, Springer, 2016, pp. 328–47, doi:<a href=\"https://doi.org/10.1007/978-3-662-49122-5_16\">10.1007/978-3-662-49122-5_16</a>.","ista":"Daca P, Gupta A, Henzinger TA. 2016. Abstraction-driven concolic testing. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 9583, 328–347.","apa":"Daca, P., Gupta, A., &#38; Henzinger, T. A. (2016). Abstraction-driven concolic testing (Vol. 9583, pp. 328–347). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, St. Petersburg, FL, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-662-49122-5_16\">https://doi.org/10.1007/978-3-662-49122-5_16</a>","ieee":"P. Daca, A. Gupta, and T. A. Henzinger, “Abstraction-driven concolic testing,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, St. Petersburg, FL, USA, 2016, vol. 9583, pp. 328–347.","chicago":"Daca, Przemyslaw, Ashutosh Gupta, and Thomas A Henzinger. “Abstraction-Driven Concolic Testing,” 9583:328–47. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-49122-5_16\">https://doi.org/10.1007/978-3-662-49122-5_16</a>."},"date_updated":"2026-04-15T10:02:12Z","abstract":[{"text":"Concolic testing is a promising method for generating test suites for large programs. However, it suffers from the path-explosion problem and often fails to find tests that cover difficult-to-reach parts of programs. In contrast, model checkers based on counterexample-guided abstraction refinement explore programs exhaustively, while failing to scale on large programs with precision. In this paper, we present a novel method that iteratively combines concolic testing and model checking to find a test suite for a given coverage criterion. If concolic testing fails to cover some test goals, then the model checker refines its program abstraction to prove more paths infeasible, which reduces the search space for concolic testing. We have implemented our method on top of the concolictesting tool Crest and the model checker CpaChecker. We evaluated our tool on a collection of programs and a category of SvComp benchmarks. In our experiments, we observed an improvement in branch coverage compared to Crest from 48% to 63% in the best case, and from 66% to 71% on average.","lang":"eng"}],"language":[{"iso":"eng"}],"oa":1,"project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"conference","volume":9583,"ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.02615"}],"date_published":"2016-01-01T00:00:00Z","publication_status":"published","department":[{"_id":"ToHe"}],"isi":1,"date_created":"2018-12-11T11:50:50Z","arxiv":1,"author":[{"first_name":"Przemyslaw","last_name":"Daca","full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gupta","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Ashutosh"},{"last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"}],"publist_id":"6104","intvolume":"      9583","year":"2016","status":"public","month":"01","scopus_import":"1","alternative_title":["LNCS"],"title":"Abstraction-driven concolic testing","quality_controlled":"1","doi":"10.1007/978-3-662-49122-5_16","external_id":{"isi":["000375148800016"],"arxiv":["1511.02615"]},"oa_version":"Preprint","acknowledgement":"We thank Andrey Kupriyanov for feedback on the manuscript,\r\nand Michael Tautschnig for help with preparing the experiments. This research was supported in part by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award).","article_processing_charge":"No"},{"status":"public","month":"10","year":"2016","author":[{"full_name":"Khorasaninejad, M.","last_name":"Khorasaninejad","first_name":"M."},{"full_name":"Zhu, A. Y.","last_name":"Zhu","first_name":"A. Y."},{"last_name":"Roques-Carmes","first_name":"Charles","full_name":"Roques-Carmes, Charles","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82"},{"full_name":"Chen, W. T.","first_name":"W. T.","last_name":"Chen"},{"full_name":"Oh, J.","last_name":"Oh","first_name":"J."},{"last_name":"Mishra","first_name":"I.","full_name":"Mishra, I."},{"full_name":"Devlin, R. C.","last_name":"Devlin","first_name":"R. C."},{"last_name":"Capasso","first_name":"F.","full_name":"Capasso, F."