[{"has_accepted_license":"1","external_id":{"isi":["000380858400001"]},"project":[{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"},{"call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"}],"publisher":"Nature Publishing Group","_id":"1358","ec_funded":1,"publication":"Nature Communications","day":"04","article_number":"12307","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"corr_author":"1","month":"08","file":[{"file_id":"4919","date_created":"2018-12-12T10:12:01Z","checksum":"fe3f3a1526d180b29fe691ab11435b78","file_size":861805,"file_name":"IST-2016-627-v1+1_ncomms12307.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:44:46Z","creator":"system"},{"file_id":"4920","checksum":"164864a1a675f3ad80e9917c27aba07f","file_size":1084703,"date_created":"2018-12-12T10:12:02Z","file_name":"IST-2016-627-v1+2_ncomms12307-s1.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:44:46Z","creator":"system"}],"volume":7,"type":"journal_article","publication_status":"published","status":"public","oa":1,"ddc":["576"],"scopus_import":"1","quality_controlled":"1","file_date_updated":"2020-07-14T12:44:46Z","pubrep_id":"627","doi":"10.1038/ncomms12307","intvolume":"         7","date_created":"2018-12-11T11:51:34Z","department":[{"_id":"GaTk"},{"_id":"NiBa"},{"_id":"CaGu"}],"abstract":[{"text":"Gene regulation relies on the specificity of transcription factor (TF)–DNA interactions. Limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate TF–DNA interactions or remains erroneously inactive. As each TF can have numerous interactions with noncognate cis-regulatory elements, crosstalk is inherently a global problem, yet has previously not been studied as such. We construct a theoretical framework to analyse the effects of global crosstalk on gene regulation. We find that crosstalk presents a significant challenge for organisms with low-specificity TFs, such as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting at equilibrium, including variants of cooperativity and combinatorial regulation. Our results suggest that crosstalk imposes a previously unexplored global constraint on the functioning and evolution of regulatory networks, which is qualitatively distinct from the known constraints that act at the level of individual gene regulatory elements.","lang":"eng"}],"date_published":"2016-08-04T00:00:00Z","article_processing_charge":"No","language":[{"iso":"eng"}],"publist_id":"5887","citation":{"chicago":"Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms12307\">https://doi.org/10.1038/ncomms12307</a>.","ista":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7, 12307.","short":"T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016).","mla":"Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” <i>Nature Communications</i>, vol. 7, 12307, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms12307\">10.1038/ncomms12307</a>.","apa":"Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., &#38; Tkačik, G. (2016). Intrinsic limits to gene regulation by global crosstalk. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms12307\">https://doi.org/10.1038/ncomms12307</a>","ama":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to gene regulation by global crosstalk. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms12307\">10.1038/ncomms12307</a>","ieee":"T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic limits to gene regulation by global crosstalk,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016."},"year":"2016","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Intrinsic limits to gene regulation by global crosstalk","author":[{"first_name":"Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","full_name":"Friedlander, Tamar","last_name":"Friedlander"},{"first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan","last_name":"Prizak"},{"first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","last_name":"Guet"},{"last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"},{"first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","last_name":"Tkacik"}],"related_material":{"record":[{"status":"public","id":"6071","relation":"dissertation_contains"}]},"isi":1,"date_updated":"2026-04-08T13:54:24Z"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Actin rings of power","author":[{"last_name":"Schwayer","full_name":"Schwayer, Cornelia","id":"3436488C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5130-2226","first_name":"Cornelia"},{"full_name":"Sikora, Mateusz K","last_name":"Sikora","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Slovakova, Jana","last_name":"Slovakova","first_name":"Jana","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kardos, Roland","last_name":"Kardos","first_name":"Roland","id":"4039350E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-04-08T13:55:28Z","isi":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"7186","status":"public"}]},"language":[{"iso":"eng"}],"publist_id":"6279","article_processing_charge":"No","year":"2016","citation":{"ieee":"C. Schwayer, M. K. Sikora, J. Slovakova, R. Kardos, and C.-P. J. Heisenberg, “Actin rings of power,” <i>Developmental Cell</i>, vol. 37, no. 6. Cell Press, pp. 493–506, 2016.","ama":"Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. Actin rings of power. <i>Developmental Cell</i>. 2016;37(6):493-506. doi:<a href=\"https://doi.org/10.1016/j.devcel.2016.05.024\">10.1016/j.devcel.2016.05.024</a>","apa":"Schwayer, C., Sikora, M. K., Slovakova, J., Kardos, R., &#38; Heisenberg, C.-P. J. (2016). Actin rings of power. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2016.05.024\">https://doi.org/10.1016/j.devcel.2016.05.024</a>","mla":"Schwayer, Cornelia, et al. “Actin Rings of Power.” <i>Developmental Cell</i>, vol. 37, no. 6, Cell Press, 2016, pp. 493–506, doi:<a href=\"https://doi.org/10.1016/j.devcel.2016.05.024\">10.1016/j.devcel.2016.05.024</a>.","short":"C. Schwayer, M.K. Sikora, J. Slovakova, R. Kardos, C.-P.J. Heisenberg, Developmental Cell 37 (2016) 493–506.","ista":"Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. 2016. Actin rings of power. Developmental Cell. 37(6), 493–506.","chicago":"Schwayer, Cornelia, Mateusz K Sikora, Jana Slovakova, Roland Kardos, and Carl-Philipp J Heisenberg. “Actin Rings of Power.” <i>Developmental Cell</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.devcel.2016.05.024\">https://doi.org/10.1016/j.devcel.2016.05.024</a>."},"department":[{"_id":"CaHe"}],"date_published":"2016-06-20T00:00:00Z","issue":"6","scopus_import":"1","quality_controlled":"1","intvolume":"        37","date_created":"2018-12-11T11:50:07Z","doi":"10.1016/j.devcel.2016.05.024","page":"493 - 506","status":"public","volume":37,"month":"06","type":"journal_article","publication_status":"published","publication":"Developmental Cell","day":"20","_id":"1096","oa_version":"None","external_id":{"isi":["000378204200005"]},"publisher":"Cell Press"},{"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:44:39Z","creator":"system","file_id":"5273","file_size":515000,"checksum":"34fa9ce681da845a1ba945ba3dc57867","date_created":"2018-12-12T10:17:20Z","file_name":"IST-2017-765-v1+1_838.pdf"}],"month":"06","volume":9696,"type":"conference","publication_status":"published","page":"285 - 303","acknowledgement":"Research  supported  by  the  European  Research  Council,  ERC  starting  grant (259668-PSPC) and ERC consolidator grant (682815 - TOCNeT).","ddc":["005","600"],"status":"public","oa":1,"has_accepted_license":"1","project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"259668","name":"Provable Security for Physical Cryptography"},{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000386324500016"]},"publisher":"Springer","ec_funded":1,"_id":"1229","day":"09","oa_version":"Submitted Version","article_processing_charge":"No","language":[{"iso":"eng"}],"publist_id":"6105","citation":{"apa":"Abusalah, H. M., Fuchsbauer, G., &#38; Pietrzak, K. Z. (2016). Offline witness encryption (Vol. 9696, pp. 285–303). Presented at the ACNS: Applied Cryptography and Network Security, Guildford, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-319-39555-5_16\">https://doi.org/10.1007/978-3-319-39555-5_16</a>","chicago":"Abusalah, Hamza M, Georg Fuchsbauer, and Krzysztof Z Pietrzak. “Offline Witness Encryption,” 9696:285–303. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-39555-5_16\">https://doi.org/10.1007/978-3-319-39555-5_16</a>.","ista":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. 2016. Offline witness encryption. ACNS: Applied Cryptography and Network Security, LNCS, vol. 9696, 285–303.","short":"H.M. Abusalah, G. Fuchsbauer, K.Z. Pietrzak, in:, Springer, 2016, pp. 285–303.","mla":"Abusalah, Hamza M., et al. <i>Offline Witness Encryption</i>. Vol. 9696, Springer, 2016, pp. 285–303, doi:<a href=\"https://doi.org/10.1007/978-3-319-39555-5_16\">10.1007/978-3-319-39555-5_16</a>.","ama":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. Offline witness encryption. In: Vol 9696. Springer; 2016:285-303. doi:<a href=\"https://doi.org/10.1007/978-3-319-39555-5_16\">10.1007/978-3-319-39555-5_16</a>","ieee":"H. M. Abusalah, G. Fuchsbauer, and K. Z. Pietrzak, “Offline witness encryption,” presented at the ACNS: Applied Cryptography and Network Security, Guildford, UK, 2016, vol. 9696, pp. 285–303."},"year":"2016","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Offline witness encryption","author":[{"last_name":"Abusalah","full_name":"Abusalah, Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87","first_name":"Hamza M"},{"last_name":"Fuchsbauer","full_name":"Fuchsbauer, Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg"},{"orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"83"}]},"date_updated":"2026-04-08T14:10:21Z","isi":1,"scopus_import":"1","quality_controlled":"1","file_date_updated":"2020-07-14T12:44:39Z","pubrep_id":"765","doi":"10.1007/978-3-319-39555-5_16","intvolume":"      9696","date_created":"2018-12-11T11:50:50Z","conference":{"start_date":"2016-06-19","name":"ACNS: Applied Cryptography and Network Security","location":"Guildford, UK","end_date":"2016-06-22"},"alternative_title":["LNCS"],"department":[{"_id":"KrPi"}],"abstract":[{"text":"Witness encryption (WE) was introduced by Garg et al. [GGSW13]. A WE scheme is defined for some NP language L and lets a sender encrypt messages relative to instances x. A ciphertext for x can be decrypted using w witnessing x ∈ L, but hides the message if x ∈ L. Garg et al. construct WE from multilinear maps and give another construction [GGH+13b] using indistinguishability obfuscation (iO) for circuits. Due to the reliance on such heavy tools, WE can cur- rently hardly be implemented on powerful hardware and will unlikely be realizable on constrained devices like smart cards any time soon. We construct a WE scheme where encryption is done by simply computing a Naor-Yung ciphertext (two CPA encryptions and a NIZK proof). To achieve this, our scheme has a setup phase, which outputs public parameters containing an obfuscated circuit (only required for decryption), two encryption keys and a common reference string (used for encryption). This setup need only be run once, and the parame- ters can be used for arbitrary many encryptions. Our scheme can also be turned into a functional WE scheme, where a message is encrypted w.r.t. a statement and a function f, and decryption with a witness w yields f (m, w). Our construction is inspired by the functional encryption scheme by Garg et al. and we prove (selective) security assuming iO and statistically simulation-sound NIZK. We give a construction of the latter in bilinear groups and combining it with ElGamal encryption, our ciphertexts are of size 1.3 kB at a 128-bit security level and can be computed on a smart card.","lang":"eng"}],"date_published":"2016-06-09T00:00:00Z"},{"month":"02","file":[{"creator":"system","content_type":"application/pdf","date_updated":"2020-07-14T12:44:41Z","access_level":"open_access","relation":"main_file","file_size":495176,"checksum":"3851cee49933ae13b1272e516f213e13","date_created":"2018-12-12T10:08:05Z","file_name":"IST-2017-764-v1+1_279.pdf","file_id":"4664"}],"volume":9610,"type":"conference","publication_status":"published","page":"413 - 428","acknowledgement":"Supported by the European Research Council, ERC Starting Grant (259668-PSPC).","oa":1,"status":"public","ddc":["005","600"],"has_accepted_license":"1","publisher":"Springer","project":[{"call_identifier":"FP7","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography"}],"external_id":{"isi":["000374102500024"]},"ec_funded":1,"_id":"1236","day":"02","oa_version":"Submitted Version","article_processing_charge":"No","publist_id":"6097","language":[{"iso":"eng"}],"citation":{"chicago":"Abusalah, Hamza M, Georg Fuchsbauer, and Krzysztof Z Pietrzak. “Constrained PRFs for Unbounded Inputs,” 9610:413–28. