[{"month":"07","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000473730600007"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1101/gr.238824.118","file_date_updated":"2020-07-14T12:47:35Z","department":[{"_id":"BeVi"}],"publisher":"CSH Press","publication_status":"published","year":"2019","volume":29,"date_updated":"2023-08-29T06:35:05Z","date_created":"2019-07-21T21:59:15Z","author":[{"first_name":"Julia","last_name":"Raices","id":"3EE67F22-F248-11E8-B48F-1D18A9856A87","full_name":"Raices, Julia"},{"full_name":"Otto, Paulo","first_name":"Paulo","last_name":"Otto"},{"full_name":"Vibranovski, Maria","first_name":"Maria","last_name":"Vibranovski"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","page":"1115-1122","citation":{"ama":"Raices J, Otto P, Vibranovski M. Haploid selection drives new gene male germline expression. Genome Research. 2019;29(7):1115-1122. doi:10.1101/gr.238824.118","ieee":"J. Raices, P. Otto, and M. Vibranovski, “Haploid selection drives new gene male germline expression,” Genome Research, vol. 29, no. 7. CSH Press, pp. 1115–1122, 2019.","apa":"Raices, J., Otto, P., & Vibranovski, M. (2019). Haploid selection drives new gene male germline expression. Genome Research. CSH Press. https://doi.org/10.1101/gr.238824.118","ista":"Raices J, Otto P, Vibranovski M. 2019. Haploid selection drives new gene male germline expression. Genome Research. 29(7), 1115–1122.","short":"J. Raices, P. Otto, M. Vibranovski, Genome Research 29 (2019) 1115–1122.","mla":"Raices, Julia, et al. “Haploid Selection Drives New Gene Male Germline Expression.” Genome Research, vol. 29, no. 7, CSH Press, 2019, pp. 1115–22, doi:10.1101/gr.238824.118.","chicago":"Raices, Julia, Paulo Otto, and Maria Vibranovski. “Haploid Selection Drives New Gene Male Germline Expression.” Genome Research. CSH Press, 2019. https://doi.org/10.1101/gr.238824.118."},"publication":"Genome Research","date_published":"2019-07-01T00:00:00Z","type":"journal_article","issue":"7","abstract":[{"lang":"eng","text":"New genes are a major source of novelties, and a disproportionate amount of them are known to show testis expression in later phases of male gametogenesis in different groups such as mammals and plants. Here, we propose that this enhanced expression is a consequence of haploid selection during the latter stages of male gametogenesis. Because emerging adaptive mutations will be fixed faster if their phenotypes are expressed by haploid rather than diploid genotypes, new genes with advantageous functions arising during this unique stage of development have a better chance to become fixed. To test this hypothesis, expression levels of genes of differing evolutionary age were examined at various stages of Drosophila spermatogenesis. We found, consistent with a model based on haploid selection, that new Drosophila genes are both expressed in later haploid phases of spermatogenesis and harbor a significant enrichment of adaptive mutations. Additionally, the observed overexpression of new genes in the latter phases of spermatogenesis was limited to the autosomes. Because all male cells exhibit hemizygous expression for X-linked genes (and therefore effectively haploid), there is no expectation that selection acting on late spermatogenesis will have a different effect on X-linked genes in comparison to initial diploid phases. Together, our proposed hypothesis and the analyzed data suggest that natural selection in haploid cells elucidates several aspects of the origin of new genes by explaining the general prevalence of their testis expression, and a parsimonious solution for new alleles to avoid being lost by genetic drift or pseudogenization. "}],"intvolume":" 29","status":"public","title":"Haploid selection drives new gene male germline expression","ddc":["576"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6658","file":[{"file_id":"6670","relation":"main_file","checksum":"4636f03a6750f90b88bf2bc3eb9d71ae","date_created":"2019-07-24T08:05:56Z","date_updated":"2020-07-14T12:47:35Z","access_level":"open_access","file_name":"2019_GenomeResearch_Raices.pdf","creator":"apreinsp","content_type":"application/pdf","file_size":2319022}],"oa_version":"Published Version"},{"scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","publication":"ACM Transactions on Graphics","citation":{"chicago":"Alderighi, Thomas, Luigi Malomo, Daniela Giorgi, Bernd Bickel, Paolo Cignoni, and Nico Pietroni. “Volume-Aware Design of Composite Molds.