}],"publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"intvolume":"        16","date_created":"2026-03-30T12:22:47Z","publication_status":"published","date_published":"2016-10-24T00:00:00Z","article_processing_charge":"No","pmid":1,"publication":"Nano Letters","doi":"10.1021/acs.nanolett.6b03626","oa_version":"None","external_id":{"pmid":["27791380"]},"ddc":["530"],"title":"Polarization-insensitive metalenses at visible wavelengths","quality_controlled":"1","scopus_import":"1","article_type":"original","_id":"21522","extern":"1","day":"24","publisher":"American Chemical Society","page":"7229-7234","OA_type":"closed access","keyword":["Metasurface","polarization-insensitive metalenses","visible wavelength","titanium dioxide"],"type":"journal_article","volume":16,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"In this Letter, we demonstrate highly efficient, polarization-insensitive planar lenses (metalenses) at red, green, and blue wavelengths (λ = 660, 532, and 405 nm). Metalenses with numerical apertures (NA) of 0.85 and 0.6 and corresponding efficiencies as high as 60% and 90% are achieved. These metalenses are less than 600 nm-thick and can focus incident light down to diffraction-limited spots as small as ∼0.64λ and provide high-resolution imaging. In addition, the focal spots are very symmetric with high Strehl ratios. The single step lithography and compatibility with large-scale fabrication processes make metalenses highly promising for widespread applications in imaging and spectroscopy.","lang":"eng"}],"language":[{"iso":"eng"}],"date_updated":"2026-04-15T11:53:17Z","citation":{"apa":"Khorasaninejad, M., Zhu, A. Y., Roques-Carmes, C., Chen, W. T., Oh, J., Mishra, I., … Capasso, F. (2016). Polarization-insensitive metalenses at visible wavelengths. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.6b03626\">https://doi.org/10.1021/acs.nanolett.6b03626</a>","ieee":"M. Khorasaninejad <i>et al.</i>, “Polarization-insensitive metalenses at visible wavelengths,” <i>Nano Letters</i>, vol. 16, no. 11. American Chemical Society, pp. 7229–7234, 2016.","chicago":"Khorasaninejad, M., A. Y. Zhu, Charles Roques-Carmes, W. T. Chen, J. Oh, I. Mishra, R. C. Devlin, and F. Capasso. “Polarization-Insensitive Metalenses at Visible Wavelengths.” <i>Nano Letters</i>. American Chemical Society, 2016. <a href=\"https://doi.org/10.1021/acs.nanolett.6b03626\">https://doi.org/10.1021/acs.nanolett.6b03626</a>.","ista":"Khorasaninejad M, Zhu AY, Roques-Carmes C, Chen WT, Oh J, Mishra I, Devlin RC, Capasso F. 2016. Polarization-insensitive metalenses at visible wavelengths. Nano Letters. 16(11), 7229–7234.","mla":"Khorasaninejad, M., et al. “Polarization-Insensitive Metalenses at Visible Wavelengths.” <i>Nano Letters</i>, vol. 16, no. 11, American Chemical Society, 2016, pp. 7229–34, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.6b03626\">10.1021/acs.nanolett.6b03626</a>.","short":"M. Khorasaninejad, A.Y. Zhu, C. Roques-Carmes, W.T. Chen, J. Oh, I. Mishra, R.C. Devlin, F. Capasso, Nano Letters 16 (2016) 7229–7234.","ama":"Khorasaninejad M, Zhu AY, Roques-Carmes C, et al. Polarization-insensitive metalenses at visible wavelengths. <i>Nano Letters</i>. 2016;16(11):7229-7234. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.6b03626\">10.1021/acs.nanolett.6b03626</a>"},"issue":"11"},{"department":[{"_id":"ToHe"}],"pubrep_id":"645","publication_status":"published","date_published":"2016-09-01T00:00:00Z","ec_funded":1,"corr_author":"1","month":"09","status":"public","year":"2016","intvolume":"      9928","publist_id":"5926","author":[{"orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Avni, Guy","first_name":"Guy","last_name":"Avni"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Kupferman, Orna","first_name":"Orna","last_name":"Kupferman"}],"isi":1,"date_created":"2018-12-11T11:51:28Z","ddc":["000"],"file_date_updated":"2020-07-14T12:44:45Z","oa_version":"Preprint","doi":"10.1007/978-3-662-53354-3_13","external_id":{"isi":["000389020400013"]},"file":[{"relation":"main_file","file_size":243458,"checksum":"0825eefd4e22774f6f62cb7d7389b05a","creator":"system","content_type":"application/pdf","file_id":"5073","date_updated":"2020-07-14T12:44:45Z","date_created":"2018-12-12T10:14:22Z","file_name":"IST-2016-645-v1+1_sagt-cr.pdf","access_level":"open_access"}],"quality_controlled":"1","title":"Dynamic resource allocation games","alternative_title":["LNCS"],"scopus_import":"1","article_processing_charge":"No","acknowledgement":"This research was supported in part by the European Research Council (ERC) under grants 267989 (QUAREM) and 278410 (QUALITY), and by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award).","page":"153 - 166","_id":"1341","related_material":{"record":[{"status":"public","id":"6761","relation":"later_version"}]},"day":"01","publisher":"Springer","citation":{"short":"G. Avni, T.A. Henzinger, O. Kupferman, in:, Springer, 