[{"acknowledged_ssus":[{"_id":"ScienComp"}],"citation":{"chicago":"Schmalhorst, Philipp S, Felix Deluweit, Roger Scherrers, Carl-Philipp J Heisenberg, and Mateusz K Sikora. “Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides.” <i>Journal of Chemical Theory and Computation</i>. American Chemical Society, 2017. <a href=\"https://doi.org/10.1021/acs.jctc.7b00374\">https://doi.org/10.1021/acs.jctc.7b00374</a>.","ama":"Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. <i>Journal of Chemical Theory and Computation</i>. 2017;13(10):5039-5053. doi:<a href=\"https://doi.org/10.1021/acs.jctc.7b00374\">10.1021/acs.jctc.7b00374</a>","mla":"Schmalhorst, Philipp S., et al. “Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides.” <i>Journal of Chemical Theory and Computation</i>, vol. 13, no. 10, American Chemical Society, 2017, pp. 5039–53, doi:<a href=\"https://doi.org/10.1021/acs.jctc.7b00374\">10.1021/acs.jctc.7b00374</a>.","ista":"Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. 2017. Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. Journal of Chemical Theory and Computation. 13(10), 5039–5053.","short":"P.S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P.J. Heisenberg, M.K. Sikora, Journal of Chemical Theory and Computation 13 (2017) 5039–5053.","apa":"Schmalhorst, P. S., Deluweit, F., Scherrers, R., Heisenberg, C.-P. J., &#38; Sikora, M. K. (2017). Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. <i>Journal of Chemical Theory and Computation</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jctc.7b00374\">https://doi.org/10.1021/acs.jctc.7b00374</a>","ieee":"P. S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P. J. Heisenberg, and M. K. Sikora, “Overcoming the limitations of the MARTINI force field in simulations of polysaccharides,” <i>Journal of Chemical Theory and Computation</i>, vol. 13, no. 10. American Chemical Society, pp. 5039–5053, 2017."},"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","abstract":[{"lang":"eng","text":"Polysaccharides (carbohydrates) are key regulators of a large number of cell biological processes. However, precise biochemical or genetic manipulation of these often complex structures is laborious and hampers experimental structure–function studies. Molecular Dynamics (MD) simulations provide a valuable alternative tool to generate and test hypotheses on saccharide function. Yet, currently used MD force fields often overestimate the aggregation propensity of polysaccharides, affecting the usability of those simulations. Here we tested MARTINI, a popular coarse-grained (CG) force field for biological macromolecules, for its ability to accurately represent molecular forces between saccharides. To this end, we calculated a thermodynamic solution property, the second virial coefficient of the osmotic pressure (B22). Comparison with light scattering experiments revealed a nonphysical aggregation of a prototypical polysaccharide in MARTINI, pointing at an imbalance of the nonbonded solute–solute, solute–water, and water–water interactions. This finding also applies to smaller oligosaccharides which were all found to aggregate in simulations even at moderate concentrations, well below their solubility limit. Finally, we explored the influence of the Lennard-Jones (LJ) interaction between saccharide molecules and propose a simple scaling of the LJ interaction strength that makes MARTINI more reliable for the simulation of saccharides."}],"publication_status":"published","publist_id":"6847","day":"10","publisher":"American Chemical Society","oa_version":"Submitted Version","doi":"10.1021/acs.jctc.7b00374","isi":1,"author":[{"full_name":"Schmalhorst, Philipp S","orcid":"0000-0002-5795-0133","last_name":"Schmalhorst","id":"309D50DA-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp S"},{"last_name":"Deluweit","full_name":"Deluweit, Felix","first_name":"Felix"},{"first_name":"Roger","last_name":"Scherrers","full_name":"Scherrers, Roger"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sikora, Mateusz K","last_name":"Sikora","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87"}],"year":"2017","department":[{"_id":"CaHe"}],"publication_identifier":{"issn":["15499618"]},"scopus_import":"1","issue":"10","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"P.S.S. was supported by research fellowship 2811/1-1 from the German Research Foundation (DFG), and M.S. was supported by EMBO Long Term Fellowship ALTF 187-2013 and Grant GC65-32 from the  Interdisciplinary Centre for Mathematical and Computational Modelling (ICM), University of Warsaw, Poland. The authors thank Antje Potthast, Marek Cieplak, Tomasz Włodarski, and Damien Thompson for fruitful discussions and the IST Austria Scientific Computing Facility for support.","intvolume":"        13","oa":1,"volume":13,"main_file_link":[{"url":"https://arxiv.org/abs/1704.03773","open_access":"1"}],"date_created":"2018-12-11T11:48:35Z","external_id":{"isi":["000412965700036"]},"_id":"804","page":"5039 - 5053","publication":"Journal of Chemical Theory and Computation","date_published":"2017-10-10T00:00:00Z","article_processing_charge":"No","month":"10","title":"Overcoming the limitations of the MARTINI force field in simulations of polysaccharides","date_updated":"2023-09-27T10:58:45Z"},{"isi":1,"author":[{"first_name":"Sabrina","full_name":"Pfurr, Sabrina","last_name":"Pfurr"},{"full_name":"Chu, Yu","last_name":"Chu","first_name":"Yu"},{"full_name":"Bohrer, Christian","last_name":"Bohrer","first_name":"Christian"},{"full_name":"Greulich, Franziska","last_name":"Greulich","first_name":"Franziska"},{"id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J","orcid":"0000-0002-8483-8753","full_name":"Beattie, Robert J","last_name":"Beattie"},{"last_name":"Mammadzada","full_name":"Mammadzada, Könül","first_name":"Könül"},{"first_name":"Miriam","full_name":"Hils, Miriam","last_name":"Hils"},{"first_name":"Sebastian","last_name":"Arnold","full_name":"Arnold, Sebastian"},{"full_name":"Taylor, Verdon","last_name":"Taylor","first_name":"Verdon"},{"first_name":"Kristina","last_name":"Schachtrup","full_name":"Schachtrup, Kristina"},{"first_name":"N Henriette","full_name":"Uhlenhaut, N Henriette","last_name":"Uhlenhaut"},{"first_name":"Christian","full_name":"Schachtrup, Christian","last_name":"Schachtrup"}],"date_published":"2017-10-31T00:00:00Z","article_processing_charge":"No","year":"2017","month":"10","title":"The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development","date_updated":"2023-09-26T16:20:09Z","department":[{"_id":"SiHi"}],"date_created":"2018-12-11T11:48:36Z","day":"31","external_id":{"isi":["000414025600007"]},"publisher":"Company of Biologists","_id":"805","oa_version":"None","page":"3917 - 3931","publication":"Development","doi":"10.1242/dev.145698","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"       144","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","volume":144,"publication_status":"published","abstract":[{"lang":"eng","text":"During corticogenesis, distinct classes of neurons are born from progenitor cells located in the ventricular and subventricular zones, from where they migrate towards the pial surface to assemble into highly organized layer-specific circuits. However, the precise and coordinated transcriptional network activity defining neuronal identity is still not understood. Here, we show that genetic depletion of the basic helix-loop-helix (bHLH) transcription factor E2A splice variant E47 increased the number of Tbr1-positive deep layer and Satb2-positive upper layer neurons at E14.5, while depletion of the alternatively spliced E12 variant did not affect layer-specific neurogenesis. While ChIP-Seq identified a big overlap for E12- and E47-specific binding sites in embryonic NSCs, including sites at the cyclin-dependent kinase inhibitor (CDKI) Cdkn1c gene locus, RNA-Seq revealed a unique transcriptional regulation by each splice variant. E47 activated the expression of the CDKI Cdkn1c through binding to a distal enhancer. Finally, overexpression of E47 in embryonic NSCs in vitro impaired neurite outgrowth and E47 overexpression in vivo by in utero electroporation disturbed proper layer-specific neurogenesis and upregulated p57(KIP2) expression. Overall, this study identified E2A target genes in embryonic NSCs and demonstrates that E47 regulates neuronal differentiation via p57(KIP2)."}],"publist_id":"6846","type":"journal_article","citation":{"apa":"Pfurr, S., Chu, Y., Bohrer, C., Greulich, F., Beattie, R. J., Mammadzada, K., … Schachtrup, C. (2017). The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.145698\">https://doi.org/10.1242/dev.145698</a>","short":"S. Pfurr, Y. Chu, C. Bohrer, F. Greulich, R.J. Beattie, K. Mammadzada, M. Hils, S. Arnold, V. Taylor, K. Schachtrup, N.H. Uhlenhaut, C. Schachtrup, Development 144 (2017) 3917–3931.","ieee":"S. Pfurr <i>et al.</i>, “The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development,” <i>Development</i>, vol. 144. Company of Biologists, pp. 3917–3931, 2017.","chicago":"Pfurr, Sabrina, Yu Chu, Christian Bohrer, Franziska Greulich, Robert J Beattie, Könül Mammadzada, Miriam Hils, et al. “The E2A Splice Variant E47 Regulates the Differentiation of Projection Neurons via P57(KIP2) during Cortical Development.” <i>Development</i>. Company of Biologists, 2017. <a href=\"https://doi.org/10.1242/dev.145698\">https://doi.org/10.1242/dev.145698</a>.","ama":"Pfurr S, Chu Y, Bohrer C, et al. The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development. <i>Development</i>. 2017;144:3917-3931. doi:<a href=\"https://doi.org/10.1242/dev.145698\">10.1242/dev.145698</a>","ista":"Pfurr S, Chu Y, Bohrer C, Greulich F, Beattie RJ, Mammadzada K, Hils M, Arnold S, Taylor V, Schachtrup K, Uhlenhaut NH, Schachtrup C. 2017. The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development. Development. 144, 3917–3931.","mla":"Pfurr, Sabrina, et al. “The E2A Splice Variant E47 Regulates the Differentiation of Projection Neurons via P57(KIP2) during Cortical Development.” <i>Development</i>, vol. 144, Company of Biologists, 2017, pp. 3917–31, doi:<a href=\"https://doi.org/10.1242/dev.145698\">10.1242/dev.145698</a>."},"scopus_import":"1"},{"month":"08","date_updated":"2021-01-12T08:16:45Z","title":"Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung","date_published":"2017-08-01T00:00:00Z","page":"274 - 280","file_date_updated":"2020-07-14T12:48:09Z","publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","date_created":"2018-12-11T11:48:36Z","_id":"807","volume":70,"issue":"2","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"intvolume":"        70","scopus_import":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"issn":["10222588"]},"department":[{"_id":"E-Lib"}],"author":[{"first_name":"Magdalena","full_name":"Andrae, Magdalena","last_name":"Andrae"},{"last_name":"Villányi","full_name":"Villányi, Márton","orcid":"0000-0001-8126-0426","first_name":"Márton","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87"}],"year":"2017","oa_version":"Published Version","doi":"10.31263/voebm.v70i2.1898","day":"01","publisher":"VÖB","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","abstract":[{"text":"On January the 1st, 2016 a new agreement between 32 Austrian scientific libraries and the publisher Springer took its effect: this deal covers accessing the licensed content on the one hand, and publishing open access on the other hand. More than 1000 papers by Austrian authors were published open access at Springer in the first year alone. The working group &quot;Springer Compact Evaluierung&quot; made the data for these articles available via the platform OpenAPC and would like to use this opportunity to give a short account of what this publishing agreement actually entails and the working group intends to do.","lang":"eng"}],"publication_status":"published","publist_id":"6843","citation":{"ama":"Andrae M, Villányi M. Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>. 