[{"publication_status":"published","citation":{"mla":"Liu, Zhijun, et al. “The CLE Gene Family in Populus Trichocarpa.” <i>Plant Signaling &#38; Behavior</i>, vol. 11, no. 6, e1191734, Taylor &#38; Francis, 2016, doi:<a href=\"https://doi.org/10.1080/15592324.2016.1191734\">10.1080/15592324.2016.1191734</a>.","apa":"Liu, Z., Yang, N., Lv, Y., Pan, L., Lv, S., Han, H., &#38; Wang, G. (2016). The CLE gene family in Populus trichocarpa. <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/15592324.2016.1191734\">https://doi.org/10.1080/15592324.2016.1191734</a>","chicago":"Liu, Zhijun, Nan Yang, Yanting Lv, Lixia Pan, Shuo Lv, Huibin Han, and Guodong Wang. “The CLE Gene Family in Populus Trichocarpa.” <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis, 2016. <a href=\"https://doi.org/10.1080/15592324.2016.1191734\">https://doi.org/10.1080/15592324.2016.1191734</a>.","ista":"Liu Z, Yang N, Lv Y, Pan L, Lv S, Han H, Wang G. 2016. The CLE gene family in Populus trichocarpa. Plant Signaling &#38; Behavior. 11(6), e1191734.","short":"Z. Liu, N. Yang, Y. Lv, L. Pan, S. Lv, H. Han, G. Wang, Plant Signaling &#38; Behavior 11 (2016).","ieee":"Z. Liu <i>et al.</i>, “The CLE gene family in Populus trichocarpa,” <i>Plant Signaling &#38; Behavior</i>, vol. 11, no. 6. Taylor &#38; Francis, 2016.","ama":"Liu Z, Yang N, Lv Y, et al. The CLE gene family in Populus trichocarpa. <i>Plant Signaling &#38; Behavior</i>. 2016;11(6). doi:<a href=\"https://doi.org/10.1080/15592324.2016.1191734\">10.1080/15592324.2016.1191734</a>"},"type":"journal_article","scopus_import":"1","abstract":[{"text":"The CLE (CLAVATA3/Embryo Surrounding Region-related) peptides are small secreted signaling peptides that are primarily involved in the regulation of stem cell homeostasis in different plant meristems. Particularly, the characterization of the CLE41-PXY/TDR signaling pathway has greatly advanced our understanding on the potential roles of CLE peptides in vascular development and wood formation. Nevertheless, our knowledge on this gene family in a tree species is limited. In a recent study, we reported on a systematically investigation of the CLE gene family in Populus trichocarpa . The potential roles of PtCLE genes were studied by comparative analysis and transcriptional pro fi ling. Among fi fty PtCLE members, many PtCLE proteins share identical CLE motifs or contain the same CLE motif as that of AtCLEs, while PtCLE genes exhibited either comparable or distinct expression patterns comparing to their Arabidopsis counterparts. These fi ndings indicate the existence of both functional conservation and functional divergence between PtCLEs and their AtCLE orthologues. Our results provide valuable resources for future functional investigations of these critical signaling molecules in woody plants. ","lang":"eng"}],"_id":"510","quality_controlled":"1","article_processing_charge":"No","department":[{"_id":"JiFr"}],"publist_id":"7308","language":[{"iso":"eng"}],"publisher":"Taylor & Francis","title":"The CLE gene family in Populus trichocarpa","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Liu","first_name":"Zhijun","full_name":"Liu, Zhijun"},{"last_name":"Yang","first_name":"Nan","full_name":"Yang, Nan"},{"last_name":"Lv","first_name":"Yanting","full_name":"Lv, Yanting"},{"full_name":"Pan, Lixia","first_name":"Lixia","last_name":"Pan"},{"first_name":"Shuo","last_name":"Lv","full_name":"Lv, Shuo"},{"full_name":"Han, Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin"},{"full_name":"Wang, Guodong","first_name":"Guodong","last_name":"Wang"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4973754/"}],"doi":"10.1080/15592324.2016.1191734","publication":"Plant Signaling & Behavior","oa_version":"Submitted Version","volume":11,"date_created":"2018-12-11T11:46:53Z","status":"public","day":"02","year":"2016","month":"06","intvolume":"        11","date_published":"2016-06-02T00:00:00Z","acknowledgement":"We are grateful to Dr. Long (Laboratoire de Reproduction et Developpement des Plantes,CNRS,INRA,ENSLyon,UCBL,Universite de Lyon,France)for critical reading of the article. Work in our group is supported by the National Natural Science Foundation of China (31271575; 31200902), the Fundamental Research Funds for the Central Univ ersities (GK201103005), the Specialized Research Fund for the Doctoral Program of Higher Education from the Ministry of Education of China (20120202120009), the Scientific Research Foundation for the Returned Overseas Chinese Scholars, State Education Ministry, and the Natural Science Basic Research Plan in Shaanxi Province of China (2014JM3064). ","article_number":"e1191734","date_updated":"2023-10-17T11:13:40Z","issue":"6","oa":1},{"author":[{"full_name":"Daniel von Wangenheim","last_name":"Von Wangenheim","orcid":"0000-0002-6862-1247","first_name":"Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fangerau, Jens","last_name":"Fangerau","first_name":"Jens"},{"last_name":"Schmitz","first_name":"Alexander","full_name":"Schmitz, Alexander"},{"last_name":"Smith","first_name":"Richard","full_name":"Smith, Richard S"},{"full_name":"Leitte, Heike","last_name":"Leitte","first_name":"Heike"},{"first_name":"Ernst","last_name":"Stelzer","full_name":"Stelzer, Ernst H"},{"last_name":"Maizel","first_name":"Alexis","full_name":"Maizel, Alexis"}],"title":"Rules and self-organizing properties of post-embryonic plant organ cell division patterns","issue":"4","date_updated":"2021-01-12T08:01:24Z","acknowledgement":"We thank M.J. Bennett, L. Laplaze, and S. Lemke for their helpful comments.\nThis work was supported by the Land Baden-Württemberg, the Chica und Heinz Schaller Stiftung, the CellNetworks cluster of excellence, and the Boehringer Ingelheim Fond (to J.F. and A.M.) and the Cluster of Excellence “Macromolecular Complexes” at the Goethe University Frankfurt am Main (CEF-MC II; DFG Project EXC 115; to D.v.W., A.S., and E.H.K.S.).\n","publisher":"Cell Press","date_published":"2016-02-22T00:00:00Z","month":"02","intvolume":"        26","year":"2016","publist_id":"7293","page":"439 - 449","quality_controlled":0,"status":"public","day":"22","_id":"526","date_created":"2018-12-11T11:46:58Z","abstract":[{"lang":"eng","text":"Plants form new organs with patterned tissue organization throughout their lifespan. It is unknown whether this robust post-embryonic organ formation results from stereotypic dynamic processes, in which the arrangement of cells follows rigid rules. Here, we combine modeling with empirical observations of whole-organ development to identify the principles governing lateral root formation in Arabidopsis. Lateral roots derive from a small pool of founder cells in which some take a dominant role as seen by lineage tracing. The first division of the founders is asymmetric, tightly regulated, and determines the formation of a layered structure. Whereas the pattern of subsequent cell divisions is not stereotypic between different samples, it is characterized by a regular switch in division plane orientation. This switch is also necessary for the appearance of patterned layers as a result of the apical growth of the primordium. Our data suggest that lateral root morphogenesis is based on a limited set of rules. They determine cell growth and division orientation. The organ-level coupling of the cell behavior ensures the emergence of the lateral root's characteristic features. We propose that self-organizing, non-deterministic modes of development account for the robustness of plant organ morphogenesis."}],"type":"journal_article","volume":26,"extern":1,"citation":{"mla":"von Wangenheim, Daniel, et al. “Rules and Self-Organizing Properties of Post-Embryonic Plant Organ Cell Division Patterns.” <i>Current Biology</i>, vol. 26, no. 4, Cell Press, 2016, pp. 439–49, doi:<a href=\"https://doi.org/10.1016/j.cub.2015.12.047\">10.1016/j.cub.2015.12.047</a>.","apa":"von Wangenheim, D., Fangerau, J., Schmitz, A., Smith, R., Leitte, H., Stelzer, E., &#38; Maizel, A. (2016). Rules and self-organizing properties of post-embryonic plant organ cell division patterns. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2015.12.047\">https://doi.org/10.1016/j.cub.2015.12.047</a>","chicago":"Wangenheim, Daniel von, Jens Fangerau, Alexander Schmitz, Richard Smith, Heike Leitte, Ernst Stelzer, and Alexis Maizel. “Rules and Self-Organizing Properties of Post-Embryonic Plant Organ Cell Division Patterns.” <i>Current Biology</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.cub.2015.12.047\">https://doi.org/10.1016/j.cub.2015.12.047</a>.","ama":"von Wangenheim D, Fangerau J, Schmitz A, et al. Rules and self-organizing properties of post-embryonic plant organ cell division patterns. <i>Current Biology</i>. 2016;26(4):439-449. doi:<a href=\"https://doi.org/10.1016/j.cub.2015.12.047\">10.1016/j.cub.2015.12.047</a>","ieee":"D. von Wangenheim <i>et al.</i>, “Rules and self-organizing properties of post-embryonic plant organ cell division patterns,” <i>Current Biology</i>, vol. 26, no. 4. Cell Press, pp. 439–449, 2016.","short":"D. von Wangenheim, J. Fangerau, A. Schmitz, R. Smith, H. Leitte, E. Stelzer, A. Maizel, Current Biology 26 (2016) 439–449.","ista":"von Wangenheim D, Fangerau J, Schmitz A, Smith R, Leitte H, Stelzer E, Maizel A. 2016. Rules and self-organizing properties of post-embryonic plant organ cell division patterns. Current Biology. 26(4), 439–449."},"publication":"Current Biology","doi":"10.1016/j.cub.2015.12.047","publication_status":"published"},{"publisher":"IST Austria","alternative_title":["IST Austria Technical Report"],"date_published":"2016-03-31T00:00:00Z","month":"03","has_accepted_license":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Quantitative interprocedural analysis","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"},{"last_name":"Velner","first_name":"Yaron","full_name":"Velner, Yaron"}],"file":[{"checksum":"cef516fa091925b5868813e355268fb4","relation":"main_file","access_level":"open_access","file_id":"5513","content_type":"application/pdf","creator":"system","file_size":1012204,"date_updated":"2020-07-14T12:46:58Z","date_created":"2018-12-12T11:53:52Z","file_name":"IST-2016-523-v1+1_main.pdf"}],"date_updated":"2023-02-23T10:06:22Z","department":[{"_id":"KrCh"}],"page":"33","year":"2016","pubrep_id":"523","language":[{"iso":"eng"}],"abstract":[{"text":"We consider the quantitative analysis problem for interprocedural control-flow graphs (ICFGs). The input consists of an ICFG, a positive weight function that assigns every transition a positive integer-valued number, and a labelling of the transitions (events) as good, bad, and neutral events. The weight function assigns to each transition a numerical value that represents ameasure of how good or bad an event is. The quantitative analysis problem asks whether there is a run of the ICFG where the ratio of the sum of the numerical weights of good events versus the sum of weights of bad events in the long-run is at least a given threshold (or equivalently, to compute the maximal ratio among all valid paths in the ICFG). The quantitative analysis problem for ICFGs can be solved in polynomial time, and we present an efficient and practical algorithm for the problem. We show that several problems relevant for static program analysis, such as estimating the worst-case execution time of a program or the average energy consumption of a mobile application, can be modeled in our framework. We have implemented our algorithm as a tool in the Java Soot framework. We demonstrate the effectiveness of our approach with two case studies. First, we show that our framework provides a sound approach (no false positives) for the analysis of inefficiently-used containers. Second, we show that our approach can also be used for static profiling of programs which reasons about methods that are frequently invoked. Our experimental results show that our tool scales to relatively large benchmarks, and discovers relevant and useful information that can be used to optimize performance of the programs. ","lang":"eng"}],"type":"technical_report","file_date_updated":"2020-07-14T12:46:58Z","publication_identifier":{"issn":["2664-1690"]},"citation":{"chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, and Yaron Velner. <i>Quantitative Interprocedural Analysis</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2016-523-v1-1\">https://doi.org/10.15479/AT:IST-2016-523-v1-1</a>.","ama":"Chatterjee K, Pavlogiannis A, Velner Y. <i>Quantitative Interprocedural Analysis</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-523-v1-1\">10.15479/AT:IST-2016-523-v1-1</a>","ista":"Chatterjee K, Pavlogiannis A, Velner Y. 2016. Quantitative interprocedural analysis, IST Austria, 33p.","ieee":"K. Chatterjee, A. Pavlogiannis, and Y. Velner, <i>Quantitative interprocedural analysis</i>. IST Austria, 2016.","short":"K. Chatterjee, A. Pavlogiannis, Y. Velner, Quantitative Interprocedural Analysis, IST Austria, 2016.","mla":"Chatterjee, Krishnendu, et al. <i>Quantitative Interprocedural Analysis</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-523-v1-1\">10.15479/AT:IST-2016-523-v1-1</a>.","apa":"Chatterjee, K., Pavlogiannis, A., &#38; Velner, Y. (2016). <i>Quantitative interprocedural analysis</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2016-523-v1-1\">https://doi.org/10.15479/AT:IST-2016-523-v1-1</a>"},"status":"public","day":"31","_id":"5445","date_created":"2018-12-12T11:39:22Z","ddc":["005"],"publication_status":"published","doi":"10.15479/AT:IST-2016-523-v1-1","oa_version":"Published Version","related_material":{"record":[{"id":"1604","relation":"later_version","status":"public"}]}},{"publication_identifier":{"issn":["2664-1690"]},"citation":{"mla":"Anonymous, 1, et al. <i>Termination and Worst-Case Analysis of Recursive Programs</i>. IST Austria, 2016.","apa":"Anonymous, 1, Anonymous, 2, &#38; Anonymous, 3. (2016). <i>Termination and worst-case analysis of recursive programs</i>. IST Austria.","chicago":"Anonymous, 1, 2 Anonymous, and 3 Anonymous. <i>Termination and Worst-Case Analysis of Recursive Programs</i>. IST Austria, 2016.","short":"1 Anonymous, 2 Anonymous, 3 Anonymous, Termination and Worst-Case Analysis of Recursive Programs, IST Austria, 2016.","ista":"Anonymous 1, Anonymous 2, Anonymous 3. 2016. Termination and worst-case analysis of recursive programs, IST Austria, 26p.","ieee":"1 Anonymous, 2 Anonymous, and 3 Anonymous, <i>Termination and worst-case analysis of recursive programs</i>. IST Austria, 2016.","ama":"Anonymous 1, Anonymous 2, Anonymous 3. <i>Termination and Worst-Case Analysis of Recursive Programs</i>. IST Austria; 2016."