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3322981.","short":"T. Alderighi, L. Malomo, D. Giorgi, B. Bickel, P. Cignoni, N. Pietroni, ACM Transactions on Graphics 38 (2019).","mla":"Alderighi, Thomas, et al. “Volume-Aware Design of Composite Molds.” ACM Transactions on Graphics, vol. 38, no. 4, 110, ACM, 2019, doi:10.1145/3306346.3322981.","apa":"Alderighi, T., Malomo, L., Giorgi, D., Bickel, B., Cignoni, P., & Pietroni, N. (2019). Volume-aware design of composite molds. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3322981","ieee":"T. Alderighi, L. Malomo, D. Giorgi, B. Bickel, P. Cignoni, and N. Pietroni, “Volume-aware design of composite molds,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.","ista":"Alderighi T, Malomo L, Giorgi D, Bickel B, Cignoni P, Pietroni N. 2019. Volume-aware design of composite molds. ACM Transactions on Graphics. 38(4), 110.","ama":"Alderighi T, Malomo L, Giorgi D, Bickel B, Cignoni P, Pietroni N. Volume-aware design of composite molds. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3322981"},"date_published":"2019-07-01T00:00:00Z","type":"journal_article","abstract":[{"text":"We propose a novel technique for the automatic design of molds to cast highly complex shapes. The technique generates composite, two-piece molds. Each mold piece is made up of a hard plastic shell and a flexible silicone part. Thanks to the thin, soft, and smartly shaped silicone part, which is kept in place by a hard plastic shell, we can cast objects of unprecedented complexity. An innovative algorithm based on a volumetric analysis defines the layout of the internal cuts in the silicone mold part. Our approach can robustly handle thin protruding features and intertwined topologies that have caused previous methods to fail. We compare our results with state of the art techniques, and we demonstrate the casting of shapes with extremely complex geometry.","lang":"eng"}],"issue":"4","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6650","status":"public","ddc":["000"],"title":"Volume-aware design of composite molds","intvolume":" 38","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"2019_ACM_Alderighi_AuthorVersion.pdf","content_type":"application/pdf","file_size":74316182,"creator":"dernst","relation":"main_file","file_id":"6651","checksum":"b4562af94672b44d2a501046427412af","date_created":"2019-07-19T06:18:53Z","date_updated":"2020-07-14T12:47:35Z"}],"month":"07","publication_identifier":{"issn":["0730-0301"]},"external_id":{"isi":["000475740600084"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"doi":"10.1145/3306346.3322981","language":[{"iso":"eng"}],"article_number":"110","file_date_updated":"2020-07-14T12:47:35Z","ec_funded":1,"year":"2019","publication_status":"published","publisher":"ACM","department":[{"_id":"BeBi"}],"author":[{"last_name":"Alderighi","first_name":"Thomas","full_name":"Alderighi, Thomas"},{"first_name":"Luigi","last_name":"Malomo","full_name":"Malomo, Luigi"},{"last_name":"Giorgi","first_name":"Daniela","full_name":"Giorgi, Daniela"},{"full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cignoni, Paolo","first_name":"Paolo","last_name":"Cignoni"},{"full_name":"Pietroni, Nico","first_name":"Nico","last_name":"Pietroni"}],"related_material":{"link":[{"url":"https://youtu.be/SO349S8-x_w","relation":"supplementary_material","description":"YouTube Video"}]},"date_created":"2019-07-19T06:18:15Z","date_updated":"2023-08-29T06:35:52Z","volume":38},{"external_id":{"isi":["000470131200001"]},"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,"project":[{"name":"Design principles underlying genetic switch architecture (DOC Fellowship)","_id":"251EE76E-B435-11E9-9278-68D0E5697425","grant_number":"24573"}],"quality_controlled":"1","isi":1,"doi":"10.3389/fmicb.2019.01171","language":[{"iso":"eng"}],"month":"06","year":"2019","department":[{"_id":"CaGu"}],"publisher":"Frontiers","publication_status":"published","author":[{"last_name":"Igler","first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","full_name":"Igler, Claudia"},{"full_name":"Abedon, Stephen T.","first_name":"Stephen T.","last_name":"Abedon"}],"volume":10,"date_created":"2019-07-28T21:59:18Z","date_updated":"2023-08-29T06:41:20Z","article_number":"1171","file_date_updated":"2020-07-14T12:47:38Z","citation":{"ama":"Igler C, Abedon ST. Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology. 2019;10. doi:10.3389/fmicb.2019.01171","apa":"Igler, C., & Abedon, S. T. (2019). Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2019.01171","ieee":"C. Igler and S. T. Abedon, “Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision,” Frontiers in Microbiology, vol. 10. Frontiers, 2019.","ista":"Igler C, Abedon ST. 2019. Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology. 10, 1171.","short":"C. Igler, S.T. Abedon, Frontiers in Microbiology 10 (2019).","mla":"Igler, Claudia, and Stephen T. Abedon. “Commentary: A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision.” Frontiers in Microbiology, vol. 10, 1171, Frontiers, 2019, doi:10.3389/fmicb.2019.01171.","chicago":"Igler, Claudia, and Stephen T. Abedon. “Commentary: A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision.” Frontiers in Microbiology. Frontiers, 2019. https://doi.org/10.3389/fmicb.2019.01171."},"publication":"Frontiers in Microbiology","date_published":"2019-06-03T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"03","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6717","intvolume":" 10","title":"Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision","ddc":["570"],"status":"public","file":[{"checksum":"317a06067e9a8e717bb55f23e0d77ba7","date_updated":"2020-07-14T12:47:38Z","date_created":"2019-07-29T07:51:54Z","relation":"main_file","file_id":"6722","file_size":246151,"content_type":"application/pdf","creator":"apreinsp","access_level":"open_access","file_name":"2019_Frontiers_Igler.pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"With the recent publication by Silpe and Bassler (2019), considering phage detection of a bacterial quorum-sensing (QS) autoinducer, we now have as many as five examples of phage-associated intercellular communication (Table 1). Each potentially involves ecological inferences by phages as to concentrations of surrounding phage-infected or uninfected bacteria. While the utility of phage detection of bacterial QS molecules may at first glance appear to be straightforward, we suggest in this commentary that the underlying ecological explanation is unlikely to be simple."}]},{"date_published":"2019-09-01T00:00:00Z","citation":{"mla":"Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Evolution, vol. 73, no. 9, Wiley, 2019, pp. 1729–45, doi:10.1111/evo.13812.","short":"H. Sachdeva, Evolution 73 (2019) 1729–1745.","chicago":"Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Evolution. Wiley, 2019. https://doi.org/10.1111/evo.13812.","ama":"Sachdeva H. Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. 2019;73(9):1729-1745. doi:10.1111/evo.13812","ista":"Sachdeva H. 2019. Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. 73(9), 1729–1745.","ieee":"H. Sachdeva, “Effect of partial selfing and polygenic selection on establishment in a new habitat,” Evolution, vol. 73, no. 9. Wiley, pp. 1729–1745, 2019.","apa":"Sachdeva, H. (2019). Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. Wiley. https://doi.org/10.1111/evo.13812"},"publication":"Evolution","page":"1729-1745","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1","file":[{"date_updated":"2020-07-14T12:47:37Z","date_created":"2019-09-17T10:56:27Z","checksum":"772ce7035965153959b946a1033de1ca","relation":"main_file","file_id":"6881","content_type":"application/pdf","file_size":937573,"creator":"kschuh","file_name":"2019_Evolution_Sachdeva.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6680","intvolume":" 73","ddc":["576"],"status":"public","title":"Effect of partial selfing and polygenic selection on establishment in a new habitat","issue":"9","abstract":[{"text":"This paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation‐selection balance in a large, partially selfing source population under selection involving multiple non‐identical loci. I then use individual‐based simulations to study the eco‐evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long‐term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed.","lang":"eng"}],"type":"journal_article","doi":"10.1111/evo.13812","language":[{"iso":"eng"}],"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":{"isi":["000481300600001"]},"oa":1,"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"month":"09","related_material":{"record":[{"id":"9802","relation":"research_data","status":"public"}]},"author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","last_name":"Sachdeva","full_name":"Sachdeva, Himani"}],"volume":73,"date_updated":"2023-08-29T06:43:58Z","date_created":"2019-07-25T09:08:28Z","year":"2019","publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","file_date_updated":"2020-07-14T12:47:37Z"},{"intvolume":" 123","status":"public","title":"Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6710","oa_version":"Published Version","type":"journal_article","issue":"7","abstract":[{"lang":"eng","text":"Sexual dimorphism in morphology, physiology or life history traits is common in dioecious plants at reproductive maturity, but it is typically inconspicuous or absent in juveniles. Although plants of different sexes probably begin to diverge in gene expression both before their reproduction commences and before dimorphism becomes readily apparent, to our knowledge transcriptome-wide differential gene expression has yet to be demonstrated for any angiosperm species."