[{"page":"3255-3298","publication":"International Mathematics Research Notices","date_created":"2018-12-11T11:49:41Z","external_id":{"arxiv":["1608.05163"],"isi":["000441668300009"]},"_id":"1012","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"}],"month":"05","date_updated":"2023-09-22T09:44:21Z","title":"Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues","ec_funded":1,"date_published":"2018-05-18T00:00:00Z","article_processing_charge":"No","scopus_import":"1","volume":2018,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.05163"}],"related_material":{"record":[{"id":"6179","status":"public","relation":"dissertation_contains"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"10","intvolume":"      2018","oa":1,"oa_version":"Preprint","arxiv":1,"doi":"10.1093/imrn/rnw330","day":"18","publisher":"Oxford University Press","publication_identifier":{"issn":["10737928"]},"department":[{"_id":"LaEr"}],"author":[{"last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","last_name":"Schröder","first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"year":"2018","citation":{"mla":"Erdös, László, and Dominik J. Schröder. “Fluctuations of Rectangular Young Diagrams of Interlacing Wigner Eigenvalues.” <i>International Mathematics Research Notices</i>, vol. 2018, no. 10, Oxford University Press, 2018, pp. 3255–98, doi:<a href=\"https://doi.org/10.1093/imrn/rnw330\">10.1093/imrn/rnw330</a>.","ista":"Erdös L, Schröder DJ. 2018. Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues. International Mathematics Research Notices. 2018(10), 3255–3298.","chicago":"Erdös, László, and Dominik J Schröder. “Fluctuations of Rectangular Young Diagrams of Interlacing Wigner Eigenvalues.” <i>International Mathematics Research Notices</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/imrn/rnw330\">https://doi.org/10.1093/imrn/rnw330</a>.","ama":"Erdös L, Schröder DJ. Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues. <i>International Mathematics Research Notices</i>. 2018;2018(10):3255-3298. doi:<a href=\"https://doi.org/10.1093/imrn/rnw330\">10.1093/imrn/rnw330</a>","ieee":"L. Erdös and D. J. Schröder, “Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues,” <i>International Mathematics Research Notices</i>, vol. 2018, no. 10. Oxford University Press, pp. 3255–3298, 2018.","short":"L. Erdös, D.J. Schröder, International Mathematics Research Notices 2018 (2018) 3255–3298.","apa":"Erdös, L., &#38; Schröder, D. J. (2018). Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues. <i>International Mathematics Research Notices</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/imrn/rnw330\">https://doi.org/10.1093/imrn/rnw330</a>"},"type":"journal_article","language":[{"iso":"eng"}],"status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"We prove a new central limit theorem (CLT) for the difference of linear eigenvalue statistics of a Wigner random matrix H and its minor H and find that the fluctuation is much smaller than the fluctuations of the individual linear statistics, as a consequence of the strong correlation between the eigenvalues of H and H. In particular, our theorem identifies the fluctuation of Kerov's rectangular Young diagrams, defined by the interlacing eigenvalues ofH and H, around their asymptotic shape, the Vershik'Kerov'Logan'Shepp curve. Young diagrams equipped with the Plancherel measure follow the same limiting shape. For this, algebraically motivated, ensemble a CLT has been obtained in Ivanov and Olshanski [20] which is structurally similar to our result but the variance is different, indicating that the analogy between the two models has its limitations. Moreover, our theorem shows that Borodin's result [7] on the convergence of the spectral distribution of Wigner matrices to a Gaussian free field also holds in derivative sense."}],"publist_id":"6383","quality_controlled":"1"},{"article_processing_charge":"No","date_published":"2018-01-01T00:00:00Z","month":"01","title":"Evaluation and monitoring of free running oscillators serving as source of randomness","date_updated":"2021-11-15T10:48:49Z","date_created":"2021-11-14T23:01:25Z","_id":"10286","page":"214-242","publication":"IACR Transactions on Cryptographic Hardware and Embedded Systems","file_date_updated":"2021-11-15T10:27:29Z","oa":1,"intvolume":"      2018","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","issue":"3","volume":2018,"scopus_import":"1","year":"2018","author":[{"last_name":"Allini","full_name":"Allini, Elie Noumon","first_name":"Elie Noumon"},{"first_name":"Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","last_name":"Skórski","full_name":"Skórski, Maciej"},{"first_name":"Oto","full_name":"Petura, Oto","last_name":"Petura"},{"first_name":"Florent","full_name":"Bernard, Florent","last_name":"Bernard"},{"full_name":"Laban, Marek","last_name":"Laban","first_name":"Marek"},{"first_name":"Viktor","full_name":"Fischer, Viktor","last_name":"Fischer"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"KrPi"}],"publication_identifier":{"eissn":["2569-2925"]},"day":"01","publisher":"International Association for Cryptologic Research","oa_version":"Published Version","doi":"10.13154/tches.v2018.i3.214-242","quality_controlled":"1","status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"publication_status":"published","abstract":[{"text":"In this paper, we evaluate clock signals generated in ring oscillators and self-timed rings and the way their jitter can be transformed into random numbers. We show that counting the periods of the jittery clock signal produces random numbers of significantly better quality than the methods in which the jittery signal is simply sampled (the case in almost all current methods). Moreover, we use the counter values to characterize and continuously monitor the source of randomness. However, instead of using the widely used statistical variance, we propose to use Allan variance to do so. There are two main advantages: Allan variance is insensitive to low frequency noises such as flicker noise that are known to be autocorrelated and significantly less circuitry is required for its computation than that used to compute commonly used variance. We also show that it is essential to use a differential principle of randomness extraction from the jitter based on the use of two identical oscillators to avoid autocorrelations originating from external and internal global jitter sources and that this fact is valid for both kinds of rings. Last but not least, we propose a method of statistical testing based on high order Markov model to show the reduced dependencies when the proposed randomness extraction is applied.","lang":"eng"}],"article_type":"original","ddc":["000"],"type":"journal_article","citation":{"ista":"Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. 2018. Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. 2018(3), 214–242.","mla":"Allini, Elie Noumon, et al. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” <i>IACR Transactions on Cryptographic Hardware and Embedded Systems</i>, vol. 2018, no. 3, International Association for Cryptologic Research, 2018, pp. 214–42, doi:<a href=\"https://doi.org/10.13154/tches.v2018.i3.214-242\">10.13154/tches.v2018.i3.214-242</a>.","chicago":"Allini, Elie Noumon, Maciej Skórski, Oto Petura, Florent Bernard, Marek Laban, and Viktor Fischer. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” <i>IACR Transactions on Cryptographic Hardware and Embedded Systems</i>. International Association for Cryptologic Research, 2018. <a href=\"https://doi.org/10.13154/tches.v2018.i3.214-242\">https://doi.org/10.13154/tches.v2018.i3.214-242</a>.","ama":"Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. Evaluation and monitoring of free running oscillators serving as source of randomness. <i>IACR Transactions on Cryptographic Hardware and Embedded Systems</i>. 