},"abstract":[{"text":"We study the problem of developing efficient approaches for proving termination of recursive programs with one-dimensional arrays. Ranking functions serve as a sound and complete approach for proving termination of non-recursive programs without array operations. First, we generalize ranking functions to the notion of measure functions, and prove that measure functions (i) provide a sound method to prove termination of recursive programs (with one-dimensional arrays), and (ii) is both sound and complete over recursive programs without array operations. Our second contribution is the synthesis of measure functions of specific forms in polynomial time. More precisely, we prove that (i) polynomial measure functions over recursive programs can be synthesized in polynomial time through Farkas’ Lemma and Handelman’s Theorem, and (ii) measure functions involving logarithm and exponentiation can be synthesized in polynomial time through abstraction of logarithmic or exponential terms and Handelman’s Theorem. A key application of our method is the worst-case analysis of recursive programs. While previous methods obtain worst-case polynomial bounds of the form O(n^k), where k is an integer, our polynomial time methods can synthesize bounds of the form O(n log n), as well as O(n^x), where x is not an integer. We show the applicability of our automated technique to obtain worst-case complexity of classical recursive algorithms such as (i) Merge-Sort, the divideand-\r\nconquer algorithm for the Closest-Pair problem, where we obtain O(n log n) worst-case bound, and (ii) Karatsuba’s algorithm for polynomial multiplication and Strassen’s algorithm for matrix multiplication, where we obtain O(n^x) bound, where x is not an integer and close to the best-known bounds for the respective algorithms. Finally, we present experimental results to demonstrate the\r\neffectiveness of our approach.","lang":"eng"}],"type":"technical_report","file_date_updated":"2020-07-14T12:46:58Z","date_created":"2018-12-12T11:39:23Z","_id":"5446","ddc":["000"],"day":"15","status":"public","publication_status":"published","oa_version":"Published Version","date_published":"2016-07-15T00:00:00Z","alternative_title":["IST Austria Technical Report"],"has_accepted_license":"1","month":"07","publisher":"IST Austria","date_updated":"2020-07-14T23:05:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"1","last_name":"Anonymous","full_name":"Anonymous, 1"},{"last_name":"Anonymous","first_name":"2","full_name":"Anonymous, 2"},{"last_name":"Anonymous","first_name":"3","full_name":"Anonymous, 3"}],"title":"Termination and worst-case analysis of recursive programs","oa":1,"file":[{"file_name":"popl2017a.pdf","date_updated":"2020-07-14T12:46:58Z","date_created":"2019-05-10T13:27:24Z","file_size":686241,"creator":"dernst","file_id":"6403","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"689069a7abbb34b21516164cbee9e0df"},{"relation":"main_file","access_level":"closed","checksum":"fc08022bfbaac07bac047a9407c0bbb3","creator":"dernst","file_size":258,"file_id":"6404","content_type":"text/plain","date_updated":"2020-07-14T12:46:58Z","date_created":"2019-05-10T13:27:31Z","file_name":"author_names.txt"}],"page":"26","language":[{"iso":"eng"}],"year":"2016","pubrep_id":"618"},{"publisher":"IST Austria","has_accepted_license":"1","month":"07","alternative_title":["IST Austria Technical Report"],"date_published":"2016-07-15T00:00:00Z","file":[{"date_created":"2019-05-10T13:32:16Z","date_updated":"2020-07-14T12:46:58Z","file_name":"listofauthors.txt","checksum":"cf53cdb6d092e68db0b4a0a1506ef8fb","relation":"main_file","access_level":"closed","creator":"dernst","file_size":281,"content_type":"text/plain","file_id":"6406"},{"content_type":"application/pdf","file_id":"6407","creator":"dernst","file_size":563642,"relation":"main_file","checksum":"7bdd94ba13aa0dec9c46887fcf13870b","access_level":"open_access","file_name":"popl2017b.pdf","date_created":"2019-05-10T13:32:16Z","date_updated":"2020-07-14T12:46:58Z"}],"author":[{"last_name":"Anonymous","first_name":"1","full_name":"Anonymous, 1"},{"full_name":"Anonymous, 2","first_name":"2","last_name":"Anonymous"},{"full_name":"Anonymous, 3","first_name":"3","last_name":"Anonymous"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"Average-case analysis of programs: Automated recurrence analysis for almost-linear bounds","date_updated":"2020-07-14T23:05:06Z","page":"20","year":"2016","pubrep_id":"619","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:46:58Z","type":"technical_report","abstract":[{"lang":"eng","text":"We consider the problem of developing automated techniques to aid the average-case complexity analysis of programs. Several classical textbook algorithms have quite efficient average-case complexity, whereas the corresponding worst-case bounds are either inefficient (e.g., QUICK-SORT), or completely ineffective (e.g., COUPONCOLLECTOR). Since the main focus of average-case analysis is to obtain efficient bounds, we consider bounds that are either logarithmic,\r\nlinear, or almost-linear (O(log n), O(n), O(n · log n),\r\nrespectively, where n represents the size of the input). Our main contribution is a sound approach for deriving such average-case bounds for randomized recursive programs. Our approach is efficient (a simple linear-time algorithm), and it is based on (a) the analysis of recurrence relations induced by randomized algorithms, and (b) a guess-and-check technique. Our approach can infer the asymptotically optimal average-case bounds for classical randomized algorithms, including RANDOMIZED-SEARCH, QUICKSORT, QUICK-SELECT, COUPON-COLLECTOR, where the worstcase\r\nbounds are either inefficient (such as linear as compared to logarithmic of average-case, or quadratic as compared to linear or almost-linear of average-case), or ineffective. We have implemented our approach, and the experimental results show that we obtain the bounds efficiently for various classical algorithms."}],"publication_identifier":{"issn":["2664-1690"]},"citation":{"mla":"Anonymous, 1, et al. <i>Average-Case Analysis of Programs: Automated Recurrence Analysis for Almost-Linear Bounds</i>. IST Austria, 2016.","apa":"Anonymous, 1, Anonymous, 2, &#38; Anonymous, 3. (2016). <i>Average-case analysis of programs: Automated recurrence analysis for almost-linear bounds</i>. IST Austria.","chicago":"Anonymous, 1, 2 Anonymous, and 3 Anonymous. <i>Average-Case Analysis of Programs: Automated Recurrence Analysis for Almost-Linear Bounds</i>. IST Austria, 2016.","ama":"Anonymous 1, Anonymous 2, Anonymous 3. <i>Average-Case Analysis of Programs: Automated Recurrence Analysis for Almost-Linear Bounds</i>. IST Austria; 2016.","ista":"Anonymous 1, Anonymous 2, Anonymous 3. 2016. Average-case analysis of programs: Automated recurrence analysis for almost-linear bounds, IST Austria, 20p.","ieee":"1 Anonymous, 2 Anonymous, and 3 Anonymous, <i>Average-case analysis of programs: Automated recurrence analysis for almost-linear bounds</i>. IST Austria, 2016.","short":"1 Anonymous, 2 Anonymous, 3 Anonymous, Average-Case Analysis of Programs: Automated Recurrence Analysis for Almost-Linear Bounds, IST Austria, 2016."},"day":"15","status":"public","ddc":["000"],"_id":"5447","date_created":"2018-12-12T11:39:23Z","publication_status":"published","oa_version":"Published Version"},{"page":"20","external_id":{"arxiv":["1610.01188"]},"language":[{"iso":"eng"}],"year":"2016","pubrep_id":"620","date_published":"2016-07-15T00:00:00Z","alternative_title":["IST Austria Technical Report"],"month":"07","has_accepted_license":"1","publisher":"IST Austria","date_updated":"2023-02-23T12:27:16Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"author":[{"full_name":"Anonymous, 1","first_name":"1","last_name":"Anonymous"},{"last_name":"Anonymous","first_name":"2","full_name":"Anonymous, 2"},{"first_name":"3","last_name":"Anonymous","full_name":"Anonymous, 3"},{"first_name":"4","last_name":"Anonymous","full_name":"Anonymous, 4"}],"title":"Data-centric dynamic partial order reduction","file":[{"file_name":"IST-2016-620-v1+1_main.pdf","date_updated":"2020-07-14T12:46:58Z","date_created":"2018-12-12T11:53:45Z","creator":"system","file_size":538881,"content_type":"application/pdf","file_id":"5506","checksum":"1d69252d66bcdf782615ddfb911d2957","access_level":"open_access","relation":"main_file"},{"file_size":121,"creator":"dernst","file_id":"6405","content_type":"text/plain","relation":"main_file","checksum":"deabb0eb8f237cae4f9542b28b0b6eb2","access_level":"closed","file_name":"authornames.txt","date_updated":"2020-07-14T12:46:58Z","date_created":"2019-05-10T13:30:40Z"}],"publication_status":"published","related_material":{"record":[{"id":"10417","status":"public","relation":"later_version"},{"id":"5456","relation":"later_version","status":"public"}]},"oa_version":"Published Version","citation":{"chicago":"Anonymous, 1, 2 Anonymous, 3 Anonymous, and 4 Anonymous. <i>Data-Centric Dynamic Partial Order Reduction</i>. IST Austria, 2016.","ama":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. <i>Data-Centric Dynamic Partial Order Reduction</i>. IST Austria; 2016.","ista":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. 