[{"abstract":[{"text":"We consider probabilistic automata on infinite words with acceptance defined by safety, reachability, Büchi, coBüchi, and limit-average conditions. We consider quantitative and qualitative decision problems. We present extensions and adaptations of proofs for probabilistic finite automata and present a complete characterization of the decidability and undecidability frontier of the quantitative and qualitative decision problems for probabilistic automata on infinite words.","lang":"eng"}],"external_id":{"arxiv":["1104.0127"]},"project":[{"call_identifier":"FP7","grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques","_id":"25EFB36C-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"},{"grant_number":"214373","call_identifier":"FP7","_id":"25F1337C-B435-11E9-9278-68D0E5697425","name":"Design for Embedded Systems"}],"citation":{"short":"K. Chatterjee, T.A. Henzinger, M. Tracol, (n.d.).","apa":"Chatterjee, K., Henzinger, T. A., &#38; Tracol, M. (n.d.). The decidability frontier for probabilistic automata on infinite words. ArXiv.","mla":"Chatterjee, Krishnendu, et al. <i>The Decidability Frontier for Probabilistic Automata on Infinite Words</i>. ArXiv.","ista":"Chatterjee K, Henzinger TA, Tracol M. The decidability frontier for probabilistic automata on infinite words.","ama":"Chatterjee K, Henzinger TA, Tracol M. The decidability frontier for probabilistic automata on infinite words.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Mathieu Tracol. “The Decidability Frontier for Probabilistic Automata on Infinite Words.” ArXiv, n.d.","ieee":"K. Chatterjee, T. A. Henzinger, and M. Tracol, “The decidability frontier for probabilistic automata on infinite words.” ArXiv."},"arxiv":1,"main_file_link":[{"url":"https://arxiv.org/abs/1104.0127","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","type":"preprint","title":"The decidability frontier for probabilistic automata on infinite words","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"month":"04","page":"19","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"full_name":"Tracol, Mathieu","first_name":"Mathieu","id":"3F54FA38-F248-11E8-B48F-1D18A9856A87","last_name":"Tracol"}],"publisher":"ArXiv","date_published":"2011-04-01T00:00:00Z","date_updated":"2020-01-21T13:20:24Z","publication_status":"submitted","year":"2011","publist_id":"3251","oa":1,"status":"public","oa_version":"Preprint","ec_funded":1,"_id":"3363","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:02:54Z"},{"author":[{"last_name":"Didier","first_name":"Frédéric","full_name":"Didier, Frédéric"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"full_name":"Mateescu, Maria","first_name":"Maria","last_name":"Mateescu"},{"last_name":"Wolf","first_name":"Verena","full_name":"Wolf, Verena"}],"date_updated":"2023-02-23T12:15:28Z","issue":"21","file_date_updated":"2020-07-14T12:46:10Z","volume":412,"_id":"3364","date_created":"2018-12-11T12:02:55Z","citation":{"ama":"Didier F, Henzinger TA, Mateescu M, Wolf V. Approximation of event probabilities in noisy cellular processes. <i>Theoretical Computer Science</i>. 2011;412(21):2128-2141. doi:<a href=\"https://doi.org/10.1016/j.tcs.2010.10.022\">10.1016/j.tcs.2010.10.022</a>","chicago":"Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf. “Approximation of Event Probabilities in Noisy Cellular Processes.” <i>Theoretical Computer Science</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.tcs.2010.10.022\">https://doi.org/10.1016/j.tcs.2010.10.022</a>.","ista":"Didier F, Henzinger TA, Mateescu M, Wolf V. 2011. Approximation of event probabilities in noisy cellular processes. Theoretical Computer Science. 412(21), 2128–2141.","apa":"Didier, F., Henzinger, T. A., Mateescu, M., &#38; Wolf, V. (2011). Approximation of event probabilities in noisy cellular processes. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2010.10.022\">https://doi.org/10.1016/j.tcs.2010.10.022</a>","short":"F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, Theoretical Computer Science 412 (2011) 2128–2141.","mla":"Didier, Frédéric, et al. “Approximation of Event Probabilities in Noisy Cellular Processes.” <i>Theoretical Computer Science</i>, vol. 412, no. 21, Elsevier, 2011, pp. 2128–41, doi:<a href=\"https://doi.org/10.1016/j.tcs.2010.10.022\">10.1016/j.tcs.2010.10.022</a>.","ieee":"F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “Approximation of event probabilities in noisy cellular processes,” <i>Theoretical Computer Science</i>, vol. 412, no. 21. Elsevier, pp. 2128–2141, 2011."},"pubrep_id":"79","scopus_import":1,"day":"06","intvolume":"       412","department":[{"_id":"ToHe"}],"month":"05","publisher":"Elsevier","quality_controlled":"1","page":"2128 - 2141","year":"2011","publication_status":"published","date_published":"2011-05-06T00:00:00Z","status":"public","oa_version":"Submitted Version","oa":1,"publist_id":"3249","has_accepted_license":"1","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"4535"}]},"abstract":[{"lang":"eng","text":"Molecular noise, which arises from the randomness of the discrete events in the cell, significantly influences fundamental biological processes. Discrete-state continuous-time stochastic models (CTMC) can be used to describe such effects, but the calculation of the probabilities of certain events is computationally expensive. We present a comparison of two analysis approaches for CTMC. On one hand, we estimate the probabilities of interest using repeated Gillespie simulation and determine the statistical accuracy that we obtain. On the other hand, we apply a numerical reachability analysis that approximates the probability distributions of the system at several time instances. We use examples of cellular processes to demonstrate the superiority of the reachability analysis if accurate results are required."}],"publication":"Theoretical Computer Science","doi":"10.1016/j.tcs.2010.10.022","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Approximation of event probabilities in noisy cellular processes","file":[{"relation":"main_file","date_created":"2018-12-12T10:11:09Z","checksum":"e5503e25ce020d753e06b3431e16841e","creator":"system","content_type":"application/pdf","access_level":"open_access","file_name":"IST-2012-79-v1+1_Approximation_of_event_probabilities_in_noisy_cellular_processes.pdf","date_updated":"2020-07-14T12:46:10Z","file_id":"4862","file_size":230503}],"ddc":["000","004"]},{"type":"conference","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"QUASY: quantitative synthesis tool","file":[{"file_id":"5022","file_name":"IST-2012-77-v1+1_QUASY-_quantitative_synthesis_tool.pdf","date_updated":"2020-07-14T12:46:10Z","file_size":475661,"relation":"main_file","date_created":"2018-12-12T10:13:37Z","creator":"system","access_level":"open_access","content_type":"application/pdf","checksum":"762e52eb296f6dbfbf2a75d98b8ebaee"}],"ddc":["000","005"],"abstract":[{"text":"We present the tool Quasy, a quantitative synthesis tool. Quasy takes qualitative and quantitative specifications and automatically constructs a system that satisfies the qualitative specification and optimizes the quantitative specification, if such a system exists. The user can choose between a system that satisfies and optimizes the specifications (a) under all possible environment behaviors or (b) under the most-likely environment behaviors given as a probability distribution on the possible input sequences. Quasy solves these two quantitative synthesis problems by reduction to instances of 2-player games and Markov Decision Processes (MDPs) with quantitative winning objectives. Quasy can also be seen as a game solver for quantitative games. Most notable, it can solve lexicographic mean-payoff games with 2 players, MDPs with mean-payoff objectives, and ergodic MDPs with mean-payoff parity objectives.","lang":"eng"}],"doi":"10.1007/978-3-642-19835-9_24","status":"public","oa_version":"Submitted Version","oa":1,"publist_id":"3248","has_accepted_license":"1","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"publisher":"Springer","quality_controlled":"1","page":"267 - 271","publication_status":"published","year":"2011","date_published":"2011-09-29T00:00:00Z","day":"29","intvolume":"      6605","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"month":"09","citation":{"short":"K. Chatterjee, T.A. Henzinger, B. Jobstmann, R. Singh, in:, Springer, 2011, pp. 267–271.","apa":"Chatterjee, K., Henzinger, T. A., Jobstmann, B., &#38; Singh, R. (2011). QUASY: quantitative synthesis tool (Vol. 6605, pp. 267–271). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Saarbrucken, Germany: Springer. <a href=\"https://doi.org/10.1007/978-3-642-19835-9_24\">https://doi.org/10.1007/978-3-642-19835-9_24</a>","mla":"Chatterjee, Krishnendu, et al. <i>QUASY: Quantitative Synthesis Tool</i>. Vol. 6605, Springer, 2011, pp. 267–71, doi:<a href=\"https://doi.org/10.1007/978-3-642-19835-9_24\">10.1007/978-3-642-19835-9_24</a>.","ista":"Chatterjee K, Henzinger TA, Jobstmann B, Singh R. 2011. QUASY: quantitative synthesis tool. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 6605, 267–271.","ama":"Chatterjee K, Henzinger TA, Jobstmann B, Singh R. QUASY: quantitative synthesis tool. In: Vol 6605. Springer; 2011:267-271. doi:<a href=\"https://doi.org/10.1007/978-3-642-19835-9_24\">10.1007/978-3-642-19835-9_24</a>","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Barbara Jobstmann, and Rohit Singh. “QUASY: Quantitative Synthesis Tool,” 6605:267–71. Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-19835-9_24\">https://doi.org/10.1007/978-3-642-19835-9_24</a>.","ieee":"K. Chatterjee, T. A. Henzinger, B. Jobstmann, and R. Singh, “QUASY: quantitative synthesis tool,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Saarbrucken, Germany, 2011, vol. 6605, pp. 267–271."