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-29485-8_24\">https://doi.org/10.1007/978-3-319-29485-8_24</a>.","ista":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. 2016. Constrained PRFs for unbounded inputs. CT-RSA: Topics in Cryptology, LNCS, vol. 9610, 413–428.","short":"H.M. Abusalah, G. Fuchsbauer, K.Z. Pietrzak, in:, Springer, 2016, pp. 413–428.","mla":"Abusalah, Hamza M., et al. <i>Constrained PRFs for Unbounded Inputs</i>. Vol. 9610, Springer, 2016, pp. 413–28, doi:<a href=\"https://doi.org/10.1007/978-3-319-29485-8_24\">10.1007/978-3-319-29485-8_24</a>.","apa":"Abusalah, H. M., Fuchsbauer, G., &#38; Pietrzak, K. Z. (2016). Constrained PRFs for unbounded inputs (Vol. 9610, pp. 413–428). Presented at the CT-RSA: Topics in Cryptology, San Francisco, CA, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-319-29485-8_24\">https://doi.org/10.1007/978-3-319-29485-8_24</a>","ama":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. Constrained PRFs for unbounded inputs. In: Vol 9610. Springer; 2016:413-428. doi:<a href=\"https://doi.org/10.1007/978-3-319-29485-8_24\">10.1007/978-3-319-29485-8_24</a>","ieee":"H. M. Abusalah, G. Fuchsbauer, and K. Z. Pietrzak, “Constrained PRFs for unbounded inputs,” presented at the CT-RSA: Topics in Cryptology, San Francisco, CA, USA, 2016, vol. 9610, pp. 413–428."},"year":"2016","title":"Constrained PRFs for unbounded inputs","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"last_name":"Abusalah","full_name":"Abusalah, Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87","first_name":"Hamza M"},{"last_name":"Fuchsbauer","full_name":"Fuchsbauer, Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg"},{"last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"83"}]},"isi":1,"date_updated":"2026-04-08T14:10:21Z","quality_controlled":"1","scopus_import":"1","pubrep_id":"764","file_date_updated":"2020-07-14T12:44:41Z","doi":"10.1007/978-3-319-29485-8_24","date_created":"2018-12-11T11:50:52Z","intvolume":"      9610","conference":{"end_date":"2016-03-04","location":"San Francisco, CA, USA","name":"CT-RSA: Topics in Cryptology","start_date":"2016-02-29"},"department":[{"_id":"KrPi"}],"alternative_title":["LNCS"],"abstract":[{"text":"A constrained pseudorandom function F: K × X → Y for a family T ⊆ 2X of subsets of X is a function where for any key k ∈ K and set S ∈ T one can efficiently compute a constrained key kS which allows to evaluate F (k, ·) on all inputs x ∈ S, while even given this key, the outputs on all inputs x ∉ S look random. At Asiacrypt’13 Boneh and Waters gave a construction which supports the most general set family so far. Its keys kc are defined for sets decided by boolean circuits C and enable evaluation of the PRF on any x ∈ X where C(x) = 1. In their construction the PRF input length and the size of the circuits C for which constrained keys can be computed must be fixed beforehand during key generation. We construct a constrained PRF that has an unbounded input length and whose constrained keys can be defined for any set recognized by a Turing machine. The only a priori bound we make is on the description size of the machines. We prove our construction secure assuming publiccoin differing-input obfuscation. As applications of our constrained PRF we build a broadcast encryption scheme where the number of potential receivers need not be fixed at setup (in particular, the length of the keys is independent of the number of parties) and the first identity-based non-interactive key exchange protocol with no bound on the number of parties that can agree on a shared key.","lang":"eng"}],"date_published":"2016-02-02T00:00:00Z"},{"doi":"10.1007/978-3-319-39555-5_24","intvolume":"      9696","date_created":"2018-12-11T11:50:52Z","quality_controlled":"1","scopus_import":"1","abstract":[{"lang":"eng","text":"A constrained pseudorandom function (CPRF) F: K×X → Y for a family T of subsets of χ is a function where for any key k ∈ K and set S ∈ T one can efficiently compute a short constrained key kS, which allows to evaluate F(k, ·) on all inputs x ∈ S, while the outputs on all inputs x /∈ S look random even given kS. Abusalah et al. recently constructed the first constrained PRF for inputs of arbitrary length whose sets S are decided by Turing machines. They use their CPRF to build broadcast encryption and the first ID-based non-interactive key exchange for an unbounded number of users. Their constrained keys are obfuscated circuits and are therefore large. In this work we drastically reduce the key size and define a constrained key for a Turing machine M as a short signature on M. For this, we introduce a new signature primitive with constrained signing keys that let one only sign certain messages, while forging a signature on others is hard even when knowing the coins for key generation."}],"date_published":"2016-01-01T00:00:00Z","conference":{"location":"Guildford, UK","name":"ACNS: Applied Cryptography and Network Security","end_date":"2016-06-22","start_date":"2016-06-19"},"alternative_title":["LNCS"],"department":[{"_id":"KrPi"}],"citation":{"mla":"Abusalah, Hamza M., and Georg Fuchsbauer. <i>Constrained PRFs for Unbounded Inputs with Short Keys</i>. Vol. 9696, Springer, 2016, pp. 445–63, doi:<a href=\"https://doi.org/10.1007/978-3-319-39555-5_24\">10.1007/978-3-319-39555-5_24</a>.","short":"H.M. Abusalah, G. Fuchsbauer, in:, Springer, 2016, pp. 445–463.","ista":"Abusalah HM, Fuchsbauer G. 2016. Constrained PRFs for unbounded inputs with short keys. ACNS: Applied Cryptography and Network Security, LNCS, vol. 9696, 445–463.","chicago":"Abusalah, Hamza M, and Georg Fuchsbauer. “Constrained PRFs for Unbounded Inputs with Short Keys,” 9696:445–63. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-39555-5_24\">https://doi.org/10.1007/978-3-319-39555-5_24</a>.","apa":"Abusalah, H. M., &#38; Fuchsbauer, G. (2016). Constrained PRFs for unbounded inputs with short keys (Vol. 9696, pp. 445–463). Presented at the ACNS: Applied Cryptography and Network Security, Guildford, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-319-39555-5_24\">https://doi.org/10.1007/978-3-319-39555-5_24</a>","ieee":"H. M. Abusalah and G. Fuchsbauer, “Constrained PRFs for unbounded inputs with short keys,” presented at the ACNS: Applied Cryptography and Network Security, Guildford, UK, 2016, vol. 9696, pp. 445–463.","ama":"Abusalah HM, Fuchsbauer G. Constrained PRFs for unbounded inputs with short keys. In: Vol 9696. Springer; 2016:445-463. doi:<a href=\"https://doi.org/10.1007/978-3-319-39555-5_24\">10.1007/978-3-319-39555-5_24</a>"},"year":"2016","article_processing_charge":"No","language":[{"iso":"eng"}],"publist_id":"6098","related_material":{"record":[{"id":"83","relation":"dissertation_contains","status":"public"}]},"date_updated":"2026-04-08T14:10:21Z","isi":1,"author":[{"last_name":"Abusalah","full_name":"Abusalah, Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87","first_name":"Hamza M"},{"full_name":"Fuchsbauer, Georg","last_name":"Fuchsbauer","first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Constrained PRFs for unbounded inputs with short keys","main_file_link":[{"url":"https://eprint.iacr.org/2016/279.pdf","open_access":"1"}],"project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","call_identifier":"FP7","name":"Provable Security for Physical Cryptography"},{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"external_id":{"isi":["000386324500024"]},"publisher":"Springer","oa_version":"Submitted Version","_id":"1235","ec_funded":1,"day":"01","publication_status":"published","type":"conference","month":"01","volume":9696,"oa":1,"status":"public","page":"445 - 463","acknowledgement":"H. Abusalah—Research supported by the European Research Council, ERC starting grant (259668-PSPC) and ERC consolidator grant (682815 - TOCNeT)."},{"title":"A phytochrome sensory domain permits receptor activation by red light","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"full_name":"Gschaider-Reichhart, Eva","last_name":"Gschaider-Reichhart","first_name":"Eva","orcid":"0000-0002-7218-7738","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Álvaro","orcid":"0000-0002-5409-8571","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","full_name":"Inglés Prieto, Álvaro","last_name":"Inglés Prieto"},{"last_name":"Tichy","full_name":"Tichy, Alexandra-Madelaine","id":"29D8BB2C-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra-Madelaine"},{"full_name":"Mckenzie, Catherine","last_name":"Mckenzie","first_name":"Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","first_name":"Harald L","last_name":"Janovjak","full_name":"Janovjak, Harald L"}],"date_updated":"2026-04-08T14:11:53Z","isi":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"418","status":"public"}]},"language":[{"iso":"eng"}],"publist_id":"5755","article_processing_charge":"No","year":"2016","citation":{"chicago":"Gschaider-Reichhart, Eva, Álvaro Inglés Prieto, Alexandra-Madelaine Tichy, Catherine Mckenzie, and Harald L Janovjak. “A Phytochrome Sensory Domain Permits Receptor Activation by Red Light.” <i>Angewandte Chemie - International Edition</i>. Wiley, 2016. <a href=\"https://doi.org/10.1002/anie.201601736\">https://doi.org/10.1002/anie.201601736</a>.","ista":"Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL. 2016. A phytochrome sensory domain permits receptor activation by red light. Angewandte Chemie - International Edition. 55(21), 6339–6342.","short":"E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, H.L. Janovjak, Angewandte Chemie - International Edition 55 (2016) 6339–6342.","mla":"Gschaider-Reichhart, Eva, et al. “A Phytochrome Sensory Domain Permits Receptor Activation by Red Light.” <i>Angewandte Chemie - International Edition</i>, vol. 55, no. 21, Wiley, 2016, pp. 6339–42, doi:<a href=\"https://doi.org/10.1002/anie.201601736\">10.1002/anie.201601736</a>.","apa":"Gschaider-Reichhart, E., Inglés Prieto, Á., Tichy, A.-M., Mckenzie, C., &#38; Janovjak, H. L. (2016). A phytochrome sensory domain permits receptor activation by red light. <i>Angewandte Chemie - International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.201601736\">https://doi.org/10.1002/anie.201601736</a>","ama":"Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL. A phytochrome sensory domain permits receptor activation by red light. <i>Angewandte Chemie - International Edition</i>. 2016;55(21):6339-6342. doi:<a href=\"https://doi.org/10.1002/anie.201601736\">10.1002/anie.201601736</a>","ieee":"E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, and H. L. Janovjak, “A phytochrome sensory domain permits receptor activation by red light,” <i>Angewandte Chemie - International Edition</i>, vol. 55, no. 21. Wiley, pp. 6339–6342, 2016."},"department":[{"_id":"HaJa"}],"date_published":"2016-05-17T00:00:00Z","abstract":[{"text":"Optogenetics and photopharmacology enable the spatio-temporal control of cell and animal behavior by light. Although red light offers deep-tissue penetration and minimal phototoxicity, very few red-light-sensitive optogenetic methods are currently available. We have now developed a red-light-induced homodimerization domain. We first showed that an optimized sensory domain of the cyanobacterial phytochrome 1 can be expressed robustly and without cytotoxicity in human cells. We then applied this domain to induce the dimerization of two receptor tyrosine kinases—the fibroblast growth factor receptor 1 and the neurotrophin receptor trkB. This new optogenetic method was then used to activate the MAPK/ERK pathway non-invasively in mammalian tissue and in multicolor cell-signaling experiments. The light-controlled dimerizer and red-light-activated receptor tyrosine kinases will prove useful to regulate a variety of cellular processes with light. Go deep with red: The sensory domain (S) of the cyanobacterial phytochrome 1 (CPH1) was repurposed to induce the homodimerization of proteins in living cells by red light. By using this domain, light-activated protein kinases were engineered that can be activated orthogonally from many fluorescent proteins and through mammalian tissue. Pr/Pfr=red-/far-red-absorbing state of CPH1.","lang":"eng"}],"file_date_updated":"2020-07-14T12:44:55Z","pubrep_id":"840","issue":"21","quality_controlled":"1","scopus_import":"1","intvolume":"        55","date_created":"2018-12-11T11:52:02Z","doi":"10.1002/anie.201601736","acknowledgement":"A.I.