2016. Data-centric dynamic partial order reduction, IST Austria, 20p.","short":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, Data-Centric Dynamic Partial Order Reduction, IST Austria, 2016.","ieee":"1 Anonymous, 2 Anonymous, 3 Anonymous, and 4 Anonymous, <i>Data-centric dynamic partial order reduction</i>. IST Austria, 2016.","mla":"Anonymous, 1, et al. <i>Data-Centric Dynamic Partial Order Reduction</i>. IST Austria, 2016.","apa":"Anonymous, 1, Anonymous, 2, Anonymous, 3, &#38; Anonymous, 4. (2016). <i>Data-centric dynamic partial order reduction</i>. IST Austria."},"publication_identifier":{"issn":["2664-1690"]},"abstract":[{"lang":"eng","text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.\r\n1. For acyclic architectures, our algorithm is guaranteed to explore exactly one representative trace from each observation class, while spending polynomial time per class. Hence, our algorithm is optimal wrt the observation equivalence, and in several cases explores exponentially fewer traces than any enumerative method based on the Mazurkiewicz equivalence.\r\n2. For cyclic architectures, we consider an equivalence between traces which is finer than the observation equivalence; but coarser than the Mazurkiewicz equivalence, and in some cases is exponentially coarser. Our data-centric DPOR algorithm remains optimal under this trace equivalence. \r\nFinally, we perform a basic experimental comparison between the existing Mazurkiewicz-based DPOR and our data-centric DPOR on a set of academic benchmarks. Our results show a significant reduction in both running time and the number of explored equivalence classes."}],"arxiv":1,"type":"technical_report","file_date_updated":"2020-07-14T12:46:58Z","_id":"5448","date_created":"2018-12-12T11:39:23Z","ddc":["000"],"status":"public","day":"15"},{"_id":"5449","ddc":["519"],"date_created":"2018-12-12T11:39:24Z","day":"09","status":"public","citation":{"chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Amplification on Undirected Population Structures: Comets Beat Stars</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">https://doi.org/10.15479/AT:IST-2016-648-v1-1</a>.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Amplification on undirected population structures: Comets beat stars, IST Austria, 22p.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Amplification on undirected population structures: Comets beat stars</i>. IST Austria, 2016.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Amplification on Undirected Population Structures: Comets Beat Stars, IST Austria, 2016.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Amplification on Undirected Population Structures: Comets Beat Stars</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">10.15479/AT:IST-2016-648-v1-1</a>","mla":"Pavlogiannis, Andreas, et al. <i>Amplification on Undirected Population Structures: Comets Beat Stars</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">10.15479/AT:IST-2016-648-v1-1</a>.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Amplification on undirected population structures: Comets beat stars</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">https://doi.org/10.15479/AT:IST-2016-648-v1-1</a>"},"publication_identifier":{"issn":["2664-1690"]},"type":"technical_report","file_date_updated":"2020-07-14T12:46:58Z","abstract":[{"lang":"eng","text":"The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population.\r\nThe fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure.\r\nAmplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade.\r\nIn this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Comet-swarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively."}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"512"}]},"oa_version":"Updated Version","publication_status":"published","doi":"10.15479/AT:IST-2016-648-v1-1","date_updated":"2023-02-23T12:22:21Z","file":[{"relation":"main_file","access_level":"open_access","checksum":"8345a8c1e7d7f0cd92516d182b7fc59e","content_type":"application/pdf","file_id":"5529","file_size":1264221,"creator":"system","date_updated":"2020-07-14T12:46:58Z","date_created":"2018-12-12T11:54:07Z","file_name":"IST-2016-648-v1+1_tr.pdf"}],"oa":1,"title":"Amplification on undirected population structures: Comets beat stars","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas"},{"orcid":"0000-0002-1097-9684","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef","full_name":"Tkadlec, Josef"},{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"month":"11","has_accepted_license":"1","alternative_title":["IST Austria Technical Report"],"date_published":"2016-11-09T00:00:00Z","publisher":"IST Austria","language":[{"iso":"eng"}],"pubrep_id":"648","year":"2016","page":"22","department":[{"_id":"KrCh"}]},{"page":"34","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"pubrep_id":"728","year":"2016","has_accepted_license":"1","month":"12","alternative_title":["IST Austria Technical Report"],"date_published":"2016-12-30T00:00:00Z","publisher":"IST Austria","date_updated":"2023-02-23T12:27:05Z","file":[{"creator":"system","file_size":1014732,"file_id":"5465","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"7b8bb17c322c0556acba6ac169fa71c1","file_name":"IST-2016-728-v1+1_main.pdf","date_updated":"2020-07-14T12:46:59Z","date_created":"2018-12-12T11:53:04Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"Strong amplifiers of natural selection","author":[{"last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Pavlogiannis, Andreas"},{"full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","last_name":"Tkadlec","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"doi":"10.15479/AT:IST-2016-728-v1-1","publication_status":"published","oa_version":"Published Version","publication_identifier":{"issn":["2664-1690"]},"citation":{"ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Strong Amplifiers of Natural Selection</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">10.15479/AT:IST-2016-728-v1-1</a>","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Strong amplifiers of natural selection</i>. IST Austria, 2016.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Strong amplifiers of natural selection, IST Austria, 34p.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Strong Amplifiers of Natural Selection, IST Austria, 2016.","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Strong Amplifiers of Natural Selection</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">https://doi.org/10.15479/AT:IST-2016-728-v1-1</a>.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Strong amplifiers of natural selection</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">https://doi.org/10.15479/AT:IST-2016-728-v1-1</a>","mla":"Pavlogiannis, Andreas, et al. <i>Strong Amplifiers of Natural Selection</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">10.15479/AT:IST-2016-728-v1-1</a>."