[{"oa_version":"Published Version","intvolume":" 116","status":"public","title":"On the power to detect rare recombination events","_id":"6621","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"26","abstract":[{"text":"We read with great interest the recent work in PNAS by Bergero et al. (1) describing differences in male and female recombination patterns on the guppy (Poecilia reticulata) sex chromosome. We fully agree that recombination in males is largely confined to the ends of the sex chromosome. Bergero et al. interpret these results to suggest that our previous findings of population-level variation in the degree of sex chromosome differentiation in this species (2) are incorrect. However, we suggest that their results are entirely consistent with our previous report, and that their interpretation presents a false controversy.","lang":"eng"}],"type":"journal_article","date_published":"2019-06-25T00:00:00Z","page":"12607-12608","article_type":"letter_note","citation":{"chicago":"Wright, Alison E., Iulia Darolti, Natasha I. Bloch, Vicencio Oostra, Benjamin A. Sandkam, Séverine D. Buechel, Niclas Kolm, Felix Breden, Beatriz Vicoso, and Judith E. Mank. “On the Power to Detect Rare Recombination Events.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1905555116.","short":"A.E. Wright, I. Darolti, N.I. Bloch, V. Oostra, B.A. Sandkam, S.D. Buechel, N. Kolm, F. Breden, B. Vicoso, J.E. Mank, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 12607–12608.","mla":"Wright, Alison E., et al. “On the Power to Detect Rare Recombination Events.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 26, Proceedings of the National Academy of Sciences, 2019, pp. 12607–08, doi:10.1073/pnas.1905555116.","apa":"Wright, A. E., Darolti, I., Bloch, N. I., Oostra, V., Sandkam, B. A., Buechel, S. D., … Mank, J. E. (2019). On the power to detect rare recombination events. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1905555116","ieee":"A. E. Wright et al., “On the power to detect rare recombination events,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 26. Proceedings of the National Academy of Sciences, pp. 12607–12608, 2019.","ista":"Wright AE, Darolti I, Bloch NI, Oostra V, Sandkam BA, Buechel SD, Kolm N, Breden F, Vicoso B, Mank JE. 2019. On the power to detect rare recombination events. Proceedings of the National Academy of Sciences of the United States of America. 116(26), 12607–12608.","ama":"Wright AE, Darolti I, Bloch NI, et al. On the power to detect rare recombination events. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(26):12607-12608. doi:10.1073/pnas.1905555116"},"publication":"Proceedings of the National Academy of Sciences of the United States of America","article_processing_charge":"No","day":"25","scopus_import":"1","volume":116,"date_created":"2019-07-07T21:59:25Z","date_updated":"2023-10-17T12:44:15Z","author":[{"full_name":"Wright, Alison E.","last_name":"Wright","first_name":"Alison E."},{"full_name":"Darolti, Iulia","last_name":"Darolti","first_name":"Iulia"},{"full_name":"Bloch, Natasha I.","last_name":"Bloch","first_name":"Natasha I."},{"full_name":"Oostra, Vicencio","last_name":"Oostra","first_name":"Vicencio"},{"full_name":"Sandkam, Benjamin A.","last_name":"Sandkam","first_name":"Benjamin A."},{"full_name":"Buechel, Séverine D.","last_name":"Buechel","first_name":"Séverine D."},{"full_name":"Kolm, Niclas","last_name":"Kolm","first_name":"Niclas"},{"last_name":"Breden","first_name":"Felix","full_name":"Breden, Felix"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso"},{"first_name":"Judith E.","last_name":"Mank","full_name":"Mank, Judith E."}],"publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"BeVi"}],"publication_status":"published","pmid":1,"year":"2019","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1905555116","isi":1,"quality_controlled":"1","external_id":{"pmid":["31213531"],"isi":["000472719100010"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1905555116"}],"oa":1,"month":"06"},{"article_type":"original","page":"1035-1047","publication":"New Phytologist","citation":{"ista":"Pickup M, Barton NH, Brandvain Y, Fraisse C, Yakimowski S, Dixit T, Lexer C, Cereghetti E, Field D. 2019. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 224(3), 1035–1047.","ieee":"M. Pickup et al., “Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow,” New Phytologist, vol. 224, no. 3. Wiley, pp. 1035–1047, 2019.","apa":"Pickup, M., Barton, N. H., Brandvain, Y., Fraisse, C., Yakimowski, S., Dixit, T., … Field, D. (2019). Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. Wiley. https://doi.org/10.1111/nph.16180","ama":"Pickup M, Barton NH, Brandvain Y, et al. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 2019;224(3):1035-1047. doi:10.1111/nph.16180","chicago":"Pickup, Melinda, Nicholas H Barton, Yaniv Brandvain, Christelle Fraisse, Sarah Yakimowski, Tanmay Dixit, Christian Lexer, Eva Cereghetti, and David Field. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16180.","mla":"Pickup, Melinda, et al. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” New Phytologist, vol. 224, no. 3, Wiley, 2019, pp. 1035–47, doi:10.1111/nph.16180.","short":"M. Pickup, N.H. Barton, Y. Brandvain, C. Fraisse, S. Yakimowski, T. Dixit, C. Lexer, E. Cereghetti, D. Field, New Phytologist 224 (2019) 1035–1047."},"date_published":"2019-11-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","status":"public","ddc":["570"],"title":"Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow","intvolume":" 224","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6856","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":1511958,"access_level":"open_access","file_name":"2019_NewPhytologist_Pickup.pdf","checksum":"21e4c95599bbcaf7c483b89954658672","date_created":"2019-11-13T08:15:05Z","date_updated":"2020-07-14T12:47:42Z","file_id":"7011","relation":"main_file"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Plant mating systems play a key role in structuring genetic variation both within and between species. In hybrid zones, the outcomes and dynamics of hybridization are usually interpreted as the balance between gene flow and selection against hybrids. Yet, mating systems can introduce selective forces that alter these expectations; with diverse outcomes for the level and direction of gene flow depending on variation in outcrossing and whether the mating systems of the species pair are the same or divergent. We present a survey of hybridization in 133 species pairs from 41 plant families and examine how patterns of hybridization vary with mating system. We examine if hybrid zone mode, level of gene flow, asymmetries in gene flow and the frequency of reproductive isolating barriers vary in relation to mating system/s of the species pair. We combine these results with a simulation model and examples from the literature to address two general themes: (i) the two‐way interaction between introgression and the evolution of reproductive systems, and (ii) how mating system can facilitate or restrict interspecific gene flow. We conclude that examining mating system with hybridization provides unique opportunities to understand divergence and the processes underlying reproductive isolation."}],"issue":"3","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Mating system and the evolutionary dynamics of hybrid zones","_id":"25B36484-B435-11E9-9278-68D0E5697425","grant_number":"329960"},{"grant_number":"M02463","_id":"2662AADE-B435-11E9-9278-68D0E5697425","name":"Sex chromosomes and species barriers","call_identifier":"FWF"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31505037"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/nph.16180","month":"11","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","year":"2019","pmid":1,"date_created":"2019-09-07T14:35:40Z","date_updated":"2023-10-18T08:47:08Z","volume":224,"author":[{"full_name":"Pickup, Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","first_name":"Melinda","last_name":"Pickup"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"first_name":"Yaniv","last_name":"Brandvain","full_name":"Brandvain, Yaniv"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse","full_name":"Fraisse, Christelle"},{"last_name":"Yakimowski","first_name":"Sarah","full_name":"Yakimowski, Sarah"},{"first_name":"Tanmay","last_name":"Dixit","full_name":"Dixit, Tanmay"},{"last_name":"Lexer","first_name":"Christian","full_name":"Lexer, Christian"},{"last_name":"Cereghetti","first_name":"Eva","id":"71AA91B4-05ED-11EA-8BEB-F5833E63BD63","full_name":"Cereghetti, Eva"},{"full_name":"Field, David","first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"}],"file_date_updated":"2020-07-14T12:47:42Z","ec_funded":1},{"year":"2019","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"UlWa"}],"publication_status":"published","related_material":{"record":[{"relation":"later_version","status":"public","id":"13974"}]},"author":[{"full_name":"Fulek, Radoslav","first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774"},{"first_name":"Bernd","last_name":"Gärtner","full_name":"Gärtner, Bernd"},{"first_name":"Andrey","last_name":"Kupavskii","full_name":"Kupavskii, Andrey"},{"full_name":"Valtr, Pavel","first_name":"Pavel","last_name":"Valtr"},{"full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"volume":129,"date_updated":"2023-12-13T12:03:35Z","date_created":"2019-07-17T10:35:04Z","file_date_updated":"2020-07-14T12:47:35Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1812.04911"]},"oa":1,"project":[{"grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs"}],"quality_controlled":"1","doi":"10.4230/LIPICS.SOCG.2019.38","conference":{"name":"SoCG 2019: Symposium on Computational Geometry","start_date":"2019-06-18","location":"Portland, OR, United States","end_date":"2019-06-21"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783959771047"],"issn":["1868-8969"]},"month":"06","_id":"6647","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 129","status":"public","title":"The crossing Tverberg theorem","ddc":["000","510"],"oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":559837,"access_level":"open_access","file_name":"2019_LIPICS_Fulek.pdf","checksum":"d6d017f8b41291b94d102294fa96ae9c","date_updated":"2020-07-14T12:47:35Z","date_created":"2019-07-24T06:54:52Z","file_id":"6667","relation":"main_file"}],"type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"The Tverberg theorem is one of the cornerstones of discrete geometry. It states that, given a set X of at least (d+1)(r-1)+1 points in R^d, one can find a partition X=X_1 cup ... cup X_r of X, such that the convex hulls of the X_i, i=1,...,r, all share a common point. In this paper, we prove a strengthening of this theorem that guarantees a partition which, in addition to the above, has the property that the boundaries of full-dimensional convex hulls have pairwise nonempty intersections. Possible generalizations and algorithmic aspects are also discussed. As a concrete application, we show that any n points in the plane in general position span floor[n/3] vertex-disjoint triangles that are pairwise crossing, meaning that their boundaries have pairwise nonempty intersections; this number is clearly best possible. A previous result of Alvarez-Rebollar et al. guarantees floor[n/6] pairwise crossing triangles. Our result generalizes to a result about simplices in R^d,d >=2."}],"citation":{"mla":"Fulek, Radoslav, et al. “The Crossing Tverberg Theorem.” 35th International Symposium on Computational Geometry, vol. 129, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 38:1-38:13, doi:10.4230/LIPICS.SOCG.2019.38.","short":"R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, U. Wagner, in:, 35th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 38:1-38:13.","chicago":"Fulek, Radoslav, Bernd Gärtner, Andrey Kupavskii, Pavel Valtr, and Uli Wagner. “The Crossing Tverberg Theorem.” In 35th International Symposium on Computational Geometry, 129:38:1-38:13. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.SOCG.2019.38.","ama":"Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. The crossing Tverberg theorem. In: 35th International Symposium on Computational Geometry. Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:38:1-38:13. doi:10.4230/LIPICS.SOCG.2019.38","ista":"Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. 2019. The crossing Tverberg theorem. 35th International Symposium on Computational Geometry. SoCG 2019: Symposium on Computational Geometry, LIPIcs, vol. 129, 38:1-38:13.","ieee":"R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, and U. Wagner, “The crossing Tverberg theorem,” in 35th International Symposium on Computational Geometry, Portland, OR, United States, 2019, vol. 129, p. 38:1-38:13.","apa":"Fulek, R., Gärtner, B., Kupavskii, A., Valtr, P., & Wagner, U. (2019). The crossing Tverberg theorem. In 35th International Symposium on Computational Geometry (Vol. 129, p. 38:1-38:13). Portland, OR, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.SOCG.2019.38"},"publication":"35th International Symposium on Computational Geometry","page":"38:1-38:13","date_published":"2019-06-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6676","title":"Why extension-based proofs fail","status":"public","oa_version":"Preprint","type":"conference","abstract":[{"text":"It is impossible to deterministically solve wait-free consensus in an asynchronous system. The classic proof uses a valency argument, which constructs an infinite execution by repeatedly extending a finite execution. We introduce extension-based proofs, a class of impossibility proofs that are modelled as an interaction between a prover and a protocol and that include valency arguments.