-P. was supported by a Ramon Areces fellowship, and E.R. by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF): W1232) and a FemTech fellowship (Austrian Research Promotion Agency: 3580812).","page":"6339 - 6342","status":"public","oa":1,"ddc":["571","576"],"volume":55,"corr_author":"1","month":"05","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:44:55Z","creator":"system","relation":"main_file","access_level":"open_access","date_created":"2018-12-12T10:17:03Z","file_size":1268662,"checksum":"26da07960e57ac4750b54179197ce57f","file_name":"IST-2017-840-v1+1_reichhart.pdf","file_id":"5255"}],"publication_status":"published","type":"journal_article","publication":"Angewandte Chemie - International Edition","day":"17","_id":"1441","ec_funded":1,"oa_version":"Submitted Version","has_accepted_license":"1","project":[{"name":"Microbial Ion Channels for Synthetic Neurobiology","grant_number":"303564","call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"W1232-B24","_id":"255A6082-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets"}],"external_id":{"isi":["000377918400039"]},"publisher":"Wiley"},{"publication_status":"published","type":"conference","volume":35,"corr_author":"1","file":[{"file_id":"5121","file_size":12453704,"date_created":"2018-12-12T10:15:04Z","checksum":"943712d9c9dc8bb5048d4adc561d7d38","file_name":"IST-2016-632-v1+2_a104-hahn.pdf","access_level":"open_access","relation":"main_file","creator":"system","content_type":"application/pdf","date_updated":"2020-07-14T12:44:46Z"}],"month":"07","oa":1,"ddc":["000"],"status":"public","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"638176","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"external_id":{"isi":["000380112400074"]},"publisher":"ACM","has_accepted_license":"1","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_number":"104","day":"01","ec_funded":1,"_id":"1362","year":"2016","citation":{"apa":"Hahn, D., &#38; Wojtan, C. (2016). Fast approximations for boundary element based brittle fracture simulation (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2897824.2925902\">https://doi.org/10.1145/2897824.2925902</a>","mla":"Hahn, David, and Chris Wojtan. <i>Fast Approximations for Boundary Element Based Brittle Fracture Simulation</i>. Vol. 35, no. 4, 104, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2897824.2925902\">10.1145/2897824.2925902</a>.","short":"D. Hahn, C. Wojtan, in:, ACM, 2016.","chicago":"Hahn, David, and Chris Wojtan. “Fast Approximations for Boundary Element Based Brittle Fracture Simulation,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2897824.2925902\">https://doi.org/10.1145/2897824.2925902</a>.","ista":"Hahn D, Wojtan C. 2016. Fast approximations for boundary element based brittle fracture simulation. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 104.","ieee":"D. Hahn and C. Wojtan, “Fast approximations for boundary element based brittle fracture simulation,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4.","ama":"Hahn D, Wojtan C. Fast approximations for boundary element based brittle fracture simulation. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2897824.2925902\">10.1145/2897824.2925902</a>"},"language":[{"iso":"eng"}],"publist_id":"5880","article_processing_charge":"No","date_updated":"2026-04-08T14:20:15Z","isi":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"839","status":"public"}]},"title":"Fast approximations for boundary element based brittle fracture simulation","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"full_name":"Hahn, David","last_name":"Hahn","first_name":"David","id":"357A6A66-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wojtan, Christopher J","last_name":"Wojtan","first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"        35","date_created":"2018-12-11T11:51:35Z","doi":"10.1145/2897824.2925902","file_date_updated":"2020-07-14T12:44:46Z","pubrep_id":"632","issue":"4","scopus_import":"1","quality_controlled":"1","date_published":"2016-07-01T00:00:00Z","abstract":[{"text":"We present a boundary element based method for fast simulation of brittle fracture. By introducing simplifying assumptions that allow us to quickly estimate stress intensities and opening displacements during crack propagation, we build a fracture algorithm where the cost of each time step scales linearly with the length of the crackfront. The transition from a full boundary element method to our faster variant is possible at the beginning of any time step. This allows us to build a hybrid method, which uses the expensive but more accurate BEM while the number of degrees of freedom is low, and uses the fast method once that number exceeds a given threshold as the crack geometry becomes more complicated. Furthermore, we integrate this fracture simulation with a standard rigid-body solver. Our rigid-body coupling solves a Neumann boundary value problem by carefully separating translational, rotational and deformational components of the collision forces and then applying a Tikhonov regularizer to the resulting linear system. We show that our method produces physically reasonable results in standard test cases and is capable of dealing with complex scenes faster than previous finite- or boundary element approaches.","lang":"eng"}],"alternative_title":["ACM Transactions on Graphics"],"department":[{"_id":"ChWo"}],"conference":{"end_date":"2016-07-28","location":"Anaheim, CA, USA","name":"ACM SIGGRAPH","start_date":"2016-07-24"}},{"day":"08","publication":"Current Biology","_id":"1243","oa_version":"None","publisher":"Cell Press","external_id":{"isi":["000369502900034"]},"project":[{"name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level","_id":"251D65D8-B435-11E9-9278-68D0E5697425","grant_number":"24210"}],"acknowledgement":"This work was funded by an HFSP Young Investigators’ grant. M.P. is a recipient of a DOC Fellowship of the Austrian Academy of Science at the Institute of Science and Technology Austria. R.O. and Y.W. were supported by the Platform for Dynamic Approaches to Living System from MEXT, Japan. We wish to thank I. Kobayashi for providing us with the EcoRI and EcoRV plasmids, and A. Campbell for providing us with the λ vir phage. We thank D. Siekhaus and C. Uhler and members of the C.C.G. and J.P. Bollback laboratories for in-depth discussions. We thank B. Stern for comments on an earlier version of the manuscript. We especially thank B.R. Levin for advice and comments, and the anonymous reviewers for significantly improving the manuscript.","page":"404 - 409","status":"public","volume":26,"month":"02","publication_status":"published","type":"journal_article","department":[{"_id":"CaGu"}],"date_published":"2016-02-08T00:00:00Z","abstract":[{"lang":"eng","text":"Restriction-modification (RM) systems represent a minimal and ubiquitous biological system of self/non-self discrimination in prokaryotes [1], which protects hosts from exogenous DNA [2]. The mechanism is based on the balance between methyltransferase (M) and cognate restriction endonuclease (R). M tags endogenous DNA as self by methylating short specific DNA sequences called restriction sites, whereas R recognizes unmethylated restriction sites as non-self and introduces a double-stranded DNA break [3]. Restriction sites are significantly underrepresented in prokaryotic genomes [4-7], suggesting that the discrimination mechanism is imperfect and occasionally leads to autoimmunity due to self-DNA cleavage (self-restriction) [8]. Furthermore, RM systems can promote DNA recombination [9] and contribute to genetic variation in microbial populations, thus facilitating adaptive evolution [10]. However, cleavage of self-DNA by RM systems as elements shaping prokaryotic genomes has not been directly detected, and its cause, frequency, and outcome are unknown. We quantify self-restriction caused by two RM systems of Escherichia coli and find that, in agreement with levels of restriction site avoidance, EcoRI, but not EcoRV, cleaves self-DNA at a measurable rate. Self-restriction is a stochastic process, which temporarily induces the SOS response, and is followed by DNA repair, maintaining cell viability. We find that RM systems with higher restriction efficiency against bacteriophage infections exhibit a higher rate of self-restriction, and that this rate can be further increased by stochastic imbalance between R and M. Our results identify molecular noise in RM systems as a factor shaping prokaryotic genomes."}],"issue":"3","scopus_import":"1","quality_controlled":"1","date_created":"2018-12-11T11:50:54Z","intvolume":"        26","doi":"10.1016/j.cub.2015.12.041","author":[{"orcid":"0000-0001-7460-7479","first_name":"Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","full_name":"Pleska, Maros","last_name":"Pleska"},{"full_name":"Qian, Long","last_name":"Qian","first_name":"Long"},{"first_name":"Reiko","full_name":"Okura, Reiko","last_name":"Okura"},{"orcid":"0000-0001-5396-4346","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","last_name":"Bergmiller"},{"first_name":"Yuichi","full_name":"Wakamoto, Yuichi","last_name":"Wakamoto"},{"first_name":"Edo","last_name":"Kussell","full_name":"Kussell, Edo"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C"}],"title":"Bacterial autoimmunity due to a restriction-modification system","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"date_updated":"2026-04-08T14:19:43Z","related_material":{"record":[{"relation":"dissertation_contains","id":"202","status":"public"}]},"publist_id":"6087","language":[{"iso":"eng"}],"article_processing_charge":"No","year":"2016","citation":{"ieee":"M. Pleska <i>et al.</i>, “Bacterial autoimmunity due to a restriction-modification system,” <i>Current Biology</i>, vol. 26, no. 3. Cell Press, pp. 404–409, 2016.","ama":"Pleska M, Qian L, Okura R, et al. Bacterial autoimmunity due to a restriction-modification system. <i>Current Biology</i>. 2016;26(3):404-409. doi:<a href=\"https://doi.org/10.1016/j.cub.2015.12.041\">10.1016/j.cub.2015.12.041</a>","mla":"Pleska, Maros, et al. “Bacterial Autoimmunity Due to a Restriction-Modification System.” <i>Current Biology</i>, vol. 26, no. 3, Cell Press, 2016, pp. 404–09, doi:<a href=\"https://doi.org/10.1016/j.cub.2015.12.041\">10.1016/j.cub.2015.12.041</a>.","ista":"Pleska M, Qian L, Okura R, Bergmiller T, Wakamoto Y, Kussell E, Guet CC. 2016. Bacterial autoimmunity due to a restriction-modification system. Current Biology. 26(3), 404–409.","chicago":"Pleska, Maros, Long Qian, Reiko Okura, Tobias Bergmiller, Yuichi Wakamoto, Edo Kussell, and Calin C Guet. “Bacterial Autoimmunity Due to a Restriction-Modification System.” <i>Current Biology</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.cub.2015.12.041\">https://doi.org/10.1016/j.cub.2015.12.041</a>.","short":"M. Pleska, L. Qian, R. Okura, T. Bergmiller, Y. Wakamoto, E. Kussell, C.C. Guet, Current Biology 26 (2016) 404–409.","apa":"Pleska, M., Qian, L., Okura, R., Bergmiller, T., Wakamoto, Y., Kussell, E., &#38; Guet, C. C. (2016). Bacterial autoimmunity due to a restriction-modification system. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2015.12.041\">https://doi.org/10.1016/j.cub.2015.12.041</a>"}},{"scopus_import":"1","quality_controlled":"1","pubrep_id":"777","file_date_updated":"2018-12-12T10:14:31Z","doi":"10.4230/LIPIcs.ESA.2016.28","date_created":"2018-12-11T11:49:59Z","intvolume":"        57","conference":{"start_date":"2016-08-22","end_date":"2016-08-24","location":"Aarhus, Denmark","name":"ESA: European Symposium on Algorithms"},"department":[{"_id":"KrCh"}],"alternative_title":["LIPIcs"],"abstract":[{"text":"We consider data-structures for answering reachability and distance queries on constant-treewidth graphs with n nodes, on the standard RAM computational model with wordsize W=Theta(log n). Our first contribution is a data-structure that after O(n) preprocessing time, allows (1) pair reachability queries in O(1) time; and (2) single-source reachability queries in O(n/log n) time. This is (asymptotically) optimal and is faster than DFS/BFS when answering more than a constant number of single-source queries. The data-structure uses at all times O(n) space. Our second contribution is a space-time tradeoff data-structure for distance queries. For any epsilon in [1/2,1], we provide a data-structure with polynomial preprocessing time that allows pair queries in O(n^{1-\\epsilon} alpha(n)) time, where alpha is the inverse of the Ackermann function, and at all times uses O(n^epsilon) space. The input graph G is not considered in the space complexity. ","lang":"eng"}],"date_published":"2016-08-01T00:00:00Z","article_processing_charge":"No","publist_id":"6312","language":[{"iso":"eng"}],"citation":{"apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2016). Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs (Vol. 57). Presented at the ESA: European Symposium on Algorithms, Aarhus, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">https://doi.org/10.4230/LIPIcs.ESA.2016.28</a>","mla":"Chatterjee, Krishnendu, et al. <i>Optimal Reachability and a Space Time Tradeoff for Distance Queries in Constant Treewidth Graphs</i>. Vol. 57, 28, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">10.4230/LIPIcs.ESA.2016.28</a>.","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2016. Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs. ESA: European Symposium on Algorithms, LIPIcs, vol. 57, 28.