}],"page":"1119-1131","article_type":"original","citation":{"chicago":"Cossard, Guillaume, Melissa A Toups, and John Pannell. “Sexual Dimorphism and Rapid Turnover in Gene Expression in Pre-Reproductive Seedlings of a Dioecious Herb.” Annals of Botany. Oxford University Press, 2019. https://doi.org/10.1093/aob/mcy183.","short":"G. Cossard, M.A. Toups, J. Pannell, Annals of Botany 123 (2019) 1119–1131.","mla":"Cossard, Guillaume, et al. “Sexual Dimorphism and Rapid Turnover in Gene Expression in Pre-Reproductive Seedlings of a Dioecious Herb.” Annals of Botany, vol. 123, no. 7, Oxford University Press, 2019, pp. 1119–31, doi:10.1093/aob/mcy183.","ieee":"G. Cossard, M. A. Toups, and J. Pannell, “Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb,” Annals of botany, vol. 123, no. 7. Oxford University Press, pp. 1119–1131, 2019.","apa":"Cossard, G., Toups, M. A., & Pannell, J. (2019). Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of Botany. Oxford University Press. https://doi.org/10.1093/aob/mcy183","ista":"Cossard G, Toups MA, Pannell J. 2019. Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of botany. 123(7), 1119–1131.","ama":"Cossard G, Toups MA, Pannell J. Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of botany. 2019;123(7):1119-1131. doi:10.1093/aob/mcy183"},"publication":"Annals of botany","date_published":"2019-06-04T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"04","department":[{"_id":"BeVi"}],"publisher":"Oxford University Press","publication_status":"published","pmid":1,"year":"2019","volume":123,"date_created":"2019-07-28T21:59:15Z","date_updated":"2023-08-29T06:42:22Z","author":[{"full_name":"Cossard, Guillaume","first_name":"Guillaume","last_name":"Cossard"},{"full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","first_name":"Melissa A"},{"full_name":"Pannell, John ","last_name":"Pannell","first_name":"John "}],"isi":1,"quality_controlled":"1","external_id":{"pmid":["30289430"],"isi":["000493043500004"]},"main_file_link":[{"url":"https://doi.org/10.1093/aob/mcy183","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1093/aob/mcy183","publication_identifier":{"eissn":["1095-8290"],"issn":["0305-7364"]},"month":"06"},{"date_updated":"2023-08-29T06:41:51Z","date_created":"2021-08-06T11:52:54Z","oa_version":"Published Version","author":[{"full_name":"Castro, João Pl","first_name":"João Pl","last_name":"Castro"},{"full_name":"Yancoskie, Michelle N.","first_name":"Michelle N.","last_name":"Yancoskie"},{"first_name":"Marta","last_name":"Marchini","full_name":"Marchini, Marta"},{"full_name":"Belohlavy, Stefanie","orcid":"0000-0002-9849-498X","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","last_name":"Belohlavy","first_name":"Stefanie"},{"last_name":"Hiramatsu","first_name":"Layla","full_name":"Hiramatsu, Layla"},{"first_name":"Marek","last_name":"Kučka","full_name":"Kučka, Marek"},{"full_name":"Beluch, William H.","first_name":"William H.","last_name":"Beluch"},{"first_name":"Ronald","last_name":"Naumann","full_name":"Naumann, Ronald"},{"full_name":"Skuplik, Isabella","last_name":"Skuplik","first_name":"Isabella"},{"full_name":"Cobb, John","first_name":"John","last_name":"Cobb"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"first_name":"Campbell","last_name":"Rolian","full_name":"Rolian, Campbell"},{"first_name":"Yingguang Frank","last_name":"Chan","full_name":"Chan, Yingguang Frank"}],"related_material":{"record":[{"id":"6713","relation":"used_in_publication","status":"public"}]},"status":"public","title":"Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","publisher":"Dryad","department":[{"_id":"NiBa"}],"_id":"9804","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"text":"Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.","lang":"eng"}],"type":"research_data_reference","doi":"10.5061/dryad.0q2h6tk","date_published":"2019-06-06T00:00:00Z","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.0q2h6tk","open_access":"1"}],"citation":{"chicago":"Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “Data from: An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” Dryad, 2019. https://doi.org/10.5061/dryad.0q2h6tk.","mla":"Castro, João Pl, et al. Data from: An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice. Dryad, 2019, doi:10.5061/dryad.0q2h6tk.","short":"J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M. Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F. Chan, (2019).","ista":"Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice, Dryad, 10.5061/dryad.0q2h6tk.","apa":"Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. Dryad. https://doi.org/10.5061/dryad.0q2h6tk","ieee":"J. P. Castro et al., “Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice.” Dryad, 2019.","ama":"Castro JP, Yancoskie MN, Marchini M, et al. Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. 2019. doi:10.5061/dryad.0q2h6tk"},"month":"06","day":"06","article_processing_charge":"No"},{"article_processing_charge":"No","month":"07","day":"16","oa":1,"citation":{"ama":"Sachdeva H. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. 2019. doi:10.5061/dryad.8tp0900","ista":"Sachdeva H. 2019. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat, Dryad, 10.5061/dryad.8tp0900.","apa":"Sachdeva, H. (2019). Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. Dryad. https://doi.org/10.5061/dryad.8tp0900","ieee":"H. Sachdeva, “Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat.” Dryad, 2019.","mla":"Sachdeva, Himani. Data from: Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat. Dryad, 2019, doi:10.5061/dryad.8tp0900.","short":"H. Sachdeva, (2019).","chicago":"Sachdeva, Himani. “Data from: Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Dryad, 2019. https://doi.org/10.5061/dryad.8tp0900."},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.8tp0900","open_access":"1"}],"date_published":"2019-07-16T00:00:00Z","doi":"10.5061/dryad.8tp0900","type":"research_data_reference","abstract":[{"lang":"eng","text":"This paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation-selection balance in a large, partially selfing source population under selection involving multiple non-identical loci. I then use individual-based simulations to study the eco-evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long-term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed."}],"_id":"9802","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Dryad","department":[{"_id":"NiBa"}],"title":"Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat","status":"public","related_material":{"record":[{"id":"6680","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","first_name":"Himani"}],"oa_version":"Published Version","date_created":"2021-08-06T11:45:11Z","date_updated":"2023-08-29T06:43:57Z"},{"abstract":[{"text":"We study the topology generated by the temperature fluctuations of the cosmic microwave background (CMB) radiation, as quantified by the number of components and holes, formally given by the Betti numbers, in the growing excursion sets. We compare CMB maps observed by the Planck satellite with a thousand simulated maps generated according to the ΛCDM paradigm with Gaussian distributed fluctuations. The comparison is multi-scale, being performed on a sequence of degraded maps with mean pixel separation ranging from 0.05 to 7.33°. The survey of the CMB over 𝕊2 is incomplete due to obfuscation effects by bright point sources and other extended foreground objects like our own galaxy. To deal with such situations, where analysis in the presence of “masks” is of importance, we introduce the concept of relative homology. The parametric χ2-test shows differences between observations and simulations, yielding p-values at percent to less than permil levels roughly between 2 and 7°, with the difference in the number of components and holes peaking at more than 3σ sporadically at these scales. The highest observed deviation between the observations and simulations for b0 and b1 is approximately between 3σ and 4σ at scales of 3–7°. There are reports of mildly unusual behaviour of the Euler characteristic at 3.66° in the literature, computed from independent measurements of the CMB temperature fluctuations by Planck’s predecessor, the Wilkinson Microwave Anisotropy Probe (WMAP) satellite. The mildly anomalous behaviour of the Euler characteristic is phenomenologically related to the strongly anomalous behaviour of components and holes, or the zeroth and first Betti numbers, respectively. Further, since these topological descriptors show consistent anomalous behaviour over independent measurements of Planck and WMAP, instrumental and systematic errors