\r\n\r\nUsing proofs based on combinatorial topology, it has been shown that it is impossible to deterministically solve k-set agreement among n > k ≥ 2 processes in a wait-free manner. However, it was unknown whether proofs based on simpler techniques were possible. We show that this impossibility result cannot be obtained by an extension-based proof and, hence, extension-based proofs are limited in power.","lang":"eng"}],"publication":"Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing","citation":{"short":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, in:, Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, ACM Press, 2019, pp. 986–996.","mla":"Alistarh, Dan-Adrian, et al. “Why Extension-Based Proofs Fail.” Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, ACM Press, 2019, pp. 986–96, doi:10.1145/3313276.3316407.","chicago":"Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi Zhu. “Why Extension-Based Proofs Fail.” In Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, 986–96. ACM Press, 2019. https://doi.org/10.1145/3313276.3316407.","ama":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Why extension-based proofs fail. In: Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing. ACM Press; 2019:986-996. doi:10.1145/3313276.3316407","apa":"Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., & Zhu, L. (2019). Why extension-based proofs fail. In Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing (pp. 986–996). Phoenix, AZ, United States: ACM Press. https://doi.org/10.1145/3313276.3316407","ieee":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Why extension-based proofs fail,” in Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, Phoenix, AZ, United States, 2019, pp. 986–996.","ista":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2019. Why extension-based proofs fail. Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 986–996."},"page":"986-996","date_published":"2019-06-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","year":"2019","publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"ACM Press","author":[{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"last_name":"Aspnes","first_name":"James","full_name":"Aspnes, James"},{"last_name":"Ellen","first_name":"Faith","full_name":"Ellen, Faith"},{"full_name":"Gelashvili, Rati","first_name":"Rati","last_name":"Gelashvili"},{"first_name":"Leqi","last_name":"Zhu","full_name":"Zhu, Leqi"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"14364"}]},"date_created":"2019-07-24T09:13:05Z","date_updated":"2023-12-13T12:28:28Z","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1811.01421","open_access":"1"}],"external_id":{"isi":["000523199100089"],"arxiv":["1811.01421"]},"quality_controlled":"1","isi":1,"conference":{"name":"STOC: Symposium on Theory of Computing","end_date":"2019-06-26","start_date":"2019-06-23","location":"Phoenix, AZ, United States"},"doi":"10.1145/3313276.3316407","language":[{"iso":"eng"}],"month":"06","publication_identifier":{"isbn":["9781450367059"]}},{"date_published":"2019-03-16T00:00:00Z","language":[{"iso":"eng"}],"publication":"arXiv","external_id":{"arxiv":["1903.06981"]},"citation":{"short":"A. Biniaz, K. Jain, A. Lubiw, Z. Masárová, T. Miltzow, D. Mondal, A.M. Naredla, J. Tkadlec, A. Turcotte, ArXiv (n.d.).","mla":"Biniaz, Ahmad, et al. “Token Swapping on Trees.” ArXiv, 1903.06981.","chicago":"Biniaz, Ahmad, Kshitij Jain, Anna Lubiw, Zuzana Masárová, Tillmann Miltzow, Debajyoti Mondal, Anurag Murty Naredla, Josef Tkadlec, and Alexi Turcotte. “Token Swapping on Trees.” ArXiv, n.d.","ama":"Biniaz A, Jain K, Lubiw A, et al. Token swapping on trees. arXiv.","apa":"Biniaz, A., Jain, K., Lubiw, A., Masárová, Z., Miltzow, T., Mondal, D., … Turcotte, A. (n.d.). Token swapping on trees. arXiv.","ieee":"A. Biniaz et al., “Token swapping on trees,” arXiv. .","ista":"Biniaz A, Jain K, Lubiw A, Masárová Z, Miltzow T, Mondal D, Naredla AM, Tkadlec J, Turcotte A. Token swapping on trees. arXiv, 1903.06981."