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Optimal Reachability and a Space Time Tradeoff for Distance Queries in Constant Treewidth Graphs,” Vol. 57. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">https://doi.org/10.4230/LIPIcs.ESA.2016.28</a>.","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs,” presented at the ESA: European Symposium on Algorithms, Aarhus, Denmark, 2016, vol. 57.","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs. In: Vol 57. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">10.4230/LIPIcs.ESA.2016.28</a>"},"year":"2016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8943-0722","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"821","status":"public"}]},"date_updated":"2026-04-08T14:22:16Z","has_accepted_license":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"ec_funded":1,"_id":"1071","article_number":"28","day":"01","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","file":[{"file_id":"5084","date_created":"2018-12-12T10:14:31Z","file_size":579225,"file_name":"IST-2017-777-v1+1_LIPIcs-ESA-2016-28.pdf","access_level":"open_access","relation":"main_file","creator":"system","content_type":"application/pdf","date_updated":"2018-12-12T10:14:31Z"}],"month":"08","volume":57,"type":"conference","publication_status":"published","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE) and ERC Start grant (279307: Graph Games).","ddc":["004","006"],"status":"public","oa":1},{"publisher":"Institute of Science and Technology Austria","date_created":"2018-12-11T11:51:47Z","day":"01","alternative_title":["ISTA Thesis"],"department":[{"_id":"KrCh"}],"_id":"1397","oa_version":"None","date_published":"2016-02-01T00:00:00Z","abstract":[{"text":"We study partially observable Markov decision processes (POMDPs) with objectives used in verification and artificial intelligence. The qualitative analysis problem given a POMDP and an objective asks whether there is a strategy (policy) to ensure that the objective is satisfied almost surely (with probability 1), resp. with positive probability (with probability greater than 0). For POMDPs with limit-average payoff, where a reward value in the interval [0,1] is associated to every transition, and the payoff of an infinite path is the long-run average of the rewards, we consider two types of path constraints: (i) a quantitative limit-average constraint defines the set of paths where the payoff is at least a given threshold L1 = 1. Our main results for qualitative limit-average constraint under almost-sure winning are as follows: (i) the problem of deciding the existence of a finite-memory controller is EXPTIME-complete; and (ii) the problem of deciding the existence of an infinite-memory controller is undecidable. For quantitative limit-average constraints we show that the problem of deciding the existence of a finite-memory controller is undecidable. We present a prototype implementation of our EXPTIME algorithm. For POMDPs with w-regular conditions specified as parity objectives, while the qualitative analysis problems are known to be undecidable even for very special case of parity objectives, we establish decidability (with optimal complexity) of the qualitative analysis problems for POMDPs with parity objectives under finite-memory strategies. We establish optimal (exponential) memory bounds and EXPTIME-completeness of the qualitative analysis problems under finite-memory strategies for POMDPs with parity objectives. Based on our theoretical algorithms we also present a practical approach, where we design heuristics to deal with the exponential complexity, and have applied our implementation on a number of well-known POMDP examples for robotics applications. For POMDPs with a set of target states and an integer cost associated with every transition, we study the optimization objective that asks to minimize the expected total cost of reaching a state in the target set, while ensuring that the target set is reached almost surely. We show that for general integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost, both double and exponential in the POMDP state space size; (ii) we show that the problem of approximating the optimal cost is decidable and present approximation algorithms that extend existing algorithms for POMDPs with finite-horizon objectives. We show experimentally that it performs well in many examples of interest. We study more deeply the problem of almost-sure reachability, where  given a set of target states, the question is to decide whether there is a strategy to ensure that the target set is reached almost surely. While in general the problem EXPTIME-complete, in many practical cases strategies with a small amount of memory suffice. Moreover, the existing solution to the problem is explicit, which first requires to construct explicitly an exponential reduction to a belief-support MDP. We first study the existence of observation-stationary strategies, which is NP-complete, and then small-memory strategies. We present a symbolic algorithm by an efficient encoding to SAT and using a SAT solver for the problem. We report experimental results demonstrating the scalability of our symbolic (SAT-based) approach. Decentralized POMDPs (DEC-POMDPs) extend POMDPs to a multi-agent setting, where several agents operate in an uncertain environment independently to achieve a joint objective. In this work we consider Goal DEC-POMDPs, where given a set of target states, the objective is to ensure that the target set is reached with minimal cost. We consider the indefinite-horizon (infinite-horizon with either discounted-sum, or undiscounted-sum, where absorbing goal states have zero-cost) problem. We present a new and novel method to solve the problem that extends methods for finite-horizon DEC-POMDPs and the real-time dynamic programming approach for POMDPs. We present experimental results on several examples, and show that our approach presents promising results. In the end we present a short summary of a few other results related to verification of MDPs and POMDPs.","lang":"eng"}],"language":[{"iso":"eng"}],"publist_id":"5810","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","corr_author":"1","month":"02","year":"2016","supervisor":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"}],"type":"dissertation","citation":{"apa":"Chmelik, M. (2016). <i>Algorithms for partially observable markov decision processes</i>. Institute of Science and Technology Austria.","chicago":"Chmelik, Martin. “Algorithms for Partially Observable Markov Decision Processes.” Institute of Science and Technology Austria, 2016.","short":"M. Chmelik, Algorithms for Partially Observable Markov Decision Processes, Institute of Science and Technology Austria, 2016.","ista":"Chmelik M. 2016. Algorithms for partially observable markov decision processes. Institute of Science and Technology Austria.","mla":"Chmelik, Martin. <i>Algorithms for Partially Observable Markov Decision Processes</i>. Institute of Science and Technology Austria, 2016.","ama":"Chmelik M. Algorithms for partially observable markov decision processes. 2016.","ieee":"M. Chmelik, “Algorithms for partially observable markov decision processes,” Institute of Science and Technology Austria, 2016."},"publication_status":"published","title":"Algorithms for partially observable markov decision processes","author":[{"last_name":"Chmelik","full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","page":"232","OA_place":"publisher","date_updated":"2026-04-08T14:23:19Z","degree_awarded":"PhD","status":"public"},{"oa_version":"Published Version","_id":"1129","day":"01","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","status":"public","oa":1,"ddc":["570"],"page":"178","acknowledgement":"First, I would like to thank Michael Sixt for being a great supervisor, mentor and\r\nscientist. I highly appreciate his guidance and continued support. Furthermore, I\r\nam very grateful that he gave me the exceptional opportunity to pursue many\r\nideas of which some managed to be included in this thesis.\r\nI owe sincere thanks to the members of my PhD thesis committee, Daria\r\nSiekhaus, Daniel Legler and Harald Janovjak. Especially I would like to thank\r\nDaria for her advice and encouragement during our regular progress meetings.\r\nI also want to thank the team and fellows of the Boehringer Ingelheim Fond\r\n(BIF) PhD Fellowship for amazing and inspiring meetings and the BIF for\r\nfinancial support.\r\nImportant factors for the success of this thesis were the warm, creative\r\nand helpful atmosphere as well as the team spirit of the whole Sixt Lab.\r\nTherefore I would like to thank my current and former colleagues Frank Assen,\r\nMarkus Brown, Ingrid de Vries, Michelle Duggan, Alexander Eichner, Miroslav\r\nHons, Eva Kiermaier, Aglaja Kopf, Alexander Leithner, Christine Moussion, Jan\r\nMüller, Maria Nemethova, Jörg Renkawitz, Anne Reversat, Kari Vaahtomeri,\r\nMichele Weber and Stefan Wieser. We had an amazing time with many\r\nlegendary evenings and events. Along these lines I want to thank the in vitro\r\ncrew of the lab, Jörg, Anne and Alex, for lots of ideas and productive\r\ndiscussions. I am sure, some day we will reveal the secret of the ‘splodge’.\r\nI want to thank the members of the Heisenberg Lab for a great time and\r\nthrilling kicker matches. In this regard I especially want to thank Maurizio\r\n‘Gnocci’ Monti, Gabriel Krens, Alex Eichner, Martin Behrndt, Vanessa Barone,Philipp Schmalhorst, Michael Smutny, Daniel Capek, Anne Reversat, Eva\r\nKiermaier, Frank Assen and Jan Müller for wonderful after-lunch matches.\r\nI would not have been able to analyze the thousands of cell trajectories\r\nand probably hundreds of thousands of mouse clicks without the productive\r\ncollaboration with Veronika Bierbaum and Tobias Bollenbach. Thanks Vroni for\r\ncountless meetings, discussions and graphs and of course for proofreading and\r\nadvice for this thesis. For proofreading I also want to thank Evi, Jörg, Jack and\r\nAnne.\r\nI would like to acknowledge Matthias Mehling for a very productive\r\ncollaboration and for introducing me into the wild world of microfluidics. Jack\r\nMerrin, for countless wafers, PDMS coated coverslips and help with anything\r\nmicro-fabrication related. And Maria Nemethova for establishing the ‘click’\r\npatterning approach with me. Without her it still would be just one of the ideas…\r\nMany thanks to Ekaterina Papusheva, Robert Hauschild, Doreen Milius\r\nand Nasser Darwish from the Bioimaging Facility as well as the Preclinical and\r\nthe Life Science facilities of IST Austria for excellent technical support. At this\r\npoint I especially want to thank Robert for countless image analyses and\r\ntechnical ideas. Always interested and creative he played an essential role in all\r\nof my projects.\r\nAdditionally I want to thank Ingrid and Gabby for welcoming me warmly\r\nwhen I first started at IST, for scientific and especially mental support in all\r\nthose years, countless coffee sessions and Heurigen evenings. #BioimagingFacility #LifeScienceFacility #PreClinicalFacility","publication_status":"published","type":"dissertation","month":"07","file":[{"file_id":"6813","checksum":"e3cd6b28f9c5cccb8891855565a2dade","date_created":"2019-08-13T10:55:35Z","file_size":32044069,"file_name":"Thesis_JSchwarz_final.pdf","access_level":"closed","relation":"main_file","creator":"dernst","content_type":"application/pdf","date_updated":"2019-08-13T10:55:35Z"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2021-02-22T11:43:14Z","creator":"dernst","file_id":"9181","success":1,"file_size":8396717,"checksum":"c3dbe219acf87eed2f46d21d5cca00de","date_created":"2021-02-22T11:43:14Z","file_name":"2016_Thesis_JSchwarz.pdf"}],"corr_author":"1","abstract":[{"text":"Directed cell migration is a hallmark feature, present in almost all multi-cellular\r\norganisms. Despite its importance, basic questions regarding force transduction\r\nor directional sensing are still heavily investigated. Directed migration of cells\r\nguided by immobilized guidance cues - haptotaxis - occurs in key-processes,\r\nsuch as embryonic development and immunity (Middleton et al., 1997; Nguyen\r\net al., 2000; Thiery, 1984; Weber et al., 2013). Immobilized guidance cues\r\ncomprise adhesive ligands, such as collagen and fibronectin (Barczyk et al.,\r\n2009), or chemokines - the main guidance cues for migratory leukocytes\r\n(Middleton et al., 1997; Weber et al., 2013). While adhesive ligands serve as\r\nattachment sites guiding cell migration (Carter, 1965), chemokines instruct\r\nhaptotactic migration by inducing adhesion to adhesive ligands and directional\r\nguidance (Rot and Andrian, 2004; Schumann et al., 2010). Quantitative analysis\r\nof the cellular response to immobilized guidance cues requires in vitro assays\r\nthat foster cell migration, offer accurate control of the immobilized cues on a\r\nsubcellular scale and in the ideal case closely reproduce in vivo conditions. The\r\nexploration of haptotactic cell migration through design and employment of such\r\nassays represents the main focus of this work.