2018;2018(3):214-242. doi:<a href=\"https://doi.org/10.13154/tches.v2018.i3.214-242\">10.13154/tches.v2018.i3.214-242</a>","ieee":"E. N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, and V. Fischer, “Evaluation and monitoring of free running oscillators serving as source of randomness,” <i>IACR Transactions on Cryptographic Hardware and Embedded Systems</i>, vol. 2018, no. 3. International Association for Cryptologic Research, pp. 214–242, 2018.","short":"E.N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, V. Fischer, IACR Transactions on Cryptographic Hardware and Embedded Systems 2018 (2018) 214–242.","apa":"Allini, E. N., Skórski, M., Petura, O., Bernard, F., Laban, M., &#38; Fischer, V. (2018). Evaluation and monitoring of free running oscillators serving as source of randomness. <i>IACR Transactions on Cryptographic Hardware and Embedded Systems</i>. International Association for Cryptologic Research. <a href=\"https://doi.org/10.13154/tches.v2018.i3.214-242\">https://doi.org/10.13154/tches.v2018.i3.214-242</a>"},"file":[{"file_name":"2018_IACR_Allini.pdf","access_level":"open_access","success":1,"checksum":"b816b848f046c48a8357700d9305dce5","relation":"main_file","file_size":955755,"date_updated":"2021-11-15T10:27:29Z","content_type":"application/pdf","date_created":"2021-11-15T10:27:29Z","creator":"cchlebak","file_id":"10289"}]},{"department":[{"_id":"GradSch"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2018","isi":1,"author":[{"first_name":"Denise","last_name":"Seitner","full_name":"Seitner, Denise"},{"last_name":"Uhse","full_name":"Uhse, Simon","first_name":"Simon"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","last_name":"Gallei"},{"full_name":"Djamei, Armin","last_name":"Djamei","first_name":"Armin"}],"doi":"10.1111/mpp.12698","oa_version":"Published Version","publisher":"Wiley","day":"01","publist_id":"7950","publication_status":"published","abstract":[{"text":"The biotrophic pathogen Ustilago maydis, the causative agent of corn smut disease, infects one of the most important crops worldwide – Zea mays. To successfully colonize its host, U. maydis secretes proteins, known as effectors, that suppress plant defense responses and facilitate the establishment of biotrophy. In this work, we describe the U. maydis effector protein Cce1. Cce1 is essential for virulence and is upregulated during infection. Through microscopic analysis and in vitro assays, we show that Cce1 is secreted from hyphae during filamentous growth of the fungus. Strikingly, Δcce1 mutants are blocked at early stages of infection and induce callose deposition as a plant defense response. Cce1 is highly conserved among smut fungi and the Ustilago bromivora ortholog complemented the virulence defect of the SG200Δcce1 deletion strain. These data indicate that Cce1 is a core effector with apoplastic localization that is essential for U. maydis to infect its host.","lang":"eng"}],"has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","file":[{"file_size":682335,"content_type":"application/pdf","date_updated":"2018-12-18T09:46:00Z","relation":"main_file","access_level":"open_access","success":1,"file_name":"2018_MolecPlantPath_Seitner.pdf","file_id":"5740","date_created":"2018-12-18T09:46:00Z","creator":"dernst"}],"citation":{"short":"D. Seitner, S. Uhse, M.C. Gallei, A. Djamei, Molecular Plant Pathology 19 (2018) 2277–2287.","apa":"Seitner, D., Uhse, S., Gallei, M. C., &#38; Djamei, A. (2018). The core effector Cce1 is required for early infection of maize by Ustilago maydis. <i>Molecular Plant Pathology</i>. Wiley. <a href=\"https://doi.org/10.1111/mpp.12698\">https://doi.org/10.1111/mpp.12698</a>","ieee":"D. Seitner, S. Uhse, M. C. Gallei, and A. Djamei, “The core effector Cce1 is required for early infection of maize by Ustilago maydis,” <i>Molecular Plant Pathology</i>, vol. 19, no. 10. Wiley, pp. 2277–2287, 2018.","chicago":"Seitner, Denise, Simon Uhse, Michelle C Gallei, and Armin Djamei. “The Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.” <i>Molecular Plant Pathology</i>. Wiley, 2018. <a href=\"https://doi.org/10.1111/mpp.12698\">https://doi.org/10.1111/mpp.12698</a>.","ama":"Seitner D, Uhse S, Gallei MC, Djamei A. The core effector Cce1 is required for early infection of maize by Ustilago maydis. <i>Molecular Plant Pathology</i>. 2018;19(10):2277-2287. doi:<a href=\"https://doi.org/10.1111/mpp.12698\">10.1111/mpp.12698</a>","ista":"Seitner D, Uhse S, Gallei MC, Djamei A. 2018. The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. 19(10), 2277–2287.","mla":"Seitner, Denise, et al. “The Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.” <i>Molecular Plant Pathology</i>, vol. 19, no. 10, Wiley, 2018, pp. 2277–87, doi:<a href=\"https://doi.org/10.1111/mpp.12698\">10.1111/mpp.12698</a>."},"type":"journal_article","ddc":["580"],"title":"The core effector Cce1 is required for early infection of maize by Ustilago maydis","date_updated":"2023-09-19T10:06:42Z","month":"10","article_processing_charge":"No","date_published":"2018-10-01T00:00:00Z","publication":"Molecular Plant Pathology","file_date_updated":"2018-12-18T09:46:00Z","page":"2277 - 2287","_id":"104","external_id":{"isi":["000445624100006"]},"date_created":"2018-12-11T11:44:39Z","volume":19,"intvolume":"        19","oa":1,"acknowledgement":"the Austrian Science Fund (FWF): [P27429‐B22, P27818‐B22, I 3033‐B22], and the Austrian Academy of Science (OEAW).","issue":"10","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1"},{"month":"09","title":"Long geodesics on convex surfaces","date_updated":"2023-09-13T08:49:16Z","date_published":"2018-09-01T00:00:00Z","article_processing_charge":"No","page":"26 - 31","publication":"Mathematical Intelligencer","date_created":"2018-12-11T11:44:40Z","external_id":{"arxiv":["1702.05172"],"isi":["000444141200005"]},"_id":"106","volume":40,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.05172"}],"issue":"3","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"intvolume":"        40","scopus_import":"1","department":[{"_id":"HeEd"}],"isi":1,"author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","last_name":"Akopyan"},{"first_name":"Anton","full_name":"Petrunin, Anton","last_name":"Petrunin"}],"year":"2018","arxiv":1,"oa_version":"Preprint","doi":"10.1007/s00283-018-9795-5","day":"01","publisher":"Springer","language":[{"iso":"eng"}],"status":"public","abstract":[{"lang":"eng","text":"The goal of this article is to introduce the reader to the theory of intrinsic geometry of convex surfaces. We illustrate the power of the tools by proving a theorem on convex surfaces containing an arbitrarily long closed simple geodesic. Let us remind ourselves that a curve in a surface is called geodesic if every sufficiently short arc of the curve is length minimizing; if, in addition, it has no self-intersections, we call it simple geodesic. A tetrahedron with equal opposite edges is called isosceles. The axiomatic method of Alexandrov geometry allows us to work with the metrics of convex surfaces directly, without approximating it first by a smooth or polyhedral metric. Such approximations destroy the closed geodesics on the surface; therefore it is difficult (if at all possible) to apply approximations in the proof of our theorem. On the other hand, a proof in the smooth or polyhedral case usually admits a translation into Alexandrov’s language; such translation makes the result more general. In fact, our proof resembles a translation of the proof given by Protasov. Note that the main theorem implies in particular that a smooth convex surface does not have arbitrarily long simple closed geodesics. However we do not know a proof of this corollary that is essentially simpler than the one presented below."}],"publication_status":"published","publist_id":"7948","quality_controlled":"1","citation":{"mla":"Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” <i>Mathematical Intelligencer</i>, vol. 40, no. 3, Springer, 2018, pp. 26–31, doi:<a href=\"https://doi.org/10.1007/s00283-018-9795-5\">10.1007/s00283-018-9795-5</a>.","ista":"Akopyan A, Petrunin A. 2018. Long geodesics on convex surfaces. Mathematical Intelligencer. 40(3), 26–31.","chicago":"Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” <i>Mathematical Intelligencer</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00283-018-9795-5\">https://doi.org/10.1007/s00283-018-9795-5</a>.","ama":"Akopyan A, Petrunin A. Long geodesics on convex surfaces. <i>Mathematical Intelligencer</i>. 2018;40(3):26-31. doi:<a href=\"https://doi.org/10.1007/s00283-018-9795-5\">10.1007/s00283-018-9795-5</a>","ieee":"A. Akopyan and A. Petrunin, “Long geodesics on convex surfaces,” <i>Mathematical Intelligencer</i>, vol. 40, no. 3. Springer, pp. 26–31, 2018.","apa":"Akopyan, A., &#38; Petrunin, A. (2018). Long geodesics on convex surfaces. <i>Mathematical Intelligencer</i>. Springer. <a href=\"https://doi.org/10.1007/s00283-018-9795-5\">https://doi.org/10.1007/s00283-018-9795-5</a>","short":"A. Akopyan, A. Petrunin, Mathematical Intelligencer 40 (2018) 26–31."