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.06981"}],"day":"16","month":"03","article_processing_charge":"No","author":[{"first_name":"Ahmad","last_name":"Biniaz","full_name":"Biniaz, Ahmad"},{"first_name":"Kshitij","last_name":"Jain","full_name":"Jain, Kshitij"},{"first_name":"Anna","last_name":"Lubiw","full_name":"Lubiw, Anna"},{"id":"45CFE238-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6660-1322","first_name":"Zuzana","last_name":"Masárová","full_name":"Masárová, Zuzana"},{"full_name":"Miltzow, Tillmann","first_name":"Tillmann","last_name":"Miltzow"},{"first_name":"Debajyoti","last_name":"Mondal","full_name":"Mondal, Debajyoti"},{"full_name":"Naredla, Anurag Murty","last_name":"Naredla","first_name":"Anurag Murty"},{"full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef"},{"full_name":"Turcotte, Alexi","first_name":"Alexi","last_name":"Turcotte"}],"related_material":{"record":[{"id":"7944","status":"public","relation":"dissertation_contains"},{"id":"12833","relation":"later_version","status":"public"}]},"date_created":"2020-06-08T12:25:25Z","date_updated":"2024-01-04T12:42:08Z","oa_version":"Preprint","_id":"7950","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","publication_status":"submitted","status":"public","title":"Token swapping on trees","department":[{"_id":"HeEd"},{"_id":"UlWa"},{"_id":"KrCh"}],"abstract":[{"text":"The input to the token swapping problem is a graph with vertices v1, v2, . . . , vn, and n tokens with labels 1,2, . . . , n, one on each vertex. The goal is to get token i to vertex vi for all i= 1, . . . , n using a minimum number of swaps, where a swap exchanges the tokens on the endpoints of an edge.Token swapping on a tree, also known as “sorting with a transposition tree,” is not known to be in P nor NP-complete. We present some partial results:\r\n1. An optimum swap sequence may need to perform a swap on a leaf vertex that has the correct token (a “happy leaf”), disproving a conjecture of Vaughan.\r\n2. Any algorithm that fixes happy leaves—as all known approximation algorithms for the problem do—has approximation factor at least 4/3. Furthermore, the two best-known 2-approximation algorithms have approximation factor exactly 2.\r\n3. A generalized problem—weighted coloured token swapping—is NP-complete on trees, but solvable in polynomial time on paths and stars. In this version, tokens and vertices have colours, and colours have weights. The goal is to get every token to a vertex of the same colour, and the cost of a swap is the sum of the weights of the two tokens involved.","lang":"eng"}],"article_number":"1903.06981","type":"preprint"},{"volume":11,"date_created":"2019-05-13T07:58:38Z","date_updated":"2024-02-21T12:45:41Z","related_material":{"record":[{"relation":"popular_science","status":"public","id":"6060"}]},"author":[{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961","first_name":"Ann K","last_name":"Huylmans","full_name":"Huylmans, Ann K"},{"last_name":"Toups","first_name":"Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A"},{"full_name":"Macon, Ariana","last_name":"Macon","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gammerdinger","first_name":"William J","orcid":"0000-0001-9638-1220","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","full_name":"Gammerdinger, William J"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"}],"publisher":"Oxford University Press","department":[{"_id":"BeVi"}],"publication_status":"published","year":"2019","ec_funded":1,"file_date_updated":"2020-07-14T12:47:29Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1093/gbe/evz053","project":[{"grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000476569800003"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"eissn":["1759-6653"]},"month":"04","file":[{"access_level":"open_access","file_name":"2019_GBE_Huylmans.pdf","content_type":"application/pdf","file_size":1256303,"creator":"dernst","relation":"main_file","file_id":"6446","checksum":"7d0ede297b6741f3dc89cd59017c7642","date_updated":"2020-07-14T12:47:29Z","date_created":"2019-05-14T08:29:38Z"}],"oa_version":"Published Version","intvolume":" 11","status":"public","title":"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome","ddc":["570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6418","issue":"4","abstract":[{"lang":"eng","text":"Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general."