},"pubrep_id":"77","conference":{"end_date":"2011-04-03","start_date":"2011-03-26","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","location":"Saarbrucken, Germany"},"scopus_import":1,"file_date_updated":"2020-07-14T12:46:10Z","volume":6605,"_id":"3365","date_created":"2018-12-11T12:02:55Z","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"full_name":"Jobstmann, Barbara","first_name":"Barbara","last_name":"Jobstmann"},{"last_name":"Singh","first_name":"Rohit","full_name":"Singh, Rohit"}],"date_updated":"2021-01-12T07:42:58Z"},{"citation":{"ista":"Cerny P, Chatterjee K, Henzinger TA, Radhakrishna A, Singh R. 2011. Quantitative synthesis for concurrent programs. CAV: Computer Aided Verification, LNCS, vol. 6806, 243–259.","ama":"Cerny P, Chatterjee K, Henzinger TA, Radhakrishna A, Singh R. Quantitative synthesis for concurrent programs. In: Gopalakrishnan G, Qadeer S, eds. Vol 6806. Springer; 2011:243-259. doi:<a href=\"https://doi.org/10.1007/978-3-642-22110-1_20\">10.1007/978-3-642-22110-1_20</a>","chicago":"Cerny, Pavol, Krishnendu Chatterjee, Thomas A Henzinger, Arjun Radhakrishna, and Rohit Singh. “Quantitative Synthesis for Concurrent Programs.” edited by Ganesh Gopalakrishnan and Shaz Qadeer, 6806:243–59. Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-22110-1_20\">https://doi.org/10.1007/978-3-642-22110-1_20</a>.","short":"P. Cerny, K. Chatterjee, T.A. Henzinger, A. Radhakrishna, R. Singh, in:, G. Gopalakrishnan, S. Qadeer (Eds.), Springer, 2011, pp. 243–259.","apa":"Cerny, P., Chatterjee, K., Henzinger, T. A., Radhakrishna, A., &#38; Singh, R. (2011). Quantitative synthesis for concurrent programs. In G. Gopalakrishnan &#38; S. Qadeer (Eds.) (Vol. 6806, pp. 243–259). Presented at the CAV: Computer Aided Verification, Snowbird, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-642-22110-1_20\">https://doi.org/10.1007/978-3-642-22110-1_20</a>","mla":"Cerny, Pavol, et al. <i>Quantitative Synthesis for Concurrent Programs</i>. Edited by Ganesh Gopalakrishnan and Shaz Qadeer, vol. 6806, Springer, 2011, pp. 243–59, doi:<a href=\"https://doi.org/10.1007/978-3-642-22110-1_20\">10.1007/978-3-642-22110-1_20</a>.","ieee":"P. Cerny, K. Chatterjee, T. A. Henzinger, A. Radhakrishna, and R. Singh, “Quantitative synthesis for concurrent programs,” presented at the CAV: Computer Aided Verification, Snowbird, USA, 2011, vol. 6806, pp. 243–259."},"pubrep_id":"76","editor":[{"first_name":"Ganesh","last_name":"Gopalakrishnan","full_name":"Gopalakrishnan, Ganesh"},{"first_name":"Shaz","last_name":"Qadeer","full_name":"Qadeer, Shaz"}],"conference":{"start_date":"2011-07-14","name":"CAV: Computer Aided Verification","location":"Snowbird, USA","end_date":"2011-07-20"},"project":[{"call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11402-N23","call_identifier":"FWF","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"214373","_id":"25F1337C-B435-11E9-9278-68D0E5697425","name":"Design for Embedded Systems"}],"month":"04","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"day":"21","intvolume":"      6806","date_updated":"2023-02-23T12:24:01Z","author":[{"first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny","full_name":"Cerny, Pavol"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna","first_name":"Arjun"},{"first_name":"Rohit","last_name":"Singh","full_name":"Singh, Rohit"}],"_id":"3366","date_created":"2018-12-11T12:02:55Z","file_date_updated":"2020-07-14T12:46:10Z","volume":6806,"doi":"10.1007/978-3-642-22110-1_20","abstract":[{"text":"We present an algorithmic method for the quantitative, performance-aware synthesis of concurrent programs. The input consists of a nondeterministic partial program and of a parametric performance model. The nondeterminism allows the programmer to omit which (if any) synchronization construct is used at a particular program location. The performance model, specified as a weighted automaton, can capture system architectures by assigning different costs to actions such as locking, context switching, and memory and cache accesses. The quantitative synthesis problem is to automatically resolve the nondeterminism of the partial program so that both correctness is guaranteed and performance is optimal. As is standard for shared memory concurrency, correctness is formalized &quot;specification free&quot;, in particular as race freedom or deadlock freedom. For worst-case (average-case) performance, we show that the problem can be reduced to 2-player graph games (with probabilistic transitions) with quantitative objectives. While we show, using game-theoretic methods, that the synthesis problem is Nexp-complete, we present an algorithmic method and an implementation that works efficiently for concurrent programs and performance models of practical interest. We have implemented a prototype tool and used it to synthesize finite-state concurrent programs that exhibit different programming patterns, for several performance models representing different architectures. ","lang":"eng"}],"file":[{"date_updated":"2020-07-14T12:46:10Z","file_name":"IST-2012-76-v1+1_Quantitative_synthesis_for_concurrent_programs.pdf","file_id":"5174","file_size":508946,"relation":"main_file","date_created":"2018-12-12T10:15:51Z","checksum":"c033689355f45742dc7c99b5af13ce7a","access_level":"open_access","content_type":"application/pdf","creator":"system"}],"ddc":["000","004"],"type":"conference","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Quantitative synthesis for concurrent programs","year":"2011","publication_status":"published","date_published":"2011-04-21T00:00:00Z","publisher":"Springer","quality_controlled":"1","page":"243 - 259","article_processing_charge":"No","ec_funded":1,"alternative_title":["LNCS"],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5388"}]},"status":"public","oa_version":"Submitted Version","oa":1,"publist_id":"3247","has_accepted_license":"1"},{"month":"06","department":[{"_id":"HeEd"}],"day":"13","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"An output sensitive algorithm for persistent homology","conference":{"location":"Paris, France","start_date":"2011-06-13","name":"SoCG: Symposium on Computational Geometry","end_date":"2011-06-15"},"doi":"10.1145/1998196.1998228","scopus_import":1,"citation":{"ieee":"C. Chen and M. Kerber, “An output sensitive algorithm for persistent homology,” presented at the SoCG: Symposium on Computational Geometry, Paris, France, 2011, pp. 207–216.","mla":"Chen, Chao, and Michael Kerber. <i>An Output Sensitive Algorithm for Persistent Homology</i>. ACM, 2011, pp. 207–16, doi:<a href=\"https://doi.org/10.1145/1998196.1998228\">10.1145/1998196.1998228</a>.","short":"C. Chen, M. Kerber, in:, ACM, 2011, pp. 207–216.","apa":"Chen, C., &#38; Kerber, M. (2011). An output sensitive algorithm for persistent homology (pp. 207–216). Presented at the SoCG: Symposium on Computational Geometry, Paris, France: ACM. <a href=\"https://doi.org/10.1145/1998196.1998228\">https://doi.org/10.1145/1998196.1998228</a>","ista":"Chen C, Kerber M. 2011. An output sensitive algorithm for persistent homology. SoCG: Symposium on Computational Geometry, 207–216.","chicago":"Chen, Chao, and Michael Kerber. “An Output Sensitive Algorithm for Persistent Homology,” 207–16. ACM, 2011. <a href=\"https://doi.org/10.1145/1998196.1998228\">https://doi.org/10.1145/1998196.1998228</a>.","ama":"Chen C, Kerber M. An output sensitive algorithm for persistent homology. In: ACM; 2011:207-216. doi:<a href=\"https://doi.org/10.1145/1998196.1998228\">10.1145/1998196.1998228</a>"},"abstract":[{"lang":"eng","text":"In this paper, we present the first output-sensitive algorithm to compute the persistence diagram of a filtered simplicial complex. For any Γ&gt;0, it returns only those homology classes with persistence at least Γ. Instead of the classical reduction via column operations, our algorithm performs rank computations on submatrices of the boundary matrix. For an arbitrary constant δ ∈ (0,1), the running time is O(C(1-δ)ΓR(n)log n), where C(1-δ)Γ is the number of homology classes with persistence at least (1-δ)Γ, n is the total number of simplices, and R(n) is the complexity of computing the rank of an n x n matrix with O(n) nonzero entries. Depending on the choice of the rank algorithm, this yields a deterministic O(C(1-δ)Γn2.376) algorithm, a O(C(1-δ)Γn2.28) Las-Vegas algorithm, or a O(C(1-δ)Γn2+ε) Monte-Carlo algorithm for an arbitrary ε&gt;0."}],"_id":"3367","date_created":"2018-12-11T12:02:56Z","related_material":{"record":[{"id":"2939","status":"public","relation":"later_version"}]},"language":[{"iso":"eng"}],"article_processing_charge":"No","publist_id":"3245","status":"public","oa_version":"None","date_published":"2011-06-13T00:00:00Z","date_updated":"2023-02-23T11:05:04Z","publication_status":"published","year":"2011","page":"207 - 216","author":[{"full_name":"Chen, Chao","last_name":"Chen","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","first_name":"Chao"},{"full_name":"Kerber, Michael","orcid":"0000-0002-8030-9299","first_name":"Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","last_name":"Kerber"}],"publisher":"ACM","quality_controlled":"1"},{"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Enveloping cell layer differentiation at the surface of zebrafish germ layer tissue explants","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024655","open_access":"1"}],"doi":"10.1073/pnas.1010767108","abstract":[{"text":"Tissue surface tension (TST) is an important mechanical property influencing cell sorting and tissue envelopment. The study by Manning et al. (1) reported on a mathematical model describing TST on the basis of the balance between adhesive and tensile properties of the constituent cells. The model predicts that, in high-adhesion cell aggregates, surface cells will be stretched to maintain the same area of cell–cell contact as interior bulk cells, resulting in an elongated and flattened cell shape. The authors (1) observed flat and elongated cells at the surface of high-adhesion zebrafish germ-layer explants, which they argue are undifferentiated stretched germ-layer progenitor cells, and they use this observation as a validation of their model.","lang":"eng"}],"publication":"PNAS","language":[{"iso":"eng"}],"status":"public","oa_version":"Submitted Version","oa":1,"publist_id":"3244","year":"2011","publication_status":"published","date_published":"2011-01-18T00:00:00Z","publisher":"National Academy of Sciences","quality_controlled":"1","page":"E9 - E10","month":"01","department":[{"_id":"CaHe"}],"pmid":1,"day":"18","intvolume":"       108","citation":{"ista":"Krens G, Möllmert S, Heisenberg C-PJ. 2011. Enveloping cell layer differentiation at the surface of zebrafish germ layer tissue explants. PNAS. 108(3), E9–E10.","chicago":"Krens, Gabriel, Stephanie Möllmert, and Carl-Philipp J Heisenberg. “Enveloping Cell Layer Differentiation at the Surface of Zebrafish Germ Layer Tissue Explants.” <i>PNAS</i>. National Academy of Sciences, 2011. <a href=\"https://doi.org/10.1073/pnas.1010767108\">https://doi.org/10.1073/pnas.1010767108</a>.","ama":"Krens G, Möllmert S, Heisenberg C-PJ. Enveloping cell layer differentiation at the surface of zebrafish germ layer tissue explants. <i>PNAS</i>. 