may be an unlikely source. These are also the scales at which the observed maps exhibit low variance compared to the simulations, and approximately the range of scales at which the power spectrum exhibits a dip with respect to the theoretical model. Non-parametric tests show even stronger differences at almost all scales. Crucially, Gaussian simulations based on power-spectrum matching the characteristics of the observed dipped power spectrum are not able to resolve the anomaly. Understanding the origin of the anomalies in the CMB, whether cosmological in nature or arising due to late-time effects, is an extremely challenging task. Regardless, beyond the trivial possibility that this may still be a manifestation of an extreme Gaussian case, these observations, along with the super-horizon scales involved, may motivate the study of primordial non-Gaussianity. Alternative scenarios worth exploring may be models with non-trivial topology, including topological defect models.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":14420451,"creator":"dernst","access_level":"open_access","file_name":"2019_AstronomyAstrophysics_Pranav.pdf","checksum":"83b9209ed9eefbdcefd89019c5a97805","date_created":"2019-08-05T08:08:59Z","date_updated":"2020-07-14T12:47:39Z","relation":"main_file","file_id":"6766"}],"intvolume":" 627","ddc":["520","530"],"title":"Unexpected topology of the temperature fluctuations in the cosmic microwave background","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6756","article_processing_charge":"No","has_accepted_license":"1","day":"17","scopus_import":"1","date_published":"2019-07-17T00:00:00Z","article_type":"original","citation":{"ieee":"P. Pranav et al., “Unexpected topology of the temperature fluctuations in the cosmic microwave background,” Astronomy and Astrophysics, vol. 627. EDP Sciences, 2019.","apa":"Pranav, P., Adler, R. J., Buchert, T., Edelsbrunner, H., Jones, B. J. T., Schwartzman, A., … Van De Weygaert, R. (2019). Unexpected topology of the temperature fluctuations in the cosmic microwave background. Astronomy and Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201834916","ista":"Pranav P, Adler RJ, Buchert T, Edelsbrunner H, Jones BJT, Schwartzman A, Wagner H, Van De Weygaert R. 2019. Unexpected topology of the temperature fluctuations in the cosmic microwave background. Astronomy and Astrophysics. 627, A163.","ama":"Pranav P, Adler RJ, Buchert T, et al. Unexpected topology of the temperature fluctuations in the cosmic microwave background. Astronomy and Astrophysics. 2019;627. doi:10.1051/0004-6361/201834916","chicago":"Pranav, Pratyush, Robert J. Adler, Thomas Buchert, Herbert Edelsbrunner, Bernard J.T. Jones, Armin Schwartzman, Hubert Wagner, and Rien Van De Weygaert. “Unexpected Topology of the Temperature Fluctuations in the Cosmic Microwave Background.” Astronomy and Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201834916.","short":"P. Pranav, R.J. Adler, T. Buchert, H. Edelsbrunner, B.J.T. Jones, A. Schwartzman, H. Wagner, R. Van De Weygaert, Astronomy and Astrophysics 627 (2019).","mla":"Pranav, Pratyush, et al. “Unexpected Topology of the Temperature Fluctuations in the Cosmic Microwave Background.” Astronomy and Astrophysics, vol. 627, A163, EDP Sciences, 2019, doi:10.1051/0004-6361/201834916."},"publication":"Astronomy and Astrophysics","file_date_updated":"2020-07-14T12:47:39Z","article_number":"A163","volume":627,"date_created":"2019-08-04T21:59:18Z","date_updated":"2023-08-29T07:01:48Z","author":[{"first_name":"Pratyush","last_name":"Pranav","full_name":"Pranav, Pratyush"},{"full_name":"Adler, Robert J.","last_name":"Adler","first_name":"Robert J."},{"full_name":"Buchert, Thomas","last_name":"Buchert","first_name":"Thomas"},{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"last_name":"Jones","first_name":"Bernard J.T.","full_name":"Jones, Bernard J.T."},{"full_name":"Schwartzman, Armin","last_name":"Schwartzman","first_name":"Armin"},{"full_name":"Wagner, Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Hubert"},{"full_name":"Van De Weygaert, Rien","first_name":"Rien","last_name":"Van De Weygaert"}],"publisher":"EDP Sciences","department":[{"_id":"HeEd"}],"publication_status":"published","year":"2019","publication_identifier":{"eissn":["14320746"],"issn":["00046361"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.1051/0004-6361/201834916","project":[{"_id":"265683E4-B435-11E9-9278-68D0E5697425","grant_number":"M62909-18-1-2038","name":"Toward Computational Information Topology"},{"name":"Persistence and stability of geometric complexes","call_identifier":"FWF","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","oa":1,"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":["1812.07678"],"isi":["000475839300003"]}},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","page":"1909-1922","article_type":"original","citation":{"chicago":"Picard, Marion A L, Beatriz Vicoso, David Roquis, Ingo Bulla, Ronaldo C. Augusto, Nathalie Arancibia, Christoph Grunau, Jérôme Boissier, and Céline Cosseau. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” Genome Biology and Evolution. Oxford Academic Press, 2019. https://doi.org/10.1093/gbe/evz133.","short":"M.A.L. Picard, B. Vicoso, D. Roquis, I. Bulla, R.C. Augusto, N. Arancibia, C. Grunau, J. Boissier, C. Cosseau, Genome Biology and Evolution 11 (2019) 1909–1922.","mla":"Picard, Marion A. L., et al. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” Genome Biology and Evolution, vol. 11, no. 7, Oxford Academic Press, 2019, pp. 1909–22, doi:10.1093/gbe/evz133.","ieee":"M. A. L. Picard et al., “Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome,” Genome biology and evolution, vol. 11, no. 7. Oxford Academic Press, pp. 1909–1922, 2019.","apa":"Picard, M. A. L., Vicoso, B., Roquis, D., Bulla, I., Augusto, R. C., Arancibia, N., … Cosseau, C. (2019). Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome Biology and Evolution. Oxford Academic Press. https://doi.org/10.1093/gbe/evz133","ista":"Picard MAL, Vicoso B, Roquis D, Bulla I, Augusto RC, Arancibia N, Grunau C, Boissier J, Cosseau C. 2019. Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome biology and evolution. 11(7), 1909–1922.","ama":"Picard MAL, Vicoso B, Roquis D, et al. Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome biology and evolution. 2019;11(7):1909-1922. doi:10.1093/gbe/evz133"},"publication":"Genome biology and evolution","date_published":"2019-07-01T00:00:00Z","type":"journal_article","issue":"7","abstract":[{"lang":"eng","text":"Differentiated sex chromosomes are accompanied by a difference in gene dose between X/Z-specific and autosomal genes. At the transcriptomic level, these sex-linked genes can lead to expression imbalance, or gene dosage can be compensated by epigenetic mechanisms and results into expression level equalization. Schistosoma mansoni has been previously described as a ZW species (i.e., female heterogamety, in opposition to XY male heterogametic species) with a partial dosage compensation, but underlying mechanisms are still unexplored. Here, we combine transcriptomic (RNA-Seq) and epigenetic data (ChIP-Seq against H3K4me3, H3K27me3,andH4K20me1histonemarks) in free larval cercariae and intravertebrate parasitic stages. For the first time, we describe differences in dosage compensation status in ZW females, depending on the parasitic status: free cercariae display global dosage compensation, whereas intravertebrate stages show a partial dosage compensation. We also highlight regional differences of gene expression along the Z chromosome in cercariae, but not in the intravertebrate stages. Finally, we feature a consistent permissive chromatin landscape of the Z chromosome in both sexes and stages. We argue that dosage compensation in schistosomes is characterized by chromatin remodeling mechanisms in the Z-specific region."}],"intvolume":" 11","ddc":["570"],"status":"public","title":"Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6755","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6765","date_created":"2019-08-05T07:55:02Z","date_updated":"2020-07-14T12:47:39Z","checksum":"f9e8f6863a406dcc5a36b2be001c138c","file_name":"2019_GenomeBiology_Picard.pdf","access_level":"open_access","file_size":580205,"content_type":"application/pdf","creator":"dernst"}],"publication_identifier":{"eissn":["1759-6653"]},"month":"07","isi":1,"quality_controlled":"1","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":["31273378"],"isi":["000484039500018"]},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"CampIT"}],"doi":"10.1093/gbe/evz133","file_date_updated":"2020-07-14T12:47:39Z","publisher":"Oxford Academic Press","department":[{"_id":"BeVi"}],"publication_status":"published","pmid":1,"year":"2019","volume":11,"date_updated":"2023-08-29T06:53:58Z","date_created":"2019-08-04T21:59:18Z","author":[{"last_name":"Picard","first_name":"Marion A L","orcid":"0000-0002-8101-2518","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","full_name":"Picard, Marion A L"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz"},{"full_name":"Roquis, David","first_name":"David","last_name":"Roquis"},{"last_name":"Bulla","first_name":"Ingo","full_name":"Bulla, Ingo"},{"first_name":"Ronaldo C.","last_name":"Augusto","full_name":"Augusto, Ronaldo C."