}],"type":"journal_article","date_published":"2019-04-01T00:00:00Z","page":"1033-1044","citation":{"ista":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. 2019. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 11(4), 1033–1044.","ieee":"A. K. Huylmans, M. A. Toups, A. Macon, W. J. Gammerdinger, and B. Vicoso, “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome,” Genome biology and evolution, vol. 11, no. 4. Oxford University Press, pp. 1033–1044, 2019.","apa":"Huylmans, A. K., Toups, M. A., Macon, A., Gammerdinger, W. J., & Vicoso, B. (2019). Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evz053","ama":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 2019;11(4):1033-1044. doi:10.1093/gbe/evz053","chicago":"Huylmans, Ann K, Melissa A Toups, Ariana Macon, William J Gammerdinger, and Beatriz Vicoso. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/gbe/evz053.","mla":"Huylmans, Ann K., et al. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution, vol. 11, no. 4, Oxford University Press, 2019, pp. 1033–44, doi:10.1093/gbe/evz053.","short":"A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome Biology and Evolution 11 (2019) 1033–1044."},"publication":"Genome biology and evolution","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1"},{"file_date_updated":"2020-07-14T12:47:47Z","abstract":[{"lang":"eng","text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature."}],"type":"research_data","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:47Z","date_created":"2019-11-13T08:52:21Z","checksum":"72441055043eda4cbf1398a422e2c118","relation":"main_file","file_id":"7017","title":"Locus1_amplified","file_size":2456192500,"content_type":"application/octet-stream","creator":"itomanek","description":"Illumina whole genome sequence data for Locus 1 - amplified.","file_name":"D8_S35_R2_001.fastq","access_level":"open_access"},{"date_updated":"2020-07-14T12:47:47Z","date_created":"2019-11-13T08:52:59Z","checksum":"a4ac50bf655d9c751f0305ade5c2ee16","title":"Locus1_ancestral","file_id":"7018","relation":"main_file","creator":"itomanek","file_size":2833452234,"content_type":"application/octet-stream","description":"Illumina whole genome sequence data for Locus 1 - 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Tomanek, (2019).","mla":"Tomanek, Isabella. Data for the Paper “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7016.","chicago":"Tomanek, Isabella. “Data for the Paper ‘Gene Amplification as a Form of Population-Level Gene Expression Regulation.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7016.","ama":"Tomanek I. Data for the paper “Gene amplification as a form of population-level gene expression regulation.” 2019. doi:10.15479/AT:ISTA:7016","apa":"Tomanek, I. (2019). Data for the paper “Gene amplification as a form of population-level gene expression regulation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7016","ieee":"I. Tomanek, “Data for the paper ‘Gene amplification as a form of population-level gene expression regulation.’” Institute of Science and Technology Austria, 2019.","ista":"Tomanek I. 2019. Data for the paper ‘Gene amplification as a form of population-level gene expression regulation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7016."},"oa":1},{"oa":1,"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Programming Temporal Morphing of Self-Actuated Shells.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7154.","short":"R. Guseinov, (2019).","mla":"Guseinov, Ruslan. Supplementary Data for “Programming Temporal Morphing of Self-Actuated Shells.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7154.","apa":"Guseinov, R. (2019). Supplementary data for “Programming temporal morphing of self-actuated shells.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7154","ieee":"R. Guseinov, “Supplementary data for ‘Programming temporal morphing of self-actuated shells.’” Institute of Science and Technology Austria, 2019.","ista":"Guseinov R. 2019. Supplementary data for ‘Programming temporal morphing of self-actuated shells’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7154.","ama":"Guseinov R. Supplementary data for “Programming temporal morphing of self-actuated shells.” 