2016, pp. 153–166.","ama":"Avni G, Henzinger TA, Kupferman O. Dynamic resource allocation games. In: Vol 9928. Springer; 2016:153-166. doi:<a href=\"https://doi.org/10.1007/978-3-662-53354-3_13\">10.1007/978-3-662-53354-3_13</a>","mla":"Avni, Guy, et al. <i>Dynamic Resource Allocation Games</i>. Vol. 9928, Springer, 2016, pp. 153–66, doi:<a href=\"https://doi.org/10.1007/978-3-662-53354-3_13\">10.1007/978-3-662-53354-3_13</a>.","ista":"Avni G, Henzinger TA, Kupferman O. 2016. Dynamic resource allocation games. SAGT: Symposium on Algorithmic Game Theory, LNCS, vol. 9928, 153–166.","apa":"Avni, G., Henzinger, T. A., &#38; Kupferman, O. (2016). Dynamic resource allocation games (Vol. 9928, pp. 153–166). Presented at the SAGT: Symposium on Algorithmic Game Theory, Liverpool, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-662-53354-3_13\">https://doi.org/10.1007/978-3-662-53354-3_13</a>","ieee":"G. Avni, T. A. Henzinger, and O. Kupferman, “Dynamic resource allocation games,” presented at the SAGT: Symposium on Algorithmic Game Theory, Liverpool, United Kingdom, 2016, vol. 9928, pp. 153–166.","chicago":"Avni, Guy, Thomas A Henzinger, and Orna Kupferman. “Dynamic Resource Allocation Games,” 9928:153–66. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-53354-3_13\">https://doi.org/10.1007/978-3-662-53354-3_13</a>."},"has_accepted_license":"1","conference":{"start_date":"2016-09-19","name":"SAGT: Symposium on Algorithmic Game Theory","end_date":"2016-09-21","location":"Liverpool, United Kingdom"},"type":"conference","volume":9928,"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"In resource allocation games, selfish players share resources that are needed in order to fulfill their objectives. The cost of using a resource depends on the load on it. In the traditional setting, the players make their choices concurrently and in one-shot. That is, a strategy for a player is a subset of the resources. We introduce and study dynamic resource allocation games. In this setting, the game proceeds in phases. In each phase each player chooses one resource. A scheduler dictates the order in which the players proceed in a phase, possibly scheduling several players to proceed concurrently. The game ends when each player has collected a set of resources that fulfills his objective. The cost for each player then depends on this set as well as on the load on the resources in it – we consider both congestion and cost-sharing games. We argue that the dynamic setting is the suitable setting for many applications in practice. We study the stability of dynamic resource allocation games, where the appropriate notion of stability is that of subgame perfect equilibrium, study the inefficiency incurred due to selfish behavior, and also study problems that are particular to the dynamic setting, like constraints on the order in which resources can be chosen or the problem of finding a scheduler that achieves stability."}],"date_updated":"2026-04-16T09:35:14Z"},{"page":"1253 - 1259","article_type":"original","_id":"1321","publisher":"Nature Publishing Group","day":"24","related_material":{"record":[{"relation":"dissertation_contains","id":"323","status":"public"}]},"citation":{"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.","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>","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>.","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.","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>","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.","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>."},"tmp":{"short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"call_identifier":"FP7","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes"}],"oa":1,"type":"journal_article","volume":18,"date_updated":"2026-04-24T22:30:05Z","language":[{"iso":"eng"}],"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."