2011;108(3):E9-E10. doi:<a href=\"https://doi.org/10.1073/pnas.1010767108\">10.1073/pnas.1010767108</a>","short":"G. Krens, S. Möllmert, C.-P.J. Heisenberg, PNAS 108 (2011) E9–E10.","mla":"Krens, Gabriel, et al. “Enveloping Cell Layer Differentiation at the Surface of Zebrafish Germ Layer Tissue Explants.” <i>PNAS</i>, vol. 108, no. 3, National Academy of Sciences, 2011, pp. E9–10, doi:<a href=\"https://doi.org/10.1073/pnas.1010767108\">10.1073/pnas.1010767108</a>.","apa":"Krens, G., Möllmert, S., &#38; Heisenberg, C.-P. J. (2011). Enveloping cell layer differentiation at the surface of zebrafish germ layer tissue explants. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1010767108\">https://doi.org/10.1073/pnas.1010767108</a>","ieee":"G. Krens, S. Möllmert, and C.-P. J. Heisenberg, “Enveloping cell layer differentiation at the surface of zebrafish germ layer tissue explants,” <i>PNAS</i>, vol. 108, no. 3. National Academy of Sciences, pp. E9–E10, 2011."},"scopus_import":1,"external_id":{"pmid":["21212360"]},"_id":"3368","date_created":"2018-12-11T12:02:56Z","issue":"3","volume":108,"date_updated":"2021-01-12T07:43:00Z","author":[{"orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel","first_name":"Gabriel","last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Möllmert, Stephanie","first_name":"Stephanie","last_name":"Möllmert","id":"260FD49C-E911-11E9-B5EA-D9538404589B"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"}]},{"department":[{"_id":"PeJo"}],"month":"01","intvolume":"        69","title":"The multiple faces of RIM","type":"journal_article","day":"27","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"A. Pernia-Andrade and P. M. Jonas, “The multiple faces of RIM,” <i>Neuron</i>, vol. 69, no. 2. Elsevier, pp. 185–187, 2011.","mla":"Pernia-Andrade, Alejandro, and Peter M. Jonas. “The Multiple Faces of RIM.” <i>Neuron</i>, vol. 69, no. 2, Elsevier, 2011, pp. 185–87, doi:<a href=\"https://doi.org/10.1016/j.neuron.2011.01.010\">10.1016/j.neuron.2011.01.010</a>.","apa":"Pernia-Andrade, A., &#38; Jonas, P. M. (2011). The multiple faces of RIM. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2011.01.010\">https://doi.org/10.1016/j.neuron.2011.01.010</a>","short":"A. Pernia-Andrade, P.M. Jonas, Neuron 69 (2011) 185–187.","chicago":"Pernia-Andrade, Alejandro, and Peter M Jonas. “The Multiple Faces of RIM.” <i>Neuron</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.neuron.2011.01.010\">https://doi.org/10.1016/j.neuron.2011.01.010</a>.","ista":"Pernia-Andrade A, Jonas PM. 2011. The multiple faces of RIM. Neuron. 69(2), 185–187.","ama":"Pernia-Andrade A, Jonas PM. The multiple faces of RIM. <i>Neuron</i>. 2011;69(2):185-187. doi:<a href=\"https://doi.org/10.1016/j.neuron.2011.01.010\">10.1016/j.neuron.2011.01.010</a>"},"scopus_import":1,"doi":"10.1016/j.neuron.2011.01.010","abstract":[{"lang":"eng","text":"Rab3 interacting molecules (RIMs) are highly enriched in the active zones of presynaptic terminals. It is generally thought that they operate as effectors of the small G protein Rab3. Three recent papers, by Han et al. (this issue of Neuron), Deng et al. (this issue of Neuron), and Kaeser et al. (a recent issue of Cell), shed new light on the functional role of RIM in presynaptic terminals. First, RIM tethers Ca2+ channels to active zones. Second, RIM contributes to priming of synaptic vesicles by interacting with another presynaptic protein, Munc13."}],"publication":"Neuron","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:02:56Z","_id":"3369","oa_version":"None","status":"public","volume":69,"publist_id":"3243","issue":"2","year":"2011","publication_status":"published","date_updated":"2021-01-12T07:43:00Z","date_published":"2011-01-27T00:00:00Z","quality_controlled":"1","publisher":"Elsevier","author":[{"full_name":"Pernia-Andrade, Alejandro","first_name":"Alejandro","id":"36963E98-F248-11E8-B48F-1D18A9856A87","last_name":"Pernia-Andrade"},{"last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"}],"page":"185 - 187"},{"volume":60,"issue":"2","publist_id":"3241","oa":1,"oa_version":"Submitted Version","status":"public","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:02:57Z","_id":"3370","page":"218 - 225","quality_controlled":"1","publisher":"Oxford University Press","author":[{"id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Kupczok","first_name":"Anne","full_name":"Kupczok, Anne"}],"date_published":"2011-03-01T00:00:00Z","year":"2011","publication_status":"published","date_updated":"2021-01-12T07:43:01Z","main_file_link":[{"url":"http://eprints.cs.univie.ac.at/3226/","open_access":"1"}],"title":"Consequences of different null models on the tree shape bias of supertree methods","intvolume":"        60","day":"01","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JoBo"}],"month":"03","publication":"Systematic Biology","abstract":[{"lang":"eng","text":"Supertree methods are widely applied and give rise to new conclusions about phylogenies (e.g., Bininda-Emonds et al. 2007). Although several desiderata for supertree methods exist (Wilkinson, Thorley, et al. 2004), only few of them have been studied in greater detail, examples include shape bias (Wilkinson et al. 2005) or pareto properties (Wilkinson et al. 2007). Here I look more closely at two matrix representation methods, matrix representation with compatibility (MRC) and matrix representation with parsimony (MRP). Different null models of random data are studied and the resulting tree shapes are investigated. Thereby I consider unrooted trees and a bias in tree shape is determined by a tree balance measure. The measure for unrooted trees is a modification of a tree balance measure for rooted trees. I observe that depending on the underlying null model of random data, the methods may resolve conflict in favor of more balanced tree shapes. The analyses refer only to trees with the same taxon set, also known as the consensus setting (e.g., Wilkinson et al. 2007), but I will be able to draw conclusions on how to deal with missing data."}],"doi":"10.1093/sysbio/syq086","citation":{"mla":"Kupczok, Anne. “Consequences of Different Null Models on the Tree Shape Bias of Supertree Methods.” <i>Systematic Biology</i>, vol. 60, no. 2, Oxford University Press, 2011, pp. 218–25, doi:<a href=\"https://doi.org/10.1093/sysbio/syq086\">10.1093/sysbio/syq086</a>.","short":"A. Kupczok, Systematic Biology 60 (2011) 218–225.","apa":"Kupczok, A. (2011). Consequences of different null models on the tree shape bias of supertree methods. <i>Systematic Biology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/sysbio/syq086\">https://doi.org/10.1093/sysbio/syq086</a>","ista":"Kupczok A. 2011. Consequences of different null models on the tree shape bias of supertree methods. Systematic Biology. 60(2), 218–225.","chicago":"Kupczok, Anne. “Consequences of Different Null Models on the Tree Shape Bias of Supertree Methods.” <i>Systematic Biology</i>. Oxford University Press, 2011. <a href=\"https://doi.org/10.1093/sysbio/syq086\">https://doi.org/10.1093/sysbio/syq086</a>.","ama":"Kupczok A. Consequences of different null models on the tree shape bias of supertree methods. <i>Systematic Biology</i>. 2011;60(2):218-225. doi:<a href=\"https://doi.org/10.1093/sysbio/syq086\">10.1093/sysbio/syq086</a>","ieee":"A. Kupczok, “Consequences of different null models on the tree shape bias of supertree methods,” <i>Systematic Biology</i>, vol. 60, no. 2. Oxford University Press, pp. 218–225, 2011."}},{"date_created":"2018-12-11T12:02:57Z","_id":"3371","volume":22,"issue":"6","file_date_updated":"2020-07-14T12:46:11Z","date_updated":"2021-01-12T07:43:01Z","tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"author":[{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"},{"full_name":"Parent, Carole","first_name":"Carole","last_name":"Parent"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","article_type":"original","department":[{"_id":"MiSi"}],"month":"03","intvolume":"        22","day":"15","scopus_import":1,"pubrep_id":"373","citation":{"ieee":"M. K. Sixt and C. Parent, “Cells on the move in Philadelphia,” <i>Molecular Biology and Evolution</i>, vol. 22, no. 6. Oxford University Press, p. 724, 2011.","chicago":"Sixt, Michael K, and Carole Parent. “Cells on the Move in Philadelphia.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2011. <a href=\"https://doi.org/10.1091/mbc.E10-12-0958\">https://doi.org/10.1091/mbc.E10-12-0958</a>.","ista":"Sixt MK, Parent C. 2011. Cells on the move in Philadelphia. Molecular Biology and Evolution. 22(6), 724.","ama":"Sixt MK, Parent C. Cells on the move in Philadelphia. <i>Molecular Biology and Evolution</i>. 2011;22(6):724. doi:<a href=\"https://doi.org/10.1091/mbc.E10-12-0958\">10.1091/mbc.E10-12-0958</a>","apa":"Sixt, M. K., &#38; Parent, C. (2011). Cells on the move in Philadelphia. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1091/mbc.E10-12-0958\">https://doi.org/10.1091/mbc.E10-12-0958</a>","mla":"Sixt, Michael K., and Carole Parent. “Cells on the Move in Philadelphia.” <i>Molecular Biology and Evolution</i>, vol. 22, no. 6, Oxford University Press, 2011, p. 724, doi:<a href=\"https://doi.org/10.1091/mbc.E10-12-0958\">10.1091/mbc.E10-12-0958</a>.","short":"M.K. Sixt, C. Parent, Molecular Biology and Evolution 22 (2011) 724."},"language":[{"iso":"eng"}],"has_accepted_license":"1","oa":1,"publist_id":"3238","oa_version":"Published Version","status":"public","date_published":"2011-03-15T00:00:00Z","publication_status":"published","year":"2011","page":"724","quality_controlled":"1","publisher":"Oxford University Press","ddc":["570"],"file":[{"file_name":"IST-2015-373-v1+1_Mol._Biol._Cell-2011-Sixt-724.pdf","date_updated":"2020-07-14T12:46:11Z","file_id":"5283","file_size":105421,"date_created":"2018-12-12T10:17:29Z","relation":"main_file","checksum":"3467986ab7a64e7694ffd1013b5d9da9","content_type":"application/pdf","creator":"system","access_level":"open_access"}],"title":"Cells on the move in Philadelphia","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","doi":"10.1091/mbc.E10-12-0958","publication":"Molecular Biology and Evolution","abstract":[{"text":"The Minisymposium “Cell Migration and Motility” was attended by approximately 500 visitors and covered a broad range of questions in the field using diverse model systems. Topics comprised actin dynamics, cell polarity, force transduction, signal transduction, bar- rier transmigration, and chemotactic guidance.","lang":"eng"}]},{"scopus_import":1,"citation":{"apa":"Abbot, P., Abe, J., Alcock, J., Alizon, S., Alpedrinha, J., Andersson, M., … Zink, A. (2011). Inclusive fitness theory and eusociality. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature09831\">https://doi.org/10.1038/nature09831</a>","mla":"Abbot, Patrick, et al. “Inclusive Fitness Theory and Eusociality.” <i>Nature</i>, vol. 471, no. 7339, Nature Publishing Group, 2011, pp. E1–4, doi:<a href=\"https://doi.org/10.1038/nature09831\">10.1038/nature09831</a>.","short":"P. Abbot, J. Abe, J. Alcock, S. Alizon, J. Alpedrinha, M. Andersson, J. Andre, M. Van Baalen, F. Balloux, S. Balshine, N.H. Barton, L. Beukeboom, J. Biernaskie, T. Bilde, G. Borgia, M. Breed, S. Brown, R. Bshary, A. Buckling, N. Burley, M. Burton Chellew, M. Cant, M. Chapuisat, E. Charnov, T. Clutton Brock, A. Cockburn, B. Cole, N. Colegrave, L. Cosmides, I. Couzin, J. Coyne, S. Creel, B. Crespi, R. Curry, S. Dall, T. Day, J. Dickinson, L. Dugatkin, C. El Mouden, S. Emlen, J. Evans, R. Ferriere, J. Field, S. Foitzik, K. Foster, W. Foster, C. Fox, J. Gadau, S. Gandon, A. Gardner, M. Gardner, T. Getty, M. Goodisman, A. Grafen, R. Grosberg, C. Grozinger, P. Gouyon, D. Gwynne, P. Harvey, B. Hatchwell, J. Heinze, H. Helantera, K. Helms, K. Hill, N. Jiricny, R. Johnstone, A. Kacelnik, E.T. Kiers, H. Kokko, J. Komdeur, J. Korb, D. Kronauer, R. Kümmerli, L. Lehmann, T. Linksvayer, S. Lion, B. Lyon, J. Marshall, R. Mcelreath, Y. Michalakis, R. Michod, D. Mock, T. Monnin, R. Montgomerie, A. Moore, U. Mueller, R. Noë, S. Okasha, P. Pamilo, G. Parker, J. Pedersen, I. Pen, D. Pfennig, D. Queller, D. Rankin, S. Reece, H. Reeve, M. Reuter, G. Roberts, S. Robson, D. Roze, F. Rousset, O. Rueppell, J. Sachs, L. Santorelli, P. Schmid Hempel, M. Schwarz, T. Scott Phillips, J. Shellmann Sherman, P. Sherman, D. Shuker, J. Smith, J. Spagna, B. Strassmann, A. Suarez, L. Sundström, M. Taborsky, P. Taylor, G. Thompson, J. Tooby, N. Tsutsui, K. Tsuji, S. Turillazzi, F. Úbeda, E. Vargo, B. Voelkl, T. Wenseleers, S. West, M. West Eberhard, D. Westneat, D. Wiernasz, G. Wild, R. Wrangham, A. Young, D. Zeh, J. Zeh, A. Zink, Nature 471 (2011) E1–E4.","ama":"Abbot P, Abe J, Alcock J, et al. Inclusive fitness theory and eusociality. <i>Nature</i>. 2011;471(7339):E1-E4. doi:<a href=\"https://doi.org/10.1038/nature09831\">10.1038/nature09831</a>","ista":"Abbot P et al. 2011. Inclusive fitness theory and eusociality. Nature. 471(7339), E1–E4.","chicago":"Abbot, Patrick, Jun Abe, John Alcock, Samuel Alizon, Joao Alpedrinha, Malte Andersson, Jean Andre, et al. “Inclusive Fitness Theory and Eusociality.” <i>Nature</i>. Nature Publishing Group, 2011. <a href=\"https://doi.org/10.1038/nature09831\">https://doi.org/10.1038/nature09831</a>.","ieee":"P. Abbot <i>et al.</i>, “Inclusive fitness theory and eusociality,” <i>Nature</i>, vol. 471, no. 7339. Nature Publishing Group, pp. E1–E4, 2011."},"external_id":{"pmid":["21430721"]},"month":"03","department":[{"_id":"NiBa"}],"pmid":1,"day":"23","intvolume":"       471","date_updated":"2021-01-12T07:43:02Z","author":[{"full_name":"Abbot, Patrick","last_name":"Abbot","first_name":"Patrick"},{"last_name":"Abe","first_name":"Jun","full_name":"Abe, Jun"},{"full_name":"Alcock, John","last_name":"Alcock","first_name":"John"},{"last_name":"Alizon","first_name":"Samuel","full_name":"Alizon, Samuel"},{"full_name":"Alpedrinha, Joao","first_name":"Joao","last_name":"Alpedrinha"},{"last_name":"Andersson","first_name":"Malte","full_name":"Andersson, Malte"},{"full_name":"Andre, Jean","first_name":"Jean","last_name":"Andre"},{"full_name":"Van Baalen, Minus","last_name":"Van Baalen","first_name":"Minus"},{"full_name":"Balloux, Francois","last_name":"Balloux","first_name":"Francois"},{"first_name":"Sigal","last_name":"Balshine","full_name":"Balshine, Sigal"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"first_name":"Leo","last_name":"Beukeboom","full_name":"Beukeboom, Leo"},{"full_name":"Biernaskie, Jay","last_name":"Biernaskie","first_name":"Jay"},{"full_name":"Bilde, Trine","last_name":"Bilde","first_name":"Trine"},{"full_name":"Borgia, Gerald","last_name":"Borgia","first_name":"Gerald"},{"full_name":"Breed, Michael","last_name":"Breed","first_name":"Michael"},{"full_name":"Brown, Sam","last_name":"Brown","first_name":"Sam"},{"first_name":"Redouan","last_name":"Bshary","full_name":"Bshary, Redouan"},{"first_name":"Angus","last_name":"Buckling","full_name":"Buckling, Angus"},{"full_name":"Burley, Nancy","first_name":"Nancy","last_name":"Burley"},{"full_name":"Burton Chellew, Max","last_name":"Burton Chellew","first_name":"Max"},{"first_name":"Michael","last_name":"Cant","full_name":"Cant, Michael"},{"last_name":"Chapuisat","first_name":"Michel","full_name":"Chapuisat, Michel"},{"last_name":"Charnov","first_name":"Eric","full_name":"Charnov, Eric"},{"full_name":"Clutton Brock, Tim","last_name":"Clutton Brock","first_name":"Tim"},{"first_name":"Andrew","last_name":"Cockburn","full_name":"Cockburn, Andrew"},{"full_name":"Cole, Blaine","last_name":"Cole","first_name":"Blaine"},{"full_name":"Colegrave, Nick","first_name":"Nick","last_name":"Colegrave"},{"last_name":"Cosmides","first_name":"Leda","full_name":"Cosmides, Leda"},{"full_name":"Couzin, Iain","last_name":"Couzin","first_name":"Iain"},{"full_name":"Coyne, Jerry","first_name":"Jerry","last_name":"Coyne"},{"first_name":"Scott","last_name":"Creel","full_name":"Creel, Scott"},{"last_name":"Crespi","first_name":"Bernard","full_name":"Crespi, Bernard"},{"full_name":"Curry, Robert","last_name":"Curry","first_name":"Robert"},{"first_name":"Sasha","last_name":"Dall","full_name":"Dall, Sasha"},{"first_name":"Troy","last_name":"Day","full_name":"Day, Troy"},{"full_name":"Dickinson, Janis","last_name":"Dickinson","first_name":"Janis"},{"last_name":"Dugatkin","first_name":"Lee","full_name":"Dugatkin, Lee"},{"full_name":"El Mouden, Claire","last_name":"El Mouden","first_name":"Claire"},{"first_name":"Stephen","last_name":"Emlen","full_name":"Emlen, Stephen"},{"full_name":"Evans, Jay","first_name":"Jay","last_name":"Evans"},{"full_name":"Ferriere, Regis","first_name":"Regis","last_name":"Ferriere"},{"full_name":"Field, Jeremy","first_name":"Jeremy","last_name":"Field"},{"full_name":"Foitzik, Susanne","last_name":"Foitzik","first_name":"Susanne"},{"full_name":"Foster, Kevin","first_name":"Kevin","last_name":"Foster"},{"full_name":"Foster, William","first_name":"William","last_name":"Foster"},{"first_name":"Charles","last_name":"Fox","full_name":"Fox, Charles"},{"last_name":"Gadau","first_name":"Juergen","full_name":"Gadau, Juergen"},{"first_name":"Sylvain","last_name":"Gandon","full_name":"Gandon, Sylvain"},{"last_name":"Gardner","first_name":"Andy","full_name":"Gardner, Andy"},{"full_name":"Gardner, Michael","first_name":"Michael","last_name":"Gardner"},{"last_name":"Getty","first_name":"Thomas","full_name":"Getty, Thomas"},{"first_name":"Michael","last_name":"Goodisman","full_name":"Goodisman, Michael"},{"first_name":"Alan","last_name":"Grafen","full_name":"Grafen, Alan"},{"first_name":"Rick","last_name":"Grosberg","full_name":"Grosberg, Rick"},{"full_name":"Grozinger, Christina","last_name":"Grozinger","first_name":"Christina"},{"full_name":"Gouyon, Pierre","last_name":"Gouyon","first_name":"Pierre"},{"full_name":"Gwynne, Darryl","first_name":"Darryl","last_name":"Gwynne"},{"full_name":"Harvey, Paul","last_name":"Harvey","first_name":"Paul"},{"full_name":"Hatchwell, Ben","last_name":"Hatchwell","first_name":"Ben"},{"full_name":"Heinze, Jürgen","last_name":"Heinze","first_name":"Jürgen"},{"full_name":"Helantera, Heikki","last_name":"Helantera","first_name":"Heikki"},{"last_name":"Helms","first_name":"Ken","full_name":"Helms, Ken"},{"full_name":"Hill, Kim","first_name":"Kim","last_name":"Hill"},{"last_name":"Jiricny","first_name":"Natalie","full_name":"Jiricny, Natalie"},{"last_name":"Johnstone","first_name":"Rufus","full_name":"Johnstone, Rufus"},{"full_name":"Kacelnik, Alex","first_name":"Alex","last_name":"Kacelnik"},{"full_name":"Kiers, E Toby","last_name":"Kiers","first_name":"E Toby"},{"full_name":"Kokko, Hanna","last_name":"Kokko","first_name":"Hanna"},{"full_name":"Komdeur, Jan","last_name":"Komdeur","first_name":"Jan"},{"last_name":"Korb","first_name":"Judith","full_name":"Korb, Judith"},{"full_name":"Kronauer, Daniel","last_name":"Kronauer","first_name":"Daniel"},{"first_name":"Rolf","last_name":"Kümmerli","full_name":"Kümmerli, Rolf"},{"first_name":"Laurent","last_name":"Lehmann","full_name":"Lehmann, Laurent"},{"full_name":"Linksvayer, Timothy","first_name":"Timothy","last_name":"Linksvayer"},{"full_name":"Lion, Sébastien","last_name":"Lion","first_name":"Sébastien"},{"first_name":"Bruce","last_name":"Lyon","full_name":"Lyon, Bruce"},{"full_name":"Marshall, James","last_name":"Marshall","first_name":"James"},{"first_name":"Richard","last_name":"Mcelreath","full_name":"Mcelreath, Richard"},{"full_name":"Michalakis, Yannis","last_name":"Michalakis","first_name":"Yannis"},{"last_name":"Michod","first_name":"Richard","full_name":"Michod, Richard"},{"first_name":"Douglas","last_name":"Mock","full_name":"Mock, Douglas"},{"full_name":"Monnin, Thibaud","first_name":"Thibaud","last_name":"Monnin"},{"first_name":"Robert","last_name":"Montgomerie","full_name":"Montgomerie, Robert"},{"full_name":"Moore, Allen","last_name":"Moore","first_name":"Allen"},{"full_name":"Mueller, Ulrich","first_name":"Ulrich","last_name":"Mueller"},{"full_name":"Noë, Ronald","last_name":"Noë","first_name":"Ronald"},{"full_name":"Okasha, Samir","last_name":"Okasha","first_name":"Samir"},{"full_name":"Pamilo, Pekka","first_name":"Pekka","last_name":"Pamilo"},{"last_name":"Parker","first_name":"Geoff","full_name":"Parker, Geoff"},{"full_name":"Pedersen, Jes","first_name":"Jes","last_name":"Pedersen"},{"full_name":"Pen, Ido","last_name":"Pen","first_name":"Ido"},{"full_name":"Pfennig, David","first_name":"David","last_name":"Pfennig"},{"first_name":"David","last_name":"Queller","full_name":"Queller, David"},{"full_name":"Rankin, Daniel","last_name":"Rankin","first_name":"Daniel"},{"full_name":"Reece, Sarah","first_name":"Sarah","last_name":"Reece"},{"full_name":"Reeve, Hudson","first_name":"Hudson","last_name":"Reeve"},{"full_name":"Reuter, Max","first_name":"Max","last_name":"Reuter"},{"full_name":"Roberts, Gilbert","first_name":"Gilbert","last_name":"Roberts"},{"first_name":"Simon","last_name":"Robson","full_name":"Robson, Simon"},{"full_name":"Roze, Denis","last_name":"Roze","first_name":"Denis"},{"full_name":"Rousset, Francois","last_name":"Rousset","first_name":"Francois"},{"full_name":"Rueppell, Olav","last_name":"Rueppell","first_name":"Olav"},{"full_name":"Sachs, Joel","last_name":"Sachs","first_name":"Joel"},{"last_name":"Santorelli","first_name":"Lorenzo","full_name":"Santorelli, Lorenzo"},{"full_name":"Schmid