[{"publication_status":"published","file":[{"creator":"system","file_size":4950415,"date_updated":"2020-07-14T12:44:42Z","file_name":"IST-2016-696-v1+1_journal.pone.0163628.PDF","date_created":"2018-12-12T10:10:47Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"3d0d55d373096a033bd9cf79288c8586","file_id":"4837"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"9869","relation":"research_data"},{"id":"9870","status":"public","relation":"research_data"},{"id":"9871","status":"public","relation":"research_data"}]},"volume":11,"issue":"9","license":"https://creativecommons.org/licenses/by/4.0/","abstract":[{"lang":"eng","text":"A crucial step in the early development of multicellular organisms involves the establishment of spatial patterns of gene expression which later direct proliferating cells to take on different cell fates. These patterns enable the cells to infer their global position within a tissue or an organism by reading out local gene expression levels. The patterning system is thus said to encode positional information, a concept that was formalized recently in the framework of information theory. Here we introduce a toy model of patterning in one spatial dimension, which can be seen as an extension of Wolpert's paradigmatic "French Flag" model, to patterning by several interacting, spatially coupled genes subject to intrinsic and extrinsic noise. Our model, a variant of an Ising spin system, allows us to systematically explore expression patterns that optimally encode positional information. We find that optimal patterning systems use positional cues, as in the French Flag model, together with gene-gene interactions to generate combinatorial codes for position which we call "Counter" patterns. Counter patterns can also be stabilized against noise and variations in system size or morphogen dosage by longer-range spatial interactions of the type invoked in the Turing model. The simple setup proposed here qualitatively captures many of the experimentally observed properties of biological patterning systems and allows them to be studied in a single, theoretically consistent framework."}],"oa_version":"Published Version","scopus_import":1,"month":"09","intvolume":" 11","date_updated":"2023-02-23T14:11:37Z","ddc":["571"],"file_date_updated":"2020-07-14T12:44:42Z","department":[{"_id":"GaTk"}],"_id":"1270","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"696","has_accepted_license":"1","year":"2016","day":"27","publication":"PLoS One","date_published":"2016-09-27T00:00:00Z","doi":"10.1371/journal.pone.0163628","date_created":"2018-12-11T11:51:03Z","acknowledgement":"The authors would like to thank Thomas Sokolowski and Filipe Tostevin for helpful discussions. PH and UG were funded by the German Excellence Initiative via the program \"Nanosystems Initiative Munich\" (https://www.nano-initiative-munich.de) and the German Research Foundation via the SFB 1032 \"Nanoagents for Spatiotemporal Control of Molecular and Cellular Reactions\" (http://www.sfb1032.physik.uni-muenchen.de). GT was funded by the Austrian Science Fund (FWF P 28844) (http://www.fwf.ac.at).","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"citation":{"ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. PLoS One. 11(9), e0163628.","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information,” PLoS One, vol. 11, no. 9. Public Library of Science, 2016.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, PLoS One 11 (2016).","apa":"Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628","ama":"Hillenbrand P, Gerland U, Tkačik G. Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. PLoS One. 2016;11(9). doi:10.1371/journal.pone.0163628","mla":"Hillenbrand, Patrick, et al. “Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information.” PLoS One, vol. 11, no. 9, e0163628, Public Library of Science, 2016, doi:10.1371/journal.pone.0163628."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6050","author":[{"last_name":"Hillenbrand","full_name":"Hillenbrand, Patrick","first_name":"Patrick"},{"last_name":"Gerland","full_name":"Gerland, Ulrich","first_name":"Ulrich"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik"}],"title":"Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information","article_number":"e0163628","project":[{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"}]},{"_id":"9870","type":"research_data_reference","status":"public","date_updated":"2023-02-21T16:56:40Z","citation":{"chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in an Ising Model.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s002.","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information in an Ising model, Public Library of Science, 10.1371/journal.pone.0163628.s002.","mla":"Hillenbrand, Patrick, et al. Computation of Positional Information in an Ising Model. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s002.","ama":"Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in an Ising model. 2016. doi:10.1371/journal.pone.0163628.s002","apa":"Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Computation of positional information in an Ising model. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s002","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in an Ising model.” Public Library of Science, 2016.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016)."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Patrick","full_name":"Hillenbrand, Patrick","last_name":"Hillenbrand"},{"first_name":"Ulrich","full_name":"Gerland, Ulrich","last_name":"Gerland"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"}],"article_processing_charge":"No","department":[{"_id":"GaTk"}],"title":"Computation of positional information in an Ising model","abstract":[{"text":"The effect of noise in the input field on an Ising model is approximated. Furthermore, methods to compute positional information in an Ising model by transfer matrices and Monte Carlo sampling are outlined.","lang":"eng"}],"oa_version":"Published Version","publisher":"Public Library of Science","month":"09","year":"2016","day":"27","doi":"10.1371/journal.pone.0163628.s002","date_published":"2016-09-27T00:00:00Z","related_material":{"record":[{"status":"public","id":"1270","relation":"used_in_publication"}]},"date_created":"2021-08-10T09:23:45Z"},{"abstract":[{"lang":"eng","text":"A lower bound on the error of a positional estimator with limited positional information is derived."