2017;70(2):274-280. doi:<a href=\"https://doi.org/10.31263/voebm.v70i2.1898\">10.31263/voebm.v70i2.1898</a>","chicago":"Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare</i>. VÖB, 2017. <a href=\"https://doi.org/10.31263/voebm.v70i2.1898\">https://doi.org/10.31263/voebm.v70i2.1898</a>.","ista":"Andrae M, Villányi M. 2017. Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 70(2), 274–280.","mla":"Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare</i>, vol. 70, no. 2, VÖB, 2017, pp. 274–80, doi:<a href=\"https://doi.org/10.31263/voebm.v70i2.1898\">10.31263/voebm.v70i2.1898</a>.","apa":"Andrae, M., &#38; Villányi, M. (2017). Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare</i>. VÖB. <a href=\"https://doi.org/10.31263/voebm.v70i2.1898\">https://doi.org/10.31263/voebm.v70i2.1898</a>","short":"M. Andrae, M. Villányi, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare 70 (2017) 274–280.","ieee":"M. Andrae and M. Villányi, “Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung,” <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>, vol. 70, no. 2. VÖB, pp. 274–280, 2017."},"type":"journal_article","file":[{"file_name":"2017_VOEB_Andrae.pdf","access_level":"open_access","checksum":"558c18bcf5580d87dd371ec626d52075","relation":"main_file","file_size":125065,"content_type":"application/pdf","date_updated":"2020-07-14T12:48:09Z","creator":"dernst","date_created":"2019-01-18T13:39:26Z","file_id":"5851"}],"popular_science":"1","ddc":["020"]},{"oa_version":"Published Version","doi":"10.15479/AT:ISTA:th_862","day":"27","publisher":"Institute of Science and Technology Austria","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"degree_awarded":"PhD","department":[{"_id":"ToBo"}],"publication_identifier":{"issn":["2663-337X"]},"author":[{"first_name":"Karin","id":"39B66846-F248-11E8-B48F-1D18A9856A87","full_name":"Mitosch, Karin","last_name":"Mitosch"}],"year":"2017","citation":{"ama":"Mitosch K. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_862\">10.15479/AT:ISTA:th_862</a>","chicago":"Mitosch, Karin. “Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_862\">https://doi.org/10.15479/AT:ISTA:th_862</a>.","mla":"Mitosch, Karin. <i>Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_862\">10.15479/AT:ISTA:th_862</a>.","ista":"Mitosch K. 2017. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. Institute of Science and Technology Austria.","apa":"Mitosch, K. (2017). <i>Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_862\">https://doi.org/10.15479/AT:ISTA:th_862</a>","short":"K. Mitosch, Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics, Institute of Science and Technology Austria, 2017.","ieee":"K. Mitosch, “Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics,” Institute of Science and Technology Austria, 2017."},"type":"dissertation","file":[{"date_created":"2019-04-05T08:48:51Z","creator":"dernst","file_id":"6210","access_level":"closed","file_name":"Thesis_KarinMitosch.docx","date_updated":"2020-07-14T12:48:09Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":6331071,"checksum":"da3993c5f90f59a8e8623cc31ad501dd","relation":"source_file"},{"relation":"main_file","checksum":"24c3d9e51992f1b721f3df55aa13fcb8","date_updated":"2020-07-14T12:48:09Z","content_type":"application/pdf","file_size":9289852,"file_name":"Thesis_KarinMitosch.pdf","access_level":"open_access","file_id":"6211","date_created":"2019-04-05T08:48:51Z","creator":"dernst"}],"ddc":["571","579"],"language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","publication_status":"published","abstract":[{"text":"Antibiotics have diverse effects on bacteria, including massive changes in bacterial gene expression. Whereas the gene expression changes under many antibiotics have been measured, the temporal organization of these responses and their dependence on the bacterial growth rate are unclear. As described in Chapter 1, we quantified the temporal gene expression changes in the bacterium Escherichia coli in response to the sudden exposure to antibiotics using a fluorescent reporter library and a robotic system. Our data show temporally structured gene expression responses, with response times for individual genes ranging from tens of minutes to several hours. We observed that many stress response genes were activated in response to antibiotics. As certain stress responses cross-protect bacteria from other stressors, we then asked whether cellular responses to antibiotics have a similar protective role in Chapter 2. Indeed, we found that the trimethoprim-induced acid stress response protects bacteria from subsequent acid stress. We combined microfluidics with time-lapse imaging to monitor survival, intracellular pH, and acid stress response in single cells. This approach revealed that the variable expression of the acid resistance operon gadBC strongly correlates with single-cell survival time. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. Overall, we provide a way to identify single-cell cross-protection between antibiotics and environmental stressors from temporal gene expression data, and show how antibiotics can increase bacterial fitness in changing environments. While gene expression changes to antibiotics show a clear temporal structure at the population-level, it is unclear whether this clear temporal order is followed by every single cell. Using dual-reporter strains described in Chapter 3, we measured gene expression dynamics of promoter pairs in the same cells using microfluidics and microscopy. Chapter 4 shows that the oxidative stress response and the DNA stress response showed little timing variability and a clear temporal order under the antibiotic nitrofurantoin. In contrast, the acid stress response under trimethoprim ran independently from all other activated response programs including the DNA stress response, which showed particularly high timing variability in this stress condition. In summary, this approach provides insight into the temporal organization of gene expression programs at the single-cell level and suggests dependencies between response programs and the underlying variability-introducing mechanisms. Altogether, this work advances our understanding of the diverse effects that antibiotics have on bacteria. These results were obtained by taking into account gene expression dynamics, which allowed us to identify general principles, molecular mechanisms, and dependencies between genes. Our findings may have implications for infectious disease treatments, and microbial communities in the human body and in nature. ","lang":"eng"}],"publist_id":"6831","page":"113","file_date_updated":"2020-07-14T12:48:09Z","pubrep_id":"862","supervisor":[{"full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias"}],"date_created":"2018-12-11T11:48:40Z","_id":"818","month":"09","title":"Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics","date_updated":"2023-09-07T12:00:26Z","date_published":"2017-09-27T00:00:00Z","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"id":"2001","status":"public","relation":"part_of_dissertation"},{"id":"666","status":"public","relation":"part_of_dissertation"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"First of all, I would like to express great gratitude to my PhD supervisor Tobias Bollenbach. Through his open and trusting attitude I had the freedom to explore different scientific directions during this project, and follow the research lines of my interest. I am thankful for constructive and often extensive discussions and his support and commitment during the different stages of my PhD. I want to thank my committee members, Călin Guet, Terry Hwa and Nassos Typas for their interest and their valuable input to this project. Special thanks to Nassos for career guidance, and for accepting me in his lab. A big thank you goes to the past, present and affiliated members of the Bollenbach group: Guillaume Chevereau, Marjon de Vos, Marta Lukačišinová, Veronika Bierbaum, Qi Qin, Marcin Zagórski, Martin Lukačišin, Andreas Angermayr, Bor Kavčič, Julia Tischler, Dilay Ayhan, Jaroslav Ferenc, and Georg Rieckh. I enjoyed working and discussing with you very much and I will miss our lengthy group meetings, our inspiring journal clubs, and our common lunches. Special thanks to Bor for great mental and professional support during the hard months of thesis writing, and to Marta for very creative times during the beginning of our PhDs. May the ‘Bacterial Survival Guide’ decorate the walls of IST forever! A great thanks to my friend and collaborator Georg Rieckh for his enthusiasm and for getting so involved in these projects, for his endurance and for his company throughout the years. Thanks to the FriSBi crowd at IST Austria for interesting meetings and discussions. In particular I want to thank Magdalena Steinrück, and Anna Andersson for inspiring exchange, and enjoyable time together. Thanks to everybody who contributed to the cover for Cell Systems: The constructive input from Tobias Bollenbach, Bor Kavčič, Georg Rieckh, Marta Lukačišinová, and Sebastian Nozzi, and the professional implementation by the graphic designer Martina Markus from the University of Cologne. Thanks to all my office mates in the first floor Bertalanffy building throughout the years: for ensuring a pleasant working atmosphere, and for your company! In general, I want to thank all the people that make IST such a great environment, with the many possibilities to shape our own social and research environment. I want to thank my family for all kind of practical support during the years, and my second family in Argentina for their enthusiasm. Thanks to my brother Bernhard and my sister Martina for being great siblings, and to Helena and Valentin for the joy you brought to my life. My deep gratitude goes to Sebastian Nozzi, for constant support, patience, love and for believing in me. ","oa":1},{"alternative_title":["ISTA Thesis"],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"616"},{"id":"806","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"734"},{"id":"732","relation":"part_of_dissertation","status":"public"}]},"acknowledgement":"ERC FP7 programme (grant agreement no. 240371)\r\nI have been supremely spoilt to work in a lab with such good resources and I must thank the wonderful Cremer group technicians, Anna, Barbara, Eva and Florian, for all of their help and keeping the lab up and running. You guys will probably be the most missed once I realise just how much work you have been saving me! For the same reason, I must say a big Dzi ę kuj ę Ci to Wonder Woman Wanda, for her tireless efforts feeding my colonies and cranking out thousands of petri dishes and sugar tubes. Again, you will be sorely missed now that I will have to take this task on myself. Of course, I will be eternally indebted to Prof. Sylvia Cremer for taking me under her wing and being a constant source of guidance and inspiration. You have given me the perfect balance of independence and supervision. I cannot thank you enough for creating such a great working environment and allowing me the freedom to follow my own research questions. I have had so many exceptional opportunities – attending and presenting at conferences all over the world, inviting me to write the ARE with you, going to workshops in Panama and Switzerland, and even organising our own PhD course – that I often think I must have had the best PhD in the world. You have taught me so much and made me a scientist. I sincerely hope we get the chance to work together again in the future. Thank you for everything. I must also thank my PhD Committee, Daria Siekhaus and Jacobus “Koos” Boomsma, for being very supportive throughout the duration of my PhD. ","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"title":"Disease defence in garden ants","date_updated":"2023-09-28T11:31:32Z","month":"09","date_published":"2017-09-26T00:00:00Z","article_processing_charge":"No","file_date_updated":"2020-07-14T12:48:09Z","pubrep_id":"861","supervisor":[{"last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia M","first_name":"Sylvia