\r\nDendritic cells (DCs) are leukocytes, which after encountering danger\r\nsignals such as pathogens in peripheral organs instruct naïve T-cells and\r\nconsequently the adaptive immune response in the lymph node (Mellman and\r\nSteinman, 2001). To reach the lymph node from the periphery, DCs follow\r\nhaptotactic gradients of the chemokine CCL21 towards lymphatic vessels\r\n(Weber et al., 2013). Questions about how DCs interpret haptotactic CCL21\r\ngradients have not yet been addressed. The main reason for this is the lack of\r\nan assay that offers diverse haptotactic environments, hence allowing the study\r\nof DC migration as a response to different signals of immobilized guidance cue.\r\nIn this work, we developed an in vitro assay that enables us to\r\nquantitatively assess DC haptotaxis, by combining precisely controllable\r\nchemokine photo-patterning with physically confining migration conditions. With this tool at hand, we studied the influence of CCL21 gradient properties and\r\nconcentration on DC haptotaxis. We found that haptotactic gradient sensing\r\ndepends on the absolute CCL21 concentration in combination with the local\r\nsteepness of the gradient. Our analysis suggests that the directionality of\r\nmigrating DCs is governed by the signal-to-noise ratio of CCL21 binding to its\r\nreceptor CCR7. Moreover, the haptotactic CCL21 gradient formed in vivo\r\nprovides an optimal shape for DCs to recognize haptotactic guidance cue.\r\nBy reconstitution of the CCL21 gradient in vitro we were also able to\r\nstudy the influence of CCR7 signal termination on DC haptotaxis. To this end,\r\nwe used DCs lacking the G-protein coupled receptor kinase GRK6, which is\r\nresponsible for CCL21 induced CCR7 receptor phosphorylation and\r\ndesensitization (Zidar et al., 2009). We found that CCR7 desensitization by\r\nGRK6 is crucial for maintenance of haptotactic CCL21 gradient sensing in vitro\r\nand confirm those observations in vivo.\r\nIn the context of the organism, immobilized haptotactic guidance cues\r\noften coincide and compete with soluble chemotactic guidance cues. During\r\nwound healing, fibroblasts are exposed and influenced by adhesive cues and\r\nsoluble factors at the same time (Wu et al., 2012; Wynn, 2008). Similarly,\r\nmigrating DCs are exposed to both, soluble chemokines (CCL19 and truncated\r\nCCL21) inducing chemotactic behavior as well as the immobilized CCL21. To\r\nquantitatively assess these complex coinciding immobilized and soluble\r\nguidance cues, we implemented our chemokine photo-patterning technique in a\r\nmicrofluidic system allowing for chemotactic gradient generation. To validate\r\nthe assay, we observed DC migration in competing CCL19/CCL21\r\nenvironments.\r\nAdhesiveness guided haptotaxis has been studied intensively over the\r\nlast century. However, quantitative studies leading to conceptual models are\r\nlargely missing, again due to the lack of a precisely controllable in vitro assay. A\r\nrequirement for such an in vitro assay is that it must prevent any uncontrolled\r\ncell adhesion. This can be accomplished by stable passivation of the surface. In\r\naddition, controlled adhesion must be sustainable, quantifiable and dose\r\ndependent in order to create homogenous gradients. Therefore, we developed a novel covalent photo-patterning technique satisfying all these needs. In\r\ncombination with a sustainable poly-vinyl alcohol (PVA) surface coating we\r\nwere able to generate gradients of adhesive cue to direct cell migration. This\r\napproach allowed us to characterize the haptotactic migratory behavior of\r\nzebrafish keratocytes in vitro. Furthermore, defined patterns of adhesive cue\r\nallowed us to control for cell shape and growth on a subcellular scale.","lang":"eng"}],"date_published":"2016-07-01T00:00:00Z","department":[{"_id":"MiSi"}],"alternative_title":["ISTA Thesis"],"date_created":"2018-12-11T11:50:18Z","file_date_updated":"2021-02-22T11:43:14Z","degree_awarded":"PhD","date_updated":"2026-04-08T14:28:53Z","OA_place":"publisher","title":"Quantitative analysis of haptotactic cell migration","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"first_name":"Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Jan","last_name":"Schwarz"}],"citation":{"apa":"Schwarz, J. (2016). <i>Quantitative analysis of haptotactic cell migration</i>. Institute of Science and Technology Austria.","mla":"Schwarz, Jan. <i>Quantitative Analysis of Haptotactic Cell Migration</i>. Institute of Science and Technology Austria, 2016.","short":"J. Schwarz, Quantitative Analysis of Haptotactic Cell Migration, Institute of Science and Technology Austria, 2016.","chicago":"Schwarz, Jan. “Quantitative Analysis of Haptotactic Cell Migration.” Institute of Science and Technology Austria, 2016.","ista":"Schwarz J. 2016. Quantitative analysis of haptotactic cell migration. Institute of Science and Technology Austria.","ieee":"J. Schwarz, “Quantitative analysis of haptotactic cell migration,” Institute of Science and Technology Austria, 2016.","ama":"Schwarz J. Quantitative analysis of haptotactic cell migration. 2016."},"supervisor":[{"orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","last_name":"Sixt"}],"year":"2016","article_processing_charge":"No","publist_id":"6231","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}]},{"file_date_updated":"2018-12-12T10:13:02Z","date_created":"2018-12-11T11:50:16Z","doi":"10.15479/AT:ISTA:th_640","alternative_title":["ISTA Thesis"],"department":[{"_id":"ChWo"}],"date_published":"2016-07-15T00:00:00Z","abstract":[{"lang":"eng","text":"Computer graphics is an extremely exciting field for two reasons. On the one hand,\r\nthere is a healthy injection of pragmatism coming from the visual effects industry\r\nthat want robust algorithms that work so they can produce results at an increasingly\r\nfrantic pace. On the other hand, they must always try to push the envelope and\r\nachieve the impossible to wow their audiences in the next blockbuster, which means\r\nthat the industry has not succumb to conservatism, and there is plenty of room to\r\ntry out new and crazy ideas if there is a chance that it will pan into something\r\nuseful.\r\nWater simulation has been in visual effects for decades, however it still remains\r\nextremely challenging because of its high computational cost and difficult artdirectability.\r\nThe work in this thesis tries to address some of these difficulties.\r\nSpecifically, we make the following three novel contributions to the state-of-the-art\r\nin water simulation for visual effects.\r\nFirst, we develop the first algorithm that can convert any sequence of closed\r\nsurfaces in time into a moving triangle mesh. State-of-the-art methods at the time\r\ncould only handle surfaces with fixed connectivity, but we are the first to be able to\r\nhandle surfaces that merge and split apart. This is important for water simulation\r\npractitioners, because it allows them to convert splashy water surfaces extracted\r\nfrom particles or simulated using grid-based level sets into triangle meshes that can\r\nbe either textured and enhanced with extra surface dynamics as a post-process.\r\nWe also apply our algorithm to other phenomena that merge and split apart, such\r\nas morphs and noisy reconstructions of human performances.\r\nSecond, we formulate a surface-based energy that measures the deviation of a\r\nwater surface froma physically valid state. Such discrepancies arise when there is a\r\nmismatch in the degrees of freedom between the water surface and the underlying\r\nphysics solver. This commonly happens when practitioners use a moving triangle\r\nmesh with a grid-based physics solver, or when high-resolution grid-based surfaces\r\nare combined with low-resolution physics. Following the direction of steepest\r\ndescent on our surface-based energy, we can either smooth these artifacts or turn\r\nthem into high-resolution waves by interpreting the energy as a physical potential.\r\nThird, we extend state-of-the-art techniques in non-reflecting boundaries to handle spatially and time-varying background flows. This allows a novel new\r\nworkflow where practitioners can re-simulate part of an existing simulation, such\r\nas removing a solid obstacle, adding a new splash or locally changing the resolution.\r\nSuch changes can easily lead to new waves in the re-simulated region that would\r\nreflect off of the new simulation boundary, effectively ruining the illusion of a\r\nseamless simulation boundary between the existing and new simulations. Our\r\nnon-reflecting boundaries makes sure that such waves are absorbed."}],"language":[{"iso":"eng"}],"publist_id":"6238","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","full_name":"Wojtan, Christopher J"}],"year":"2016","citation":{"ieee":"M. Bojsen-Hansen, “Tracking, correcting and absorbing water surface waves,” Institute of Science and Technology Austria, 2016.","ama":"Bojsen-Hansen M. Tracking, correcting and absorbing water surface waves. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_640\">10.15479/AT:ISTA:th_640</a>","mla":"Bojsen-Hansen, Morten. <i>Tracking, Correcting and Absorbing Water Surface Waves</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_640\">10.15479/AT:ISTA:th_640</a>.","short":"M. Bojsen-Hansen, Tracking, Correcting and Absorbing Water Surface Waves, Institute of Science and Technology Austria, 2016.","chicago":"Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:th_640\">https://doi.org/10.15479/AT:ISTA:th_640</a>.","ista":"Bojsen-Hansen M. 2016. Tracking, correcting and absorbing water surface waves. Institute of Science and Technology Austria.","apa":"Bojsen-Hansen, M. (2016). <i>Tracking, correcting and absorbing water surface waves</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_640\">https://doi.org/10.15479/AT:ISTA:th_640</a>"},"author":[{"full_name":"Bojsen-Hansen, Morten","last_name":"Bojsen-Hansen","first_name":"Morten","orcid":"0000-0002-4417-3224","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87"}],"title":"Tracking, correcting and absorbing water surface waves","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","date_updated":"2026-04-08T14:24:06Z","related_material":{"record":[{"status":"public","id":"5558","relation":"other"}]},"degree_awarded":"PhD","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","day":"15","_id":"1122","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"corr_author":"1","file":[{"file_id":"4982","file_name":"IST-2016-640-v1+1_2016_Bojsen-Hansen_TCaAWSW.pdf","date_created":"2018-12-12T10:13:02Z","file_size":13869345,"relation":"main_file","access_level":"open_access","date_updated":"2018-12-12T10:13:02Z","content_type":"application/pdf","creator":"system"}],"month":"07","publication_status":"published","type":"dissertation","acknowledgement":"First and foremost I would like to thank Chris. I have been incredibly lucky to have\r\nyou as my advisor. Your integrity and aspiration to do the right thing in all walks of\r\nlife is something I admire and aspire to. I also really appreciate the fact that when\r\nworking with you it felt like we were equals. I think we had a very synergetic work\r\nrelationship: I learned immensely from you, but I dare say that you learned a few\r\nthings from me as well. ;)\r\nNext, I would like to thank my amazing committee. Hao, it was a fantastic\r\nexperience working with you. You showed me how to persevere and keep morale\r\nhigh when things were looking the most bleak before the deadline. You are an\r\nincredible motivator and super fun to be around! Vladimir, thanks for the shared\r\nlunches and the poker games. Sorry for not bringing them back when I got busy.\r\nAlso, sorry for embarrassing you by asking about your guitar playing that one\r\ntime. You really are quite awesome! Nils, one of the friendliest and most humble\r\npeople you will meet and a top notch researcher to boot! Thank you for joining\r\nmy committee late!\r\nI would also like to acknowledge the Visual Computing group at IST Austria\r\nfrom whom I have learned so much. The excellent discussions we had in reading\r\ngroups and research meetings really helped me become a better researcher!