},"type":"technical_report","file_date_updated":"2020-07-14T12:46:59Z","ddc":["000"],"_id":"5451","date_created":"2018-12-12T11:39:24Z","status":"public","day":"30"},{"publisher":"IST Austria","has_accepted_license":"1","file":[{"file_name":"IST-2017-728-v2+1_main.pdf","date_updated":"2020-07-14T12:46:59Z","date_created":"2018-12-12T11:52:59Z","creator":"system","file_size":811558,"content_type":"application/pdf","file_id":"5460","access_level":"open_access","relation":"main_file","checksum":"58e895f26c82f560c0f0989bf8b08599"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis"},{"full_name":"Tkadlec, Josef","last_name":"Tkadlec","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"title":"Arbitrarily strong amplifiers of natural selection","department":[{"_id":"KrCh"}],"article_processing_charge":"No","pubrep_id":"750","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:46:59Z","type":"technical_report","publication_identifier":{"issn":["2664-1690"]},"citation":{"apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Arbitrarily strong amplifiers of natural selection</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2017-728-v2-1\">https://doi.org/10.15479/AT:IST-2017-728-v2-1</a>","mla":"Pavlogiannis, Andreas, et al. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-728-v2-1\">10.15479/AT:IST-2017-728-v2-1</a>.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-728-v2-1\">10.15479/AT:IST-2017-728-v2-1</a>","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Arbitrarily Strong Amplifiers of Natural Selection, IST Austria, 2016.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Arbitrarily strong amplifiers of natural selection</i>. IST Austria, 2016.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Arbitrarily strong amplifiers of natural selection, IST Austria, 32p.","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2017-728-v2-1\">https://doi.org/10.15479/AT:IST-2017-728-v2-1</a>."},"_id":"5452","publication_status":"published","project":[{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"month":"12","date_published":"2016-12-30T00:00:00Z","alternative_title":["IST Austria Technical Report"],"oa":1,"date_updated":"2024-02-21T13:48:42Z","page":"32","year":"2016","status":"public","day":"30","ddc":["000"],"date_created":"2018-12-12T11:39:25Z","doi":"10.15479/AT:IST-2017-728-v2-1","oa_version":"Published Version","ec_funded":1,"related_material":{"record":[{"relation":"later_version","status":"public","id":"5453"},{"id":"5559","status":"public","relation":"popular_science"}]}},{"date_created":"2018-12-12T11:39:25Z","_id":"5453","ddc":["000"],"status":"public","day":"30","publication_identifier":{"issn":["2664-1690"]},"citation":{"apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Arbitrarily strong amplifiers of natural selection</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2017-749-v3-1\">https://doi.org/10.15479/AT:IST-2017-749-v3-1</a>","mla":"Pavlogiannis, Andreas, et al. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-749-v3-1\">10.15479/AT:IST-2017-749-v3-1</a>.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-749-v3-1\">10.15479/AT:IST-2017-749-v3-1</a>","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Arbitrarily strong amplifiers of natural selection</i>. IST Austria, 2016.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Arbitrarily Strong Amplifiers of Natural Selection, IST Austria, 2016.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Arbitrarily strong amplifiers of natural selection, IST Austria, 34p.","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2017-749-v3-1\">https://doi.org/10.15479/AT:IST-2017-749-v3-1</a>."},"type":"technical_report","file_date_updated":"2020-07-14T12:46:59Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5452"}]},"oa_version":"Published Version","publication_status":"published","doi":"10.15479/AT:IST-2017-749-v3-1","date_updated":"2023-02-23T12:27:07Z","file":[{"content_type":"application/pdf","file_id":"5474","file_size":1015647,"creator":"system","relation":"main_file","checksum":"83b0313dab3bff4bdb6ac38695026fda","access_level":"open_access","file_name":"IST-2017-749-v3+1_main.pdf","date_created":"2018-12-12T11:53:13Z","date_updated":"2020-07-14T12:46:59Z"}],"author":[{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"},{"full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","last_name":"Tkadlec","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Arbitrarily strong amplifiers of natural selection","month":"12","has_accepted_license":"1","alternative_title":["IST Austria Technical Report"],"date_published":"2016-12-30T00:00:00Z","publisher":"IST Austria","language":[{"iso":"eng"}],"year":"2016","pubrep_id":"755","page":"34","department":[{"_id":"KrCh"}]},{"has_accepted_license":"1","month":"02","date_published":"2016-02-19T00:00:00Z","datarep_id":"34","publisher":"Institute of Science and Technology Austria","date_updated":"2024-02-21T13:49:54Z","file":[{"file_name":"IST-2016-34-v1+1_tellis_flower_colour_data.zip","date_updated":"2020-07-14T12:47:00Z","date_created":"2018-12-12T13:02:27Z","file_size":4468543,"creator":"system","file_id":"5594","content_type":"application/zip","relation":"main_file","checksum":"950f85b80427d357bfeff09608ba02e9","access_level":"open_access"}],"oa":1,"author":[{"full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"full_name":"Field, David","last_name":"Field","orcid":"0000-0002-4014-8478","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"}],"title":"Flower colour data and phylogeny (NEXUS) files","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publist_id":"5828","license":"https://creativecommons.org/publicdomain/zero/1.0/","department":[{"_id":"NiBa"}],"year":"2016","citation":{"apa":"Ellis, T., &#38; Field, D. (2016). Flower colour data and phylogeny (NEXUS) files. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:34\">https://doi.org/10.15479/AT:ISTA:34</a>","mla":"Ellis, Thomas, and David Field. <i>Flower Colour Data and Phylogeny (NEXUS) Files</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>.","ama":"Ellis T, Field D. Flower colour data and phylogeny (NEXUS) files. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>","short":"T. Ellis, D. Field, (2016).","ista":"Ellis T, Field D. 2016. Flower colour data and phylogeny (NEXUS) files, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>.","ieee":"T. Ellis and D. Field, “Flower colour data and phylogeny (NEXUS) files.” Institute of Science and Technology Austria, 2016.","chicago":"Ellis, Thomas, and David Field. “Flower Colour Data and Phylogeny (NEXUS) Files.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:34\">https://doi.org/10.15479/AT:ISTA:34</a>."},"file_date_updated":"2020-07-14T12:47:00Z","type":"research_data","abstract":[{"text":"We collected flower colour information on species in the tribe Antirrhineae from taxonomic literature. We also retreived molecular data from GenBank for as many of these species as possible to estimate phylogenetic relationships among these taxa. We then used the R package 'diversitree' to examine patterns of evolutionary transitions between anthocyanin and yellow pigmentation across the phylogeny.\r\n\r\nFor full details of the methods see:\r\nEllis TJ and Field DL \"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae”, Annals of Botany (in press)","lang":"eng"}],"date_created":"2018-12-12T12:31:29Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"_id":"5550","ddc":["576"],"day":"19","status":"public","doi":"10.15479/AT:ISTA:34","related_material":{"record":[{"id":"1382","relation":"research_paper","status":"public"}]},"oa_version":"Published Version"},{"file_date_updated":"2020-07-14T12:47:01Z","type":"research_data","abstract":[{"text":"Data from array experiments investigating pollinator behaviour on snapdragons in controlled conditions, and their effect on plant mating. Data were collected as part of Tom Ellis' PhD thesis , submitted February 2016.\r\n\r\nWe placed a total of 36 plants in a grid inside a closed organza tent, with a single hive of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus, at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6.\r\n\r\nAfter 24 hours to learn how to deal with snapdragons, I observed pollinators foraging on plants, and recorded the transitions between plants. Thereafter seeds on plants were allowed to develops. A sample of these were grown to maturity when their flower colour could be determined, and they were scored as yellow, magenta, or hybrid.","lang":"eng"}],"citation":{"chicago":"Ellis, Thomas. “Data on Pollinator Observations and Offpsring Phenotypes.