Hempel, Paul","first_name":"Paul","last_name":"Schmid Hempel"},{"full_name":"Schwarz, Michael","last_name":"Schwarz","first_name":"Michael"},{"full_name":"Scott Phillips, Tom","first_name":"Tom","last_name":"Scott Phillips"},{"full_name":"Shellmann Sherman, Janet","first_name":"Janet","last_name":"Shellmann Sherman"},{"last_name":"Sherman","first_name":"Paul","full_name":"Sherman, Paul"},{"full_name":"Shuker, David","first_name":"David","last_name":"Shuker"},{"last_name":"Smith","first_name":"Jeff","full_name":"Smith, Jeff"},{"full_name":"Spagna, Joseph","last_name":"Spagna","first_name":"Joseph"},{"first_name":"Beverly","last_name":"Strassmann","full_name":"Strassmann, Beverly"},{"last_name":"Suarez","first_name":"Andrew","full_name":"Suarez, Andrew"},{"last_name":"Sundström","first_name":"Liselotte","full_name":"Sundström, Liselotte"},{"first_name":"Michael","last_name":"Taborsky","full_name":"Taborsky, Michael"},{"full_name":"Taylor, Peter","last_name":"Taylor","first_name":"Peter"},{"last_name":"Thompson","first_name":"Graham","full_name":"Thompson, Graham"},{"last_name":"Tooby","first_name":"John","full_name":"Tooby, John"},{"first_name":"Neil","last_name":"Tsutsui","full_name":"Tsutsui, Neil"},{"first_name":"Kazuki","last_name":"Tsuji","full_name":"Tsuji, Kazuki"},{"last_name":"Turillazzi","first_name":"Stefano","full_name":"Turillazzi, Stefano"},{"first_name":"Francisco","last_name":"Úbeda","full_name":"Úbeda, Francisco"},{"full_name":"Vargo, Edward","last_name":"Vargo","first_name":"Edward"},{"full_name":"Voelkl, Bernard","last_name":"Voelkl","first_name":"Bernard"},{"full_name":"Wenseleers, Tom","first_name":"Tom","last_name":"Wenseleers"},{"last_name":"West","first_name":"Stuart","full_name":"West, Stuart"},{"full_name":"West Eberhard, Mary","last_name":"West Eberhard","first_name":"Mary"},{"full_name":"Westneat, David","first_name":"David","last_name":"Westneat"},{"full_name":"Wiernasz, Diane","last_name":"Wiernasz","first_name":"Diane"},{"full_name":"Wild, Geoff","last_name":"Wild","first_name":"Geoff"},{"full_name":"Wrangham, Richard","last_name":"Wrangham","first_name":"Richard"},{"last_name":"Young","first_name":"Andrew","full_name":"Young, Andrew"},{"first_name":"David","last_name":"Zeh","full_name":"Zeh, David"},{"full_name":"Zeh, Jeanne","last_name":"Zeh","first_name":"Jeanne"},{"first_name":"Andrew","last_name":"Zink","full_name":"Zink, Andrew"}],"_id":"3372","date_created":"2018-12-11T12:02:57Z","issue":"7339","volume":471,"doi":"10.1038/nature09831","publication":"Nature","abstract":[{"lang":"eng","text":"Nowak et al.1 argue that inclusive fitness theory has been of little value in explaining the natural world, and that it has led to negligible progress in explaining the evolution of eusociality. However, we believe that their arguments are based upon a misunderstanding of evolutionary theory and a misrepresentation of the empirical literature. We will focus our comments on three general issues."}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836173/","open_access":"1"}],"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Inclusive fitness theory and eusociality","date_published":"2011-03-23T00:00:00Z","year":"2011","publication_status":"published","page":"E1 - E4","publisher":"Nature Publishing Group","quality_controlled":"1","language":[{"iso":"eng"}],"publist_id":"3237","oa":1,"status":"public","oa_version":"Submitted Version"},{"citation":{"ieee":"M. Jahnel, M. Behrndt, A. Jannasch, E. Schaeffer, and S. Grill, “Measuring the complete force field of an optical trap,” <i>Optics Letters</i>, vol. 36, no. 7. Optica Publishing Group, pp. 1260–1262, 2011.","apa":"Jahnel, M., Behrndt, M., Jannasch, A., Schaeffer, E., &#38; Grill, S. (2011). Measuring the complete force field of an optical trap. <i>Optics Letters</i>. Optica Publishing Group. <a href=\"https://doi.org/10.1364/OL.36.001260\">https://doi.org/10.1364/OL.36.001260</a>","short":"M. Jahnel, M. Behrndt, A. Jannasch, E. Schaeffer, S. Grill, Optics Letters 36 (2011) 1260–1262.","mla":"Jahnel, Marcus, et al. “Measuring the Complete Force Field of an Optical Trap.” <i>Optics Letters</i>, vol. 36, no. 7, Optica Publishing Group, 2011, pp. 1260–62, doi:<a href=\"https://doi.org/10.1364/OL.36.001260\">10.1364/OL.36.001260</a>.","ama":"Jahnel M, Behrndt M, Jannasch A, Schaeffer E, Grill S. Measuring the complete force field of an optical trap. <i>Optics Letters</i>. 2011;36(7):1260-1262. doi:<a href=\"https://doi.org/10.1364/OL.36.001260\">10.1364/OL.36.001260</a>","ista":"Jahnel M, Behrndt M, Jannasch A, Schaeffer E, Grill S. 2011. Measuring the complete force field of an optical trap. Optics Letters. 36(7), 1260–1262.","chicago":"Jahnel, Marcus, Martin Behrndt, Anita Jannasch, Erik Schaeffer, and Stephan Grill. “Measuring the Complete Force Field of an Optical Trap.” <i>Optics Letters</i>. Optica Publishing Group, 2011. <a href=\"https://doi.org/10.1364/OL.36.001260\">https://doi.org/10.1364/OL.36.001260</a>."},"scopus_import":"1","intvolume":"        36","day":"30","month":"03","department":[{"_id":"CaHe"}],"author":[{"first_name":"Marcus","last_name":"Jahnel","full_name":"Jahnel, Marcus"},{"id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","last_name":"Behrndt","first_name":"Martin","full_name":"Behrndt, Martin"},{"full_name":"Jannasch, Anita","last_name":"Jannasch","first_name":"Anita"},{"first_name":"Erik","last_name":"Schaeffer","full_name":"Schaeffer, Erik"},{"full_name":"Grill, Stephan","first_name":"Stephan","last_name":"Grill"}],"date_updated":"2023-10-17T12:16:58Z","volume":36,"issue":"7","date_created":"2018-12-11T12:02:58Z","_id":"3373","abstract":[{"lang":"eng","text":"The use of optical traps to measure or apply forces on the molecular level requires a precise knowledge of the trapping force field. Close to the trap center, this field is typically approximated as linear in the displacement of the trapped microsphere. However, applications demanding high forces at low laser intensities can probe the light-microsphere interaction beyond the linear regime. Here, we measured the full nonlinear force and displacement response of an optical trap in two dimensions using a dual-beam optical trap setup with back-focal-plane photodetection. We observed a substantial stiffening of the trap beyond the linear regime that depends on microsphere size, in agreement with Mie theory calculations. Surprisingly, we found that the linear detection range for forces exceeds the one for displacement by far. Our approach allows for a complete calibration of an optical trap."}],"publication":"Optics Letters","doi":"10.1364/OL.36.001260","title":"Measuring the complete force field of an optical trap","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://www.osapublishing.org/ol/abstract.cfm?uri=ol-36-7-1260"}],"quality_controlled":"1","publisher":"Optica Publishing Group","page":"1260 - 1262","year":"2011","publication_status":"published","date_published":"2011-03-30T00:00:00Z","oa_version":"Published Version","status":"public","oa":1,"publist_id":"3234","article_processing_charge":"No","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1403"}]}},{"status":"public","oa_version":"Submitted Version","publist_id":"3233","oa":1,"issue":"15","volume":23,"_id":"3374","article_number":"153102","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:02:58Z","author":[{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"},{"full_name":"Walczak, Aleksandra","first_name":"Aleksandra","last_name":"Walczak"}],"publisher":"IOP Publishing Ltd.","quality_controlled":"1","date_updated":"2021-01-12T07:43:03Z","year":"2011","publication_status":"published","date_published":"2011-04-01T00:00:00Z","type":"journal_article","day":"01","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Information transmission in genetic regulatory networks a review","intvolume":"        23","main_file_link":[{"url":"http://arxiv.org/abs/1101.4240","open_access":"1"}],"month":"04","department":[{"_id":"GaTk"}],"abstract":[{"text":"Genetic regulatory networks enable cells to respond to changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits has deepened our understanding of what kinds of computations genetic regulatory networks can perform, and with what reliability. These advances have motivated researchers to look for connections between the architecture and function of genetic regulatory networks. Transmitting information between a network's inputs and outputs has been proposed as one such possible measure of function, relevant in certain biological contexts. Here we summarize recent developments in the application of information theory to gene regulatory networks. We first review basic concepts in information theory necessary for understanding recent work. We then discuss the functional complexity of gene regulation, which arises from the molecular nature of the regulatory interactions. We end by reviewing some experiments that support the view that genetic networks responsible for early development of multicellular organisms might be maximizing transmitted 'positional information'.","lang":"eng"}],"publication":"Journal of Physics: Condensed Matter","citation":{"apa":"Tkačik, G., &#38; Walczak, A. (2011). Information transmission in genetic regulatory networks a review. <i>Journal of Physics: Condensed Matter</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/0953-8984/23/15/153102\">https://doi.org/10.1088/0953-8984/23/15/153102</a>","short":"G. Tkačik, A. Walczak, Journal of Physics: Condensed Matter 23 (2011).","mla":"Tkačik, Gašper, and Aleksandra Walczak. “Information Transmission in Genetic Regulatory Networks a Review.” <i>Journal of Physics: Condensed Matter</i>, vol. 23, no. 15, 153102, IOP Publishing Ltd., 2011, doi:<a href=\"https://doi.org/10.1088/0953-8984/23/15/153102\">10.1088/0953-8984/23/15/153102</a>.","chicago":"Tkačik, Gašper, and Aleksandra Walczak. “Information Transmission in Genetic Regulatory Networks a Review.” <i>Journal of Physics: Condensed Matter</i>. IOP Publishing Ltd., 2011. <a href=\"https://doi.org/10.1088/0953-8984/23/15/153102\">https://doi.org/10.1088/0953-8984/23/15/153102</a>.","ama":"Tkačik G, Walczak A. Information transmission in genetic regulatory networks a review. <i>Journal of Physics: Condensed Matter</i>. 