\r\nNext, I would like to thank all the amazing people that I met during my PhD\r\nstudies, both at IST Austria, in Vienna and elsewhere. ","page":"114","status":"public","ddc":["004","005","006","532","621"],"oa":1},{"date_created":"2018-12-11T11:50:16Z","file_date_updated":"2021-02-22T11:36:34Z","abstract":[{"lang":"eng","text":"Motivated by topological Tverberg-type problems  in topological combinatorics and by classical\r\nresults about embeddings (maps without double points), we study the question whether a finite\r\nsimplicial complex K  can be mapped into Rd  without triple, quadruple, or, more generally, r-fold points  (image points with at least r  distinct preimages), for a given multiplicity r ≤ 2. In particular, we are interested in maps f : K → Rd  that have no global r -fold intersection points, i.e., no r -fold points with preimages in r pairwise disjoint  simplices of K , and we seek necessary and sufficient conditions for the existence of such maps.\r\n\r\nWe present higher-multiplicity analogues of several classical results for embeddings, in particular of the completeness of the Van Kampen obstruction  for embeddability of k -dimensional\r\ncomplexes into R2k , k ≥ 3. Speciffically, we show that under suitable restrictions on the dimensions(viz., if dimK  = (r ≥ 1)k  and d  = rk \\ for some k ≥ 3), a well-known deleted product criterion (DPC ) is not only necessary but also sufficient for the existence of maps without global r -fold points. Our main technical tool is a higher-multiplicity version of the classical Whitney trick , by which pairs of isolated r -fold points of opposite sign  can be eliminated by local modiffications of the map, assuming codimension d – dimK ≥ 3.\r\n\r\nAn important guiding idea for our work was that suffciency of the DPC, together with an old\r\nresult of Özaydin's on the existence of equivariant maps, might yield an approach to disproving the remaining open cases of the the long-standing topological Tverberg conjecture , i.e., to construct maps from the N -simplex σN  to Rd  without r-Tverberg points when r not a prime power  and\r\nN  = (d  + 1)(r – 1). Unfortunately, our proof of the sufficiency of the DPC requires codimension d – dimK ≥ 3, which is not satisfied for K  = σN .\r\n\r\nIn 2015, Frick [16] found a very elegant way to overcome this \\codimension 3 obstacle&quot; and\r\nto construct the first counterexamples to the topological Tverberg conjecture for all parameters(d; r ) with d ≥ 3r  + 1 and r  not a prime power, by a reduction1  to a suitable lower-dimensional skeleton, for which the codimension 3 restriction is satisfied and maps without r -Tverberg points exist by Özaydin's result and sufficiency of the DPC.\r\n\r\nIn this thesis, we present a different construction (which does not use the constraint method) that yields counterexamples for d ≥ 3r , r  not a prime power.     "}],"date_published":"2016-08-01T00:00:00Z","department":[{"_id":"UlWa"}],"alternative_title":["ISTA Thesis"],"citation":{"mla":"Mabillard, Isaac. <i>Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture</i>. Institute of Science and Technology Austria, 2016.","ista":"Mabillard I. 2016. Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture. Institute of Science and Technology Austria.","chicago":"Mabillard, Isaac. “Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture.” Institute of Science and Technology Austria, 2016.","short":"I. Mabillard, Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture, Institute of Science and Technology Austria, 2016.","apa":"Mabillard, I. (2016). <i>Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture</i>. Institute of Science and Technology Austria.","ieee":"I. Mabillard, “Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture,” Institute of Science and Technology Austria, 2016.","ama":"Mabillard I. Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture. 2016."},"year":"2016","supervisor":[{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner","full_name":"Wagner, Uli"}],"article_processing_charge":"No","publist_id":"6237","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"2159","relation":"part_of_dissertation","status":"public"}]},"degree_awarded":"PhD","date_updated":"2026-04-08T14:24:23Z","OA_place":"publisher","author":[{"first_name":"Isaac","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","full_name":"Mabillard, Isaac","last_name":"Mabillard"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","oa_version":"Published Version","_id":"1123","day":"01","publication_status":"published","type":"dissertation","file":[{"file_name":"Thesis_final version_Mabillard_w_signature_page.pdf","checksum":"2d140cc924cd1b764544906fc22684ef","date_created":"2019-08-13T08:45:27Z","file_size":2227916,"file_id":"6809","creator":"dernst","date_updated":"2019-08-13T08:45:27Z","content_type":"application/pdf","access_level":"closed","relation":"main_file"},{"file_id":"9178","success":1,"file_name":"2016_Mabillard_Thesis.pdf","file_size":2227916,"checksum":"2d140cc924cd1b764544906fc22684ef","date_created":"2021-02-22T11:36:34Z","relation":"main_file","access_level":"open_access","date_updated":"2021-02-22T11:36:34Z","content_type":"application/pdf","creator":"dernst"}],"month":"08","corr_author":"1","status":"public","ddc":["500"],"oa":1,"page":"55","acknowledgement":"Foremost, I would like to thank Uli Wagner for introducing me to the exciting interface between\r\ntopology and combinatorics, and for our subsequent years of fruitful collaboration.\r\nIn our creative endeavors to eliminate intersection points, we had the chance to be joined later\r\nby Sergey Avvakumov and Arkadiy Skopenkov, which led us to new surprises in dimension 12.\r\nMy stay at EPFL and IST Austria was made very agreeable thanks to all these wonderful\r\npeople: Cyril Becker, Marek Filakovsky, Peter Franek, Radoslav Fulek, Peter Gazi, Kristof Huszar,\r\nMarek Krcal, Zuzana Masarova, Arnaud de Mesmay, Filip Moric, Michal Rybar, Martin Tancer,\r\nand Stephan Zhechev.\r\nFinally, I would like to thank my thesis committee Herbert Edelsbrunner and Roman Karasev\r\nfor their careful reading of the present manuscript and for the many improvements they suggested."},{"date_published":"2016-08-01T00:00:00Z","abstract":[{"text":"The process of gene expression is central to the modern understanding of how cellular systems\r\nfunction. In this process, a special kind of regulatory proteins, called transcription factors,\r\nare important to determine how much protein is produced from a given gene. As biological\r\ninformation is transmitted from transcription factor concentration to mRNA levels to amounts of\r\nprotein, various sources of noise arise and pose limits to the fidelity of intracellular signaling.\r\nThis thesis concerns itself with several aspects of stochastic gene expression: (i) the mathematical\r\ndescription of complex promoters responsible for the stochastic production of biomolecules,\r\n(ii) fundamental limits to information processing the cell faces due to the interference from multiple\r\nfluctuating signals, (iii) how the presence of gene expression noise influences the evolution\r\nof regulatory sequences, (iv) and tools for the experimental study of origins and consequences\r\nof cell-cell heterogeneity, including an application to bacterial stress response systems.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"department":[{"_id":"GaTk"}],"date_created":"2018-12-11T11:50:18Z","file_date_updated":"2020-09-21T11:30:40Z","date_updated":"2026-04-08T14:24:58Z","degree_awarded":"PhD","title":"Studying the complexities of transcriptional regulation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"full_name":"Rieckh, Georg","last_name":"Rieckh","first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","supervisor":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper"}],"year":"2016","citation":{"ieee":"G. Rieckh, “Studying the complexities of transcriptional regulation,” Institute of Science and Technology Austria, 2016.","ama":"Rieckh G. Studying the complexities of transcriptional regulation. 2016.","apa":"Rieckh, G. (2016). <i>Studying the complexities of transcriptional regulation</i>. Institute of Science and Technology Austria.","mla":"Rieckh, Georg. <i>Studying the Complexities of Transcriptional Regulation</i>. Institute of Science and Technology Austria, 2016.","short":"G. Rieckh, Studying the Complexities of Transcriptional Regulation, Institute of Science and Technology Austria, 2016.","ista":"Rieckh G. 2016. Studying the complexities of transcriptional regulation. Institute of Science and Technology Austria.","chicago":"Rieckh, Georg. “Studying the Complexities of Transcriptional Regulation.” Institute of Science and Technology Austria, 2016."},"publist_id":"6232","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"article_processing_charge":"No","oa_version":"Published Version","day":"01","_id":"1128","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","oa":1,"status":"public","ddc":["570"],"page":"114","publication_status":"published","type":"dissertation","file":[{"file_name":"Thesis_Georg_Rieckh_w_signature_page.pdf","file_size":2614660,"date_created":"2019-08-13T11:46:25Z","checksum":"ec453918c3bf8e6f460fd1156ef7b493","file_id":"6815","date_updated":"2019-08-13T11:46:25Z","content_type":"application/pdf","creator":"dernst","relation":"main_file","access_level":"closed"},{"access_level":"open_access","relation":"main_file","creator":"dernst","content_type":"application/pdf","date_updated":"2020-09-21T11:30:40Z","success":1,"file_id":"8542","checksum":"51ae398166370d18fd22478b6365c4da","file_size":6096178,"date_created":"2020-09-21T11:30:40Z","file_name":"Thesis_Georg_Rieckh.pdf"}],"month":"08","corr_author":"1"},{"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","oa_version":"Published Version","day":"01","_id":"1124","type":"dissertation","publication_status":"published","corr_author":"1","month":"03","file":[{"content_type":"application/pdf","date_updated":"2019-08-13T10:50:00Z","creator":"dernst","relation":"main_file","access_level":"closed","file_size":4785167,"checksum":"b439803ac0827cdddd56562a54e3b53b","date_created":"2019-08-13T10:50:00Z","file_name":"MORRI_PhD_thesis_FINALPLUSSIGNATURES (2).pdf","file_id":"6812"},{"access_level":"open_access","relation":"main_file","creator":"dernst","content_type":"application/pdf","date_updated":"2021-02-22T11:42:06Z","success":1,"file_id":"9180","checksum":"dd4136247fe472e7d47880ec68ac8de0","date_created":"2021-02-22T11:42:06Z","file_size":4495669,"file_name":"2016_MORRI_Thesis.pdf"}],"ddc":["570"],"oa":1,"status":"public","page":"129","date_created":"2018-12-11T11:50:17Z","file_date_updated":"2021-02-22T11:42:06Z","date_published":"2016-03-01T00:00:00Z","alternative_title":["ISTA Thesis"],"department":[{"_id":"HaJa"}],"year":"2016","supervisor":[{"orcid":"0000-0002-8023-9315","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L","last_name":"Janovjak"}],"citation":{"ama":"Morri M. Optical functionalization of human class A orphan G-protein coupled receptors. 2016.","ieee":"M. Morri, “Optical functionalization of human class A orphan G-protein coupled receptors,” Institute of Science and Technology Austria, 2016.","chicago":"Morri, Maurizio. “Optical Functionalization of Human Class A Orphan G-Protein Coupled Receptors.” Institute of Science and Technology Austria, 2016.","short":"M. Morri, Optical Functionalization of Human Class A Orphan G-Protein Coupled Receptors, Institute of Science and Technology Austria, 2016.","ista":"Morri M. 2016. Optical functionalization of human class A orphan G-protein coupled receptors. Institute of Science and Technology Austria.","mla":"Morri, Maurizio. <i>Optical Functionalization of Human Class A Orphan G-Protein Coupled Receptors</i>. Institute of Science and Technology Austria, 2016.","apa":"Morri, M. (2016). <i>Optical functionalization of human class A orphan G-protein coupled receptors</i>. Institute of Science and Technology Austria."},"language":[{"iso":"eng"}],"publist_id":"6236","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","date_updated":"2026-04-08T14:26:54Z","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"id":"4863116E-F248-11E8-B48F-1D18A9856A87","first_name":"Maurizio","last_name":"Morri","full_name":"Morri, Maurizio"}],"title":"Optical functionalization of human class A orphan G-protein coupled receptors","OA_place":"publisher"},{"oa_version":"Published Version","date_published":"2016-09-23T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"PhD thesis LaTeX source code"}],"day":"23","department":[{"_id":"ChWo"}],"_id":"5558","publisher":"Institute of Science and Technology Austria","date_created":"2018-12-12T12:31:31Z","doi":"10.15479/AT:ISTA:48","file_date_updated":"2020-07-14T12:47:02Z","has_accepted_license":"1","pubrep_id":"640","date_updated":"2026-04-08T14:24:05Z","status":"public","related_material":{"record":[{"id":"1122","relation":"other","status":"public"}]},"oa":1,"ddc":["004"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4417-3224","first_name":"Morten","last_name":"Bojsen-Hansen","full_name":"Bojsen-Hansen, Morten"}],"title":"Tracking, Correcting and Absorbing Water Surface Waves","year":"2016","type":"research_data","citation":{"ama":"Bojsen-Hansen M. Tracking, Correcting and Absorbing Water Surface Waves. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:48\">10.15479/AT:ISTA:48</a>","ieee":"M. Bojsen-Hansen, “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016.","apa":"Bojsen-Hansen, M. (2016). Tracking, Correcting and Absorbing Water Surface Waves. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:48\">https://doi.org/10.15479/AT:ISTA:48</a>","chicago":"Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:48\">https://doi.org/10.15479/AT:ISTA:48</a>.","ista":"Bojsen-Hansen M. 2016. Tracking, Correcting and Absorbing Water Surface Waves, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:48\">10.15479/AT:ISTA:48</a>.","short":"M. Bojsen-Hansen, (2016).","mla":"Bojsen-Hansen, Morten. <i>Tracking, Correcting and Absorbing Water Surface Waves</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:48\">10.15479/AT:ISTA:48</a>."},"datarep_id":"48","publist_id":"6238","article_processing_charge":"No","month":"09","file":[{"date_created":"2018-12-12T13:02:18Z","checksum":"5b1b256ad796fbddb4b7729f5e45e444","file_size":55237885,"file_name":"IST-2016-48-v1+1_2016_Bojsen-Hansen_TCaAWSW.tar.bz2","file_id":"5589","content_type":"application/x-bzip2","date_updated":"2020-07-14T12:47:02Z","creator":"system","relation":"main_file","access_level":"open_access"}]},{"oa_version":"Published Version","ec_funded":1,"_id":"1126","day":"01","publisher":"Institute of Science and Technology Austria","project":[{"name":"Lifelong Learning of Visual Scene Understanding","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"308036"}],"has_accepted_license":"1","status":"public","ddc":["006"],"oa":1,"page":"127","acknowledgement":"First and foremost I would like to express my gratitude to my supervisor, Christoph\r\nLampert. Thank you for your patience in teaching me all aspects of doing research\r\n(including English grammar), for your trust in my capabilities and endless support. Thank\r\nyou for granting me freedom in my research and, at the same time, having time and\r\nhelping me cope with the consequences whenever I needed it. Thank you for creating\r\nan excellent atmosphere in the group, it was a great pleasure and honor to be a part of\r\nit. There could not have been a better and more inspiring adviser and mentor.\r\nI thank Shai Ben-David for welcoming me into his group at the University of Waterloo,\r\nfor inspiring discussions and support. It was a great pleasure to work together. I am\r\nalso thankful to Ruth Urner for hosting me at the Max-Planck Institute Tübingen, for the\r\nfruitful collaboration and for taking care of me during that not-so-sunny month of May.\r\nI thank Jan Maas for kindly joining my thesis committee despite the short notice and\r\nproviding me with insightful comments.\r\nI would like to thank my colleagues for their support, entertaining conversations and\r\nendless table soccer games we shared together: Georg, Jan, Amelie and Emilie, Michal\r\nand Alex, Alex K. and Alex Z., Thomas, Sameh, Vlad, Mayu, Nathaniel, Silvester, Neel,\r\nCsaba, Vladimir, Morten. Thank you, Mabel and Ram, for the wonderful time we spent\r\ntogether. I am thankful to Shrinu and Samira for taking care of me during my stay at the\r\nUniversity of Waterloo. Special thanks to Viktoriia for her never-ending optimism and for\r\nbeing so inspiring and supportive, especially at the beginning of my PhD journey.\r\nThanks to IST administration, in particular, Vlad and Elisabeth for shielding me from\r\nmost of the bureaucratic paperwork.\r\n\r\nThis dissertation would not have been possible without funding from the European\r\nResearch Council under the European Union's Seventh Framework Programme\r\n(FP7/2007-2013)/ERC grant agreement no 308036.","type":"dissertation","publication_status":"published","month":"11","file":[{"access_level":"open_access","relation":"main_file","creator":"system","date_updated":"2018-12-12T10:14:07Z","content_type":"application/pdf","file_id":"5056","file_name":"IST-2017-776-v1+1_Pentina_Thesis_2016.pdf","file_size":2140062,"date_created":"2018-12-12T10:14:07Z"}],"corr_author":"1","abstract":[{"lang":"eng","text":"Traditionally machine learning has been focusing on the problem of solving a single\r\ntask in isolation. While being quite well understood, this approach disregards an\r\nimportant aspect of human learning: when facing a new problem, humans are able to\r\nexploit knowledge acquired from previously learned tasks. Intuitively, access to several\r\nproblems simultaneously or sequentially could also be advantageous for a machine\r\nlearning system, especially if these tasks are closely related. Indeed, results of many\r\nempirical studies have provided justification for this intuition. However, theoretical\r\njustifications of this idea are rather limited.\r\nThe focus of this thesis is to expand the understanding of potential benefits of information\r\ntransfer between several related learning problems. We provide theoretical\r\nanalysis for three scenarios of multi-task learning - multiple kernel learning, sequential\r\nlearning and active task selection. We also provide a PAC-Bayesian perspective on\r\nlifelong learning and investigate how the task generation process influences the generalization\r\nguarantees in this scenario. In addition, we show how some of the obtained\r\ntheoretical results can be used to derive principled multi-task and lifelong learning\r\nalgorithms and illustrate their performance on various synthetic and real-world datasets."}],"date_published":"2016-11-01T00:00:00Z","department":[{"_id":"ChLa"}],"alternative_title":["ISTA Thesis"],"doi":"10.15479/AT:ISTA:TH_776","date_created":"2018-12-11T11:50:17Z","pubrep_id":"776","file_date_updated":"2018-12-12T10:14:07Z","degree_awarded":"PhD","date_updated":"2026-04-09T10:49:34Z","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Theoretical foundations of multi-task lifelong learning","author":[{"full_name":"Pentina, Anastasia","last_name":"Pentina","first_name":"Anastasia","id":"42E87FC6-F248-11E8-B48F-1D18A9856A87"}],"citation":{"short":"A. Pentina, Theoretical Foundations of Multi-Task Lifelong Learning, Institute of Science and Technology Austria, 2016.","chicago":"Pentina, Anastasia. “Theoretical Foundations of Multi-Task Lifelong Learning.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_776\">https://doi.org/10.15479/AT:ISTA:TH_776</a>.","ista":"Pentina A. 2016. Theoretical foundations of multi-task lifelong learning. Institute of Science and Technology Austria.","mla":"Pentina, Anastasia. <i>Theoretical Foundations of Multi-Task Lifelong Learning</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_776\">10.15479/AT:ISTA:TH_776</a>.","apa":"Pentina, A. (2016). <i>Theoretical foundations of multi-task lifelong learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_776\">https://doi.org/10.15479/AT:ISTA:TH_776</a>","ama":"Pentina A. Theoretical foundations of multi-task lifelong learning. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_776\">10.15479/AT:ISTA:TH_776</a>","ieee":"A. Pentina, “Theoretical foundations of multi-task lifelong learning,” Institute of Science and Technology Austria, 2016."},"supervisor":[{"last_name":"Lampert","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph"}],"year":"2016","article_processing_charge":"No","publist_id":"6234","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}]},{"type":"dissertation","publication_status":"published","corr_author":"1","file":[{"file_id":"6814","file_name":"PhDThesis_HandeAcar_1230.pdf","date_created":"2019-08-13T11:17:50Z","checksum":"94bbbc754c36115bf37f8fc11fad43c4","file_size":3682711,"access_level":"closed","relation":"main_file","creator":"dernst","date_updated":"2019-08-13T11:17:50Z","content_type":"application/pdf"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2021-02-22T11:51:13Z","creator":"dernst","file_id":"9184","success":1,"file_size":3682711,"date_created":"2021-02-22T11:51:13Z","checksum":"94bbbc754c36115bf37f8fc11fad43c4","file_name":"2016_Thesis_HandeAcar.pdf"}],"month":"12","oa":1,"status":"public","ddc":["570"],"acknowledgement":"This study was supported by European Research Council ERC CoG 2014 – EVOLHGT,\r\nunder the grant number 648440.\r\n\r\nIt is a pleasure to thank the many people who made this thesis possible.\r\nI would like to first thank my advisor, Jonathan Paul Bollback for providing guidance in\r\nall aspects of my life, encouragement, sound advice, and good teaching over the last six\r\nyears.\r\nI would also like to thank the members of my dissertation committee – Călin C. Guet\r\nand John F. Baines – not only for their time and guidance, but for their intellectual\r\ncontributions to my development as a scientist.\r\nI would like to thank Flavia Gama and Rodrigo Redondo who have taught me all the\r\nskills in the laboratory with their graciousness and friendship. Also special thanks to\r\nBollback group for their support and for providing a stimulating and fun environment:\r\nIsabella Tomanek, Fabienne Jesse, Claudia Igler, and Pavel Payne.\r\nJerneja Beslagic is not only an amazing assistant, she also has a smile brighter and\r\nwarmer than the sunshine, bringing happiness to every moment. Always keep your light\r\nNeja, I will miss our invaluable chatters a lot.","page":"75","project":[{"grant_number":"648440","call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","oa_version":"Published Version","day":"01","ec_funded":1,"_id":"1121","year":"2016","supervisor":[{"orcid":"0000-0002-4624-4612","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P","last_name":"Bollback"}],"citation":{"ieee":"H. Acar, “Selective barriers to horizontal gene transfer,” Institute of Science and Technology Austria, 2016.","ama":"Acar H. Selective barriers to horizontal gene transfer. 2016.","mla":"Acar, Hande. <i>Selective Barriers to Horizontal Gene Transfer</i>. Institute of Science and Technology Austria, 2016.","chicago":"Acar, Hande. “Selective Barriers to Horizontal Gene Transfer.” Institute of Science and Technology Austria, 2016.","short":"H. Acar, Selective Barriers to Horizontal Gene Transfer, Institute of Science and Technology Austria, 2016.","ista":"Acar H. 2016. Selective barriers to horizontal gene transfer. Institute of Science and Technology Austria.","apa":"Acar, H. (2016). <i>Selective barriers to horizontal gene transfer</i>. Institute of Science and Technology Austria."},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publist_id":"6239","article_processing_charge":"No","date_updated":"2026-04-09T10:51:38Z","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Selective barriers to horizontal gene transfer","author":[{"full_name":"Acar, Hande","last_name":"Acar","orcid":"0000-0003-1986-9753","first_name":"Hande","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","date_created":"2018-12-11T11:50:16Z","file_date_updated":"2021-02-22T11:51:13Z","date_published":"2016-12-01T00:00:00Z","abstract":[{"lang":"eng","text":"Horizontal gene transfer (HGT), the lateral acquisition of genes across existing species\r\nboundaries, is a major evolutionary force shaping microbial genomes that facilitates\r\nadaptation to new environments as well as resistance to antimicrobial drugs. As such,\r\nunderstanding the mechanisms and constraints that determine the outcomes of HGT\r\nevents is crucial to understand the dynamics of HGT and to design better strategies to\r\novercome the challenges that originate from it.\r\nFollowing the insertion and expression of a newly transferred gene, the success of an\r\nHGT event will depend on the fitness effect it has on the recipient (host) cell. Therefore,\r\npredicting the impact of HGT on the genetic composition of a population critically\r\ndepends on the distribution of fitness effects (DFE) of horizontally transferred genes.\r\nHowever, to date, we have little knowledge of the DFE of newly transferred genes, and\r\nhence little is known about the shape and scale of this distribution.\r\nIt is particularly important to better understand the selective barriers that determine\r\nthe fitness effects of newly transferred genes. In spite of substantial bioinformatics\r\nefforts to identify horizontally transferred genes and selective barriers, a systematic\r\nexperimental approach to elucidate the roles of different selective barriers in defining\r\nthe fate of a transfer event has largely been absent. Similarly, although the fact that\r\nenvironment might alter the fitness effect of a horizontally transferred gene may seem\r\nobvious, little attention has been given to it in a systematic experimental manner.\r\nIn this study, we developed a systematic experimental approach that consists of\r\ntransferring 44 arbitrarily selected Salmonella typhimurium orthologous genes into an\r\nEscherichia coli host, and estimating the fitness effects of these transferred genes at a\r\nconstant expression level by performing competition assays against the wild type.