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:35\">https://doi.org/10.15479/AT:ISTA:35</a>.","ama":"Ellis T. Data on pollinator observations and offpsring phenotypes. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:35\">10.15479/AT:ISTA:35</a>","ieee":"T. Ellis, “Data on pollinator observations and offpsring phenotypes.” Institute of Science and Technology Austria, 2016.","short":"T. Ellis, (2016).","ista":"Ellis T. 2016. Data on pollinator observations and offpsring phenotypes, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:35\">10.15479/AT:ISTA:35</a>.","mla":"Ellis, Thomas. <i>Data on Pollinator Observations and Offpsring Phenotypes</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:35\">10.15479/AT:ISTA:35</a>.","apa":"Ellis, T. (2016). Data on pollinator observations and offpsring phenotypes. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:35\">https://doi.org/10.15479/AT:ISTA:35</a>"},"status":"public","day":"19","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"date_created":"2018-12-12T12:31:29Z","_id":"5551","doi":"10.15479/AT:ISTA:35","oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"research_paper","id":"1398"}]},"contributor":[{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","month":"02","datarep_id":"35","date_published":"2016-02-19T00:00:00Z","file":[{"date_updated":"2020-07-14T12:47:01Z","date_created":"2018-12-12T13:05:12Z","file_name":"IST-2016-35-v1+1_array_data.zip","relation":"main_file","access_level":"open_access","checksum":"aa3eb85d52b110cd192aa23147c4d4f3","file_id":"5640","content_type":"application/zip","file_size":32775,"creator":"system"}],"title":"Data on pollinator observations and offpsring phenotypes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"author":[{"full_name":"Ellis, Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","orcid":"0000-0002-8511-0254","last_name":"Ellis"}],"date_updated":"2024-02-21T13:51:27Z","department":[{"_id":"NiBa"}],"article_processing_charge":"No","year":"2016"},{"article_processing_charge":"No","department":[{"_id":"NiBa"}],"year":"2016","has_accepted_license":"1","month":"02","date_published":"2016-02-19T00:00:00Z","datarep_id":"36","publisher":"Institute of Science and Technology Austria","date_updated":"2024-02-21T13:51:40Z","file":[{"file_name":"IST-2016-36-v1+1_tag_assay_archive.zip","date_created":"2018-12-12T13:03:07Z","date_updated":"2020-07-14T12:47:01Z","file_size":44905,"creator":"system","content_type":"application/zip","file_id":"5625","checksum":"cbc61b523d4d475a04a737d50dc470ef","access_level":"open_access","relation":"main_file"}],"author":[{"full_name":"Ellis, Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","orcid":"0000-0002-8511-0254","last_name":"Ellis"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.","doi":"10.15479/AT:ISTA:36","related_material":{"record":[{"id":"1398","status":"public","relation":"research_paper"}]},"contributor":[{"last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"oa_version":"Published Version","citation":{"apa":"Ellis, T. (2016). Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:36\">https://doi.org/10.15479/AT:ISTA:36</a>","mla":"Ellis, Thomas. <i>Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data.</i> Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:36\">10.15479/AT:ISTA:36</a>.","ama":"Ellis T. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:36\">10.15479/AT:ISTA:36</a>","short":"T. Ellis, (2016).","ieee":"T. Ellis, “Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.” Institute of Science and Technology Austria, 2016.","ista":"Ellis T. 2016. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data., Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:36\">10.15479/AT:ISTA:36</a>.","chicago":"Ellis, Thomas. “Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:36\">https://doi.org/10.15479/AT:ISTA:36</a>."},"type":"research_data","file_date_updated":"2020-07-14T12:47:01Z","abstract":[{"lang":"eng","text":"Data on pollinator visitation to wild snapdragons in a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted February 2016).\r\n\r\nSnapdragon flowers have a mouth-like structure which pollinators must open to access nectar. We placed 5mm cellophane tags in these mouths, which are held in place by the pressure of the flower until a pollinator visits. When she opens the flower, the tag drops out, and one can infer a visit. We surveyed plants over multiple days in 2010, 2011 and 2012.\r\n\r\nAlso included are data on phenotypic and demographic variables which may be explanatory variables for pollinator visitation."}],"date_created":"2018-12-12T12:31:30Z","_id":"5552","day":"19","status":"public"},{"doi":"10.15479/AT:ISTA:37","oa_version":"Published Version","contributor":[{"contributor_type":"project_manager","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"related_material":{"record":[{"id":"1398","relation":"research_paper","status":"public"}]},"abstract":[{"text":"Genotypic, phenotypic and demographic data for 2128 wild snapdragons and 1127 open-pollinated progeny from a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted) February 2016).\r\n\r\nTissue samples were sent to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been removed from this dataset.\r\n\r\nOther data were retreived from an online database of this population at www.antspec.org.","lang":"eng"}],"type":"research_data","file_date_updated":"2020-07-14T12:47:01Z","citation":{"apa":"Field, D., &#38; Ellis, T. (2016). Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:37\">https://doi.org/10.15479/AT:ISTA:37</a>","mla":"Field, David, and Thomas Ellis. <i>Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>.","short":"D. Field, T. Ellis, (2016).","ieee":"D. Field and T. Ellis, “Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012.” Institute of Science and Technology Austria, 2016.","ista":"Field D, Ellis T. 2016. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>.","ama":"Field D, Ellis T. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>","chicago":"Field, David, and Thomas Ellis. “Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:37\">https://doi.org/10.15479/AT:ISTA:37</a>."},"day":"19","status":"public","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"date_created":"2018-12-12T12:31:30Z","_id":"5553","ddc":["576"],"department":[{"_id":"NiBa"}],"article_processing_charge":"No","year":"2016","publisher":"Institute of Science and Technology Austria","date_published":"2016-02-19T00:00:00Z","datarep_id":"37","month":"02","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"author":[{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","orcid":"0000-0002-4014-8478","full_name":"Field, David"},{"last_name":"Ellis","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","full_name":"Ellis, Thomas"}],"title":"Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012","file":[{"date_created":"2018-12-12T13:03:02Z","date_updated":"2020-07-14T12:47:01Z","file_name":"IST-2016-37-v1+1_paternity_archive.zip","relation":"main_file","checksum":"4ae751b1fa4897fa216241f975a57313","access_level":"open_access","file_size":132808,"creator":"system","file_id":"5620","content_type":"application/zip"}],"keyword":["paternity assignment","pedigree","matting patterns","assortative mating","Antirrhinum majus","frequency-dependent selection","plant-pollinator