2011;23(15). doi:<a href=\"https://doi.org/10.1088/0953-8984/23/15/153102\">10.1088/0953-8984/23/15/153102</a>","ista":"Tkačik G, Walczak A. 2011. Information transmission in genetic regulatory networks a review. Journal of Physics: Condensed Matter. 23(15), 153102.","ieee":"G. Tkačik and A. Walczak, “Information transmission in genetic regulatory networks a review,” <i>Journal of Physics: Condensed Matter</i>, vol. 23, no. 15. IOP Publishing Ltd., 2011."},"doi":"10.1088/0953-8984/23/15/153102","scopus_import":1},{"article_processing_charge":"No","ec_funded":1,"language":[{"iso":"eng"}],"status":"public","oa_version":"Submitted Version","publist_id":"3232","oa":1,"publication_status":"published","year":"2011","date_published":"2011-05-01T00:00:00Z","publisher":"The Royal Society","quality_controlled":"1","page":"720 - 739","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","title":"The statistical mechanics of a polygenic character under stabilizing selection mutation and drift","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061091/"}],"doi":"10.1098/rsif.2010.0438","abstract":[{"lang":"eng","text":"By exploiting an analogy between population genetics and statistical mechanics, we study the evolution of a polygenic trait under stabilizing selection, mutation and genetic drift. This requires us to track only four macroscopic variables, instead of the distribution of all the allele frequencies that influence the trait. These macroscopic variables are the expectations of: the trait mean and its square, the genetic variance, and of a measure of heterozygosity, and are derived from a generating function that is in turn derived by maximizing an entropy measure. These four macroscopics are enough to accurately describe the dynamics of the trait mean and of its genetic variance (and in principle of any other quantity). Unlike previous approaches that were based on an infinite series of moments or cumulants, which had to be truncated arbitrarily, our calculations provide a well-defined approximation procedure. We apply the framework to abrupt and gradual changes in the optimum, as well as to changes in the strength of stabilizing selection. Our approximations are surprisingly accurate, even for systems with as few as five loci. We find that when the effects of drift are included, the expected genetic variance is hardly altered by directional selection, even though it fluctuates in any particular instance. We also find hysteresis, showing that even after averaging over the microscopic variables, the macroscopic trajectories retain a memory of the underlying genetic states."}],"publication":"Journal of the Royal Society Interface","_id":"3375","date_created":"2018-12-11T12:02:58Z","issue":"58","volume":8,"date_updated":"2025-05-28T11:42:45Z","author":[{"last_name":"de Vladar","id":"2A181218-F248-11E8-B48F-1D18A9856A87","first_name":"Harold","orcid":"0000-0002-5985-7653","full_name":"de Vladar, Harold"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"article_type":"original","department":[{"_id":"NiBa"}],"month":"05","pmid":1,"day":"01","intvolume":"         8","citation":{"ieee":"H. de Vladar and N. H. Barton, “The statistical mechanics of a polygenic character under stabilizing selection mutation and drift,” <i>Journal of the Royal Society Interface</i>, vol. 8, no. 58. The Royal Society, pp. 720–739, 2011.","ista":"de Vladar H, Barton NH. 2011. The statistical mechanics of a polygenic character under stabilizing selection mutation and drift. Journal of the Royal Society Interface. 8(58), 720–739.","ama":"de Vladar H, Barton NH. The statistical mechanics of a polygenic character under stabilizing selection mutation and drift. <i>Journal of the Royal Society Interface</i>. 2011;8(58):720-739. doi:<a href=\"https://doi.org/10.1098/rsif.2010.0438\">10.1098/rsif.2010.0438</a>","chicago":"Vladar, Harold de, and Nicholas H Barton. “The Statistical Mechanics of a Polygenic Character under Stabilizing Selection Mutation and Drift.” <i>Journal of the Royal Society Interface</i>. The Royal Society, 2011. <a href=\"https://doi.org/10.1098/rsif.2010.0438\">https://doi.org/10.1098/rsif.2010.0438</a>.","apa":"de Vladar, H., &#38; Barton, N. H. (2011). The statistical mechanics of a polygenic character under stabilizing selection mutation and drift. <i>Journal of the Royal Society Interface</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsif.2010.0438\">https://doi.org/10.1098/rsif.2010.0438</a>","mla":"de Vladar, Harold, and Nicholas H. Barton. “The Statistical Mechanics of a Polygenic Character under Stabilizing Selection Mutation and Drift.” <i>Journal of the Royal Society Interface</i>, vol. 8, no. 58, The Royal Society, 2011, pp. 720–39, doi:<a href=\"https://doi.org/10.1098/rsif.2010.0438\">10.1098/rsif.2010.0438</a>.","short":"H. de Vladar, N.H. Barton, Journal of the Royal Society Interface 8 (2011) 720–739."},"scopus_import":"1","project":[{"name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152"}],"external_id":{"pmid":["21084341"]}},{"department":[{"_id":"ToBo"}],"month":"05","intvolume":"        42","day":"20","scopus_import":1,"citation":{"chicago":"Bollenbach, Mark Tobias, and Roy Kishony. “Resolution of Gene Regulatory Conflicts Caused by Combinations of Antibiotics.” <i>Molecular Cell</i>. Cell Press, 2011. <a href=\"https://doi.org/10.1016/j.molcel.2011.04.016\">https://doi.org/10.1016/j.molcel.2011.04.016</a>.","ama":"Bollenbach MT, Kishony R. Resolution of gene regulatory conflicts caused by combinations of antibiotics. <i>Molecular Cell</i>. 2011;42(4):413-425. doi:<a href=\"https://doi.org/10.1016/j.molcel.2011.04.016\">10.1016/j.molcel.2011.04.016</a>","ista":"Bollenbach MT, Kishony R. 2011. Resolution of gene regulatory conflicts caused by combinations of antibiotics. Molecular Cell. 42(4), 413–425.","apa":"Bollenbach, M. T., &#38; Kishony, R. (2011). Resolution of gene regulatory conflicts caused by combinations of antibiotics. <i>Molecular Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.molcel.2011.04.016\">https://doi.org/10.1016/j.molcel.2011.04.016</a>","mla":"Bollenbach, Mark Tobias, and Roy Kishony. “Resolution of Gene Regulatory Conflicts Caused by Combinations of Antibiotics.” <i>Molecular Cell</i>, vol. 42, no. 4, Cell Press, 2011, pp. 413–25, doi:<a href=\"https://doi.org/10.1016/j.molcel.2011.04.016\">10.1016/j.molcel.2011.04.016</a>.","short":"M.T. Bollenbach, R. Kishony, Molecular Cell 42 (2011) 413–425.","ieee":"M. T. Bollenbach and R. Kishony, “Resolution of gene regulatory conflicts caused by combinations of antibiotics,” <i>Molecular Cell</i>, vol. 42, no. 4. Cell Press, pp. 413–425, 2011."},"date_created":"2018-12-11T12:02:59Z","_id":"3376","volume":42,"acknowledgement":"This work was supported by a Feodor Lynen Fellowship of the Alexander von Humboldt Foundation (to T.B.).","issue":"4","date_updated":"2021-01-12T07:43:03Z","author":[{"last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias"},{"full_name":"Kishony, Roy","first_name":"Roy","last_name":"Kishony"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3143497/","open_access":"1"}],"title":"Resolution of gene regulatory conflicts caused by combinations of antibiotics","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.molcel.2011.04.016","publication":"Molecular Cell","abstract":[{"text":"Regulatory conflicts occur when two signals that individually trigger opposite cellular responses are present simultaneously. Here, we investigate regulatory conflicts in the bacterial response to antibiotic combinations. We use an Escherichia coli promoter-GFP library to study the transcriptional response of many promoters to either additive or antagonistic drug pairs at fine two-dimensional (2D) resolution of drug concentration. Surprisingly, we find that this data set can be characterized as a linear sum of only two principal components. Component one, accounting for over 70% of the response, represents the response to growth inhibition by the drugs. Component two describes how regulatory conflicts are resolved. For the additive drug pair, conflicts are resolved by linearly interpolating the single drug responses, while for the antagonistic drug pair, the growth-limiting drug dominates the response. Importantly, for a given drug pair, the same conflict resolution strategy applies to almost all genes. These results provide a recipe for predicting gene expression responses to antibiotic combinations.","lang":"eng"}],"language":[{"iso":"eng"}],"publist_id":"3231","oa":1,"oa_version":"Submitted Version","status":"public","date_published":"2011-05-20T00:00:00Z","publication_status":"published","year":"2011","page":"413 - 425","quality_controlled":"1","publisher":"Cell Press"},{"main_file_link":[{"url":"http://arxiv.org/abs/0911.2142","open_access":"1"}],"type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Quantifying transversality by measuring the robustness of intersections","publication":"Foundations of Computational Mathematics","abstract":[{"lang":"eng","text":"By definition, transverse intersections are stable under in- finitesimal perturbations. Using persistent homology, we ex- tend this notion to sizeable perturbations. Specifically, we assign to each homology class of the intersection its robust- ness, the magnitude of a perturbation necessary to kill it, and prove that robustness is stable. Among the applications of this result is a stable notion of robustness for fixed points of continuous mappings and a statement of stability for con- tours of smooth mappings."