},"type":"journal_article"},{"volume":59,"oa":1,"intvolume":"        59","issue":"4","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","title":"On the circle covering theorem by A.W. Goodman and R.E. Goodman","date_updated":"2023-09-20T12:08:51Z","month":"06","article_processing_charge":"Yes (via OA deal)","date_published":"2018-06-01T00:00:00Z","ec_funded":1,"publication":"Discrete & Computational Geometry","file_date_updated":"2019-01-18T09:27:36Z","page":"1001-1009","_id":"1064","project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"external_id":{"isi":["000432205500011"]},"date_created":"2018-12-11T11:49:57Z","publist_id":"6324","abstract":[{"lang":"eng","text":"In 1945, A.W. Goodman and R.E. Goodman proved the following conjecture by P. Erdős: Given a family of (round) disks of radii r1, … , rn in the plane, it is always possible to cover them by a disk of radius R= ∑ ri, provided they cannot be separated into two subfamilies by a straight line disjoint from the disks. In this note we show that essentially the same idea may work for different analogues and generalizations of their result. In particular, we prove the following: Given a family of positive homothetic copies of a fixed convex body K⊂ Rd with homothety coefficients τ1, … , τn> 0 , it is always possible to cover them by a translate of d+12(∑τi)K, provided they cannot be separated into two subfamilies by a hyperplane disjoint from the homothets."}],"publication_status":"published","status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"quality_controlled":"1","file":[{"file_id":"5844","creator":"dernst","date_created":"2019-01-18T09:27:36Z","relation":"main_file","file_size":482518,"date_updated":"2019-01-18T09:27:36Z","content_type":"application/pdf","file_name":"2018_DiscreteComp_Akopyan.pdf","access_level":"open_access","success":1}],"type":"journal_article","citation":{"ama":"Akopyan A, Balitskiy A, Grigorev M. On the circle covering theorem by A.W. Goodman and R.E. Goodman. <i>Discrete &#38; Computational Geometry</i>. 2018;59(4):1001-1009. doi:<a href=\"https://doi.org/10.1007/s00454-017-9883-x\">10.1007/s00454-017-9883-x</a>","chicago":"Akopyan, Arseniy, Alexey Balitskiy, and Mikhail Grigorev. “On the Circle Covering Theorem by A.W. Goodman and R.E. Goodman.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00454-017-9883-x\">https://doi.org/10.1007/s00454-017-9883-x</a>.","ista":"Akopyan A, Balitskiy A, Grigorev M. 2018. On the circle covering theorem by A.W. Goodman and R.E. Goodman. Discrete &#38; Computational Geometry. 59(4), 1001–1009.","mla":"Akopyan, Arseniy, et al. “On the Circle Covering Theorem by A.W. Goodman and R.E. Goodman.” <i>Discrete &#38; Computational Geometry</i>, vol. 59, no. 4, Springer, 2018, pp. 1001–09, doi:<a href=\"https://doi.org/10.1007/s00454-017-9883-x\">10.1007/s00454-017-9883-x</a>.","apa":"Akopyan, A., Balitskiy, A., &#38; Grigorev, M. (2018). On the circle covering theorem by A.W. Goodman and R.E. Goodman. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-017-9883-x\">https://doi.org/10.1007/s00454-017-9883-x</a>","short":"A. Akopyan, A. Balitskiy, M. Grigorev, Discrete &#38; Computational Geometry 59 (2018) 1001–1009.","ieee":"A. Akopyan, A. Balitskiy, and M. Grigorev, “On the circle covering theorem by A.W. Goodman and R.E. Goodman,” <i>Discrete &#38; Computational Geometry</i>, vol. 59, no. 4. Springer, pp. 1001–1009, 2018."},"ddc":["516","000"],"article_type":"original","department":[{"_id":"HeEd"}],"publication_identifier":{"issn":["01795376"],"eissn":["14320444"]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2018","author":[{"last_name":"Akopyan","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy"},{"full_name":"Balitskiy, Alexey","last_name":"Balitskiy","first_name":"Alexey"},{"first_name":"Mikhail","full_name":"Grigorev, Mikhail","last_name":"Grigorev"}],"isi":1,"doi":"10.1007/s00454-017-9883-x","oa_version":"Published Version","publisher":"Springer","day":"01"},{"publication":"Journal of the ACM","date_created":"2018-12-11T11:44:40Z","external_id":{"isi":["000442938200004"]},"project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"},{"name":"Provable Security for Physical Cryptography","call_identifier":"FP7","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"_id":"107","month":"08","date_updated":"2023-09-13T09:05:17Z","title":"Non-malleable codes","ec_funded":1,"date_published":"2018-08-01T00:00:00Z","article_processing_charge":"No","scopus_import":"1","volume":65,"main_file_link":[{"url":"https://eprint.iacr.org/2009/608","open_access":"1"}],"issue":"4","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"        65","oa":1,"article_number":"20","oa_version":"Preprint","doi":"10.1145/3178432","day":"01","publisher":"ACM","department":[{"_id":"KrPi"}],"author":[{"full_name":"Dziembowski, Stefan","last_name":"Dziembowski","first_name":"Stefan"},{"last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wichs, Daniel","last_name":"Wichs","first_name":"Daniel"}],"isi":1,"year":"2018","citation":{"ieee":"S. Dziembowski, K. Z. Pietrzak, and D. Wichs, “Non-malleable codes,” <i>Journal of the ACM</i>, vol. 65, no. 4. ACM, 2018.","short":"S. Dziembowski, K.Z. Pietrzak, D. Wichs, Journal of the ACM 65 (2018).","apa":"Dziembowski, S., Pietrzak, K. Z., &#38; Wichs, D. (2018). Non-malleable codes. <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/3178432\">https://doi.org/10.1145/3178432</a>","ista":"Dziembowski S, Pietrzak KZ, Wichs D. 2018. Non-malleable codes. Journal of the ACM. 65(4), 20.","mla":"Dziembowski, Stefan, et al. “Non-Malleable Codes.” <i>Journal of the ACM</i>, vol. 65, no. 4, 20, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3178432\">10.1145/3178432</a>.","ama":"Dziembowski S, Pietrzak KZ, Wichs D. Non-malleable codes. <i>Journal of the ACM</i>. 2018;65(4). doi:<a href=\"https://doi.org/10.1145/3178432\">10.1145/3178432</a>","chicago":"Dziembowski, Stefan, Krzysztof Z Pietrzak, and Daniel Wichs. “Non-Malleable Codes.” <i>Journal of the ACM</i>. ACM, 2018. <a href=\"https://doi.org/10.1145/3178432\">https://doi.org/10.1145/3178432</a>."},"type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"status":"public","publication_status":"published","abstract":[{"text":"We introduce the notion of “non-malleable codes” which relaxes the notion of error correction and error detection. Informally, a code is non-malleable if the message contained in a modified codeword is either the original message, or a completely unrelated value. In contrast to error correction and error detection, non-malleability can be achieved for very rich classes of modifications. We construct an efficient code that is non-malleable with respect to modifications that affect each bit of the codeword arbitrarily (i.e., leave it untouched, flip it, or set it to either 0 or 1), but independently of the value of the other bits of the codeword. Using the probabilistic method, we also show a very strong and general statement: there exists a non-malleable code for every “small enough” family F of functions via which codewords can be modified. Although this probabilistic method argument does not directly yield efficient constructions, it gives us efficient non-malleable codes in the random-oracle model for very general classes of tampering functions—e.g., functions where every bit in the tampered codeword can depend arbitrarily on any 99% of the bits in the original codeword. As an application of non-malleable codes, we show that they provide an elegant algorithmic solution to the task of protecting functionalities implemented in hardware (e.g., signature cards) against “tampering attacks.” In such attacks, the secret state of a physical system is tampered, in the hopes that future interaction with the modified system will reveal some secret information. This problem was previously studied in the work of Gennaro et al. in 2004 under the name “algorithmic tamper proof security” (ATP). We show that non-malleable codes can be used to achieve important improvements over the prior work. In particular, we show that any functionality can be made secure against a large class of tampering attacks, simply by encoding the secret state with a non-malleable code while it is stored in memory.","lang":"eng"}],"publist_id":"7947","quality_controlled":"1"},{"department":[{"_id":"KrPi"}],"author":[{"full_name":"Obremski, Marciej","last_name":"Obremski","first_name":"Marciej"},{"first_name":"Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","last_name":"Skorski","full_name":"Skorski, Maciej"}],"isi":1,"year":"2018","conference":{"name":"ISIT: International Symposium on Information Theory","end_date":"2018-06-22","location":"Vail, CO, USA","start_date":"2018-06-17 "},"doi":"10.1109/ISIT.2018.8437654","oa_version":"Submitted Version","publisher":"IEEE","day":"16","abstract":[{"lang":"eng","text":"Universal hashing found a lot of applications in computer science. In cryptography the most important fact about universal families is the so called Leftover Hash Lemma, proved by Impagliazzo, Levin and Luby. In the language of modern cryptography it states that almost universal families are good extractors. In this work we provide a somewhat surprising characterization in the opposite direction. Namely, every extractor with sufficiently good parameters yields a universal family on a noticeable fraction of its inputs. Our proof technique is based on tools from extremal graph theory applied to the \\'collision graph\\' induced by the extractor, and may be of independent interest. We discuss possible applications to the theory of randomness extractors and non-malleable codes."