}],"oa_version":"Published Version","publisher":"Public Library of Science","month":"09","year":"2016","day":"27","date_created":"2021-08-10T08:53:48Z","doi":"10.1371/journal.pone.0163628.s001","date_published":"2016-09-27T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1270"}]},"_id":"9869","type":"research_data_reference","status":"public","date_updated":"2023-02-21T16:56:40Z","citation":{"chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Error Bound on an Estimator of Position.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s001.","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Error bound on an estimator of position, Public Library of Science, 10.1371/journal.pone.0163628.s001.","mla":"Hillenbrand, Patrick, et al. Error Bound on an Estimator of Position. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s001.","ama":"Hillenbrand P, Gerland U, Tkačik G. Error bound on an estimator of position. 2016. doi:10.1371/journal.pone.0163628.s001","apa":"Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Error bound on an estimator of position. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s001","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Error bound on an estimator of position.” Public Library of Science, 2016."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"full_name":"Hillenbrand, Patrick","last_name":"Hillenbrand","first_name":"Patrick"},{"first_name":"Ulrich","last_name":"Gerland","full_name":"Gerland, Ulrich"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"}],"title":"Error bound on an estimator of position","department":[{"_id":"GaTk"}]},{"abstract":[{"text":"The positional information in a discrete morphogen field with Gaussian noise is computed.","lang":"eng"}],"oa_version":"Published Version","publisher":"Public Library of Science","month":"09","year":"2016","day":"27","doi":"10.1371/journal.pone.0163628.s003","related_material":{"record":[{"relation":"used_in_publication","id":"1270","status":"public"}]},"date_created":"2021-08-10T09:27:35Z","_id":"9871","type":"research_data_reference","status":"public","date_updated":"2023-02-21T16:56:40Z","citation":{"ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information in a discrete morphogen field, Public Library of Science, 10.1371/journal.pone.0163628.s003.","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in a Discrete Morphogen Field.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s003.","apa":"Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Computation of positional information in a discrete morphogen field. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s003","ama":"Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in a discrete morphogen field. 2016. doi:10.1371/journal.pone.0163628.s003","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in a discrete morphogen field.” Public Library of Science, 2016.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","mla":"Hillenbrand, Patrick, et al. Computation of Positional Information in a Discrete Morphogen Field. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s003."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"full_name":"Hillenbrand, Patrick","last_name":"Hillenbrand","first_name":"Patrick"},{"first_name":"Ulrich","full_name":"Gerland, Ulrich","last_name":"Gerland"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"article_processing_charge":"No","department":[{"_id":"GaTk"}],"title":"Computation of positional information in a discrete morphogen field"},{"alternative_title":["ISTA Thesis"],"month":"08","abstract":[{"lang":"eng","text":"The process of gene expression is central to the modern understanding of how cellular systems\r\nfunction. In this process, a special kind of regulatory proteins, called transcription factors,\r\nare important to determine how much protein is produced from a given gene. As biological\r\ninformation is transmitted from transcription factor concentration to mRNA levels to amounts of\r\nprotein, various sources of noise arise and pose limits to the fidelity of intracellular signaling.\r\nThis thesis concerns itself with several aspects of stochastic gene expression: (i) the mathematical\r\ndescription of complex promoters responsible for the stochastic production of biomolecules,\r\n(ii) fundamental limits to information processing the cell faces due to the interference from multiple\r\nfluctuating signals, (iii) how the presence of gene expression noise influences the evolution\r\nof regulatory sequences, (iv) and tools for the experimental study of origins and consequences\r\nof cell-cell heterogeneity, including an application to bacterial stress response systems."}],"oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"access_level":"closed","relation":"main_file","content_type":"application/pdf","file_id":"6815","checksum":"ec453918c3bf8e6f460fd1156ef7b493","creator":"dernst","date_updated":"2019-08-13T11:46:25Z","file_size":2614660,"date_created":"2019-08-13T11:46:25Z","file_name":"Thesis_Georg_Rieckh_w_signature_page.pdf"},{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"51ae398166370d18fd22478b6365c4da","file_id":"8542","success":1,"date_updated":"2020-09-21T11:30:40Z","file_size":6096178,"creator":"dernst","date_created":"2020-09-21T11:30:40Z","file_name":"Thesis_Georg_Rieckh.pdf"}],"language":[{"iso":"eng"}],"type":"dissertation","status":"public","_id":"1128","file_date_updated":"2020-09-21T11:30:40Z","department":[{"_id":"GaTk"}],"supervisor":[{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik"}],"date_updated":"2023-09-07T11:44:34Z","ddc":["570"],"publisher":"Institute of Science and Technology Austria","oa":1,"page":"114","date_published":"2016-08-01T00:00:00Z","date_created":"2018-12-11T11:50:18Z","has_accepted_license":"1","year":"2016","day":"01","author":[{"full_name":"Rieckh, Georg","last_name":"Rieckh","first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6232","article_processing_charge":"No","title":"Studying the complexities of transcriptional regulation","citation":{"apa":"Rieckh, G. (2016). Studying the complexities of transcriptional regulation. Institute of Science and Technology Austria.","ama":"Rieckh G. Studying the complexities of transcriptional regulation. 2016.","ieee":"G. Rieckh, “Studying the complexities of transcriptional regulation,” Institute of Science and Technology Austria, 2016.","short":"G. Rieckh, Studying the Complexities of Transcriptional Regulation, Institute of Science and Technology Austria, 2016.","mla":"Rieckh, Georg. Studying the Complexities of Transcriptional Regulation. Institute of Science and Technology Austria, 2016.","ista":"Rieckh G. 2016. Studying the complexities of transcriptional regulation. Institute of Science and Technology Austria.","chicago":"Rieckh, Georg. “Studying the Complexities of Transcriptional Regulation.” Institute of Science and Technology Austria, 2016."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"}]