interaction"],"date_updated":"2024-02-21T13:51:14Z"},{"year":"2016","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"article_processing_charge":"No","file":[{"file_name":"IST-2016-43-v1+1_DATA_MTugrul_PhDThesis_Chapter3.zip","date_updated":"2020-07-14T12:47:01Z","date_created":"2018-12-12T13:03:08Z","content_type":"application/zip","file_id":"5626","file_size":1123495,"creator":"system","relation":"main_file","checksum":"1fc0a10bb7ce110fcb5e1fbe3cf0c4e2","access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase","author":[{"last_name":"Tugrul","orcid":"0000-0002-8523-0758","first_name":"Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","full_name":"Tugrul, Murat"}],"date_updated":"2024-02-21T13:50:34Z","keyword":["RNAP binding","de novo promoter evolution","lac promoter"],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","month":"05","datarep_id":"43","date_published":"2016-05-12T00:00:00Z","oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1131"}]},"contributor":[{"last_name":"Steinrück","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","first_name":"Magdalena","contributor_type":"researcher"},{"last_name":"Jesse","first_name":"Fabienne","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher"}],"doi":"10.15479/AT:ISTA:43","status":"public","day":"12","date_created":"2018-12-12T12:31:30Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"_id":"5554","type":"research_data","file_date_updated":"2020-07-14T12:47:01Z","abstract":[{"text":"The data stored here is used in Murat Tugrul's PhD thesis (Chapter 3), which is related to the evolution of bacterial RNA polymerase binding.\r\nMagdalena Steinrueck (PhD Student in Calin Guet's group at IST Austria) performed the experiments and created the data on de novo promoter evolution. Fabienne Jesse (PhD Student in Jon Bollback's group at IST Austria) performed the experiments and created the data on lac promoter evolution.","lang":"eng"}],"citation":{"ista":"Tugrul M. 2016. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:43\">10.15479/AT:ISTA:43</a>.","ieee":"M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016.","short":"M. Tugrul, (2016).","ama":"Tugrul M. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:43\">10.15479/AT:ISTA:43</a>","chicago":"Tugrul, Murat. “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:43\">https://doi.org/10.15479/AT:ISTA:43</a>.","apa":"Tugrul, M. (2016). Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:43\">https://doi.org/10.15479/AT:ISTA:43</a>","mla":"Tugrul, Murat. <i>Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:43\">10.15479/AT:ISTA:43</a>."}},{"doi":"10.15479/AT:ISTA:44","oa_version":"Published Version","citation":{"chicago":"Hauschild, Robert. “Fiji Script to Determine Average Speed and Direction of Migration of Cells.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:44\">https://doi.org/10.15479/AT:ISTA:44</a>.","ama":"Hauschild R. Fiji script to determine average speed and direction of migration of cells. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:44\">10.15479/AT:ISTA:44</a>","ista":"Hauschild R. 2016. Fiji script to determine average speed and direction of migration of cells, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:44\">10.15479/AT:ISTA:44</a>.","ieee":"R. Hauschild, “Fiji script to determine average speed and direction of migration of cells.” Institute of Science and Technology Austria, 2016.","short":"R. Hauschild, (2016).","mla":"Hauschild, Robert. <i>Fiji Script to Determine Average Speed and Direction of Migration of Cells</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:44\">10.15479/AT:ISTA:44</a>.","apa":"Hauschild, R. (2016). Fiji script to determine average speed and direction of migration of cells. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:44\">https://doi.org/10.15479/AT:ISTA:44</a>"},"file_date_updated":"2020-07-14T12:47:02Z","type":"research_data","abstract":[{"text":"This FIJI script calculates the population average of the migration speed as a function of time of all cells from wide field microscopy movies.","lang":"eng"}],"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"_id":"5555","ddc":["570"],"date_created":"2018-12-12T12:31:31Z","status":"public","day":"08","article_processing_charge":"No","department":[{"_id":"Bio"}],"year":"2016","has_accepted_license":"1","month":"07","datarep_id":"44","date_published":"2016-07-08T00:00:00Z","publisher":"Institute of Science and Technology Austria","date_updated":"2024-02-21T13:50:06Z","keyword":["cell migration","wide field microscopy","FIJI"],"file":[{"file_name":"IST-2016-44-v1+1_migrationAnalyzer.zip","date_updated":"2020-07-14T12:47:02Z","date_created":"2018-12-12T13:03:03Z","content_type":"application/zip","file_id":"5621","creator":"system","file_size":20692,"access_level":"open_access","relation":"main_file","checksum":"9f96cddbcd4ed689f48712ffe234d5e5"}],"author":[{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Fiji script to determine average speed and direction of migration of cells","oa":1},{"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","month":"08","datarep_id":"45","date_published":"2016-08-25T00:00:00Z","file":[{"file_name":"IST-2016-45-v1+1_PaperCode.zip","date_created":"2018-12-12T13:02:58Z","date_updated":"2020-07-14T12:47:02Z","file_id":"5616","content_type":"application/zip","creator":"system","file_size":296722548,"relation":"main_file","checksum":"ee697f2b1ade4dc14d6ac0334dd832ab","access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'","author":[{"full_name":"Lukacisin, Martin","orcid":"0000-0001-6549-4177","last_name":"Lukacisin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"first_name":"Matthieu","last_name":"Landon","full_name":"Landon, Matthieu"},{"last_name":"Jajoo","first_name":"Rishi","full_name":"Jajoo, Rishi"}],"date_updated":"2024-02-21T13:51:53Z","keyword":["transcription","pausing","backtracking","polymerase","RNA","NET-seq","nucleosome","basepairing"],"license":"https://creativecommons.org/licenses/by-sa/4.0/","department":[{"_id":"ToBo"}],"article_processing_charge":"No","year":"2016","type":"research_data","file_date_updated":"2020-07-14T12:47:02Z","abstract":[{"lang":"eng","text":"MATLAB code and processed datasets available for reproducing the results in: \r\nLukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.\r\n*equal contributions"}],"citation":{"apa":"Lukacisin, M., Landon, M., &#38; Jajoo, R. (2016). MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:45\">https://doi.org/10.15479/AT:ISTA:45</a>","mla":"Lukacisin, Martin, et al. <i>MATLAB Analysis Code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.”</i> Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:45\">10.15479/AT:ISTA:45</a>.","ieee":"M. Lukacisin, M. Landon, and R. Jajoo, “MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016.","short":"M. Lukacisin, M. Landon, R. Jajoo, (2016).","ista":"Lukacisin M, Landon M, Jajoo R. 2016. MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:45\">10.15479/AT:ISTA:45</a>.","ama":"Lukacisin M, Landon M, Jajoo R. MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:45\">10.15479/AT:ISTA:45</a>","chicago":"Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “MATLAB Analysis Code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:45\">https://doi.org/10.15479/AT:ISTA:45</a>."},"status":"public","day":"25","date_created":"2018-12-12T12:31:31Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)"},"_id":"5556","ddc":["571"],"doi":"10.15479/AT:ISTA:45","oa_version":"Published Version","related_material":{"record":[{"id":"8431","status":"deleted","relation":"used_in_publication"},{"relation":"research_paper","status":"public","id":"1029"}]}},{"doi":"10.15479/AT:ISTA:46","oa_version":"Published Version","contributor":[{"contributor_type":"data_collector","last_name":"Kuske","first_name":"Jan"}],"file_date_updated":"2020-07-14T12:47:02Z","type":"research_data","abstract":[{"text":"Small synthetic discrete tomography problems.\r\nSizes are 32x32, 64z64 and 256x256.\r\nProjection angles are 2, 4, and 6.\r\nNumber of labels are 3 and 5.","lang":"eng"}],"citation":{"chicago":"Swoboda, Paul. “Synthetic Discrete Tomography Problems.