M","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"page":"122","_id":"819","date_created":"2018-12-11T11:48:40Z","publication_status":"published","abstract":[{"text":"Contagious diseases must transmit from infectious to susceptible hosts in order to reproduce. Whilst vectored pathogens can rely on intermediaries to find new hosts for them, many infectious pathogens require close contact or direct interaction between hosts for transmission. Hence, this means that conspecifics are often the main source of infection for most animals and so, in theory, animals should avoid conspecifics to reduce their risk of infection. Of course, in reality animals must interact with one another, as a bare minimum, to mate. However, being social provides many additional benefits and group living has become a taxonomically diverse and widespread trait. How then do social animals overcome the issue of increased disease? Over the last few decades, the social insects (ants, termites and some bees and wasps) have become a model system for studying disease in social animals. On paper, a social insect colony should be particularly susceptible to disease, given that they often contain thousands of potential hosts that are closely related and frequently interact, as well as exhibiting stable environmental conditions that encourage microbial growth. Yet, disease outbreaks appear to be rare and attempts to eradicate pest species using pathogens have failed time and again. Evolutionary biologists investigating this observation have discovered that the reduced disease susceptibility in social insects is, in part, due to collectively performed disease defences of the workers. These defences act like a “social immune system” for the colony, resulting in a per capita decrease in disease, termed social immunity. Our understanding of social immunity, and its importance in relation to the immunological defences of each insect, continues to grow, but there remain many open questions. In this thesis I have studied disease defence in garden ants. In the first data chapter, I use the invasive garden ant, Lasius neglectus, to investigate how colonies mitigate lethal infections and prevent them from spreading systemically. I find that ants have evolved ‘destructive disinfection’ – a behaviour that uses endogenously produced acidic poison to kill diseased brood and to prevent the pathogen from replicating. In the second experimental chapter, I continue to study the use of poison in invasive garden ant colonies, finding that it is sprayed prophylactically within the nest. However, this spraying has negative effects on developing pupae when they have had their cocoons artificially removed. Hence, I suggest that acidic nest sanitation may be maintaining larval cocoon spinning in this species. In the next experimental chapter, I investigated how colony founding black garden ant queens (Lasius niger) prevent disease when a co-foundress dies. I show that ant queens prophylactically perform undertaking behaviours, similar to those performed by the workers in mature nests. When a co-foundress was infected, these undertaking behaviours improved the survival of the healthy queen. In the final data chapter, I explored how immunocompetence (measured as antifungal activity) changes as incipient black garden ant colonies grow and mature, from the solitary queen phase to colonies with several hundred workers. Queen and worker antifungal activity varied throughout this time period, but despite social immunity, did not decrease as colonies matured. In addition to the above data chapters, this thesis includes two co-authored reviews. In the first, we examine the state of the art in the field of social immunity and how it might develop in the future. In the second, we identify several challenges and open questions in the study of disease defence in animals. We highlight how social insects offer a unique model to tackle some of these problems, as disease defence can be studied from the cell to the society. ","lang":"eng"}],"publist_id":"6830","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","file":[{"file_id":"6199","date_created":"2019-04-05T07:53:04Z","creator":"dernst","file_size":18580400,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2020-07-14T12:48:09Z","checksum":"4993cdd5382295758ecc3ecbd2a9aaff","relation":"source_file","access_level":"closed","file_name":"2017_Thesis_Pull.docx"},{"date_created":"2019-04-05T07:53:04Z","creator":"dernst","file_id":"6200","access_level":"open_access","file_name":"2017_Thesis_Pull.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:48:09Z","file_size":14400681,"relation":"main_file","checksum":"ee2e3ebb5b53c154c866f5b052b25153"}],"citation":{"ama":"Pull C. Disease defence in garden ants. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_861\">10.15479/AT:ISTA:th_861</a>","chicago":"Pull, Christopher. “Disease Defence in Garden Ants.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_861\">https://doi.org/10.15479/AT:ISTA:th_861</a>.","ista":"Pull C. 2017. Disease defence in garden ants. Institute of Science and Technology Austria.","mla":"Pull, Christopher. <i>Disease Defence in Garden Ants</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_861\">10.15479/AT:ISTA:th_861</a>.","apa":"Pull, C. (2017). <i>Disease defence in garden ants</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_861\">https://doi.org/10.15479/AT:ISTA:th_861</a>","short":"C. Pull, Disease Defence in Garden Ants, Institute of Science and Technology Austria, 2017.","ieee":"C. Pull, “Disease defence in garden ants,” Institute of Science and Technology Austria, 2017."},"type":"dissertation","ddc":["576","577","578","579","590","592"],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"department":[{"_id":"SyCr"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher","orcid":"0000-0003-1122-3982","full_name":"Pull, Christopher","last_name":"Pull"}],"year":"2017","doi":"10.15479/AT:ISTA:th_861","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","day":"26"},{"volume":167,"oa":1,"intvolume":"       167","acknowledgement":"Z. Bao was supported by ERC Advanced Grant RANMAT No. 338804; L. Erdős was partially supported by ERC Advanced Grant RANMAT No. 338804.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria). The authors are very grateful to the anonymous referees for careful reading and valuable comments, which helped to improve the organization.","issue":"3-4","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","date_updated":"2023-09-20T09:42:12Z","title":"Delocalization for a class of random block band matrices","month":"04","article_processing_charge":"Yes (via OA deal)","date_published":"2017-04-01T00:00:00Z","ec_funded":1,"publication":"Probability Theory and Related Fields","file_date_updated":"2020-07-14T12:45:00Z","pubrep_id":"489","page":"673 - 776","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"}],"_id":"1528","external_id":{"isi":["000398842700004"]},"date_created":"2018-12-11T11:52:32Z","publist_id":"5644","abstract":[{"text":"We consider N×N Hermitian random matrices H consisting of blocks of size M≥N6/7. The matrix elements are i.i.d. within the blocks, close to a Gaussian in the four moment matching sense, but their distribution varies from block to block to form a block-band structure, with an essential band width M. We show that the entries of the Green’s function G(z)=(H−z)−1 satisfy the local semicircle law with spectral parameter z=E+iη down to the real axis for any η≫N−1, using a combination of the supersymmetry method inspired by Shcherbina (J Stat Phys 155(3): 466–499, 2014) and the Green’s function comparison strategy. Previous estimates were valid only for η≫M−1. The new estimate also implies that the eigenvectors in the middle of the spectrum are fully delocalized.","lang":"eng"}],"publication_status":"published","status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"quality_controlled":"1","file":[{"checksum":"67afa85ff1e220cbc1f9f477a828513c","relation":"main_file","file_size":1615755,"date_updated":"2020-07-14T12:45:00Z","content_type":"application/pdf","file_name":"IST-2016-489-v1+1_s00440-015-0692-y.pdf","access_level":"open_access","file_id":"4665","date_created":"2018-12-12T10:08:05Z","creator":"system"}],"type":"journal_article","citation":{"ama":"Bao Z, Erdös L. Delocalization for a class of random block band matrices. <i>Probability Theory and Related Fields</i>. 2017;167(3-4):673-776. doi:<a href=\"https://doi.org/10.1007/s00440-015-0692-y\">10.1007/s00440-015-0692-y</a>","chicago":"Bao, Zhigang, and László Erdös. “Delocalization for a Class of Random Block Band Matrices.” <i>Probability Theory and Related Fields</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00440-015-0692-y\">https://doi.org/10.1007/s00440-015-0692-y</a>.","mla":"Bao, Zhigang, and László Erdös. “Delocalization for a Class of Random Block Band Matrices.” <i>Probability Theory and Related Fields</i>, vol. 167, no. 3–4, Springer, 2017, pp. 673–776, doi:<a href=\"https://doi.org/10.1007/s00440-015-0692-y\">10.1007/s00440-015-0692-y</a>.","ista":"Bao Z, Erdös L. 2017. Delocalization for a class of random block band matrices. Probability Theory and Related Fields. 167(3–4), 673–776.","apa":"Bao, Z., &#38; Erdös, L. (2017). Delocalization for a class of random block band matrices. <i>Probability Theory and Related Fields</i>. Springer. <a href=\"https://doi.org/10.1007/s00440-015-0692-y\">https://doi.org/10.1007/s00440-015-0692-y</a>","short":"Z. Bao, L. Erdös, Probability Theory and Related Fields 167 (2017) 673–776.","ieee":"Z. Bao and L. Erdös, “Delocalization for a class of random block band matrices,” <i>Probability Theory and Related Fields</i>, vol. 167, no. 3–4. Springer, pp. 673–776, 2017."},"ddc":["530"],"article_type":"original","publication_identifier":{"issn":["01788051"]},"department":[{"_id":"LaEr"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2017","isi":1,"author":[{"first_name":"Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","full_name":"Bao, Zhigang","orcid":"0000-0003-3036-1475","last_name":"Bao"},{"last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1007/s00440-015-0692-y","oa_version":"Published Version","publisher":"Springer","day":"01"},{"citation":{"chicago":"Martin Del Campo Sanchez, Abraham, Sarah A Cepeda Humerez, and Caroline Uhler. “Exact Goodness-of-Fit Testing for the Ising Model.” <i>Scandinavian Journal of Statistics</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/sjos.12251\">https://doi.org/10.1111/sjos.12251</a>.","ama":"Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. Exact goodness-of-fit testing for the Ising model. <i>Scandinavian Journal of Statistics</i>. 2017;44(2):285-306. doi:<a href=\"https://doi.org/10.1111/sjos.12251\">10.1111/sjos.12251</a>","ista":"Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. 2017. Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of Statistics. 44(2), 285–306.","mla":"Martin Del Campo Sanchez, Abraham, et al. “Exact Goodness-of-Fit Testing for the Ising Model.” <i>Scandinavian Journal of Statistics</i>, vol. 44, no. 2, Wiley-Blackwell, 2017, pp. 285–306, doi:<a href=\"https://doi.org/10.1111/sjos.12251\">10.1111/sjos.12251</a>.","apa":"Martin Del Campo Sanchez, A., Cepeda Humerez, S. A., &#38; Uhler, C. (2017). Exact goodness-of-fit testing for the Ising model. <i>Scandinavian Journal of Statistics</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/sjos.12251\">https://doi.org/10.1111/sjos.12251</a>","short":"A. Martin Del Campo Sanchez, S.A. Cepeda Humerez, C. Uhler, Scandinavian Journal of Statistics 44 (2017) 285–306.","ieee":"A. Martin Del Campo Sanchez, S. A. Cepeda Humerez, and C. Uhler, “Exact goodness-of-fit testing for the Ising model,” <i>Scandinavian Journal of Statistics</i>, vol. 44, no. 2. Wiley-Blackwell, pp. 285–306, 2017."