}],"publication_status":"published","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"}],"corr_author":"1","date_published":"2016-10-24T00:00:00Z","ec_funded":1,"year":"2016","month":"10","status":"public","date_created":"2018-12-11T11:51:21Z","isi":1,"intvolume":"        18","publist_id":"5949","author":[{"id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X","last_name":"Leithner","first_name":"Alexander F"},{"first_name":"Alexander","last_name":"Eichner","id":"4DFA52AE-F248-11E8-B48F-1D18A9856A87","full_name":"Eichner, Alexander"},{"first_name":"Jan","last_name":"Müller","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","full_name":"Müller, Jan"},{"last_name":"Reversat","first_name":"Anne","id":"35B76592-F248-11E8-B48F-1D18A9856A87","full_name":"Reversat, Anne","orcid":"0000-0003-0666-8928"},{"first_name":"Markus","last_name":"Brown","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Markus"},{"id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Jan","first_name":"Jan","last_name":"Schwarz"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin","first_name":"Jack"},{"last_name":"De Gorter","first_name":"David","full_name":"De Gorter, David"},{"last_name":"Schur","first_name":"Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian","orcid":"0000-0003-4790-8078"},{"full_name":"Bayerl, Jonathan","first_name":"Jonathan","last_name":"Bayerl"},{"last_name":"De Vries","first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","full_name":"De Vries, Ingrid"},{"last_name":"Wieser","first_name":"Stefan","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","full_name":"Wieser, Stefan","orcid":"0000-0002-2670-2217"},{"last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522"},{"full_name":"Lai, Frank","last_name":"Lai","first_name":"Frank"},{"last_name":"Moser","first_name":"Markus","full_name":"Moser, Markus"},{"first_name":"Dontscho","last_name":"Kerjaschki","full_name":"Kerjaschki, Dontscho"},{"full_name":"Rottner, Klemens","last_name":"Rottner","first_name":"Klemens"},{"first_name":"Victor","last_name":"Small","full_name":"Small, Victor"},{"full_name":"Stradal, Theresia","first_name":"Theresia","last_name":"Stradal"},{"last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"}],"file":[{"relation":"main_file","content_type":"application/pdf","creator":"dernst","file_id":"7844","checksum":"e1411cb7c99a2d9089c178a6abef25e7","file_size":4433280,"access_level":"open_access","file_name":"2018_NatureCell_Leithner.pdf","date_updated":"2020-07-14T12:44:43Z","date_created":"2020-05-14T16:33:46Z"}],"ddc":["570"],"file_date_updated":"2020-07-14T12:44:43Z","oa_version":"Submitted Version","doi":"10.1038/ncb3426","external_id":{"isi":["000387165600018"]},"scopus_import":"1","quality_controlled":"1","acknowledged_ssus":[{"_id":"SSU"}],"title":"Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes","article_processing_charge":"No","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.","publication":"Nature Cell Biology"},{"page":"1481 - 1494","related_material":{"record":[{"relation":"dissertation_contains","id":"395","status":"public"}]},"day":"01","publisher":"Cell Press","article_type":"original","_id":"1183","has_accepted_license":"1","issue":"6","citation":{"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>.","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.","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>","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.","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>.","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>","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."},"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"}],"language":[{"iso":"eng"}],"date_updated":"2026-04-24T22:30:54Z","type":"journal_article","volume":167,"oa":1,"project":[{"name":"Transmembrane Transporters in Health and Disease","grant_number":"F03523","_id":"25473368-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2016-12-01T00:00:00Z","pubrep_id":"771","department":[{"_id":"GaNo"}],"publication_status":"published","author":[{"id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","full_name":"Tarlungeanu, Dora-Clara","first_name":"Dora-Clara","last_name":"Tarlungeanu"},{"orcid":"0000-0002-7370-5293","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","full_name":"Deliu, Elena","first_name":"Elena","last_name":"Deliu"},{"orcid":"0000-0002-9033-9096","full_name":"Dotter, Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Dotter"},{"full_name":"Kara, Majdi","first_name":"Majdi","last_name":"Kara"},{"last_name":"Janiesch","first_name":"Philipp","full_name":"Janiesch, Philipp"},{"full_name":"Scalise, Mariafrancesca","first_name":"Mariafrancesca","last_name":"Scalise"},{"last_name":"Galluccio","first_name":"Michele","full_name":"Galluccio, Michele"},{"first_name":"Mateja","last_name":"Tesulov","full_name":"Tesulov, Mateja"},{"id":"3F4D1282-F248-11E8-B48F-1D18A9856A87","full_name":"Morelli, Emanuela","last_name":"Morelli","first_name":"Emanuela"},{"full_name":"Sönmez, Fatma","first_name":"Fatma","last_name":"Sönmez"},{"first_name":"Kaya","last_name":"Bilgüvar","full_name":"Bilgüvar, Kaya"},{"full_name":"Ohgaki, Ryuichi","last_name":"Ohgaki","first_name":"Ryuichi"},{"last_name":"Kanai","first_name":"Yoshikatsu","full_name":"Kanai, Yoshikatsu"},{"full_name":"Johansen, Anide","last_name":"Johansen","first_name":"Anide"},{"full_name":"Esharif, Seham","last_name":"Esharif","first_name":"Seham"},{"last_name":"Ben