\r\nIn chapter 2, we performed one-to-one competition assays between a mutant strain\r\ncarrying a transferred gene and the wild type strain. By using flow cytometry we\r\nestimated selection coefficients for the transferred genes with a precision level of 10-3,and obtained the DFE of horizontally transferred genes. We then investigated if these\r\nfitness effects could be predicted by any of the intrinsic properties of the genes, namely,\r\nfunctional category, degree of complexity (protein-protein interactions), GC content,\r\ncodon usage and length. Our analyses revealed that the functional category and length\r\nof the genes act as potential selective barriers. Finally, using the same procedure with\r\nthe endogenous E. coli orthologs of these 44 genes, we demonstrated that gene dosage is\r\nthe most prominent selective barrier to HGT.\r\nIn chapter 3, using the same set of genes we investigated the role of environment on the\r\nsuccess of HGT events. Under six different environments with different levels of stress\r\nwe performed more complex competition assays, where we mixed all 44 mutant strains\r\ncarrying transferred genes with the wild type strain. To estimate the fitness effects of\r\ngenes relative to wild type we used next generation sequencing. We found that the DFEs\r\nof horizontally transferred genes are highly dependent on the environment, with\r\nabundant gene–by-environment interactions. Furthermore, we demonstrated a\r\nrelationship between average fitness effect of a gene across all environments and its\r\nenvironmental variance, and thus its predictability. Finally, in spite of the fitness effects\r\nof genes being highly environment-dependent, we still observed a common shape of\r\nDFEs across all tested environments."}],"department":[{"_id":"JoBo"}],"alternative_title":["ISTA Thesis"]},{"citation":{"apa":"Ellis, T. (2016). <i>The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">https://doi.org/10.15479/AT:ISTA:TH_526 </a>","chicago":"Ellis, Thomas. “The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">https://doi.org/10.15479/AT:ISTA:TH_526 </a>.","short":"T. Ellis, The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone, Institute of Science and Technology Austria, 2016.","ista":"Ellis T. 2016. The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute of Science and Technology Austria.","mla":"Ellis, Thomas. <i>The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">10.15479/AT:ISTA:TH_526 </a>.","ama":"Ellis T. The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">10.15479/AT:ISTA:TH_526 </a>","ieee":"T. Ellis, “The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone,” Institute of Science and Technology Austria, 2016."},"supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H"}],"year":"2016","article_processing_charge":"No","language":[{"iso":"eng"}],"publist_id":"5809","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"5553"},{"relation":"dissertation_contains","id":"5551","status":"public"},{"id":"5552","relation":"dissertation_contains","status":"public"}]},"date_updated":"2026-04-09T10:52:07Z","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone","author":[{"last_name":"Ellis","full_name":"Ellis, Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","orcid":"0000-0002-8511-0254"}],"doi":"10.15479/AT:ISTA:TH_526 ","date_created":"2018-12-11T11:51:47Z","file_date_updated":"2025-07-03T06:24:39Z","pubrep_id":"526","abstract":[{"text":"Hybrid zones represent evolutionary laboratories, where recombination brings together alleles in combinations which have not previously been tested by selection. This provides an excellent opportunity to test the effect of molecular variation on fitness, and how this variation is able to spread through populations in a natural context. The snapdragon Antirrhinum majus is polymorphic in the wild for two loci controlling the distribution of yellow and magenta floral pigments. Where the yellow A. m. striatum and the magenta A. m. pseudomajus meet along a valley in the Spanish Pyrenees they form a stable hybrid zone Alleles at these loci recombine to give striking transgressive variation for flower colour. The sharp transition in phenotype over ~1km implies strong selection maintaining the hybrid zone. An indirect assay of pollinator visitation in the field found that pollinators forage in a positive-frequency dependent manner on Antirrhinum, matching previous data on fruit set. Experimental arrays and paternity analysis of wild-pollinated seeds demonstrated assortative mating for pigmentation alleles, and that pollinator behaviour alone is sufficient to explain this pattern. Selection by pollinators should be sufficiently strong to maintain the hybrid zone, although other mechanisms may be at work. At a broader scale I examined evolutionary transitions between yellow and anthocyanin pigmentation in the tribe Antirrhinae, and found that selection has acted strate that pollinators are a major determinant of reproductive success and mating patterns in wild Antirrhinum.","lang":"eng"}],"date_published":"2016-02-18T00:00:00Z","alternative_title":["ISTA Thesis"],"department":[{"_id":"NiBa"},{"_id":"GradSch"}],"publication_status":"published","type":"dissertation","corr_author":"1","file":[{"file_name":"2016_Thesis_Ellis_noSignatures.pdf","checksum":"f0f7c260e19ec1416824b165afe2d5fd","file_size":7590862,"date_created":"2025-07-03T06:24:17Z","file_id":"19957","creator":"dernst","date_updated":"2025-07-03T06:24:17Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"date_created":"2018-12-12T10:14:51Z","checksum":"a89b17ff27cf92c9a15f6b3d46bd7e53","file_size":11928241,"file_name":"IST-2016-526-v1+1_Ellis_signed_thesis.pdf","file_id":"5106","creator":"system","content_type":"application/pdf","date_updated":"2025-07-03T06:24:39Z","access_level":"closed","relation":"main_file"}],"month":"02","ddc":["576"],"oa":1,"status":"public","page":"130","acknowledgement":"I am indebted to many people for their support during my PhD, but I particularly wish to thank Nick Barton for his guidance and intuition, and for encouraging me to take the time to look beyond the immediate topic of my PhD to understand the broader context. I am also especially grateful to David Field his bottomless patience, invaluable advice on experimental design, analysis and scientific writing, and for tireless work on the population surveys and genomic work without most of my thesis could not have happened. \r\n\r\nIt has been a pleasure to work with the combined strengths of the groups at The John Innes Centre, University of Toulouse and IST Austria. Thanks to Enrico Coen and his group for hosting me in Norwich in 2011 and especially for setting up the tag experiment. \r\n\r\nI thank David Field, Desmond Bradley and Maria Clara Melo-Hurtado for organising field collections, as well as Monique Burrus and Christophe Andalo and a large number of volunteers for their e ff orts helping with the field work. Furthermore I thank Coline Jaworski for providing seeds and for her input into the design of the experimental arrays, and Matthew Couchman for maintaining the database of. \r\n\r\nIn addition to those mentioned above, I am grateful to Melinda Pickup, Spencer Barrett, and four anonymous reviewers for their insightful comments on sections of this manuscript. I also thank Jana Porsche for her e ff orts in tracking down the more obscure references for chapter 5, and Jon Bollback for his advice about the analysis. \r\n\r\nI am indebted to Jon Ågren for his patience whilst I finished this thesis, and to Sylvia Cremer and Magnus Nordborg for taking the time to read and evaluate the thesis given a shorter deadline than was fair. \r\n\r\nA very positive aspect of my PhD has been the supportive atmosphere of IST. In particular, I have come to appreciate the enormous support from our group assistants Nicole Hotzy, Julia Asimakis, Christine Ostermann and Jerneja Beslagic. I also thank Christian Chaloupka and Stefan Hipfinger for their enthusiasm and readiness to help where possible in setting up our greenhouse and experiments. ","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","oa_version":"Published Version","_id":"1398","day":"18"},{"publication_status":"published","type":"journal_article","volume":7,"corr_author":"1","file":[{"date_updated":"2020-07-14T12:44:53Z","content_type":"application/pdf","creator":"system","relation":"main_file","access_level":"open_access","file_name":"IST-2016-582-v1+1_ncomms11552.pdf","date_created":"2018-12-12T10:18:33Z","checksum":"7e84d0392348c874d473b62f1042de22","file_size":4510512,"file_id":"5355"}],"month":"05","ddc":["570"],"oa":1,"status":"public","acknowledgement":"We thank Jozsef Csicsvari and Nelson Spruston for critically reading the manuscript. We also thank A. Schlögl for programming, F. Marr for technical assistance and E. Kramberger for manuscript editing. ","project":[{"name":"Mechanisms of transmitter release at GABAergic synapses","grant_number":"P24909-B24","call_identifier":"FWF","_id":"25C26B1E-B435-11E9-9278-68D0E5697425"},{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"268548"}],"external_id":{"isi":["000375938200001"]},"publisher":"Nature Publishing Group","has_accepted_license":"1","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_number":"11552","day":"13","publication":"Nature Communications","_id":"1432","ec_funded":1,"year":"2016","citation":{"short":"R.K. Mishra, S. Kim, J. Guzmán, P.M. Jonas, Nature Communications 7 (2016).","chicago":"Mishra, Rajiv Kumar, Sooyun Kim, José Guzmán, and Peter M Jonas. “Symmetric Spike Timing-Dependent Plasticity at CA3–CA3 Synapses Optimizes Storage and Recall in Autoassociative Networks.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms11552\">https://doi.org/10.1038/ncomms11552</a>.","ista":"Mishra RK, Kim S, Guzmán J, Jonas PM. 2016. Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. Nature Communications. 7, 11552.","mla":"Mishra, Rajiv Kumar, et al. “Symmetric Spike Timing-Dependent Plasticity at CA3–CA3 Synapses Optimizes Storage and Recall in Autoassociative Networks.” <i>Nature Communications</i>, vol. 7, 11552, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms11552\">10.1038/ncomms11552</a>.","apa":"Mishra, R. K., Kim, S., Guzmán, J., &#38; Jonas, P. M. (2016). Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms11552\">https://doi.org/10.1038/ncomms11552</a>","ama":"Mishra RK, Kim S, Guzmán J, Jonas PM. Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms11552\">10.1038/ncomms11552</a>","ieee":"R. K. Mishra, S. Kim, J. Guzmán, and P. M. Jonas, “Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016."},"language":[{"iso":"eng"}],"publist_id":"5766","article_processing_charge":"No","isi":1,"date_updated":"2026-04-09T10:52:26Z","related_material":{"record":[{"relation":"dissertation_contains","id":"1396","status":"public"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"last_name":"Mishra","full_name":"Mishra, Rajiv Kumar","id":"46CB58F2-F248-11E8-B48F-1D18A9856A87","first_name":"Rajiv Kumar"},{"first_name":"Sooyun","id":"394AB1C8-F248-11E8-B48F-1D18A9856A87","full_name":"Kim, Sooyun","last_name":"Kim"},{"id":"30CC5506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2209-5242","first_name":"José","last_name":"Guzmán","full_name":"Guzmán, José"},{"full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"title":"Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks","intvolume":"         7","date_created":"2018-12-11T11:51:59Z","doi":"10.1038/ncomms11552","file_date_updated":"2020-07-14T12:44:53Z","pubrep_id":"582","quality_controlled":"1","scopus_import":"1","date_published":"2016-05-13T00:00:00Z","abstract":[{"text":"CA3–CA3 recurrent excitatory synapses are thought to play a key role in memory storage and pattern completion. Whether the plasticity properties of these synapses are consistent with their proposed network functions remains unclear. Here, we examine the properties of spike timing-dependent plasticity (STDP) at CA3–CA3 synapses. Low-frequency pairing of excitatory postsynaptic potentials (EPSPs) and action potentials (APs) induces long-term potentiation (LTP), independent of temporal order. The STDP curve is symmetric and broad (half-width ~150 ms). Consistent with these STDP induction properties, AP–EPSP sequences lead to supralinear summation of spine [Ca2+] transients. Furthermore, afterdepolarizations (ADPs) following APs efficiently propagate into dendrites of CA3 pyramidal neurons, and EPSPs summate with dendritic ADPs. In autoassociative network models, storage and recall are more robust with symmetric than with asymmetric STDP rules. Thus, a specialized STDP induction rule allows reliable storage and recall of information in the hippocampal CA3 network.","lang":"eng"}],"department":[{"_id":"PeJo"}]}]