}],"publication_status":"published","publist_id":"7946","language":[{"iso":"eng"}],"status":"public","quality_controlled":"1","type":"conference","citation":{"mla":"Obremski, Marciej, and Maciej Skórski. <i>Inverted Leftover Hash Lemma</i>. Vol. 2018, IEEE, 2018, doi:<a href=\"https://doi.org/10.1109/ISIT.2018.8437654\">10.1109/ISIT.2018.8437654</a>.","ista":"Obremski M, Skórski M. 2018. Inverted leftover hash lemma. ISIT: International Symposium on Information Theory, ISIT Proceedings, vol. 2018.","ama":"Obremski M, Skórski M. Inverted leftover hash lemma. In: Vol 2018. IEEE; 2018. doi:<a href=\"https://doi.org/10.1109/ISIT.2018.8437654\">10.1109/ISIT.2018.8437654</a>","chicago":"Obremski, Marciej, and Maciej Skórski. “Inverted Leftover Hash Lemma,” Vol. 2018. IEEE, 2018. <a href=\"https://doi.org/10.1109/ISIT.2018.8437654\">https://doi.org/10.1109/ISIT.2018.8437654</a>.","ieee":"M. Obremski and M. Skórski, “Inverted leftover hash lemma,” presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA, 2018, vol. 2018.","apa":"Obremski, M., &#38; Skórski, M. (2018). Inverted leftover hash lemma (Vol. 2018). Presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA: IEEE. <a href=\"https://doi.org/10.1109/ISIT.2018.8437654\">https://doi.org/10.1109/ISIT.2018.8437654</a>","short":"M. Obremski, M. Skórski, in:, IEEE, 2018."},"date_updated":"2023-09-13T08:23:18Z","title":"Inverted leftover hash lemma","month":"08","date_published":"2018-08-16T00:00:00Z","article_processing_charge":"No","_id":"108","date_created":"2018-12-11T11:44:40Z","external_id":{"isi":["000448139300368"]},"volume":2018,"alternative_title":["ISIT Proceedings"],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/507"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"intvolume":"      2018","scopus_import":"1"},{"month":"05","title":"FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis","date_updated":"2021-12-14T07:53:40Z","keyword":["Multidisciplinary"],"article_processing_charge":"No","date_published":"2018-05-15T00:00:00Z","page":"E4720-E4729","publication":"Proceedings of the National Academy of Sciences","file_date_updated":"2021-06-07T06:16:38Z","external_id":{"pmid":["29712855"]},"date_created":"2021-06-07T06:11:28Z","_id":"9471","related_material":{"link":[{"url":"https://doi.org/10.1101/187674 ","relation":"earlier_version"}]},"volume":115,"intvolume":"       115","oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","issue":"20","extern":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"department":[{"_id":"DaZi"}],"year":"2018","author":[{"first_name":"Jennifer M.","full_name":"Frost, Jennifer M.","last_name":"Frost"},{"full_name":"Kim, M. Yvonne","last_name":"Kim","first_name":"M. Yvonne"},{"first_name":"Guen Tae","last_name":"Park","full_name":"Park, Guen Tae"},{"last_name":"Hsieh","full_name":"Hsieh, Ping-Hung","first_name":"Ping-Hung"},{"full_name":"Nakamura, Miyuki","last_name":"Nakamura","first_name":"Miyuki"},{"first_name":"Samuel J. H.","last_name":"Lin","full_name":"Lin, Samuel J. H."},{"last_name":"Yoo","full_name":"Yoo, Hyunjin","first_name":"Hyunjin"},{"first_name":"Jaemyung","full_name":"Choi, Jaemyung","last_name":"Choi"},{"last_name":"Ikeda","full_name":"Ikeda, Yoko","first_name":"Yoko"},{"first_name":"Tetsu","last_name":"Kinoshita","full_name":"Kinoshita, Tetsu"},{"first_name":"Yeonhee","last_name":"Choi","full_name":"Choi, Yeonhee"},{"last_name":"Zilberman","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"first_name":"Robert L.","full_name":"Fischer, Robert L.","last_name":"Fischer"}],"oa_version":"Published Version","doi":"10.1073/pnas.1713333115","day":"15","publisher":"National Academy of Sciences","status":"public","has_accepted_license":"1","pmid":1,"language":[{"iso":"eng"}],"abstract":[{"text":"The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin.","lang":"eng"}],"publication_status":"published","quality_controlled":"1","citation":{"apa":"Frost, J. M., Kim, M. Y., Park, G. T., Hsieh, P.-H., Nakamura, M., Lin, S. J. H., … Fischer, R. L. (2018). FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1713333115\">https://doi.org/10.1073/pnas.1713333115</a>","short":"J.M. Frost, M.Y. Kim, G.T. Park, P.-H. Hsieh, M. Nakamura, S.J.H. Lin, H. Yoo, J. Choi, Y. Ikeda, T. Kinoshita, Y. Choi, D. Zilberman, R.L. Fischer, Proceedings of the National Academy of Sciences 115 (2018) E4720–E4729.","ieee":"J. M. Frost <i>et al.</i>, “FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis,” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 20. National Academy of Sciences, pp. E4720–E4729, 2018.","chicago":"Frost, Jennifer M., M. Yvonne Kim, Guen Tae Park, Ping-Hung Hsieh, Miyuki Nakamura, Samuel J. H. Lin, Hyunjin Yoo, et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1713333115\">https://doi.org/10.1073/pnas.1713333115</a>.","ama":"Frost JM, Kim MY, Park GT, et al. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. <i>Proceedings of the National Academy of Sciences</i>. 2018;115(20):E4720-E4729. doi:<a href=\"https://doi.org/10.1073/pnas.1713333115\">10.1073/pnas.1713333115</a>","mla":"Frost, Jennifer M., et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 20, National Academy of Sciences, 2018, pp. E4720–29, doi:<a href=\"https://doi.org/10.1073/pnas.1713333115\">10.1073/pnas.1713333115</a>.","ista":"Frost JM, Kim MY, Park GT, Hsieh P-H, Nakamura M, Lin SJH, Yoo H, Choi J, Ikeda Y, Kinoshita T, Choi Y, Zilberman D, Fischer RL. 2018. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. 115(20), E4720–E4729."},"type":"journal_article","file":[{"creator":"asandaue","date_created":"2021-06-07T06:16:38Z","file_id":"9472","success":1,"access_level":"open_access","file_name":"2018_PNAS_Frost.pdf","content_type":"application/pdf","date_updated":"2021-06-07T06:16:38Z","file_size":3045260,"checksum":"810260dc0e3cc3033e15c19ad0dc123e","relation":"main_file"}],"article_type":"original","ddc":["580"]},{"type":"research_data_reference","citation":{"chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” Springer Nature, 2018. <a href=\"https://doi.org/10.6084/m9.figshare.7295339.v1\">https://doi.org/10.6084/m9.figshare.7295339.v1</a>.","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. 2018. doi:<a href=\"https://doi.org/10.6084/m9.figshare.7295339.v1\">10.6084/m9.figshare.7295339.v1</a>","mla":"Higareda Almaraz, Juan, et al. <i>Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes</i>. Springer Nature, 2018, doi:<a href=\"https://doi.org/10.6084/m9.figshare.7295339.v1\">10.6084/m9.figshare.7295339.v1</a>.","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.7295339.v1\">10.6084/m9.figshare.7295339.v1</a>.","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018).","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., &#38; Scheideler, M. (2018). Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.7295339.v1\">https://doi.org/10.6084/m9.figshare.7295339.v1</a>","ieee":"J. Higareda Almaraz <i>et al.</i>, “Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018."