},"type":"journal_article","quality_controlled":"1","publist_id":"5060","publication_status":"published","abstract":[{"text":"The Ising model is one of the simplest and most famous models of interacting systems. It was originally proposed to model ferromagnetic interactions in statistical physics and is now widely used to model spatial processes in many areas such as ecology, sociology, and genetics, usually without testing its goodness-of-fit. Here, we propose an exact goodness-of-fit test for the finite-lattice Ising model. The theory of Markov bases has been developed in algebraic statistics for exact goodness-of-fit testing using a Monte Carlo approach. However, this beautiful theory has fallen short of its promise for applications, because finding a Markov basis is usually computationally intractable. We develop a Monte Carlo method for exact goodness-of-fit testing for the Ising model which avoids computing a Markov basis and also leads to a better connectivity of the Markov chain and hence to a faster convergence. We show how this method can be applied to analyze the spatial organization of receptors on the cell membrane.","lang":"eng"}],"status":"public","language":[{"iso":"eng"}],"publisher":"Wiley-Blackwell","day":"01","doi":"10.1111/sjos.12251","oa_version":"Preprint","arxiv":1,"year":"2017","author":[{"first_name":"Abraham","last_name":"Martin Del Campo Sanchez","full_name":"Martin Del Campo Sanchez, Abraham"},{"last_name":"Cepeda Humerez","full_name":"Cepeda Humerez, Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","first_name":"Sarah A"},{"last_name":"Uhler","orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline","first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"publication_identifier":{"issn":["03036898"]},"department":[{"_id":"GaTk"}],"scopus_import":"1","intvolume":"        44","oa":1,"issue":"2","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"id":"6473","relation":"part_of_dissertation","status":"public"}]},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1410.1242"}],"volume":44,"_id":"2016","external_id":{"isi":["000400985000001"],"arxiv":["1410.1242"]},"date_created":"2018-12-11T11:55:13Z","publication":"Scandinavian Journal of Statistics","page":"285 - 306","article_processing_charge":"No","date_published":"2017-06-01T00:00:00Z","date_updated":"2023-09-19T15:13:27Z","title":"Exact goodness-of-fit testing for the Ising model","month":"06"},{"article_processing_charge":"No","date_published":"2017-10-01T00:00:00Z","date_updated":"2023-09-15T12:04:56Z","title":"Biology of restriction-modification systems at the single-cell and population level","month":"10","project":[{"name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)","_id":"251D65D8-B435-11E9-9278-68D0E5697425","grant_number":"24210"}],"_id":"202","date_created":"2018-12-11T11:45:10Z","supervisor":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"}],"pubrep_id":"916","file_date_updated":"2020-07-14T12:45:24Z","page":"126","oa":1,"acknowledgement":"During my PhD studies, I received help from many people, all of which unfortunately cannot be listed here. I thank them deeply and hope that I never made them regret their kindness.\r\nI would like to express my deepest gratitude to Călin Guet, who went far beyond his responsibilities as an advisor and was to me also a great mentor and a friend. Călin never questioned my potential or lacked compassion and I cannot thank him enough for cultivating in me an independent scientist. I was amazed by his ability to recognize the most fascinating scientific problems in objects of study that others would find mundane. I hope I adopted at least a fraction of this ability.\r\nI will be forever grateful to Bruce Levin for all his support and especially for giving me the best possible example of how one can practice excellent science with humor and style. Working with Bruce was a true privilege.\r\nI thank Jonathan Bollback and Gašper Tkačik for serving in my PhD committee and the Austrian Academy of Science for funding my PhD research via the DOC fellowship.\r\nI thank all our lab members: Tobias Bergmiller for his guidance, especially in the first years of my research, and for being a good friend throughout; Remy Chait for staying in the lab at unreasonable hours and for the good laughs at bad jokes we shared; Anna Staron for supportively listening to my whines whenever I had to run a gel; Magdalena Steinrück for her pioneering work in the lab; Kathrin Tomasek for keeping the entropic forces in check and for her FACS virtuosity; Isabella Tomanek for always being nice to me, no matter how much bench space I took from her.\r\nI thank all my collaborators: Reiko Okura and Yuichi Wakamoto for performing and analyzing the microfluidic experiments; Long Qian and Edo Kussell for their bioinformatics analysis; Dominik Refardt for the λ kan phage; Moritz for his help with the mathematical modeling. I thank Fabienne Jesse for her tireless editorial work on all our manuscripts.\r\nFinally, I would like to thank my family and especially my wife Edita, who sacrificed a lot so that I can pursue my goals and dreams.\r\n","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"id":"1243","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"561"},{"status":"public","relation":"part_of_dissertation","id":"457"}]},"alternative_title":["ISTA Thesis"],"year":"2017","author":[{"full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479","last_name":"Pleska","first_name":"Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"department":[{"_id":"CaGu"}],"degree_awarded":"PhD","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Institute of Science and Technology Austria","day":"01","doi":"10.15479/AT:ISTA:th_916","oa_version":"Published Version","publist_id":"7711","abstract":[{"lang":"eng","text":"Restriction-modification (RM) represents the simplest and possibly the most widespread mechanism of self/non-self discrimination in nature. In order to provide bacteria with immunity against bacteriophages and other parasitic genetic elements, RM systems rely on a balance between two enzymes: the restriction enzyme, which cleaves non-self DNA at specific restriction sites, and the modification enzyme, which tags the host’s DNA as self and thus protects it from cleavage. In this thesis, I use population and single-cell level experiments in combination with mathematical modeling to study different aspects of the interplay between RM systems, bacteria and bacteriophages. First, I analyze how mutations in phage restriction sites affect the probability of phage escape – an inherently stochastic process, during which phages accidently get modified instead of restricted. Next, I use single-cell experiments to show that RM systems can, with a low probability, attack the genome of their bacterial host and that this primitive form of autoimmunity leads to a tradeoff between the evolutionary cost and benefit of RM systems. Finally, I investigate the nature of interactions between bacteria, RM systems and temperate bacteriophages to find that, as a consequence of phage escape and its impact on population dynamics, RM systems can promote acquisition of symbiotic bacteriophages, rather than limit it. The results presented here uncover new fundamental biological properties of RM systems and highlight their importance in the ecology and evolution of bacteria, bacteriophages and their interactions."}],"publication_status":"published","status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"ddc":["576","579"],"file":[{"relation":"main_file","checksum":"33cfb59674e91f82e3738396d3fb3776","file_size":18569590,"date_updated":"2020-07-14T12:45:24Z","content_type":"application/pdf","file_name":"IST-2018-916-v1+3_2017_Pleska_Maros_Thesis.pdf","access_level":"open_access","file_id":"4710","creator":"system","date_created":"2018-12-12T10:08:48Z"},{"access_level":"closed","file_name":"2017_Pleska_Maros_Thesis.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2020-07-14T12:45:24Z","file_size":2801649,"checksum":"dcc239968decb233e7f98cf1083d8c26","relation":"source_file","creator":"dernst","date_created":"2019-04-05T08:33:14Z","file_id":"6204"}],"type":"dissertation","citation":{"mla":"Pleska, Maros. <i>Biology of Restriction-Modification Systems at the Single-Cell and Population Level</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">10.15479/AT:ISTA:th_916</a>.","ista":"Pleska M. 2017. Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria.","chicago":"Pleska, Maros. “Biology of Restriction-Modification Systems at the Single-Cell and Population Level.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">https://doi.org/10.15479/AT:ISTA:th_916</a>.","ama":"Pleska M. Biology of restriction-modification systems at the single-cell and population level. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">10.15479/AT:ISTA:th_916</a>","ieee":"M. Pleska, “Biology of restriction-modification systems at the single-cell and population level,” Institute of Science and Technology Austria, 2017.","short":"M. Pleska, Biology of Restriction-Modification Systems at the Single-Cell and Population Level, Institute of Science and Technology Austria, 2017.","apa":"Pleska, M. (2017). <i>Biology of restriction-modification systems at the single-cell and population level</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">https://doi.org/10.15479/AT:ISTA:th_916</a>"}},{"ec_funded":1,"date_published":"2017-06-01T00:00:00Z","article_processing_charge":"No","month":"06","date_updated":"2023-09-20T11:14:42Z","title":"Towards a runtime comparison of natural and artificial evolution","date_created":"2018-12-11T11:51:27Z","external_id":{"isi":["000400379500013"]},"_id":"1336","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091"}],"page":"681 - 713","pubrep_id":"658","file_date_updated":"2020-07-14T12:44:44Z","publication":"Algorithmica","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"2","intvolume":"        78","oa":1,"volume":78,"scopus_import":"1","author":[{"last_name":"Paixao","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago"},{"full_name":"Pérez Heredia, Jorge","last_name":"Pérez Heredia","first_name":"Jorge"},{"full_name":"Sudholt, Dirk","last_name":"Sudholt","first_name":"Dirk"},{"id":"42302D54-F248-11E8-B48F-1D18A9856A87","first_name":"Barbora","last_name":"Trubenova","full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967"}],"isi":1,"year":"2017","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publication_identifier":{"issn":["01784617"]},"day":"01","publisher":"Springer","oa_version":"Published Version","doi":"10.1007/s00453-016-0212-1","quality_controlled":"1","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","publication_status":"published","abstract":[{"text":"Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse the runtimes of EAs on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrences of new mutations is much longer than the time it takes for a mutated genotype to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a stochastic process evolving one genotype by means of mutation and selection between the resident and the mutated genotype. The probability of accepting the mutated genotype then depends on the change in fitness. We study this process, SSWM, from an algorithmic perspective, quantifying its expected optimisation time for various parameters and investigating differences to a similar evolutionary algorithm, the well-known (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient.","lang":"eng"}],"publist_id":"5931","ddc":["576"],"type":"journal_article","citation":{"ista":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2017. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 78(2), 681–713.","mla":"Paixao, Tiago, et al. “Towards a Runtime Comparison of Natural and Artificial Evolution.” <i>Algorithmica</i>, vol. 78, no. 2, Springer, 2017, pp. 681–713, doi:<a href=\"https://doi.org/10.1007/s00453-016-0212-1\">10.1007/s00453-016-0212-1</a>.","chicago":"Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “Towards a Runtime Comparison of Natural and Artificial Evolution.” <i>Algorithmica</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00453-016-0212-1\">https://doi.org/10.1007/s00453-016-0212-1</a>.","ama":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison of natural and artificial evolution. <i>Algorithmica</i>. 