},{"last_name":"Arancibia","first_name":"Nathalie","full_name":"Arancibia, Nathalie"},{"last_name":"Grunau","first_name":"Christoph","full_name":"Grunau, Christoph"},{"full_name":"Boissier, Jérôme","first_name":"Jérôme","last_name":"Boissier"},{"first_name":"Céline","last_name":"Cosseau","full_name":"Cosseau, Céline"}]},{"author":[{"orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","first_name":"Guy","full_name":"Avni, Guy"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"full_name":"Chonev, Ventsislav K","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Chonev","first_name":"Ventsislav K"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"950"}]},"date_created":"2019-08-04T21:59:16Z","date_updated":"2023-08-29T07:02:13Z","volume":66,"year":"2019","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"ACM","article_number":"31","doi":"10.1145/3340295","language":[{"iso":"eng"}],"external_id":{"isi":["000487714900008"],"arxiv":["1705.01433"]},"main_file_link":[{"url":"https://arxiv.org/abs/1705.01433","open_access":"1"}],"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"},{"name":"Formal Methods meets Algorithmic Game Theory","call_identifier":"FWF","_id":"264B3912-B435-11E9-9278-68D0E5697425","grant_number":"M02369"}],"month":"07","publication_identifier":{"eissn":["1557735X"],"issn":["00045411"]},"oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6752","status":"public","title":"Infinite-duration bidding games","intvolume":" 66","abstract":[{"lang":"eng","text":"Two-player games on graphs are widely studied in formal methods, as they model the interaction between a system and its environment. The game is played by moving a token throughout a graph to produce an infinite path. There are several common modes to determine how the players move the token through the graph; e.g., in turn-based games the players alternate turns in moving the token. We study the bidding mode of moving the token, which, to the best of our knowledge, has never been studied in infinite-duration games. The following bidding rule was previously defined and called Richman bidding. Both players have separate budgets, which sum up to 1. In each turn, a bidding takes place: Both players submit bids simultaneously, where a bid is legal if it does not exceed the available budget, and the higher bidder pays his bid to the other player and moves the token. The central question studied in bidding games is a necessary and sufficient initial budget for winning the game: a threshold budget in a vertex is a value t ∈ [0, 1] such that if Player 1’s budget exceeds t, he can win the game; and if Player 2’s budget exceeds 1 − t, he can win the game. Threshold budgets were previously shown to exist in every vertex of a reachability game, which have an interesting connection with random-turn games—a sub-class of simple stochastic games in which the player who moves is chosen randomly. We show the existence of threshold budgets for a qualitative class of infinite-duration games, namely parity games, and a quantitative class, namely mean-payoff games. The key component of the proof is a quantitative solution to strongly connected mean-payoff bidding games in which we extend the connection with random-turn games to these games, and construct explicit optimal strategies for both players."}],"issue":"4","type":"journal_article","date_published":"2019-07-16T00:00:00Z","publication":"Journal of the ACM","citation":{"chicago":"Avni, Guy, Thomas A Henzinger, and Ventsislav K Chonev. “Infinite-Duration Bidding Games.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3340295.","mla":"Avni, Guy, et al. “Infinite-Duration Bidding Games.” Journal of the ACM, vol. 66, no. 4, 31, ACM, 2019, doi:10.1145/3340295.","short":"G. Avni, T.A. Henzinger, V.K. Chonev, Journal of the ACM 66 (2019).","ista":"Avni G, Henzinger TA, Chonev VK. 2019. Infinite-duration bidding games. Journal of the ACM. 66(4), 31.","ieee":"G. Avni, T. A. Henzinger, and V. K. Chonev, “Infinite-duration bidding games,” Journal of the ACM, vol. 66, no. 4. ACM, 2019.","apa":"Avni, G., Henzinger, T. A., & Chonev, V. K. (2019). Infinite-duration bidding games. Journal of the ACM. ACM. https://doi.org/10.1145/3340295","ama":"Avni G, Henzinger TA, Chonev VK. Infinite-duration bidding games. Journal of the ACM. 2019;66(4). doi:10.1145/3340295"},"day":"16","article_processing_charge":"No","scopus_import":"1"}]