Omran","first_name":"Tawfeg","full_name":"Ben Omran, Tawfeg"},{"first_name":"Meral","last_name":"Topcu","full_name":"Topcu, Meral"},{"full_name":"Schlessinger, Avner","first_name":"Avner","last_name":"Schlessinger"},{"last_name":"Indiveri","first_name":"Cesare","full_name":"Indiveri, Cesare"},{"last_name":"Duncan","first_name":"Kent","full_name":"Duncan, Kent"},{"last_name":"Caglayan","first_name":"Ahmet","full_name":"Caglayan, Ahmet"},{"first_name":"Murat","last_name":"Günel","full_name":"Günel, Murat"},{"last_name":"Gleeson","first_name":"Joseph","full_name":"Gleeson, Joseph"},{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","last_name":"Novarino","first_name":"Gaia"}],"publist_id":"6170","intvolume":"       167","isi":1,"date_created":"2018-12-11T11:50:35Z","status":"public","month":"12","year":"2016","title":"Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder","quality_controlled":"1","scopus_import":"1","oa_version":"Submitted Version","doi":"10.1016/j.cell.2016.11.013","external_id":{"isi":["000389470500012"]},"file_date_updated":"2020-07-14T12:44:37Z","ddc":["576","616"],"file":[{"relation":"main_file","date_updated":"2020-07-14T12:44:37Z","date_created":"2018-12-12T10:13:44Z","access_level":"open_access","file_name":"IST-2017-771-v1+1_Tarlungeanu_et_al._Final_edited.pdf","checksum":"7fe01ab12a6610d3db421e0136db2f77","file_size":73907957,"creator":"system","content_type":"application/pdf","file_id":"5030"}],"publication":"Cell","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","article_processing_charge":"No"},{"page":"866 - 877","_id":"1100","day":"19","publisher":"Cell Press","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"961"},{"status":"public","id":"50","relation":"dissertation_contains"}]},"citation":{"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.","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>","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.","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>.","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.","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>","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>."},"issue":"3","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","project":[{"name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation","_id":"2529486C-B435-11E9-9278-68D0E5697425","grant_number":"T 560-B17","call_identifier":"FWF"},{"name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","call_identifier":"FWF","_id":"2527D5CC-B435-11E9-9278-68D0E5697425","grant_number":"I812-B12"},{"grant_number":"303564","_id":"25548C20-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Microbial Ion Channels for Synthetic Neurobiology"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"type":"journal_article","volume":16,"date_updated":"2026-04-24T22:31:01Z","language":[{"iso":"eng"}],"abstract":[{"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.","lang":"eng"}],"publication_status":"published","department":[{"_id":"CaHe"},{"_id":"HaJa"}],"pubrep_id":"754","date_published":"2016-07-19T00:00:00Z","ec_funded":1,"year":"2016","month":"07","status":"public","isi":1,"date_created":"2018-12-11T11:50:08Z","intvolume":"        16","publist_id":"6275","author":[{"full_name":"Sako, Keisuke","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6453-8075","last_name":"Sako","first_name":"Keisuke"},{"first_name":"Saurabh","last_name":"Pradhan","full_name":"Pradhan, Saurabh"},{"first_name":"Vanessa","last_name":"Barone","orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Álvaro","last_name":"Inglés Prieto","orcid":"0000-0002-5409-8571","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","full_name":"Inglés