}],"doi":"10.1007/s10208-011-9090-8","publist_id":"3230","oa":1,"status":"public","oa_version":"Submitted Version","language":[{"iso":"eng"}],"page":"345 - 361","publisher":"Springer","quality_controlled":"1","date_published":"2011-06-01T00:00:00Z","year":"2011","publication_status":"published","day":"01","intvolume":"        11","month":"06","department":[{"_id":"HeEd"}],"scopus_import":1,"citation":{"ieee":"H. Edelsbrunner, D. Morozov, and A. Patel, “Quantifying transversality by measuring the robustness of intersections,” <i>Foundations of Computational Mathematics</i>, vol. 11, no. 3. Springer, pp. 345–361, 2011.","apa":"Edelsbrunner, H., Morozov, D., &#38; Patel, A. (2011). Quantifying transversality by measuring the robustness of intersections. <i>Foundations of Computational Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s10208-011-9090-8\">https://doi.org/10.1007/s10208-011-9090-8</a>","mla":"Edelsbrunner, Herbert, et al. “Quantifying Transversality by Measuring the Robustness of Intersections.” <i>Foundations of Computational Mathematics</i>, vol. 11, no. 3, Springer, 2011, pp. 345–61, doi:<a href=\"https://doi.org/10.1007/s10208-011-9090-8\">10.1007/s10208-011-9090-8</a>.","short":"H. Edelsbrunner, D. Morozov, A. Patel, Foundations of Computational Mathematics 11 (2011) 345–361.","chicago":"Edelsbrunner, Herbert, Dmitriy Morozov, and Amit Patel. “Quantifying Transversality by Measuring the Robustness of Intersections.” <i>Foundations of Computational Mathematics</i>. Springer, 2011. <a href=\"https://doi.org/10.1007/s10208-011-9090-8\">https://doi.org/10.1007/s10208-011-9090-8</a>.","ista":"Edelsbrunner H, Morozov D, Patel A. 2011. Quantifying transversality by measuring the robustness of intersections. Foundations of Computational Mathematics. 11(3), 345–361.","ama":"Edelsbrunner H, Morozov D, Patel A. Quantifying transversality by measuring the robustness of intersections. <i>Foundations of Computational Mathematics</i>. 2011;11(3):345-361. doi:<a href=\"https://doi.org/10.1007/s10208-011-9090-8\">10.1007/s10208-011-9090-8</a>"},"issue":"3","volume":11,"acknowledgement":"This research is partially supported by the Defense Advanced Research Projects Agency (DARPA) under grants HR0011-05-1-0007 and HR0011-05-1-0057.","_id":"3377","date_created":"2018-12-11T12:02:59Z","author":[{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Morozov, Dmitriy","first_name":"Dmitriy","last_name":"Morozov"},{"full_name":"Patel, Amit","id":"34A254A0-F248-11E8-B48F-1D18A9856A87","last_name":"Patel","first_name":"Amit"}],"date_updated":"2021-01-12T07:43:04Z"},{"department":[{"_id":"HeEd"}],"month":"06","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","day":"01","title":"Persistent intersection homology","intvolume":"        11","doi":"10.1007/s10208-010-9081-1","scopus_import":1,"citation":{"chicago":"Bendich, Paul, and John Harer. “Persistent Intersection Homology.” <i>Foundations of Computational Mathematics</i>. Springer, 2011. <a href=\"https://doi.org/10.1007/s10208-010-9081-1\">https://doi.org/10.1007/s10208-010-9081-1</a>.","ista":"Bendich P, Harer J. 2011. Persistent intersection homology. Foundations of Computational Mathematics. 11(3), 305–336.","ama":"Bendich P, Harer J. Persistent intersection homology. <i>Foundations of Computational Mathematics</i>. 2011;11(3):305-336. doi:<a href=\"https://doi.org/10.1007/s10208-010-9081-1\">10.1007/s10208-010-9081-1</a>","short":"P. Bendich, J. Harer, Foundations of Computational Mathematics 11 (2011) 305–336.","mla":"Bendich, Paul, and John Harer. “Persistent Intersection Homology.” <i>Foundations of Computational Mathematics</i>, vol. 11, no. 3, Springer, 2011, pp. 305–36, doi:<a href=\"https://doi.org/10.1007/s10208-010-9081-1\">10.1007/s10208-010-9081-1</a>.","apa":"Bendich, P., &#38; Harer, J. (2011). Persistent intersection homology. <i>Foundations of Computational Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s10208-010-9081-1\">https://doi.org/10.1007/s10208-010-9081-1</a>","ieee":"P. Bendich and J. Harer, “Persistent intersection homology,” <i>Foundations of Computational Mathematics</i>, vol. 11, no. 3. Springer, pp. 305–336, 2011."},"publication":"Foundations of Computational Mathematics","abstract":[{"lang":"eng","text":"The theory of intersection homology was developed to study the singularities of a topologically stratified space. This paper in- corporates this theory into the already developed framework of persistent homology. We demonstrate that persistent intersec- tion homology gives useful information about the relationship between an embedded stratified space and its singularities. We give, and prove the correctness of, an algorithm for the computa- tion of the persistent intersection homology groups of a filtered simplicial complex equipped with a stratification by subcom- plexes. We also derive, from Poincare ́ Duality, some structural results about persistent intersection homology."}],"_id":"3378","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:02:59Z","publist_id":"3229","issue":"3","acknowledgement":"This research was partially supported by the Defense Advanced Research Projects Agency (DARPA) under grant HR0011-05-1-0007.","volume":11,"status":"public","oa_version":"None","date_published":"2011-06-01T00:00:00Z","date_updated":"2021-01-12T07:43:04Z","publication_status":"published","year":"2011","page":"305 - 336","publisher":"Springer","author":[{"full_name":"Bendich, Paul","first_name":"Paul","id":"43F6EC54-F248-11E8-B48F-1D18A9856A87","last_name":"Bendich"},{"full_name":"Harer, John","first_name":"John","last_name":"Harer"}],"quality_controlled":"1"},{"doi":"10.1016/j.ydbio.2011.03.025","abstract":[{"lang":"eng","text":"The process of gastrulation is highly conserved across vertebrates on both the genetic and morphological levels, despite great variety in embryonic shape and speed of development. This mechanism spatially separates the germ layers and establishes the organizational foundation for future development. Mesodermal identity is specified in a superficial layer of cells, the epiblast, where cells maintain an epithelioid morphology. These cells involute to join the deeper hypoblast layer where they adopt a migratory, mesenchymal morphology. Expression of a cascade of related transcription factors orchestrates the parallel genetic transition from primitive to mature mesoderm. Although the early and late stages of this process are increasingly well understood, the transition between them has remained largely mysterious. We present here the first high resolution in vivo observations of the blebby transitional morphology of involuting mesodermal cells in a vertebrate embryo. We further demonstrate that the zebrafish spadetail mutation creates a reversible block in the maturation program, stalling cells in the transition state. This mutation creates an ideal system for dissecting the specific properties of cells undergoing the morphological transition of maturing mesoderm, as we demonstrate with a direct measurement of cell–cell adhesion."}],"publication":"Developmental Biology","title":"Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3090540/"}],"year":"2011","publication_status":"published","date_published":"2011-06-01T00:00:00Z","quality_controlled":"1","publisher":"Elsevier","page":"102 - 110","language":[{"iso":"eng"}],"oa_version":"Submitted Version","status":"public","publist_id":"3228","oa":1,"citation":{"ieee":"R. Row, J.-L. Maître, B. Martin, P. Stockinger, C.-P. J. Heisenberg, and D. Kimelman, “Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail,” <i>Developmental Biology</i>, vol. 354, no. 1. Elsevier, pp. 102–110, 2011.","chicago":"Row, Richard, Jean-Léon Maître, Benjamin Martin, Petra Stockinger, Carl-Philipp J Heisenberg, and David Kimelman. “Completion of the Epithelial to Mesenchymal Transition in Zebrafish Mesoderm Requires Spadetail.” <i>Developmental Biology</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.ydbio.2011.03.025\">https://doi.org/10.1016/j.ydbio.2011.03.025</a>.","ista":"Row R, Maître J-L, Martin B, Stockinger P, Heisenberg C-PJ, Kimelman D. 2011. Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail. Developmental Biology. 354(1), 102–110.","ama":"Row R, Maître J-L, Martin B, Stockinger P, Heisenberg C-PJ, Kimelman D. Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail. <i>Developmental Biology</i>. 2011;354(1):102-110. doi:<a href=\"https://doi.org/10.1016/j.ydbio.2011.03.025\">10.1016/j.ydbio.2011.03.025</a>","apa":"Row, R., Maître, J.-L., Martin, B., Stockinger, P., Heisenberg, C.-P. J., &#38; Kimelman, D. (2011). Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail. <i>Developmental Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ydbio.2011.03.025\">https://doi.org/10.1016/j.ydbio.2011.03.025</a>","short":"R. Row, J.-L. Maître, B. Martin, P. Stockinger, C.-P.J. Heisenberg, D. Kimelman, Developmental Biology 354 (2011) 102–110.","mla":"Row, Richard, et al. “Completion of the Epithelial to Mesenchymal Transition in Zebrafish Mesoderm Requires Spadetail.” <i>Developmental Biology</i>, vol. 354, no. 1, Elsevier, 2011, pp. 102–10, doi:<a href=\"https://doi.org/10.1016/j.ydbio.2011.03.025\">10.1016/j.ydbio.2011.03.025</a>."},"scopus_import":1,"external_id":{"pmid":["1463614"]},"pmid":1,"month":"06","department":[{"_id":"CaHe"}],"intvolume":"       354","day":"01","date_updated":"2021-01-12T07:43:04Z","article_type":"original","author":[{"full_name":"Row, Richard","last_name":"Row","first_name":"Richard"},{"id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","last_name":"Maître","first_name":"Jean-Léon","full_name":"Maître, Jean-Léon","orcid":"0000-0002-3688-1474"},{"full_name":"Martin, Benjamin","first_name":"Benjamin","last_name":"Martin"},{"first_name":"Petra","id":"261CB030-E90D-11E9-B182-F697D44B663C","last_name":"Stockinger","full_name":"Stockinger, Petra"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg"},{"last_name":"Kimelman","first_name":"David","full_name":"Kimelman, David"}],"date_created":"2018-12-11T12:03:00Z","_id":"3379","volume":354,"issue":"1"},{"main_file_link":[{"url":"https://www.pure.ed.ac.uk/ws/files/8144621/GR_2011_Barton.pdf","open_access":"1"}],"title":"Mapping Mendelian traits in asexual progeny using changes in marker allele frequency","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","doi":"10.1017/S0016672311000115","publication":"Genetical Research","abstract":[{"text":"Linkage between markers and genes that affect a phenotype of interest may be determined by examining differences in marker allele frequency in the extreme progeny of a cross between two inbred lines. This strategy is usually employed when pooling is used to reduce genotyping costs. When the cross progeny are asexual, the extreme progeny may be selected by multiple generations of asexual reproduction and selection. We analyse this method of measuring phenotype in asexual progeny and examine the changes in marker allele frequency due to selection over many generations. Stochasticity in marker frequency in the selected population arises due to the finite initial population size. We derive the distribution of marker frequency as a result of selection at a single major locus, and show that in order to avoid spurious changes in marker allele frequency in the selected population, the initial population size should be in the low to mid hundreds.","lang":"eng"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","oa":1,"publist_id":"3227","oa_version":"Published Version","status":"public","date_published":"2011-05-18T00:00:00Z","year":"2011","publication_status":"published","page":"221 - 232","quality_controlled":"1","publisher":"Cambridge University Press","month":"05","department":[{"_id":"NiBa"}],"intvolume":"        93","day":"18","scopus_import":1,"citation":{"ieee":"S. Logeswaran and N. H. Barton, “Mapping Mendelian traits in asexual progeny using changes in marker allele frequency,” <i>Genetical Research</i>, vol. 93, no. 3. Cambridge University Press, pp. 221–232, 2011.","ista":"Logeswaran S, Barton NH. 2011. Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. Genetical Research. 93(3), 221–232.","ama":"Logeswaran S, Barton NH. Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. <i>Genetical Research</i>. 2011;93(3):221-232. doi:<a href=\"https://doi.org/10.1017/S0016672311000115\">10.1017/S0016672311000115</a>","chicago":"Logeswaran, Sayanthan, and Nicholas H Barton. “Mapping Mendelian Traits in Asexual Progeny Using Changes in Marker Allele Frequency.” <i>Genetical Research</i>. Cambridge University Press, 2011. <a href=\"https://doi.org/10.1017/S0016672311000115\">https://doi.org/10.1017/S0016672311000115</a>.","short":"S. Logeswaran, N.H. Barton, Genetical Research 93 (2011) 221–232.","apa":"Logeswaran, S., &#38; Barton, N. H. (2011). Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. <i>Genetical Research</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/S0016672311000115\">https://doi.org/10.1017/S0016672311000115</a>","mla":"Logeswaran, Sayanthan, and Nicholas H. Barton. “Mapping Mendelian Traits in Asexual Progeny Using Changes in Marker Allele Frequency.” <i>Genetical Research</i>, vol. 93, no. 3, Cambridge University Press, 2011, pp. 221–32, doi:<a href=\"https://doi.org/10.1017/S0016672311000115\">10.1017/S0016672311000115</a>."},"date_created":"2018-12-11T12:03:00Z","_id":"3380","volume":93,"issue":"3","date_updated":"2021-01-12T07:43:05Z","article_type":"original","author":[{"full_name":"Logeswaran, Sayanthan","last_name":"Logeswaran","first_name":"Sayanthan"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}]},{"title":"Formalisms for specifying Markovian population models","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"file":[{"file_id":"4707","date_updated":"2020-07-14T12:46:11Z","file_name":"IST-2016-628-v1+1_journals-ijfcs-HenzingerJW11.pdf","file_size":222840,"relation":"main_file","date_created":"2018-12-12T10:08:45Z","content_type":"application/pdf","creator":"system","access_level":"open_access","checksum":"df88431872586c773fbcfea37d7b36a2"}],"abstract":[{"lang":"eng","text":"In this survey, we compare several languages for specifying Markovian population models such as queuing networks and chemical reaction networks. All these languages — matrix descriptions, stochastic Petri nets, stoichiometric equations, stochastic process algebras, and guarded command models — describe continuous-time Markov chains, but they differ according to important properties, such as compositionality, expressiveness and succinctness, executability, and ease of use. Moreover, they provide different support for checking the well-formedness of a model and for analyzing a model."}],"publication":"IJFCS: International Journal of Foundations of Computer Science","doi":"10.1142/S0129054111008441","oa_version":"Submitted Version","status":"public","has_accepted_license":"1","publist_id":"3226","oa":1,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"3841"}]},"language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"World Scientific Publishing","page":"823 - 841","publication_status":"published","year":"2011","date_published":"2011-06-01T00:00:00Z","intvolume":"        22","day":"01","month":"06","department":[{"_id":"ToHe"}],"pubrep_id":"628","citation":{"ieee":"T. A. Henzinger, B. Jobstmann, and V. Wolf, “Formalisms for specifying Markovian population models,” <i>IJFCS: International Journal of Foundations of Computer Science</i>, vol. 22, no. 4. World Scientific Publishing, pp. 823–841, 2011.","apa":"Henzinger, T. A., Jobstmann, B., &#38; Wolf, V. (2011). Formalisms for specifying Markovian population models. <i>IJFCS: International Journal of Foundations of Computer Science</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0129054111008441\">https://doi.org/10.1142/S0129054111008441</a>","short":"T.A. Henzinger, B. Jobstmann, V. Wolf, IJFCS: International Journal of Foundations of Computer Science 22 (2011) 823–841.","mla":"Henzinger, Thomas A., et al. “Formalisms for Specifying Markovian Population Models.” <i>IJFCS: International Journal of Foundations of Computer Science</i>, vol. 22, no. 4, World Scientific Publishing, 2011, pp. 823–41, doi:<a href=\"https://doi.org/10.1142/S0129054111008441\">10.1142/S0129054111008441</a>.","ama":"Henzinger TA, Jobstmann B, Wolf V. Formalisms for specifying Markovian population models. <i>IJFCS: International Journal of Foundations of Computer Science</i>. 2011;22(4):823-841. doi:<a href=\"https://doi.org/10.1142/S0129054111008441\">10.1142/S0129054111008441</a>","chicago":"Henzinger, Thomas A, Barbara Jobstmann, and Verena Wolf. “Formalisms for Specifying Markovian Population Models.” <i>IJFCS: International Journal of Foundations of Computer Science</i>. World Scientific Publishing, 2011. <a href=\"https://doi.org/10.1142/S0129054111008441\">https://doi.org/10.1142/S0129054111008441</a>.","ista":"Henzinger TA, Jobstmann B, Wolf V. 2011. Formalisms for specifying Markovian population models. IJFCS: International Journal of Foundations of Computer Science. 22(4), 823–841."},"scopus_import":1,"volume":22,"file_date_updated":"2020-07-14T12:46:11Z","issue":"4","date_created":"2018-12-11T12:03:00Z","_id":"3381","author":[{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"first_name":"Barbara","last_name":"Jobstmann","full_name":"Jobstmann, Barbara"},{"full_name":"Wolf, Verena","last_name":"Wolf","first_name":"Verena"}],"date_updated":"2023-02-23T11:45:03Z"},{"date_published":"2011-05-21T00:00:00Z","year":"2011","publication_status":"published","date_updated":"2021-01-12T07:43:06Z","page":"545 - 557","quality_controlled":"1","publisher":"IEEE","author":[{"first_name":"Oliver","last_name":"Kroemer","full_name":"Kroemer, Oliver"},{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Peters, Jan","last_name":"Peters","first_name":"Jan"}],"date_created":"2018-12-11T12:03:01Z","language":[{"iso":"eng"}],"_id":"3382","volume":27,"publist_id":"3225","issue":"3","oa_version":"None","status":"public","scopus_import":1,"doi":"10.1109/TRO.2011.2121130","citation":{"ieee":"O. Kroemer, C. Lampert, and J. Peters, “Learning dynamic tactile sensing with robust vision based training,” <i>IEEE Transactions on Robotics</i>, vol. 27, no. 3. IEEE, pp. 545–557, 2011.","chicago":"Kroemer, Oliver, Christoph Lampert, and Jan Peters. “Learning Dynamic Tactile Sensing with Robust Vision Based Training.” <i>IEEE Transactions on Robotics</i>. IEEE, 2011. <a href=\"https://doi.org/10.1109/TRO.2011.2121130\">https://doi.org/10.1109/TRO.2011.2121130</a>.","ama":"Kroemer O, Lampert C, Peters J. Learning dynamic tactile sensing with robust vision based training. <i>IEEE Transactions on Robotics</i>. 2011;27(3):545-557. doi:<a href=\"https://doi.org/10.1109/TRO.2011.2121130\">10.1109/TRO.2011.2121130</a>","ista":"Kroemer O, Lampert C, Peters J. 2011. Learning dynamic tactile sensing with robust vision based training. IEEE Transactions on Robotics. 27(3), 545–557.","apa":"Kroemer, O., Lampert, C., &#38; Peters, J. (2011). Learning dynamic tactile sensing with robust vision based training. <i>IEEE Transactions on Robotics</i>. IEEE. <a href=\"https://doi.org/10.1109/TRO.2011.2121130\">https://doi.org/10.1109/TRO.2011.2121130</a>","short":"O. Kroemer, C. Lampert, J. Peters, IEEE Transactions on Robotics 27 (2011) 545–557.","mla":"Kroemer, Oliver, et al. “Learning Dynamic Tactile Sensing with Robust Vision Based Training.” <i>IEEE Transactions on Robotics</i>, vol. 27, no. 3, IEEE, 2011, pp. 545–57, doi:<a href=\"https://doi.org/10.1109/TRO.2011.2121130\">10.1109/TRO.2011.2121130</a>."},"publication":"IEEE Transactions on Robotics","abstract":[{"lang":"eng","text":"Dynamic tactile sensing is a fundamental ability to recognize materials and objects. However, while humans are born with partially developed dynamic tactile sensing and quickly master this skill, today's robots remain in their infancy. The development of such a sense requires not only better sensors but the right algorithms to deal with these sensors' data as well. For example, when classifying a material based on touch, the data are noisy, high-dimensional, and contain irrelevant signals as well as essential ones. Few classification methods from machine learning can deal with such problems. In this paper, we propose an efficient approach to infer suitable lower dimensional representations of the tactile data. In order to classify materials based on only the sense of touch, these representations are autonomously discovered using visual information of the surfaces during training. However, accurately pairing vision and tactile samples in real-robot applications is a difficult problem. The proposed approach, therefore, works with weak pairings between the modalities. Experiments show that the resulting approach is very robust and yields significantly higher classification performance based on only dynamic tactile sensing."}],"month":"05","department":[{"_id":"ChLa"}],"title":"Learning dynamic tactile sensing with robust vision based training","intvolume":"        27","day":"21","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article"}]