2019. doi:10.15479/AT:ISTA:7154"},"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"date_published":"2019-12-06T00:00:00Z","doi":"10.15479/AT:ISTA:7154","has_accepted_license":"1","article_processing_charge":"No","month":"12","day":"06","_id":"7154","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","department":[{"_id":"BeBi"}],"status":"public","title":"Supplementary data for \"Programming temporal morphing of self-actuated shells\"","ddc":["000"],"contributor":[{"id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9819-5077","first_name":"Ruslan","last_name":"Guseinov"},{"last_name":"McMahan","first_name":"Connor"},{"last_name":"Perez Rodriguez","first_name":"Jesus","id":"2DC83906-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Daraio","first_name":"Chiara"},{"last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"used_in_publication","status":"deleted","id":"8433"},{"id":"7262","status":"public","relation":"used_in_publication"}]},"author":[{"id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9819-5077","first_name":"Ruslan","last_name":"Guseinov","full_name":"Guseinov, Ruslan"}],"file":[{"relation":"main_file","file_id":"7155","date_updated":"2020-07-14T12:47:50Z","date_created":"2019-12-09T07:52:17Z","checksum":"155133e6e188e85b3c0676a5e70b9341","file_name":"temporal_morphing_supp_data.zip","access_level":"open_access","file_size":65307107,"content_type":"application/x-zip-compressed","creator":"dernst"}],"oa_version":"Published Version","date_created":"2019-12-09T07:52:46Z","date_updated":"2024-02-21T12:45:03Z","type":"research_data","ec_funded":1,"file_date_updated":"2020-07-14T12:47:50Z"},{"citation":{"chicago":"Vicoso, Beatriz. “Supplementary Data for ‘Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome’ (Huylman, Toups et Al., 2019). .” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6060.","short":"B. Vicoso, (2019).","mla":"Vicoso, Beatriz. Supplementary Data for “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome” (Huylman, Toups et Al., 2019). . Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6060.","ieee":"B. Vicoso, “Supplementary data for ‘Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al., 2019). .” Institute of Science and Technology Austria, 2019.","apa":"Vicoso, B. (2019). Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6060","ista":"Vicoso B. 2019. Supplementary data for ‘Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al., 2019). , Institute of Science and Technology Austria, 10.15479/AT:ISTA:6060.","ama":"Vicoso B. Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . 2019. doi:10.15479/AT:ISTA:6060"},"oa":1,"doi":"10.15479/AT:ISTA:6060","date_published":"2019-02-28T00:00:00Z","day":"28","month":"02","article_processing_charge":"No","has_accepted_license":"1","_id":"6060","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","title":"Supplementary data for \"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome\" (Huylman, Toups et al., 2019). ","status":"public","department":[{"_id":"BeVi"}],"publisher":"Institute of Science and Technology Austria","author":[{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"related_material":{"record":[{"relation":"research_paper","status":"public","id":"6418"}]},"date_updated":"2024-02-21T12:45:42Z","date_created":"2019-02-28T10:55:15Z","file":[{"checksum":"a338a622d728af0e3199cb07e6dd64d3","date_updated":"2020-07-14T12:47:17Z","date_created":"2019-02-28T10:54:27Z","relation":"main_file","file_id":"6061","content_type":"application/zip","file_size":36646050,"creator":"bvicoso","access_level":"open_access","file_name":"SupData.zip"}],"oa_version":"Published Version","type":"research_data","file_date_updated":"2020-07-14T12:47:17Z"},{"abstract":[{"lang":"eng","text":"This dataset contains the supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\".\r\n\r\nThe contained files have the following content:\r\n'Supplementary Figures.pdf'\r\n\tAdditional figures (as referenced in the paper).\r\n'Supplementary Table 1. Statistics.xlsx'\r\n\tDetails on statistical tests performed in the paper.\r\n'Supplementary Table 2. Differentially expressed gene analysis.xlsx'\r\n\tResults for the differential gene expression analysis for embryonic (E9.5; analysis with edgeR) and in vitro (ESCs, EBs, NPCs; analysis with DESeq2) samples.