Prieto, Álvaro"},{"first_name":"Patrick","last_name":"Mueller","full_name":"Mueller, Patrick"},{"first_name":"Verena","last_name":"Ruprecht","orcid":"0000-0003-4088-8633","full_name":"Ruprecht, Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87"},{"id":"31C42484-F248-11E8-B48F-1D18A9856A87","full_name":"Capek, Daniel","orcid":"0000-0001-5199-9940","last_name":"Capek","first_name":"Daniel"},{"first_name":"Sanjeev","last_name":"Galande","full_name":"Galande, Sanjeev"},{"first_name":"Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"file":[{"content_type":"application/pdf","file_id":"4857","creator":"system","file_size":3921947,"file_name":"IST-2017-754-v1+1_1-s2.0-S2211124716307768-main.pdf","access_level":"open_access","date_updated":"2018-12-12T10:11:04Z","date_created":"2018-12-12T10:11:04Z","relation":"main_file"}],"ddc":["570","576"],"file_date_updated":"2018-12-12T10:11:04Z","oa_version":"Published Version","doi":"10.1016/j.celrep.2016.06.036","external_id":{"isi":["000380264200024"]},"scopus_import":"1","quality_controlled":"1","acknowledged_ssus":[{"_id":"SSU"}],"title":"Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation","article_processing_charge":"No","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.","publication":"Cell Reports"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"oa":1,"volume":"20-22","type":"conference","date_updated":"2026-04-24T22:31:03Z","language":[{"iso":"eng"}],"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"}],"citation":{"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.","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>.","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.","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>","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>."},"conference":{"name":"POPL: Principles of Programming Languages","end_date":"2016-01-22","location":"St. Petersburg, FL, USA","start_date":"2016-01-20"},"_id":"1437","publisher":"ACM","day":"11","related_material":{"record":[{"relation":"earlier_version","id":"5441","status":"public"},{"relation":"earlier_version","id":"5442","status":"public"},{"relation":"later_version","status":"public","id":"6009"},{"id":"821","status":"public","relation":"dissertation_contains"},{"id":"8934","status":"public","relation":"dissertation_contains"}]},"page":"733 - 747","external_id":{"arxiv":["1510.07565"]},"doi":"10.1145/2837614.2837624","oa_version":"Preprint","alternative_title":["POPL"],"scopus_import":1,"quality_controlled":"1","title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","year":"2016","month":"01","status":"public","arxiv":1,"date_created":"2018-12-11T11:52:01Z","publist_id":"5761","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Goharshady","first_name":"Amir","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir","orcid":"0000-0003-1702-6584"},{"first_name":"Rasmus","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","first_name":"Andreas"}],"publication_status":"published","department":[{"_id":"KrCh"}],"corr_author":"1","date_published":"2016-01-11T00:00:00Z","main_file_link":[{"url":"http://arxiv.org/abs/1510.07565","open_access":"1"}],"ec_funded":1},{"page":"3 - 22","day":"01","publisher":"Springer","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"_id":"1386","conference":{"start_date":"2016-07-17","end_date":"2016-07-23","name":"CAV: Computer Aided Verification","location":"Toronto, Canada"},"citation":{"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.","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>.","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>","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>."},"date_updated":"2026-04-24T22:31:04Z","language":[{"iso":"eng"}],"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"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"}],"oa":1,"volume":9779,"type":"conference","corr_author":"1","date_published":"2016-07-01T00:00:00Z","main_file_link":[{"url":"http://arxiv.org/abs/1604.07169","open_access":"1"}],"ec_funded":1,"publication_status":"published","department":[{"_id":"KrCh"}],"arxiv":1,"isi":1,"date_created":"2018-12-11T11:51:43Z","publist_id":"5824","intvolume":"      9779","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Fu","first_name":"Hongfei","full_name":"Fu, Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Goharshady","first_name":"Amir","full_name":"Goharshady, Amir","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584"}],"year":"2016","month":"07","status":"public","alternative_title":["LNCS"],"scopus_import":"1","quality_controlled":"1","title":"Termination analysis of probabilistic programs through Positivstellensatz's","oa_version":"Preprint","doi":"10.1007/978-3-319-41528-4_1","external_id":{"arxiv":["1604.07169"],"isi":["000387731200001"]},"article_processing_charge":"No"}]