},"status":"public","related_material":{"record":[{"id":"20","status":"public","relation":"used_in_publication"}]},"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.7295339.v1","open_access":"1"}],"abstract":[{"text":"Table S1. Genes with highest betweenness. Table S2. Local and Master regulators up-regulated. Table S3. Local and Master regulators down-regulated (XLSX 23 kb).","lang":"eng"}],"oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","doi":"10.6084/m9.figshare.7295339.v1","day":"03","date_created":"2021-08-06T12:26:53Z","_id":"9807","publisher":"Springer Nature","month":"11","department":[{"_id":"SiHi"}],"date_updated":"2023-09-13T09:10:47Z","title":"Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","year":"2018","article_processing_charge":"No","date_published":"2018-11-03T00:00:00Z","author":[{"last_name":"Higareda Almaraz","full_name":"Higareda Almaraz, Juan","first_name":"Juan"},{"full_name":"Karbiener, Michael","last_name":"Karbiener","first_name":"Michael"},{"first_name":"Maude","last_name":"Giroud","full_name":"Giroud, Maude"},{"orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"first_name":"Teresa","full_name":"Gerhalter, Teresa","last_name":"Gerhalter"},{"last_name":"Herzig","full_name":"Herzig, Stephan","first_name":"Stephan"},{"first_name":"Marcel","last_name":"Scheideler","full_name":"Scheideler, Marcel"}]},{"oa_version":"Published Version","doi":"10.6084/m9.figshare.7295369.v1","date_created":"2021-08-06T12:31:57Z","day":"03","_id":"9808","publisher":"Springer Nature","month":"11","title":"Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","date_updated":"2023-09-13T09:10:47Z","department":[{"_id":"SiHi"}],"author":[{"first_name":"Juan","full_name":"Higareda Almaraz, Juan","last_name":"Higareda Almaraz"},{"first_name":"Michael","last_name":"Karbiener","full_name":"Karbiener, Michael"},{"full_name":"Giroud, Maude","last_name":"Giroud","first_name":"Maude"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","last_name":"Pauler"},{"full_name":"Gerhalter, Teresa","last_name":"Gerhalter","first_name":"Teresa"},{"full_name":"Herzig, Stephan","last_name":"Herzig","first_name":"Stephan"},{"full_name":"Scheideler, Marcel","last_name":"Scheideler","first_name":"Marcel"}],"date_published":"2018-11-03T00:00:00Z","year":"2018","article_processing_charge":"No","citation":{"ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. 2018. doi:<a href=\"https://doi.org/10.6084/m9.figshare.7295369.v1\">10.6084/m9.figshare.7295369.v1</a>","chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 3: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” Springer Nature, 2018. <a href=\"https://doi.org/10.6084/m9.figshare.7295369.v1\">https://doi.org/10.6084/m9.figshare.7295369.v1</a>.","mla":"Higareda Almaraz, Juan, et al. <i>Additional File 3: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes</i>. Springer Nature, 2018, doi:<a href=\"https://doi.org/10.6084/m9.figshare.7295369.v1\">10.6084/m9.figshare.7295369.v1</a>.","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.7295369.v1\">10.6084/m9.figshare.7295369.v1</a>.","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., &#38; Scheideler, M. (2018). Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.7295369.v1\">https://doi.org/10.6084/m9.figshare.7295369.v1</a>","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018).","ieee":"J. Higareda Almaraz <i>et al.</i>, “Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018."},"type":"research_data_reference","status":"public","abstract":[{"text":"Table S4. Counts per Gene per Million Reads Mapped. (XLSX 2751 kb).","lang":"eng"}],"related_material":{"record":[{"id":"20","relation":"used_in_publication","status":"public"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.7295369.v1"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1},{"type":"research_data_reference","citation":{"ista":"Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Numerical data used in figures, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2005971.s008\">10.1371/journal.pbio.2005971.s008</a>.","mla":"Chaudhry, Waqas, et al. <i>Numerical Data Used in Figures</i>. Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005971.s008\">10.1371/journal.pbio.2005971.s008</a>.","chicago":"Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Numerical Data Used in Figures.” Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pbio.2005971.s008\">https://doi.org/10.1371/journal.pbio.2005971.s008</a>.","ama":"Chaudhry W, Pleska M, Shah N, et al. Numerical data used in figures. 2018. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005971.s008\">10.1371/journal.pbio.2005971.s008</a>","ieee":"W. Chaudhry <i>et al.</i>, “Numerical data used in figures.” Public Library of Science, 2018.","short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, (2018).","apa":"Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Numerical data used in figures. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2005971.s008\">https://doi.org/10.1371/journal.pbio.2005971.s008</a>"},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","related_material":{"record":[{"id":"82","status":"public","relation":"used_in_publication"}]},"date_created":"2021-08-06T12:43:44Z","day":"16","_id":"9810","publisher":"Public Library of Science","oa_version":"Published Version","doi":"10.1371/journal.pbio.2005971.s008","author":[{"last_name":"Chaudhry","full_name":"Chaudhry, Waqas","first_name":"Waqas"},{"first_name":"Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479","last_name":"Pleska"},{"first_name":"Nilang","last_name":"Shah","full_name":"Shah, Nilang"},{"full_name":"Weiss, Howard","last_name":"Weiss","first_name":"Howard"},{"first_name":"Ingrid","last_name":"Mccall","full_name":"Mccall, Ingrid"},{"last_name":"Meyer","full_name":"Meyer, Justin","first_name":"Justin"},{"first_name":"Animesh","full_name":"Gupta, Animesh","last_name":"Gupta"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"},{"first_name":"Bruce","full_name":"Levin, Bruce","last_name":"Levin"}],"date_published":"2018-08-16T00:00:00Z","year":"2018","article_processing_charge":"No","month":"08","date_updated":"2023-09-13T08:45:41Z","title":"Numerical data used in figures","department":[{"_id":"CaGu"}]},{"department":[{"_id":"FyKo"}],"title":"Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","date_updated":"2023-09-13T09:01:31Z","month":"05","article_processing_charge":"No","year":"2018","date_published":"2018-05-31T00:00:00Z","author":[{"full_name":"Zapata, Luis","last_name":"Zapata","first_name":"Luis"},{"full_name":"Pich, Oriol","last_name":"Pich","first_name":"Oriol"},{"first_name":"Luis","last_name":"Serrano","full_name":"Serrano, Luis"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694"},{"last_name":"Ossowski","full_name":"Ossowski, Stephan","first_name":"Stephan"},{"first_name":"Martin","last_name":"Schaefer","full_name":"Schaefer, Martin"}],"doi":"10.6084/m9.figshare.6401390.v1","oa_version":"Preprint","publisher":"Springer Nature","_id":"9811","day":"31","date_created":"2021-08-06T12:53:49Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.6401390.v1"}],"related_material":{"record":[{"id":"279","status":"public","relation":"used_in_publication"}]},"abstract":[{"lang":"eng","text":"This document contains additional supporting evidence presented as supplemental tables. 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Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:<a href=\"https://doi.org/10.6084/m9.figshare.6401390.v1\">10.6084/m9.figshare.6401390.v1</a>"}},{"article_processing_charge":"No","year":"2018","author":[{"first_name":"Luis","last_name":"Zapata","full_name":"Zapata, Luis"},{"full_name":"Pich, Oriol","last_name":"Pich","first_name":"Oriol"},{"full_name":"Serrano, Luis","last_name":"Serrano","first_name":"Luis"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"full_name":"Ossowski, Stephan","last_name":"Ossowski","first_name":"Stephan"},{"last_name":"Schaefer","full_name":"Schaefer, Martin","first_name":"Martin"}],"date_published":"2018-05-31T00:00:00Z","month":"05","department":[{"_id":"FyKo"}],"date_updated":"2023-09-13T09:01:31Z","title":"Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","day":"31","date_created":"2021-08-06T12:58:25Z","publisher":"Springer Nature","_id":"9812","oa_version":"Published Version","doi":"10.6084/m9.figshare.6401414.v1","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","related_material":{"record":[{"id":"279","status":"public","relation":"used_in_publication"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.6401414.v1"}],"abstract":[{"text":"This document contains the full list of genes with their respective significance and dN/dS values. (TXT 4499Â kb)","lang":"eng"}],"type":"research_data_reference","citation":{"ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:<a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">10.6084/m9.figshare.6401414.v1</a>","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. <a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">https://doi.org/10.6084/m9.figshare.6401414.v1</a>.","mla":"Zapata, Luis, et al. <i>Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome</i>. Springer Nature, 2018, doi:<a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">10.6084/m9.figshare.6401414.v1</a>.","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">10.6084/m9.figshare.6401414.v1</a>.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., &#38; Schaefer, M. (2018). Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">https://doi.org/10.6084/m9.figshare.6401414.v1</a>","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018."