\r\n'Supplementary Table 3. Gene Ontology (GO) term enrichment analysis.xlsx'\r\n\tResults for the GO term enrichment analysis for differentially expressed genes in embryonic (GO E9.5) and in vitro (GO ESC, GO EBs, GO NPCs) samples. Differentially expressed genes for in vitro samples were split into upregulated and downregulated genes (up/down) and the analysis was performed on each subset (e.g. GO ESC up / GO ESC down).\r\n'Supplementary Table 4. Differentially expressed gene analysis for CFC samples.xlsx'\r\n\tResults for the differential gene expression analysis for samples from adult mice before (HC - Homecage) and 1h and 3h after contextual fear conditioning (1h and 3h, respectively). Each sheet shows the results for a different comparison. Sheets 1-3 show results for comparisons between timepoints for wild type (WT) samples only and sheets 4-6 for the same comparisons in mutant (Het) samples. Sheets 7-9 show results for comparisons between genotypes at each time point and sheet 10 contains the results for the analysis of differential expression trajectories between wild type and mutant.\r\n'Supplementary Table 5. Cluster identification.xlsx'\r\n\tResults for k-means clustering of genes by expression. Sheet 1 shows clustering of just the genes with significantly different expression trajectories between genotypes. Sheet 2 shows clustering of all genes that are significantly differentially expressed in any of the comparisons (includes also genes with same trajectories).\r\n'Supplementary Table 6. GO term cluster analysis.xlsx'\r\n\tResults for the GO term enrichment analysis and EWCE analysis for enrichment of cell type specific genes for each cluster identified by clustering genes with different expression trajectories (see Table S5, sheet 1).\r\n'Supplementary Table 7. Setd5 mass spectrometry results.xlsx'\r\n\tResults showing proteins interacting with Setd5 as identified by mass spectrometry. Sheet 1 shows protein protein interaction data generated from these results (combined with data from the STRING database. Sheet 2 shows the results of the statistical analysis with limma.\r\n'Supplementary Table 8. PolII ChIP-seq analysis.xlsx'\r\n\tResults for the Chip-Seq analysis for binding of RNA polymerase II (PolII). Sheet 1 shows results for differential binding of PolII at the transcription start site (TSS) between genotypes and sheets 2+3 show the corresponding GO enrichment analysis for these differentially bound genes. Sheet 4 shows RNAseq counts for genes with increased binding of PolII at the TSS."}],"file_date_updated":"2020-07-14T12:47:18Z","type":"research_data","date_updated":"2024-02-21T13:41:01Z","date_created":"2019-03-07T13:32:35Z","file":[{"file_name":"Setd5_paper.zip","access_level":"open_access","file_size":33202743,"content_type":"application/zip","creator":"dernst","relation":"supplementary_material","file_id":"6084","date_updated":"2020-07-14T12:47:18Z","date_created":"2019-03-07T13:37:19Z","checksum":"bc1b285edca9e98a2c63d153c79bb75b"}],"oa_version":"Published Version","author":[{"full_name":"Dotter, Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9033-9096","first_name":"Christoph","last_name":"Dotter"},{"first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"related_material":{"record":[{"id":"3","status":"public","relation":"research_paper"}]},"ddc":["570"],"title":"Supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\"","status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaNo"}],"year":"2019","_id":"6074","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"09","month":"01","has_accepted_license":"1","article_processing_charge":"No","doi":"10.15479/AT:ISTA:6074","date_published":"2019-01-09T00:00:00Z","citation":{"chicago":"Dotter, Christoph, and Gaia Novarino. “Supplementary Data for the Research Paper ‘Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6074.","short":"C. Dotter, G. Novarino, (2019).","mla":"Dotter, Christoph, and Gaia Novarino. Supplementary Data for the Research Paper “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6074.","ieee":"C. Dotter and G. Novarino, “Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.’” Institute of Science and Technology Austria, 2019.","apa":"Dotter, C., & Novarino, G. (2019). Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6074","ista":"Dotter C, Novarino G. 2019. Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:6074.","ama":"Dotter C, Novarino G. Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” 2019. doi:10.15479/AT:ISTA:6074"},"oa":1}]