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:46\">https://doi.org/10.15479/AT:ISTA:46</a>.","ieee":"P. Swoboda, “Synthetic discrete tomography problems.” Institute of Science and Technology Austria, 2016.","short":"P. Swoboda, (2016).","ista":"Swoboda P. 2016. Synthetic discrete tomography problems, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:46\">10.15479/AT:ISTA:46</a>.","ama":"Swoboda P. Synthetic discrete tomography problems. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:46\">10.15479/AT:ISTA:46</a>","mla":"Swoboda, Paul. <i>Synthetic Discrete Tomography Problems</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:46\">10.15479/AT:ISTA:46</a>.","apa":"Swoboda, P. (2016). Synthetic discrete tomography problems. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:46\">https://doi.org/10.15479/AT:ISTA:46</a>"},"status":"public","day":"20","_id":"5557","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"date_created":"2018-12-12T12:31:31Z","ddc":["006"],"department":[{"_id":"VlKo"}],"article_processing_charge":"No","year":"2016","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","month":"09","date_published":"2016-09-20T00:00:00Z","datarep_id":"46","file":[{"access_level":"open_access","checksum":"aa5a16a0dc888da7186fb8fc45e88439","relation":"main_file","file_size":36058401,"creator":"system","file_id":"5645","content_type":"application/zip","date_updated":"2020-07-14T12:47:02Z","date_created":"2018-12-12T13:05:19Z","file_name":"IST-2016-46-v1+1_discrete_tomography_synthetic.zip"}],"title":"Synthetic discrete tomography problems","author":[{"full_name":"Swoboda, Paul","first_name":"Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T13:50:21Z","keyword":["discrete tomography"]},{"related_material":{"record":[{"id":"1122","status":"public","relation":"other"}]},"oa_version":"Published Version","doi":"10.15479/AT:ISTA:48","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"5558","date_created":"2018-12-12T12:31:31Z","ddc":["004"],"status":"public","day":"23","citation":{"ieee":"M. Bojsen-Hansen, “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016.","ista":"Bojsen-Hansen M. 2016. Tracking, Correcting and Absorbing Water Surface Waves, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:48\">10.15479/AT:ISTA:48</a>.","short":"M. Bojsen-Hansen, (2016).","ama":"Bojsen-Hansen M. Tracking, Correcting and Absorbing Water Surface Waves. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:48\">10.15479/AT:ISTA:48</a>","chicago":"Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:48\">https://doi.org/10.15479/AT:ISTA:48</a>.","apa":"Bojsen-Hansen, M. (2016). Tracking, Correcting and Absorbing Water Surface Waves. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:48\">https://doi.org/10.15479/AT:ISTA:48</a>","mla":"Bojsen-Hansen, Morten. <i>Tracking, Correcting and Absorbing Water Surface Waves</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:48\">10.15479/AT:ISTA:48</a>."},"abstract":[{"lang":"eng","text":"PhD thesis LaTeX source code"}],"type":"research_data","file_date_updated":"2020-07-14T12:47:02Z","pubrep_id":"640","year":"2016","article_processing_charge":"No","publist_id":"6238","department":[{"_id":"ChWo"}],"date_updated":"2024-02-21T13:50:48Z","oa":1,"author":[{"full_name":"Bojsen-Hansen, Morten","first_name":"Morten","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","last_name":"Bojsen-Hansen","orcid":"0000-0002-4417-3224"}],"title":"Tracking, Correcting and Absorbing Water Surface Waves","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2018-12-12T13:02:18Z","date_updated":"2020-07-14T12:47:02Z","file_name":"IST-2016-48-v1+1_2016_Bojsen-Hansen_TCaAWSW.tar.bz2","checksum":"5b1b256ad796fbddb4b7729f5e45e444","relation":"main_file","access_level":"open_access","file_id":"5589","content_type":"application/x-bzip2","creator":"system","file_size":55237885}],"datarep_id":"48","date_published":"2016-09-23T00:00:00Z","has_accepted_license":"1","month":"09","publisher":"Institute of Science and Technology Austria"},{"author":[{"full_name":"Wielgoss, Sébastien","last_name":"Wielgoss","first_name":"Sébastien"},{"orcid":"0000-0001-5396-4346","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","full_name":"Bergmiller, Tobias"},{"first_name":"Anna M.","last_name":"Bischofberger","full_name":"Bischofberger, Anna M."},{"full_name":"Hall, Alex R.","last_name":"Hall","first_name":"Alex R."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria","file":[{"file_name":"2016_MolBiolEvol_Wielgoss.pdf","date_updated":"2020-07-14T12:47:10Z","date_created":"2018-12-18T13:21:45Z","file_id":"5750","content_type":"application/pdf","creator":"dernst","file_size":634037,"checksum":"47d9010690b6c5c17f2ac830cc63ac5c","relation":"main_file","access_level":"open_access"}],"publisher":"Oxford University Press","has_accepted_license":"1","pubrep_id":"587","language":[{"iso":"eng"}],"department":[{"_id":"CaGu"}],"article_processing_charge":"No","quality_controlled":"1","_id":"5749","scopus_import":"1","abstract":[{"lang":"eng","text":"Parasitism creates selection for resistance mechanisms in host populations and is hypothesized to promote increased host evolvability. However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance."}],"type":"journal_article","file_date_updated":"2020-07-14T12:47:10Z","citation":{"apa":"Wielgoss, S., Bergmiller, T., Bischofberger, A. M., &#38; Hall, A. R. (2016). Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msv270\">https://doi.org/10.1093/molbev/msv270</a>","mla":"Wielgoss, Sébastien, et al. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.” <i>Molecular Biology and Evolution</i>, vol. 33, no. 3, Oxford University Press, 2016, pp. 770–82, doi:<a href=\"https://doi.org/10.1093/molbev/msv270\">10.1093/molbev/msv270</a>.","ista":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. 2016. Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. Molecular Biology and Evolution. 33(3), 770–782.","short":"S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, Molecular Biology and Evolution 33 (2016) 770–782.","ieee":"S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. Hall, “Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria,” <i>Molecular Biology and Evolution</i>, vol. 33, no. 3. Oxford University Press, pp. 770–782, 2016.","ama":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. <i>Molecular Biology and Evolution</i>. 2016;33(3):770-782. doi:<a href=\"https://doi.org/10.1093/molbev/msv270\">10.1093/molbev/msv270</a>","chicago":"Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex R. Hall. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/molbev/msv270\">https://doi.org/10.1093/molbev/msv270</a>."},"publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"publication_status":"published","oa":1,"issue":"3","date_updated":"2023-09-05T13:46:05Z","acknowledgement":"The authors thank three anonymous reviewers and the editor for helpful comments on the manuscript, as well as Dominique Schneider for feedback on an earlier draft, Jenna Gallie for lytic λ and Julien Capelle for T5 and T6. This work was supported by the Swiss National Science Foundation (PZ00P3_148255 to A.H.) and an EU Marie Curie PEOPLE Postdoctoral Fellowship for Career Development (FP7-PEOPLE-2012-IEF-331824 to S.W.).","date_published":"2016-03-01T00:00:00Z","month":"03","intvolume":"        33","year":"2016","license":"https://creativecommons.org/licenses/by-nc/4.0/","external_id":{"pmid":["26609077"]},"page":"770-782","status":"public","day":"01","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"date_created":"2018-12-18T13:18:10Z","ddc":["576"],"volume":33,"pmid":1,"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"research_data","id":"9719"}]},"publication":"Molecular Biology and Evolution","doi":"10.1093/molbev/msv270"}]