}},{"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"date_updated":"2025-05-28T11:57:01Z","title":"Supplemental material for Bodova et al., 2018","month":"04","year":"2018","article_processing_charge":"No","author":[{"first_name":"Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","full_name":"Bod'ová, Katarína","orcid":"0000-0002-7214-0171","last_name":"Bod'ová"},{"full_name":"Priklopil, Tadeas","last_name":"Priklopil","first_name":"Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Field","full_name":"Field, David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2018-04-30T00:00:00Z","doi":"10.25386/genetics.6148304.v1","oa_version":"Published Version","_id":"9813","publisher":"Genetics Society of America","day":"30","date_created":"2021-08-06T13:04:32Z","main_file_link":[{"url":"https://doi.org/10.25386/genetics.6148304.v1","open_access":"1"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"316"}]},"abstract":[{"text":"File S1 contains figures that clarify the following features: (i) effect of population size on the average number/frequency of SI classes, (ii) changes in the minimal completeness deficit in time for a single class, and (iii) diversification diagrams for all studied pathways, including the summary figure for k = 8. File S2 contains the code required for a stochastic simulation of the SLF system with an example. This file also includes the output in the form of figures and tables.","lang":"eng"}],"status":"public","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","citation":{"ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Supplemental material for Bodova et al., 2018.” Genetics Society of America, 2018.","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., &#38; Pickup, M. (2018). Supplemental material for Bodova et al., 2018. Genetics Society of America. <a href=\"https://doi.org/10.25386/genetics.6148304.v1\">https://doi.org/10.25386/genetics.6148304.v1</a>","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Supplemental material for Bodova et al., 2018, Genetics Society of America, <a href=\"https://doi.org/10.25386/genetics.6148304.v1\">10.25386/genetics.6148304.v1</a>.","mla":"Bodova, Katarina, et al. <i>Supplemental Material for Bodova et Al., 2018</i>. Genetics Society of America, 2018, doi:<a href=\"https://doi.org/10.25386/genetics.6148304.v1\">10.25386/genetics.6148304.v1</a>.","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Supplemental material for Bodova et al., 2018. 2018. doi:<a href=\"https://doi.org/10.25386/genetics.6148304.v1\">10.25386/genetics.6148304.v1</a>","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Supplemental Material for Bodova et Al., 2018.” Genetics Society of America, 2018. <a href=\"https://doi.org/10.25386/genetics.6148304.v1\">https://doi.org/10.25386/genetics.6148304.v1</a>."}},{"doi":"10.1371/journal.pone.0193049.s001","oa_version":"Published Version","_id":"9831","publisher":"Public Library of Science","day":"07","date_created":"2021-08-09T07:01:24Z","department":[{"_id":"GaTk"}],"title":"Implementation of the inference method in Matlab","date_updated":"2023-09-15T12:06:18Z","month":"03","year":"2018","article_processing_charge":"No","author":[{"first_name":"Katarína","last_name":"Bod’Ová","full_name":"Bod’Ová, Katarína"},{"first_name":"Gabriel","id":"315BCD80-F248-11E8-B48F-1D18A9856A87","last_name":"Mitchell","full_name":"Mitchell, Gabriel"},{"last_name":"Harpaz","full_name":"Harpaz, Roy","first_name":"Roy"},{"first_name":"Elad","last_name":"Schneidman","full_name":"Schneidman, Elad"},{"last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"}],"date_published":"2018-03-07T00:00:00Z","type":"research_data_reference","citation":{"ieee":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Implementation of the inference method in Matlab.” Public Library of Science, 2018.","apa":"Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., &#38; Tkačik, G. (2018). Implementation of the inference method in Matlab. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0193049.s001\">https://doi.org/10.1371/journal.pone.0193049.s001</a>","short":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, (2018).","ista":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Implementation of the inference method in Matlab, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0193049.s001\">10.1371/journal.pone.0193049.s001</a>.","mla":"Bod’Ová, Katarína, et al. <i>Implementation of the Inference Method in Matlab</i>. Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pone.0193049.s001\">10.1371/journal.pone.0193049.s001</a>.","ama":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Implementation of the inference method in Matlab. 2018. doi:<a href=\"https://doi.org/10.1371/journal.pone.0193049.s001\">10.1371/journal.pone.0193049.s001</a>","chicago":"Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Implementation of the Inference Method in Matlab.” Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pone.0193049.s001\">https://doi.org/10.1371/journal.pone.0193049.s001</a>."},"related_material":{"record":[{"id":"406","relation":"used_in_publication","status":"public"}]},"abstract":[{"text":"Implementation of the inference method in Matlab, including three applications of the method: The first one for the model of ant motion, the second one for bacterial chemotaxis, and the third one for the motion of fish.","lang":"eng"}],"status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"citation":{"short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, (2018).","apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Dryad. <a href=\"https://doi.org/10.5061/dryad.72cg113\">https://doi.org/10.5061/dryad.72cg113</a>","ieee":"R. Faria <i>et al.</i>, “Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.","chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.72cg113\">https://doi.org/10.5061/dryad.72cg113</a>.","ama":"Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.72cg113\">10.5061/dryad.72cg113</a>","ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes, Dryad, <a href=\"https://doi.org/10.5061/dryad.72cg113\">10.5061/dryad.72cg113</a>.","mla":"Faria, Rui, et al. <i>Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.72cg113\">10.5061/dryad.72cg113</a>."},"type":"research_data_reference","main_file_link":[{"url":"https://doi.org/10.5061/dryad.72cg113","open_access":"1"}],"related_material":{"record":[{"id":"6095","status":"public","relation":"used_in_publication"}]},"abstract":[{"text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.","lang":"eng"}],"status":"public","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","doi":"10.5061/dryad.72cg113","oa_version":"Published Version","_id":"9837","publisher":"Dryad","day":"09","date_created":"2021-08-09T12:46:39Z","department":[{"_id":"NiBa"}],"date_updated":"2023-08-24T14:50:26Z","title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","month":"10","year":"2018","article_processing_charge":"No","date_published":"2018-10-09T00:00:00Z","author":[{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"first_name":"Pragya","full_name":"Chaube, Pragya","last_name":"Chaube"},{"full_name":"Morales, Hernán E.","last_name":"Morales","first_name":"Hernán E."},{"last_name":"Larsson","full_name":"Larsson, Tomas","first_name":"Tomas"},{"first_name":"Alan R.","full_name":"Lemmon, Alan R.","last_name":"Lemmon"},{"first_name":"Emily M.","full_name":"Lemmon, Emily M.","last_name":"Lemmon"},{"first_name":"Marina","full_name":"Rafajlović, Marina","last_name":"Rafajlović"},{"last_name":"Panova","full_name":"Panova, Marina","first_name":"Marina"},{"last_name":"Ravinet","full_name":"Ravinet, Mark","first_name":"Mark"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."