2017;78(2):681-713. doi:<a href=\"https://doi.org/10.1007/s00453-016-0212-1\">10.1007/s00453-016-0212-1</a>","ieee":"T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime comparison of natural and artificial evolution,” <i>Algorithmica</i>, vol. 78, no. 2. Springer, pp. 681–713, 2017.","short":"T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017) 681–713.","apa":"Paixao, T., Pérez Heredia, J., Sudholt, D., &#38; Trubenova, B. (2017). Towards a runtime comparison of natural and artificial evolution. <i>Algorithmica</i>. Springer. <a href=\"https://doi.org/10.1007/s00453-016-0212-1\">https://doi.org/10.1007/s00453-016-0212-1</a>"},"file":[{"file_size":710206,"content_type":"application/pdf","date_updated":"2020-07-14T12:44:44Z","checksum":"7873f665a0c598ac747c908f34cb14b9","relation":"main_file","access_level":"open_access","file_name":"IST-2016-658-v1+1_s00453-016-0212-1.pdf","file_id":"4805","date_created":"2018-12-12T10:10:19Z","creator":"system"}]},{"oa_version":"Published Version","doi":"10.1007/s00440-016-0740-2","day":"01","publisher":"Springer","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"issn":["01788051"]},"department":[{"_id":"LaEr"}],"author":[{"id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87","first_name":"Oskari H","full_name":"Ajanki, Oskari H","last_name":"Ajanki"},{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös"},{"first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H"}],"isi":1,"year":"2017","citation":{"ieee":"O. H. Ajanki, L. Erdös, and T. H. Krüger, “Universality for general Wigner-type matrices,” <i>Probability Theory and Related Fields</i>, vol. 169, no. 3–4. Springer, pp. 667–727, 2017.","apa":"Ajanki, O. H., Erdös, L., &#38; Krüger, T. H. (2017). Universality for general Wigner-type matrices. <i>Probability Theory and Related Fields</i>. Springer. <a href=\"https://doi.org/10.1007/s00440-016-0740-2\">https://doi.org/10.1007/s00440-016-0740-2</a>","short":"O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields 169 (2017) 667–727.","ista":"Ajanki OH, Erdös L, Krüger TH. 2017. Universality for general Wigner-type matrices. Probability Theory and Related Fields. 169(3–4), 667–727.","mla":"Ajanki, Oskari H., et al. “Universality for General Wigner-Type Matrices.” <i>Probability Theory and Related Fields</i>, vol. 169, no. 3–4, Springer, 2017, pp. 667–727, doi:<a href=\"https://doi.org/10.1007/s00440-016-0740-2\">10.1007/s00440-016-0740-2</a>.","ama":"Ajanki OH, Erdös L, Krüger TH. Universality for general Wigner-type matrices. <i>Probability Theory and Related Fields</i>. 2017;169(3-4):667-727. doi:<a href=\"https://doi.org/10.1007/s00440-016-0740-2\">10.1007/s00440-016-0740-2</a>","chicago":"Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Universality for General Wigner-Type Matrices.” <i>Probability Theory and Related Fields</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00440-016-0740-2\">https://doi.org/10.1007/s00440-016-0740-2</a>."},"type":"journal_article","file":[{"access_level":"open_access","file_name":"IST-2017-657-v1+2_s00440-016-0740-2.pdf","file_size":988843,"date_updated":"2020-07-14T12:44:44Z","content_type":"application/pdf","relation":"main_file","checksum":"29f5a72c3f91e408aeb9e78344973803","date_created":"2018-12-12T10:08:25Z","creator":"system","file_id":"4686"}],"ddc":["510","530"],"language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","abstract":[{"lang":"eng","text":"We consider the local eigenvalue distribution of large self-adjoint N×N random matrices H=H∗ with centered independent entries. In contrast to previous works the matrix of variances sij=\\mathbbmE|hij|2 is not assumed to be stochastic. Hence the density of states is not the Wigner semicircle law. Its possible shapes are described in the companion paper (Ajanki et al. in Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095). We show that as N grows, the resolvent, G(z)=(H−z)−1, converges to a diagonal matrix, diag(m(z)), where m(z)=(m1(z),…,mN(z)) solves the vector equation −1/mi(z)=z+∑jsijmj(z) that has been analyzed in Ajanki et al. (Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095). We prove a local law down to the smallest spectral resolution scale, and bulk universality for both real symmetric and complex hermitian symmetry classes."}],"publication_status":"published","publist_id":"5930","quality_controlled":"1","page":"667 - 727","pubrep_id":"657","file_date_updated":"2020-07-14T12:44:44Z","publication":"Probability Theory and Related Fields","date_created":"2018-12-11T11:51:27Z","external_id":{"isi":["000414358400002"]},"_id":"1337","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"month":"12","date_updated":"2023-09-20T11:14:17Z","title":"Universality for general Wigner-type matrices","ec_funded":1,"date_published":"2017-12-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","volume":169,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"3-4","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).  ","intvolume":"       169","oa":1},{"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1729"}]},"volume":50,"oa":1,"intvolume":"        50","issue":"2-3","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","month":"06","title":"From non-preemptive to preemptive scheduling using synchronization synthesis","date_updated":"2023-09-20T11:13:51Z","ec_funded":1,"article_processing_charge":"No","date_published":"2017-06-01T00:00:00Z","page":"97 - 139","publication":"Formal Methods in System Design","pubrep_id":"656","file_date_updated":"2020-07-14T12:44:44Z","external_id":{"isi":["000399888900001"]},"date_created":"2018-12-11T11:51:27Z","_id":"1338","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"publist_id":"5929","abstract":[{"lang":"eng","text":"We present a computer-aided programming approach to concurrency. The approach allows programmers to program assuming a friendly, non-preemptive scheduler, and our synthesis procedure inserts synchronization to ensure that the final program works even with a preemptive scheduler. The correctness specification is implicit, inferred from the non-preemptive behavior. Let us consider sequences of calls that the program makes to an external interface. The specification requires that any such sequence produced under a preemptive scheduler should be included in the set of sequences produced under a non-preemptive scheduler. We guarantee that our synthesis does not introduce deadlocks and that the synchronization inserted is optimal w.r.t. a given objective function. The solution is based on a finitary abstraction, an algorithm for bounded language inclusion modulo an independence relation, and generation of a set of global constraints over synchronization placements. Each model of the global constraints set corresponds to a correctness-ensuring synchronization placement. The placement that is optimal w.r.t. the given objective function is chosen as the synchronization solution. We apply the approach to device-driver programming, where the driver threads call the software interface of the device and the API provided by the operating system. Our experiments demonstrate that our synthesis method is precise and efficient. The implicit specification helped us find one concurrency bug previously missed when model-checking using an explicit, user-provided specification. We implemented objective functions for coarse-grained and fine-grained locking and observed that different synchronization placements are produced for our experiments, favoring a minimal number of synchronization operations or maximum concurrency, respectively."}],"publication_status":"published","quality_controlled":"1","citation":{"mla":"Cerny, Pavol, et al. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” <i>Formal Methods in System Design</i>, vol. 50, no. 2–3, Springer, 2017, pp. 97–139, doi:<a href=\"https://doi.org/10.1007/s10703-016-0256-5\">10.1007/s10703-016-0256-5</a>.","ista":"Cerny P, Clarke E, Henzinger TA, Radhakrishna A, Ryzhyk L, Samanta R, Tarrach T. 2017. From non-preemptive to preemptive scheduling using synchronization synthesis. Formal Methods in System Design. 50(2–3), 97–139.","chicago":"Cerny, Pavol, Edmund Clarke, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, Roopsha Samanta, and Thorsten Tarrach. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” <i>Formal Methods in System Design</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s10703-016-0256-5\">https://doi.org/10.1007/s10703-016-0256-5</a>.","ama":"Cerny P, Clarke E, Henzinger TA, et al. From non-preemptive to preemptive scheduling using synchronization synthesis. <i>Formal Methods in System Design</i>. 2017;50(2-3):97-139. doi:<a href=\"https://doi.org/10.1007/s10703-016-0256-5\">10.1007/s10703-016-0256-5</a>","ieee":"P. Cerny <i>et al.</i>, “From non-preemptive to preemptive scheduling using synchronization synthesis,” <i>Formal Methods in System Design</i>, vol. 50, no. 2–3. Springer, pp. 97–139, 2017.","apa":"Cerny, P., Clarke, E., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., Samanta, R., &#38; Tarrach, T. (2017). From non-preemptive to preemptive scheduling using synchronization synthesis. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-016-0256-5\">https://doi.org/10.1007/s10703-016-0256-5</a>","short":"P. Cerny, E. Clarke, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, R. Samanta, T. Tarrach, Formal Methods in System Design 50 (2017) 97–139."},"type":"journal_article","file":[{"date_created":"2018-12-12T10:13:05Z","creator":"system","file_id":"4985","access_level":"open_access","file_name":"IST-2016-656-v1+1_s10703-016-0256-5.pdf","file_size":1416170,"content_type":"application/pdf","date_updated":"2020-07-14T12:44:44Z","checksum":"1163dfd997e8212c789525d4178b1653","relation":"main_file"}],"ddc":["000"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"ToHe"}],"year":"2017","author":[{"first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny","full_name":"Cerny, Pavol"},{"last_name":"Clarke","full_name":"Clarke, Edmund","first_name":"Edmund"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun"},{"first_name":"Leonid","last_name":"Ryzhyk","full_name":"Ryzhyk, Leonid"},{"first_name":"Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","last_name":"Samanta","full_name":"Samanta, Roopsha"},{"first_name":"Thorsten","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","full_name":"Tarrach, Thorsten","orcid":"0000-0003-4409-8487","last_name":"Tarrach"}],"isi":1,"oa_version":"Published Version","doi":"10.1007/s10703-016-0256-5","day":"01","publisher":"Springer"},{"year":"2017","isi":1,"author":[{"first_name":"Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8180-0904","full_name":"Giacobbe, Mirco","last_name":"Giacobbe"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet"},{"id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh","full_name":"Gupta, Ashutosh","last_name":"Gupta"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","last_name":"Paixao"},{"id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","first_name":"Tatjana","orcid":"0000-0002-9041-0905","full_name":"Petrov, Tatjana","last_name":"Petrov"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"publication_identifier":{"issn":["00015903"]},"day":"01","publisher":"Springer","oa_version":"Published Version","doi":"10.1007/s00236-016-0278-x","quality_controlled":"1","status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"publist_id":"5898","publication_status":"published","abstract":[{"lang":"eng","text":"The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs—an important problem of interest in evolutionary biology—more efficiently than the classical simulation method. We specify the property in linear temporal logic. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights."}],"ddc":["006","576"],"citation":{"ieee":"M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking the evolution of gene regulatory networks,” <i>Acta Informatica</i>, vol. 54, no. 8. Springer, pp. 765–787, 2017.","short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, Acta Informatica 54 (2017) 765–787.","apa":"Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., &#38; Petrov, T. (2017). Model checking the evolution of gene regulatory networks. <i>Acta Informatica</i>. Springer. <a href=\"https://doi.org/10.1007/s00236-016-0278-x\">https://doi.org/10.1007/s00236-016-0278-x</a>","ista":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2017. Model checking the evolution of gene regulatory networks. Acta Informatica. 54(8), 765–787.","mla":"Giacobbe, Mirco, et al. “Model Checking the Evolution of Gene Regulatory Networks.” <i>Acta Informatica</i>, vol. 54, no. 8, Springer, 2017, pp. 765–87, doi:<a href=\"https://doi.org/10.1007/s00236-016-0278-x\">10.1007/s00236-016-0278-x</a>.","chicago":"Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking the Evolution of Gene Regulatory Networks.” <i>Acta Informatica</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00236-016-0278-x\">https://doi.org/10.1007/s00236-016-0278-x</a>.","ama":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking the evolution of gene regulatory networks. <i>Acta Informatica</i>. 2017;54(8):765-787. doi:<a href=\"https://doi.org/10.1007/s00236-016-0278-x\">10.1007/s00236-016-0278-x</a>"},"type":"journal_article","file":[{"file_id":"5841","date_created":"2019-01-17T15:57:29Z","creator":"dernst","checksum":"4e661d9135d7f8c342e8e258dee76f3e","relation":"main_file","date_updated":"2020-07-14T12:44:46Z","content_type":"application/pdf","file_size":755241,"file_name":"2017_ActaInformatica_Giacobbe.pdf","access_level":"open_access"}],"ec_funded":1,"article_processing_charge":"No","date_published":"2017-12-01T00:00:00Z","month":"12","date_updated":"2025-05-28T11:57:04Z","title":"Model checking the evolution of gene regulatory networks","external_id":{"isi":["000414343200003"]},"date_created":"2018-12-11T11:51:32Z","project":[{"call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF"},{"grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"_id":"1351","page":"765 - 787","publication":"Acta Informatica","file_date_updated":"2020-07-14T12:44:46Z","pubrep_id":"649","oa":1,"intvolume":"        54","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"8","related_material":{"record":[{"id":"1835","relation":"earlier_version","status":"public"}]},"volume":54,"scopus_import":"1"},{"external_id":{"isi":["000408634200019"]},"date_created":"2018-12-11T11:51:37Z","_id":"1367","page":"312 - 337","publication":"Computer Graphics Forum","pubrep_id":"634","file_date_updated":"2020-07-14T12:44:47Z","article_processing_charge":"No","date_published":"2017-09-01T00:00:00Z","month":"09","date_updated":"2023-09-20T11:05:36Z","title":"Adaptive physically based models in computer graphics","scopus_import":"1","oa":1,"intvolume":"        36","issue":"6","acknowledgement":"This work was partly supported by the starting grants ADAPT and BigSplash, as well as the advanced grant EXPRESSIVE from the European Research Council (ERC-2012-StG_20111012, ERC-2014-StG_638176 and ERC-2011-ADG_20110209).","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":36,"day":"01","publisher":"Wiley-Blackwell","oa_version":"Submitted Version","doi":"10.1111/cgf.12941","year":"2017","author":[{"full_name":"Manteaux, Pierre","last_name":"Manteaux","first_name":"Pierre"},{"orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","last_name":"Wojtan","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rahul","full_name":"Narain, Rahul","last_name":"Narain"},{"full_name":"Redon, Stéphane","last_name":"Redon","first_name":"Stéphane"},{"last_name":"Faure","full_name":"Faure, François","first_name":"François"},{"last_name":"Cani","full_name":"Cani, Marie","first_name":"Marie"}],"isi":1,"publication_identifier":{"issn":["01677055"]},"department":[{"_id":"ChWo"}],"ddc":["000"],"citation":{"ama":"Manteaux P, Wojtan C, Narain R, Redon S, Faure F, Cani M. Adaptive physically based models in computer graphics. <i>Computer Graphics Forum</i>. 2017;36(6):312-337. doi:<a href=\"https://doi.org/10.1111/cgf.12941\">10.1111/cgf.12941</a>","chicago":"Manteaux, Pierre, Chris Wojtan, Rahul Narain, Stéphane Redon, François Faure, and Marie Cani. “Adaptive Physically Based Models in Computer Graphics.” <i>Computer Graphics Forum</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/cgf.12941\">https://doi.org/10.1111/cgf.12941</a>.","ista":"Manteaux P, Wojtan C, Narain R, Redon S, Faure F, Cani M. 2017. Adaptive physically based models in computer graphics. Computer Graphics Forum. 36(6), 312–337.","mla":"Manteaux, Pierre, et al. “Adaptive Physically Based Models in Computer Graphics.” <i>Computer Graphics Forum</i>, vol. 36, no. 6, Wiley-Blackwell, 2017, pp. 312–37, doi:<a href=\"https://doi.org/10.1111/cgf.12941\">10.1111/cgf.12941</a>.","apa":"Manteaux, P., Wojtan, C., Narain, R., Redon, S., Faure, F., &#38; Cani, M. (2017). Adaptive physically based models in computer graphics. <i>Computer Graphics Forum</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/cgf.12941\">https://doi.org/10.1111/cgf.12941</a>","short":"P. Manteaux, C. Wojtan, R. Narain, S. Redon, F. Faure, M. Cani, Computer Graphics Forum 36 (2017) 312–337.","ieee":"P. Manteaux, C. Wojtan, R. Narain, S. Redon, F. Faure, and M. Cani, “Adaptive physically based models in computer graphics,” <i>Computer Graphics Forum</i>, vol. 36, no. 6. Wiley-Blackwell, pp. 312–337, 2017."},"type":"journal_article","file":[{"checksum":"7676e9a9ead6d58c3000988c97deb2ef","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:44:47Z","file_size":1434439,"file_name":"IST-2016-634-v1+1_starAdaptivity-cgf.pdf","access_level":"open_access","file_id":"5208","date_created":"2018-12-12T10:16:21Z","creator":"system"}],"quality_controlled":"1","status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"publist_id":"5873","publication_status":"published","abstract":[{"lang":"eng","text":"One of the major challenges in physically based modelling is making simulations efficient. Adaptive models provide an essential solution to these efficiency goals. These models are able to self-adapt in space and time, attempting to provide the best possible compromise between accuracy and speed. This survey reviews the adaptive solutions proposed so far in computer graphics. Models are classified according to the strategy they use for adaptation, from time-stepping and freezing techniques to geometric adaptivity in the form of structured grids, meshes and particles. Applications range from fluids, through deformable bodies, to articulated solids."}]},{"issue":"2","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"        23","oa":1,"volume":23,"main_file_link":[{"url":"http://arxiv.org/abs/1410.5387","open_access":"1"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1689"}]},"scopus_import":"1","ec_funded":1,"date_published":"2017-02-01T00:00:00Z","article_processing_charge":"No","month":"02","date_updated":"2023-09-20T09:43:09Z","title":"Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games","date_created":"2018-12-11T11:51:50Z","external_id":{"arxiv":["1410.5387"],"isi":["000390637000014"]},"_id":"1407","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"}],"page":"230 - 253","publication":"Nonlinear Analysis: Hybrid Systems","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"We consider the problem of computing the set of initial states of a dynamical system such that there exists a control strategy to ensure that the trajectories satisfy a temporal logic specification with probability 1 (almost-surely). We focus on discrete-time, stochastic linear dynamics and specifications given as formulas of the Generalized Reactivity(1) fragment of Linear Temporal Logic over linear predicates in the states of the system. We propose a solution based on iterative abstraction-refinement, and turn-based 2-player probabilistic games. While the theoretical guarantee of our algorithm after any finite number of iterations is only a partial solution, we show that if our algorithm terminates, then the result is the set of all satisfying initial states. Moreover, for any (partial) solution our algorithm synthesizes witness control strategies to ensure almost-sure satisfaction of the temporal logic specification. While the proposed algorithm guarantees progress and soundness in every iteration, it is computationally demanding. We offer an alternative, more efficient solution for the reachability properties that decomposes the problem into a series of smaller problems of the same type. All algorithms are demonstrated on an illustrative case study."}],"publist_id":"5800","citation":{"apa":"Svoreňová, M., Kretinsky, J., Chmelik, M., Chatterjee, K., Cěrná, I., &#38; Belta, C. (2017). Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. <i>Nonlinear Analysis: Hybrid Systems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.nahs.2016.04.006\">https://doi.org/10.1016/j.nahs.2016.04.006</a>","short":"M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, C. Belta, Nonlinear Analysis: Hybrid Systems 23 (2017) 230–253.","ieee":"M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, and C. Belta, “Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games,” <i>Nonlinear Analysis: Hybrid Systems</i>, vol. 23, no. 2. Elsevier, pp. 230–253, 2017.","chicago":"Svoreňová, Mária, Jan Kretinsky, Martin Chmelik, Krishnendu Chatterjee, Ivana Cěrná, and Cǎlin Belta. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” <i>Nonlinear Analysis: Hybrid Systems</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.nahs.2016.04.006\">https://doi.org/10.1016/j.nahs.2016.04.006</a>.","ama":"Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. <i>Nonlinear Analysis: Hybrid Systems</i>. 2017;23(2):230-253. doi:<a href=\"https://doi.org/10.1016/j.nahs.2016.04.006\">10.1016/j.nahs.2016.04.006</a>","mla":"Svoreňová, Mária, et al. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” <i>Nonlinear Analysis: Hybrid Systems</i>, vol. 23, no. 2, Elsevier, 2017, pp. 230–53, doi:<a href=\"https://doi.org/10.1016/j.nahs.2016.04.006\">10.1016/j.nahs.2016.04.006</a>.","ista":"Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. 2017. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Nonlinear Analysis: Hybrid Systems. 23(2), 230–253."},"type":"journal_article","isi":1,"author":[{"first_name":"Mária","full_name":"Svoreňová, Mária","last_name":"Svoreňová"},{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Kretinsky","full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881"},{"full_name":"Chmelik, Martin","last_name":"Chmelik","first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Cěrná","full_name":"Cěrná, Ivana","first_name":"Ivana"},{"first_name":"Cǎlin","last_name":"Belta","full_name":"Belta, Cǎlin"}],"year":"2017","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"day":"01","publisher":"Elsevier","arxiv":1,"oa_version":"Preprint","doi":"10.1016/j.nahs.2016.04.006"},{"external_id":{"arxiv":["1702.06457"]},"date_created":"2023-08-22T14:17:19Z","_id":"14205","page":"860-868","publication":"Proceedings of the 20th International Conference on Artificial Intelligence and Statistics","article_processing_charge":"No","date_published":"2017-02-21T00:00:00Z","month":"02","date_updated":"2023-09-13T09:49:10Z","title":"A unified optimization view on generalized matching pursuit and Frank-Wolfe","extern":"1","intvolume":"        54","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1702.06457","open_access":"1"}],"volume":54,"day":"21","publisher":"ML Research Press","oa_version":"Preprint","arxiv":1,"year":"2017","conference":{"name":"AISTATS: Conference on Artificial Intelligence and Statistics","end_date":"2017-04-22","start_date":"2017-04-20","location":"Fort Lauderdale, FL, United States"},"author":[{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"last_name":"Khanna","full_name":"Khanna, Rajiv","first_name":"Rajiv"},{"first_name":"Michael","full_name":"Tschannen, Michael","last_name":"Tschannen"},{"full_name":"Jaggi, Martin","last_name":"Jaggi","first_name":"Martin"}],"department":[{"_id":"FrLo"}],"type":"conference","citation":{"short":"F. Locatello, R. Khanna, M. Tschannen, M. Jaggi, in:, Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, ML Research Press, 2017, pp. 860–868.","apa":"Locatello, F., Khanna, R., Tschannen, M., &#38; Jaggi, M. (2017). A unified optimization view on generalized matching pursuit and Frank-Wolfe. In <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i> (Vol. 54, pp. 860–868). Fort Lauderdale, FL, United States: ML Research Press.","ieee":"F. Locatello, R. Khanna, M. Tschannen, and M. Jaggi, “A unified optimization view on generalized matching pursuit and Frank-Wolfe,” in <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i>, Fort Lauderdale, FL, United States, 2017, vol. 54, pp. 860–868.","chicago":"Locatello, Francesco, Rajiv Khanna, Michael Tschannen, and Martin Jaggi. “A Unified Optimization View on Generalized Matching Pursuit and Frank-Wolfe.” In <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i>, 54:860–68. ML Research Press, 2017.","ama":"Locatello F, Khanna R, Tschannen M, Jaggi M. A unified optimization view on generalized matching pursuit and Frank-Wolfe. In: <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i>. Vol 54. ML Research Press; 2017:860-868.","ista":"Locatello F, Khanna R, Tschannen M, Jaggi M. 2017. A unified optimization view on generalized matching pursuit and Frank-Wolfe. Proceedings of the 20th International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics vol. 54, 860–868.","mla":"Locatello, Francesco, et al. “A Unified Optimization View on Generalized Matching Pursuit and Frank-Wolfe.” <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i>, vol. 54, ML Research Press, 2017, pp. 860–68."