}]},{"year":"2018","article_processing_charge":"No","author":[{"first_name":"Marketa","last_name":"Kaucka","full_name":"Kaucka, Marketa"},{"last_name":"Petersen","full_name":"Petersen, Julian","first_name":"Julian"},{"first_name":"Marketa","last_name":"Tesarova","full_name":"Tesarova, Marketa"},{"first_name":"Bara","full_name":"Szarowska, Bara","last_name":"Szarowska"},{"last_name":"Kastriti","full_name":"Kastriti, Maria Eleni","first_name":"Maria Eleni"},{"first_name":"Meng","last_name":"Xie","full_name":"Xie, Meng"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","last_name":"Kicheva"},{"first_name":"Karl","full_name":"Annusver, Karl","last_name":"Annusver"},{"first_name":"Maria","full_name":"Kasper, Maria","last_name":"Kasper"},{"first_name":"Orsolya","full_name":"Symmons, Orsolya","last_name":"Symmons"},{"full_name":"Pan, Leslie","last_name":"Pan","first_name":"Leslie"},{"full_name":"Spitz, Francois","last_name":"Spitz","first_name":"Francois"},{"first_name":"Jozef","last_name":"Kaiser","full_name":"Kaiser, Jozef"},{"last_name":"Hovorakova","full_name":"Hovorakova, Maria","first_name":"Maria"},{"full_name":"Zikmund, Tomas","last_name":"Zikmund","first_name":"Tomas"},{"first_name":"Kazunori","full_name":"Sunadome, Kazunori","last_name":"Sunadome"},{"full_name":"Matise, Michael P","last_name":"Matise","first_name":"Michael P"},{"first_name":"Hui","last_name":"Wang","full_name":"Wang, Hui"},{"first_name":"Ulrika","last_name":"Marklund","full_name":"Marklund, Ulrika"},{"full_name":"Abdo, Hind","last_name":"Abdo","first_name":"Hind"},{"last_name":"Ernfors","full_name":"Ernfors, Patrik","first_name":"Patrik"},{"last_name":"Maire","full_name":"Maire, Pascal","first_name":"Pascal"},{"full_name":"Wurmser, Maud","last_name":"Wurmser","first_name":"Maud"},{"full_name":"Chagin, Andrei S","last_name":"Chagin","first_name":"Andrei S"},{"first_name":"Kaj","full_name":"Fried, Kaj","last_name":"Fried"},{"first_name":"Igor","full_name":"Adameyko, Igor","last_name":"Adameyko"}],"date_published":"2018-06-14T00:00:00Z","month":"06","department":[{"_id":"AnKi"}],"title":"Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","date_updated":"2023-09-18T09:29:07Z","day":"14","date_created":"2021-08-09T12:54:35Z","publisher":"Dryad","_id":"9838","oa_version":"Published Version","doi":"10.5061/dryad.f1s76f2","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.f1s76f2"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"162"}]},"abstract":[{"text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts.","lang":"eng"}],"type":"research_data_reference","citation":{"ieee":"M. Kaucka <i>et al.</i>, “Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage.” Dryad, 2018.","short":"M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M.E. Kastriti, M. Xie, A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, (2018).","apa":"Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M. E., Xie, M., … Adameyko, I. (2018). Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. Dryad. <a href=\"https://doi.org/10.5061/dryad.f1s76f2\">https://doi.org/10.5061/dryad.f1s76f2</a>","mla":"Kaucka, Marketa, et al. <i>Data from: Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.f1s76f2\">10.5061/dryad.f1s76f2</a>.","ista":"Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti ME, Xie M, Kicheva A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser M, Chagin AS, Fried K, Adameyko I. 2018. Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage, Dryad, <a href=\"https://doi.org/10.5061/dryad.f1s76f2\">10.5061/dryad.f1s76f2</a>.","chicago":"Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Eleni Kastriti, Meng Xie, Anna Kicheva, et al. “Data from: Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.f1s76f2\">https://doi.org/10.5061/dryad.f1s76f2</a>.","ama":"Kaucka M, Petersen J, Tesarova M, et al. Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.f1s76f2\">10.5061/dryad.f1s76f2</a>"}},{"date_published":"2018-03-12T00:00:00Z","author":[{"id":"35F78294-F248-11E8-B48F-1D18A9856A87","first_name":"Pavel","last_name":"Payne","full_name":"Payne, Pavel","orcid":"0000-0002-2711-9453"},{"first_name":"Lukas","full_name":"Geyrhofer, Lukas","last_name":"Geyrhofer"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","last_name":"Bollback","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612"}],"article_processing_charge":"No","year":"2018","date_updated":"2023-09-11T12:49:17Z","title":"Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"month":"03","_id":"9840","publisher":"Dryad","date_created":"2021-08-09T13:10:02Z","day":"12","doi":"10.5061/dryad.42n44","oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"abstract":[{"lang":"eng","text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity."}],"main_file_link":[{"url":"https://doi.org/10.5061/dryad.42n44","open_access":"1"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"423"}]},"status":"public","citation":{"chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.42n44\">https://doi.org/10.5061/dryad.42n44</a>.","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.42n44\">10.5061/dryad.42n44</a>","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations, Dryad, <a href=\"https://doi.org/10.5061/dryad.42n44\">10.5061/dryad.42n44</a>.","mla":"Payne, Pavel, et al. <i>Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.42n44\">10.5061/dryad.42n44</a>.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., &#38; Bollback, J. P. (2018). Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. Dryad. <a href=\"https://doi.org/10.5061/dryad.42n44\">https://doi.org/10.5061/dryad.42n44</a>","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018."},"type":"research_data_reference"},{"date_published":"2018-12-12T00:00:00Z","author":[{"full_name":"Harrison, Mark C.","last_name":"Harrison","first_name":"Mark C."},{"first_name":"Evelien","last_name":"Jongepier","full_name":"Jongepier, Evelien"},{"last_name":"Robertson","full_name":"Robertson, Hugh M.","first_name":"Hugh M."},{"full_name":"Arning, Nicolas","last_name":"Arning","first_name":"Nicolas"},{"last_name":"Bitard-Feildel","full_name":"Bitard-Feildel, Tristan","first_name":"Tristan"},{"first_name":"Hsu","full_name":"Chao, Hsu","last_name":"Chao"},{"first_name":"Christopher P.","full_name":"Childers, Christopher P.","last_name":"Childers"},{"full_name":"Dinh, Huyen","last_name":"Dinh","first_name":"Huyen"},{"first_name":"Harshavardhan","full_name":"Doddapaneni, Harshavardhan","last_name":"Doddapaneni"},{"first_name":"Shannon","last_name":"Dugan","full_name":"Dugan, Shannon"},{"first_name":"Johannes","last_name":"Gowin","full_name":"Gowin, Johannes"},{"first_name":"Carolin","last_name":"Greiner","full_name":"Greiner, Carolin"},{"full_name":"Han, Yi","last_name":"Han","first_name":"Yi"},{"last_name":"Hu","full_name":"Hu, Haofu","first_name":"Haofu"},{"first_name":"Daniel S. T.","full_name":"Hughes, Daniel S. T.","last_name":"Hughes"},{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K","full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","last_name":"Huylmans"},{"first_name":"Carsten","last_name":"Kemena","full_name":"Kemena, Carsten"},{"first_name":"Lukas P. M.","last_name":"Kremer","full_name":"Kremer, Lukas P. M."},{"first_name":"Sandra L.","full_name":"Lee, Sandra L.","last_name":"Lee"},{"last_name":"Lopez-Ezquerra","full_name":"Lopez-Ezquerra, Alberto","first_name":"Alberto"},{"last_name":"Mallet","full_name":"Mallet, Ludovic","first_name":"Ludovic"},{"last_name":"Monroy-Kuhn","full_name":"Monroy-Kuhn, Jose M.","first_name":"Jose M."},{"first_name":"Annabell","last_name":"Moser","full_name":"Moser, Annabell"},{"last_name":"Murali","full_name":"Murali, Shwetha C.","first_name":"Shwetha C."},{"last_name":"Muzny","full_name":"Muzny, Donna M.","first_name":"Donna M."},{"last_name":"Otani","full_name":"Otani, Saria","first_name":"Saria"},{"full_name":"Piulachs, Maria-Dolors","last_name":"Piulachs","first_name":"Maria-Dolors"},{"full_name":"Poelchau, Monica","last_name":"Poelchau","first_name":"Monica"},{"full_name":"Qu, Jiaxin","last_name":"Qu","first_name":"Jiaxin"},{"full_name":"Schaub, Florentine","last_name":"Schaub","first_name":"Florentine"},{"first_name":"Ayako","full_name":"Wada-Katsumata, Ayako","last_name":"Wada-Katsumata"},{"last_name":"Worley","full_name":"Worley, Kim C.","first_name":"Kim C."},{"first_name":"Qiaolin","full_name":"Xie, Qiaolin","last_name":"Xie"},{"full_name":"Ylla, Guillem","last_name":"Ylla","first_name":"Guillem"},{"last_name":"Poulsen","full_name":"Poulsen, Michael","first_name":"Michael"},{"first_name":"Richard A.","full_name":"Gibbs, Richard A.","last_name":"Gibbs"},{"first_name":"Coby","last_name":"Schal","full_name":"Schal, Coby"},{"first_name":"Stephen","last_name":"Richards","full_name":"Richards, Stephen"},{"full_name":"Belles, Xavier","last_name":"Belles","first_name":"Xavier"},{"first_name":"Judith","full_name":"Korb, Judith","last_name":"Korb"},{"full_name":"Bornberg-Bauer, Erich","last_name":"Bornberg-Bauer","first_name":"Erich"}],"article_processing_charge":"No","year":"2018","month":"12","title":"Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality","date_updated":"2023-09-11T14:10:56Z","department":[{"_id":"BeVi"}],"date_created":"2021-08-09T13:13:48Z","day":"12","_id":"9841","publisher":"Dryad","oa_version":"Published Version","doi":"10.5061/dryad.51d4r","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"status":"public","abstract":[{"lang":"eng","text":"Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity."}],"main_file_link":[{"url":"https://doi.org/10.5061/dryad.51d4r","open_access":"1"}],"related_material":{"record":[{"id":"448","relation":"used_in_publication","status":"public"}]},"citation":{"mla":"Harrison, Mark C., et al. <i>Data from: Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.51d4r\">10.5061/dryad.51d4r</a>.","ista":"Harrison MC, Jongepier E, Robertson HM, Arning N, Bitard-Feildel T, Chao H, Childers CP, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu H, Hughes DST, Huylmans AK, Kemena C, Kremer LPM, Lee SL, Lopez-Ezquerra A, Mallet L, Monroy-Kuhn JM, Moser A, Murali SC, Muzny DM, Otani S, Piulachs M-D, Poelchau M, Qu J, Schaub F, Wada-Katsumata A, Worley KC, Xie Q, Ylla G, Poulsen M, Gibbs RA, Schal C, Richards S, Belles X, Korb J, Bornberg-Bauer E. 2018. Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality, Dryad, <a href=\"https://doi.org/10.5061/dryad.51d4r\">10.5061/dryad.51d4r</a>.","chicago":"Harrison, Mark C., Evelien Jongepier, Hugh M. Robertson, Nicolas Arning, Tristan Bitard-Feildel, Hsu Chao, Christopher P. Childers, et al. “Data from: Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.51d4r\">https://doi.org/10.5061/dryad.51d4r</a>.","ama":"Harrison MC, Jongepier E, Robertson HM, et al. Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.51d4r\">10.5061/dryad.51d4r</a>","ieee":"M. C. Harrison <i>et al.</i>, “Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality.” Dryad, 2018.","short":"M.C. Harrison, E. Jongepier, H.M. Robertson, N. Arning, T. Bitard-Feildel, H. Chao, C.P. Childers, H. Dinh, H. Doddapaneni, S. Dugan, J. Gowin, C. Greiner, Y. Han, H. Hu, D.S.T. Hughes, A.K. Huylmans, C. Kemena, L.P.M. Kremer, S.L. Lee, A. Lopez-Ezquerra, L. Mallet, J.M. Monroy-Kuhn, A. Moser, S.C. Murali, D.M. Muzny, S. Otani, M.-D. Piulachs, M. Poelchau, J. Qu, F. Schaub, A. Wada-Katsumata, K.C. Worley, Q. Xie, G. Ylla, M. Poulsen, R.A. Gibbs, C. Schal, S. Richards, X. Belles, J. Korb, E. Bornberg-Bauer, (2018).","apa":"Harrison, M. C., Jongepier, E., Robertson, H. M., Arning, N., Bitard-Feildel, T., Chao, H., … Bornberg-Bauer, E. (2018). Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality. Dryad. <a href=\"https://doi.org/10.5061/dryad.51d4r\">https://doi.org/10.5061/dryad.51d4r</a>"},"type":"research_data_reference"},{"publication_identifier":{"eissn":["2056-3744"],"issn":[" 2056-3744"]},"department":[{"_id":"BeVi"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"isi":1,"author":[{"first_name":"Johan","full_name":"Hollander, Johan","last_name":"Hollander"},{"full_name":"Montaño-Rendón, Mauricio","last_name":"Montaño-Rendón","first_name":"Mauricio"},{"first_name":"Giuseppe","full_name":"Bianco, Giuseppe","last_name":"Bianco"},{"first_name":"Xi","last_name":"Yang","full_name":"Yang, Xi"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram"},{"first_name":"Ludovic","last_name":"Duvaux","full_name":"Duvaux, Ludovic"},{"last_name":"Reid","full_name":"Reid, David G.","first_name":"David G."},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."}],"year":"2018","doi":"10.1002/evl3.85","oa_version":"Published Version","publisher":"Wiley","day":"13","publication_status":"published","abstract":[{"lang":"eng","text":"The evolution of assortative mating is a key part of the speciation process. Stronger assortment, or greater divergence in mating traits, between species pairs with overlapping ranges is commonly observed, but possible causes of this pattern of reproductive character displacement are difficult to distinguish. We use a multidisciplinary approach to provide a rare example where it is possible to distinguish among hypotheses concerning the evolution of reproductive character displacement. We build on an earlier comparative analysis that illustrated a strong pattern of greater divergence in penis form between pairs of sister species with overlapping ranges than between allopatric sister-species pairs, in a large clade of marine gastropods (Littorinidae). We investigate both assortative mating and divergence in male genitalia in one of the sister-species pairs, discriminating among three contrasting processes each of which can generate a pattern of reproductive character displacement: reinforcement, reproductive interference and the Templeton effect. We demonstrate reproductive character displacement in assortative mating, but not in genital form between this pair of sister species and use demographic models to distinguish among the different processes. Our results support a model with no gene flow since secondary contact and thus favor reproductive interference as the cause of reproductive character displacement for mate choice, rather than reinforcement. High gene flow within species argues against the Templeton effect. Secondary contact appears to have had little impact on genital divergence."}],"language":[{"iso":"eng"}],"pmid":1,"status":"public","has_accepted_license":"1","quality_controlled":"1","file":[{"relation":"main_file","checksum":"997a78ac41c809975ca69cbdea441f88","file_size":584606,"date_updated":"2021-08-16T07:37:28Z","content_type":"application/pdf","file_name":"2018_EvolutionLetters_Hollander.pdf","access_level":"open_access","success":1,"file_id":"9916","creator":"asandaue","date_created":"2021-08-16T07:37:28Z"}],"type":"journal_article","citation":{"chicago":"Hollander, Johan, Mauricio Montaño-Rendón, Giuseppe Bianco, Xi Yang, Anja M Westram, Ludovic Duvaux, David G. Reid, and Roger K. Butlin. “Are Assortative Mating and Genital Divergence Driven by Reinforcement?” <i>Evolution Letters</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/evl3.85\">https://doi.org/10.1002/evl3.85</a>.","ama":"Hollander J, Montaño-Rendón M, Bianco G, et al. Are assortative mating and genital divergence driven by reinforcement? <i>Evolution Letters</i>. 2018;2(6):557-566. doi:<a href=\"https://doi.org/10.1002/evl3.85\">10.1002/evl3.85</a>","mla":"Hollander, Johan, et al. “Are Assortative Mating and Genital Divergence Driven by Reinforcement?” <i>Evolution Letters</i>, vol. 2, no. 6, Wiley, 2018, pp. 557–66, doi:<a href=\"https://doi.org/10.1002/evl3.85\">10.1002/evl3.85</a>.","ista":"Hollander J, Montaño-Rendón M, Bianco G, Yang X, Westram AM, Duvaux L, Reid DG, Butlin RK. 2018. Are assortative mating and genital divergence driven by reinforcement? Evolution Letters. 2(6), 557–566.","short":"J. Hollander, M. Montaño-Rendón, G. Bianco, X. Yang, A.M. Westram, L. Duvaux, D.G. Reid, R.K. Butlin, Evolution Letters 2 (2018) 557–566.","apa":"Hollander, J., Montaño-Rendón, M., Bianco, G., Yang, X., Westram, A. M., Duvaux, L., … Butlin, R. K. (2018). Are assortative mating and genital divergence driven by reinforcement? <i>Evolution Letters</i>. Wiley. <a href=\"https://doi.org/10.1002/evl3.85\">https://doi.org/10.1002/evl3.85</a>","ieee":"J. Hollander <i>et al.</i>, “Are assortative mating and genital divergence driven by reinforcement?,” <i>Evolution Letters</i>, vol. 2, no. 6. Wiley, pp. 557–566, 2018."},"ddc":["570"],"article_type":"letter_note","date_updated":"2023-09-19T15:08:53Z","title":"Are assortative mating and genital divergence driven by reinforcement?","month":"12","date_published":"2018-12-13T00:00:00Z","article_processing_charge":"Yes","file_date_updated":"2021-08-16T07:37:28Z","publication":"Evolution Letters","page":"557-566","_id":"9915","date_created":"2021-08-16T07:30:00Z","external_id":{"isi":["000452990000002"],"pmid":["30564439"]},"volume":2,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9929"}]},"issue":"6","acknowledgement":"The authors express a special thanks to Dr Richard Willan at the Museum and Art Gallery of the Northern Territory for guidance and support in the field, and to Carole Smadja for reading and commenting on the manuscript. The authors thank the Government of Western Australia Department of Parks and Wildlife (license no. 009254) and Fishery Research Division (exemption no. 2262) for assistance with permits. Khalid Belkhir modified the coalescent sampler msnsam for the specific needs of this project and Martin Hirsch helped to set up the ABC pipeline and to modify the summary statistic calculator mscalc. The authors are grateful to the Crafoord Foundation for supporting this project. R.K.B., A.M.W., and L.D. were supported by grants from the Natural Environment Research Council, R.K.B. and A.M.W. were also supported by the European Research Council and R.K.B. and L.D. by the Leverhulme Trust. M.M.R. was supported by Consejo Nacional de Ciencia y Tecnología and Secretaría de Educación Pública, Mexico. G.B. was supported by the Centre for Animal Movement Research (CAnMove) financed by a Linnaeus grant (No. 349-2007-8690) from the Swedish Research Council and Lund University.","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"         2","oa":1}]