},"quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"publication_status":"published","abstract":[{"text":"Two of the most fundamental prototypes of greedy optimization are the matching pursuit and Frank-Wolfe algorithms. In this paper, we take a unified view on both classes of methods, leading to the first explicit convergence rates of matching pursuit methods in an optimization sense, for general sets of atoms. We derive sublinear (1/t) convergence for both classes on general smooth objectives, and linear convergence on strongly convex objectives, as well as a clear correspondence of algorithm variants. Our presented algorithms and rates are affine invariant, and do not need any incoherence or sparsity assumptions.","lang":"eng"}]},{"type":"conference","citation":{"mla":"Locatello, Francesco, et al. “Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.” <i>Advances in Neural Information Processing Systems</i>, 2017.","ista":"Locatello F, Tschannen M, Rätsch G, Jaggi M. 2017. Greedy algorithms for cone constrained optimization with convergence guarantees. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems.","ama":"Locatello F, Tschannen M, Rätsch G, Jaggi M. Greedy algorithms for cone constrained optimization with convergence guarantees. In: <i>Advances in Neural Information Processing Systems</i>. ; 2017.","chicago":"Locatello, Francesco, Michael Tschannen, Gunnar Rätsch, and Martin Jaggi. “Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.” In <i>Advances in Neural Information Processing Systems</i>, 2017.","ieee":"F. Locatello, M. Tschannen, G. Rätsch, and M. Jaggi, “Greedy algorithms for cone constrained optimization with convergence guarantees,” in <i>Advances in Neural Information Processing Systems</i>, Long Beach, CA, United States, 2017.","short":"F. Locatello, M. Tschannen, G. Rätsch, M. Jaggi, in:, Advances in Neural Information Processing Systems, 2017.","apa":"Locatello, F., Tschannen, M., Rätsch, G., &#38; Jaggi, M. (2017). Greedy algorithms for cone constrained optimization with convergence guarantees. In <i>Advances in Neural Information Processing Systems</i>. Long Beach, CA, United States."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","publication_status":"published","abstract":[{"text":"Greedy optimization methods such as Matching Pursuit (MP) and Frank-Wolfe (FW) algorithms regained popularity in recent years due to their simplicity, effectiveness and theoretical guarantees. MP and FW address optimization over the linear span and the convex hull of a set of atoms, respectively. In this paper, we consider the intermediate case of optimization over the convex cone, parametrized as the conic hull of a generic atom set, leading to the first principled definitions of non-negative MP algorithms for which we give explicit convergence rates and demonstrate excellent empirical performance. In particular, we derive sublinear (O(1/t)) convergence on general smooth and convex objectives, and linear convergence (O(e−t)) on strongly convex objectives, in both cases for general sets of atoms. Furthermore, we establish a clear correspondence of our algorithms to known algorithms from the MP and FW literature. Our novel algorithms and analyses target general atom sets and general objective functions, and hence are directly applicable to a large variety of learning settings.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.11041"}],"date_created":"2023-08-22T14:17:38Z","day":"31","external_id":{"arxiv":["1705.11041"]},"_id":"14206","oa_version":"Preprint","arxiv":1,"publication":"Advances in Neural Information Processing Systems","date_published":"2017-05-31T00:00:00Z","author":[{"last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"last_name":"Tschannen","full_name":"Tschannen, Michael","first_name":"Michael"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"},{"first_name":"Martin","last_name":"Jaggi","full_name":"Jaggi, Martin"}],"conference":{"location":"Long Beach, CA, United States","start_date":"2017-12-04","end_date":"2017-12-09","name":"NeurIPS: Neural Information Processing Systems"},"year":"2017","article_processing_charge":"No","month":"05","date_updated":"2023-09-13T08:32:23Z","title":"Greedy algorithms for cone constrained optimization with convergence guarantees","department":[{"_id":"FrLo"}],"publication_identifier":{"isbn":["9781510860964"]}},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"intvolume":"        78","volume":78,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jsc.2016.03.008"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"10894"}]},"scopus_import":"1","date_published":"2017-01-01T00:00:00Z","article_processing_charge":"No","ec_funded":1,"date_updated":"2023-09-20T09:42:40Z","title":"Phat - Persistent homology algorithms toolbox","month":"01","_id":"1433","project":[{"name":"Topological Complex Systems","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_created":"2018-12-11T11:51:59Z","external_id":{"isi":["000384396000005"]},"publication":"Journal of Symbolic Computation","page":"76 - 90","quality_controlled":"1","publication_status":"published","abstract":[{"text":"Phat is an open-source C. ++ library for the computation of persistent homology by matrix reduction, targeted towards developers of software for topological data analysis. We aim for a simple generic design that decouples algorithms from data structures without sacrificing efficiency or user-friendliness. We provide numerous different reduction strategies as well as data types to store and manipulate the boundary matrix. We compare the different combinations through extensive experimental evaluation and identify optimization techniques that work well in practical situations. We also compare our software with various other publicly available libraries for persistent homology.","lang":"eng"}],"publist_id":"5765","language":[{"iso":"eng"}],"status":"public","article_type":"original","citation":{"apa":"Bauer, U., Kerber, M., Reininghaus, J., &#38; Wagner, H. (2017). Phat - Persistent homology algorithms toolbox. <i>Journal of Symbolic Computation</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jsc.2016.03.008\">https://doi.org/10.1016/j.jsc.2016.03.008</a>","short":"U. Bauer, M. Kerber, J. Reininghaus, H. Wagner, Journal of Symbolic Computation 78 (2017) 76–90.","ieee":"U. Bauer, M. Kerber, J. Reininghaus, and H. Wagner, “Phat - Persistent homology algorithms toolbox,” <i>Journal of Symbolic Computation</i>, vol. 78. Academic Press, pp. 76–90, 2017.","chicago":"Bauer, Ulrich, Michael Kerber, Jan Reininghaus, and Hubert Wagner. “Phat - Persistent Homology Algorithms Toolbox.” <i>Journal of Symbolic Computation</i>. Academic Press, 2017. <a href=\"https://doi.org/10.1016/j.jsc.2016.03.008\">https://doi.org/10.1016/j.jsc.2016.03.008</a>.","ama":"Bauer U, Kerber M, Reininghaus J, Wagner H. Phat - Persistent homology algorithms toolbox. <i>Journal of Symbolic Computation</i>. 2017;78:76-90. doi:<a href=\"https://doi.org/10.1016/j.jsc.2016.03.008\">10.1016/j.jsc.2016.03.008</a>","ista":"Bauer U, Kerber M, Reininghaus J, Wagner H. 2017. Phat - Persistent homology algorithms toolbox. Journal of Symbolic Computation. 78, 76–90.","mla":"Bauer, Ulrich, et al. “Phat - Persistent Homology Algorithms Toolbox.” <i>Journal of Symbolic Computation</i>, vol. 78, Academic Press, 2017, pp. 76–90, doi:<a href=\"https://doi.org/10.1016/j.jsc.2016.03.008\">10.1016/j.jsc.2016.03.008</a>."},"type":"journal_article","isi":1,"author":[{"last_name":"Bauer","full_name":"Bauer, Ulrich","first_name":"Ulrich"},{"first_name":"Michael","full_name":"Kerber, Michael","last_name":"Kerber"},{"first_name":"Jan","full_name":"Reininghaus, Jan","last_name":"Reininghaus"},{"first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","full_name":"Wagner, Hubert"}],"year":"2017","department":[{"_id":"HeEd"}],"publication_identifier":{"issn":[" 07477171"]},"publisher":"Academic Press","day":"01","doi":"10.1016/j.jsc.2016.03.008","oa_version":"Published Version"},{"has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"publist_id":"7276","abstract":[{"lang":"eng","text":"RNA-dependent RNA polymerases (RdRps) play a key role in the life cycle of RNA viruses and impact their immunobiology. The arenavirus lymphocytic choriomeningitis virus (LCMV) strain Clone 13 provides a benchmark model for studying chronic infection. A major genetic determinant for its ability to persist maps to a single amino acid exchange in the viral L protein, which exhibits RdRp activity, yet its functional consequences remain elusive. To unravel the L protein interactions with the host proteome, we engineered infectious L protein-tagged LCMV virions by reverse genetics. A subsequent mass-spectrometric analysis of L protein pulldowns from infected human cells revealed a comprehensive network of interacting host proteins. The obtained LCMV L protein interactome was bioinformatically integrated with known host protein interactors of RdRps from other RNA viruses, emphasizing interconnected modules of human proteins. Functional characterization of selected interactors highlighted proviral (DDX3X) as well as antiviral (NKRF, TRIM21) host factors. To corroborate these findings, we infected Trim21-/-mice with LCMV and found impaired virus control in chronic infection. These results provide insights into the complex interactions of the arenavirus LCMV and other viral RdRps with the host proteome and contribute to a better molecular understanding of how chronic viruses interact with their host."}],"publication_status":"published","quality_controlled":"1","citation":{"chicago":"Khamina, Kseniya, Alexander Lercher, Michael Caldera, Christopher Schliehe, Bojan Vilagos, Mehmet Sahin, Lindsay Kosack, et al. “Characterization of Host Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” <i>PLoS Pathogens</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.ppat.1006758\">https://doi.org/10.1371/journal.ppat.1006758</a>.","ama":"Khamina K, Lercher A, Caldera M, et al. Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. <i>PLoS Pathogens</i>. 2017;13(12). doi:<a href=\"https://doi.org/10.1371/journal.ppat.1006758\">10.1371/journal.ppat.1006758</a>","ista":"Khamina K, Lercher A, Caldera M, Schliehe C, Vilagos B, Sahin M, Kosack L, Bhattacharya A, Májek P, Stukalov A, Sacco R, James L, Pinschewer D, Bennett K, Menche J, Bergthaler A. 2017. Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. 13(12), e1006758.","mla":"Khamina, Kseniya, et al. “Characterization of Host Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” <i>PLoS Pathogens</i>, vol. 13, no. 12, e1006758, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.ppat.1006758\">10.1371/journal.ppat.1006758</a>.","short":"K. Khamina, A. Lercher, M. Caldera, C. Schliehe, B. Vilagos, M. Sahin, L. Kosack, A. Bhattacharya, P. Májek, A. Stukalov, R. Sacco, L. James, D. Pinschewer, K. Bennett, J. Menche, A. Bergthaler, PLoS Pathogens 13 (2017).","apa":"Khamina, K., Lercher, A., Caldera, M., Schliehe, C., Vilagos, B., Sahin, M., … Bergthaler, A. (2017). Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. <i>PLoS Pathogens</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.ppat.1006758\">https://doi.org/10.1371/journal.ppat.1006758</a>","ieee":"K. Khamina <i>et al.</i>, “Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein,” <i>PLoS Pathogens</i>, vol. 13, no. 12. Public Library of Science, 2017."},"type":"journal_article","file":[{"access_level":"open_access","file_name":"IST-2018-931-v1+1_journal.ppat.1006758.pdf","date_updated":"2020-07-14T12:46:44Z","content_type":"application/pdf","file_size":4106772,"checksum":"1aa20f19a1e90664fadce6e7d5284fdc","relation":"main_file","creator":"system","date_created":"2018-12-12T10:12:26Z","file_id":"4944"}],"ddc":["576","616"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"issn":["15537366"]},"department":[{"_id":"GaNo"}],"year":"2017","author":[{"first_name":"Kseniya","full_name":"Khamina, Kseniya","last_name":"Khamina"},{"first_name":"Alexander","full_name":"Lercher, Alexander","last_name":"Lercher"},{"full_name":"Caldera, Michael","last_name":"Caldera","first_name":"Michael"},{"last_name":"Schliehe","full_name":"Schliehe, Christopher","first_name":"Christopher"},{"first_name":"Bojan","last_name":"Vilagos","full_name":"Vilagos, Bojan"},{"full_name":"Sahin, Mehmet","last_name":"Sahin","first_name":"Mehmet"},{"first_name":"Lindsay","last_name":"Kosack","full_name":"Kosack, Lindsay"},{"first_name":"Anannya","full_name":"Bhattacharya, Anannya","last_name":"Bhattacharya"},{"first_name":"Peter","last_name":"Májek","full_name":"Májek, Peter"},{"first_name":"Alexey","last_name":"Stukalov","full_name":"Stukalov, Alexey"},{"full_name":"Sacco, Roberto","last_name":"Sacco","first_name":"Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Leo","last_name":"James","full_name":"James, Leo"},{"full_name":"Pinschewer, Daniel","last_name":"Pinschewer","first_name":"Daniel"},{"full_name":"Bennett, Keiryn","last_name":"Bennett","first_name":"Keiryn"},{"full_name":"Menche, Jörg","last_name":"Menche","first_name":"Jörg"},{"last_name":"Bergthaler","full_name":"Bergthaler, Andreas","first_name":"Andreas"}],"oa_version":"Published Version","doi":"10.1371/journal.ppat.1006758","day":"01","publisher":"Public Library of Science","volume":13,"intvolume":"        13","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"12","article_number":"e1006758","scopus_import":1,"month":"12","date_updated":"2021-01-12T08:01:48Z","title":"Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein","date_published":"2017-12-01T00:00:00Z","publication":"PLoS Pathogens","pubrep_id":"931","file_date_updated":"2020-07-14T12:46:44Z","date_created":"2018-12-11T11:47:03Z","_id":"540"},{"file":[{"access_level":"open_access","file_name":"IST-2018-959-v1+1_2017_Nikolic_Cell-to-cell.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:46Z","file_size":1308475,"checksum":"22426d9382f21554bad5fa5967afcfd0","relation":"main_file","date_created":"2018-12-12T10:14:35Z","creator":"system","file_id":"5088"}],"citation":{"ieee":"N. Nikolic <i>et al.</i>, “Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations,” <i>PLoS Genetics</i>, vol. 13, no. 12. Public Library of Science, 2017.","short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, PLoS Genetics 13 (2017).","apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1007122\">https://doi.org/10.1371/journal.pgen.1007122</a>","mla":"Nikolic, Nela, et al. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.” <i>PLoS Genetics</i>, vol. 13, no. 12, e1007122, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007122\">10.1371/journal.pgen.1007122</a>.","ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. 13(12), e1007122.","ama":"Nikolic N, Schreiber F, Dal Co A, et al. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. <i>PLoS Genetics</i>. 2017;13(12). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007122\">10.1371/journal.pgen.1007122</a>","chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.” <i>PLoS Genetics</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pgen.1007122\">https://doi.org/10.1371/journal.pgen.1007122</a>."},"type":"journal_article","ddc":["576","579"],"publist_id":"7275","abstract":[{"text":"While we have good understanding of bacterial metabolism at the population level, we know little about the metabolic behavior of individual cells: do single cells in clonal populations sometimes specialize on different metabolic pathways? Such metabolic specialization could be driven by stochastic gene expression and could provide individual cells with growth benefits of specialization. We measured the degree of phenotypic specialization in two parallel metabolic pathways, the assimilation of glucose and arabinose. We grew Escherichia coli in chemostats, and used isotope-labeled sugars in combination with nanometer-scale secondary ion mass spectrometry and mathematical modeling to quantify sugar assimilation at the single-cell level. We found large variation in metabolic activities between single cells, both in absolute assimilation and in the degree to which individual cells specialize in the assimilation of different sugars. Analysis of transcriptional reporters indicated that this variation was at least partially based on cell-to-cell variation in gene expression. Metabolic differences between cells in clonal populations could potentially reduce metabolic incompatibilities between different pathways, and increase the rate at which parallel reactions can be performed.","lang":"eng"}],"publication_status":"published","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","doi":"10.1371/journal.pgen.1007122","oa_version":"Published Version","publisher":"Public Library of Science","day":"18","publication_identifier":{"issn":["15537390"]},"department":[{"_id":"CaGu"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2017","author":[{"last_name":"Nikolic","full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090","first_name":"Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schreiber","full_name":"Schreiber, Frank","first_name":"Frank"},{"full_name":"Dal Co, Alma","last_name":"Dal Co","first_name":"Alma"},{"first_name":"Daniel","full_name":"Kiviet, Daniel","last_name":"Kiviet"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","last_name":"Bergmiller"},{"full_name":"Littmann, Sten","last_name":"Littmann","first_name":"Sten"},{"first_name":"Marcel","full_name":"Kuypers, Marcel","last_name":"Kuypers"},{"full_name":"Ackermann, Martin","last_name":"Ackermann","first_name":"Martin"}],"scopus_import":1,"related_material":{"record":[{"status":"public","relation":"research_data","id":"9844"},{"id":"9845","status":"public","relation":"research_data"},{"status":"public","relation":"research_data","id":"9846"}]},"volume":13,"article_number":"e1007122","oa":1,"intvolume":"        13","issue":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"PLoS Genetics","pubrep_id":"959","file_date_updated":"2020-07-14T12:46:46Z","_id":"541","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_created":"2018-12-11T11:47:04Z","title":"Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations","date_updated":"2023-02-23T14:10:34Z","month":"12","date_published":"2017-12-18T00:00:00Z","ec_funded":1},{"doi":"10.5772/intechopen.69712","oa_version":"Published Version","publisher":"InTech","series_title":"Plant Engineering","day":"17","department":[{"_id":"JiFr"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2017","author":[{"last_name":"Mazur","full_name":"Mazur, Ewa","first_name":"Ewa"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"editor":[{"last_name":"Jurić","full_name":"Jurić, Snježana","first_name":"Snježana"}],"file":[{"file_id":"4969","creator":"system","date_created":"2018-12-12T10:12:49Z","relation":"main_file","checksum":"e1f05e5850dfd9f9434d2d373ca61941","file_size":7443683,"content_type":"application/pdf","date_updated":"2020-07-14T12:46:58Z","file_name":"IST-2018-929-v1+1_56106.pdf","access_level":"open_access"}],"citation":{"chicago":"Mazur, Ewa, and Jiří Friml. “Vascular Tissue Development and Regeneration in the Model Plant Arabidopsis.” In <i>Plant Engineering</i>, edited by Snježana Jurić, 113–40. Plant Engineering. InTech, 2017. <a href=\"https://doi.org/10.5772/intechopen.69712\">https://doi.org/10.5772/intechopen.69712</a>.","ama":"Mazur E, Friml J. Vascular tissue development and regeneration in the model plant arabidopsis. In: Jurić S, ed. <i>Plant Engineering</i>. Plant Engineering. InTech; 2017:113-140. doi:<a href=\"https://doi.org/10.5772/intechopen.69712\">10.5772/intechopen.69712</a>","ista":"Mazur E, Friml J. 2017.Vascular tissue development and regeneration in the model plant arabidopsis. In: Plant Engineering. Agricultural and Biological Sciences, , 113–140.","mla":"Mazur, Ewa, and Jiří Friml. “Vascular Tissue Development and Regeneration in the Model Plant Arabidopsis.” <i>Plant Engineering</i>, edited by Snježana Jurić, InTech, 2017, pp. 113–40, doi:<a href=\"https://doi.org/10.5772/intechopen.69712\">10.5772/intechopen.69712</a>.","apa":"Mazur, E., &#38; Friml, J. (2017). Vascular tissue development and regeneration in the model plant arabidopsis. In S. Jurić (Ed.), <i>Plant Engineering</i> (pp. 113–140). InTech. <a href=\"https://doi.org/10.5772/intechopen.69712\">https://doi.org/10.5772/intechopen.69712</a>","short":"E. Mazur, J. Friml, in:, S. Jurić (Ed.), Plant Engineering, InTech, 2017, pp. 113–140.","ieee":"E. Mazur and J. Friml, “Vascular tissue development and regeneration in the model plant arabidopsis,” in <i>Plant Engineering</i>, S. Jurić, Ed. InTech, 2017, pp. 113–140."},"type":"book_chapter","ddc":["581"],"publist_id":"7269","abstract":[{"lang":"eng","text":"Development of vascular tissue is a remarkable example of intercellular communication and coordinated development involving hormonal signaling and tissue polarity. Thus far, studies on vascular patterning and regeneration have been conducted mainly in trees—woody plants—with a well-developed layer of vascular cambium and secondary tissues. Trees are difficult to use as genetic models, i.e., due to long generation time, unstable environmental conditions, and lack of available mutants and transgenic lines. Therefore, the use of the main genetic model plant Arabidopsis thaliana (L.) Heynh., with a wealth of available marker and transgenic lines, provides a unique opportunity to address molecular mechanism of vascular tissue formation and regeneration. With specific treatments, the tiny weed Arabidopsis can serve as a model to understand the growth of mighty trees and interconnect a tree physiology with molecular genetics and cell biology of Arabidopsis."}],"publication_status":"published","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","publication":"Plant Engineering","pubrep_id":"929","file_date_updated":"2020-07-14T12:46:58Z","page":"113 - 140","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"_id":"545","date_created":"2018-12-11T11:47:05Z","title":"Vascular tissue development and regeneration in the model plant arabidopsis","date_updated":"2024-02-12T12:03:42Z","month":"11","date_published":"2017-11-17T00:00:00Z","ec_funded":1,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1274"}]},"alternative_title":["Agricultural and Biological Sciences"],"oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"}]