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Aggarwal, et. al. \r\nThe measurements were done using Labber Software and the data is stored in the hdf5 file format. 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Valentini, et. al. \r\nThe measurements were done using Labber Software and the data is stored in the hdf5 file format.\r\nInstructions of how to read the data are in \"Notebook_Valentini.pdf\"."}],"acknowledged_ssus":[{"_id":"NanoFab"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2021","file":[{"creator":"mvalenti","file_size":10572981,"date_updated":"2021-05-14T11:42:23Z","file_name":"Notebook_Valentini.pdf","date_created":"2021-05-14T11:42:23Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"9390","checksum":"80a905c4eef24dab6fb247e81a3d67f5"},{"content_type":"application/x-zip-compressed","access_level":"open_access","relation":"main_file","file_id":"9391","checksum":"1e61a7e63949448a8db0091cdac23570","date_updated":"2021-05-14T11:56:48Z","file_size":99076111,"creator":"mvalenti","date_created":"2021-05-14T11:56:48Z","file_name":"Experimental_data.zip"}],"doi":"10.15479/AT:ISTA:9389","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8910"}]},"date_published":"2021-01-01T00:00:00Z","date_created":"2021-05-14T12:07:53Z","contributor":[{"last_name":"Valentini","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","contributor_type":"contact_person","first_name":"Marco"}]},{"type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"9192","author":[{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","first_name":"Parvathy","full_name":"Surendranadh, Parvathy","last_name":"Surendranadh"},{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S","orcid":"0000-0003-1771-714X","full_name":"Arathoon, Louise S","last_name":"Arathoon"},{"full_name":"Baskett, Carina","orcid":"0000-0002-7354-8574","last_name":"Baskett","first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Field","orcid":"0000-0002-4014-8478","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"last_name":"Pickup","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"article_processing_charge":"No","file_date_updated":"2021-02-24T17:45:13Z","title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"citation":{"chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9192.","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2021. 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Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9192"},"date_updated":"2024-02-21T12:41:09Z","ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","oa":1,"month":"02","abstract":[{"text":"Here are the research data underlying the publication \" Effects of fine-scale population structure on inbreeding in a long-term study of snapdragons (Antirrhinum majus).\" Further information are summed up in the README document.","lang":"eng"}],"oa_version":"Published Version","doi":"10.15479/AT:ISTA:9192","related_material":{"record":[{"status":"public","id":"11411","relation":"used_in_publication"},{"status":"public","id":"11321","relation":"later_version"},{"id":"8254","status":"public","relation":"earlier_version"}]},"date_published":"2021-02-26T00:00:00Z","date_created":"2021-02-24T17:49:21Z","contributor":[{"last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87","first_name":"Parvathy","contributor_type":"project_member"},{"last_name":"Arathoon","contributor_type":"project_member","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","contributor_type":"project_member","last_name":"Baskett"},{"first_name":"David","contributor_type":"project_member","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","orcid":"0000-0002-4014-8478"},{"last_name":"Pickup","orcid":"0000-0001-6118-0541","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","contributor_type":"project_leader","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","year":"2021","file":[{"date_created":"2021-02-24T17:45:13Z","file_name":"Data_Code.zip","date_updated":"2021-02-24T17:45:13Z","file_size":5934452,"creator":"larathoo","file_id":"9193","checksum":"f85537815809a8a4b7da9d01163f88c0","success":1,"content_type":"application/x-zip-compressed","access_level":"open_access","relation":"main_file"}],"day":"26"},{"article_processing_charge":"No","author":[{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"title":"Data from Hyulmans et al 2021, \"Transitions to asexuality and evolution of gene expression in Artemia brine shrimp\"","department":[{"_id":"BeVi"}],"file_date_updated":"2021-08-21T13:43:59Z","citation":{"apa":"Vicoso, B. (2021). Data from Hyulmans et al 2021, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9949","ama":"Vicoso B. Data from Hyulmans et al 2021, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.” 2021. doi:10.15479/AT:ISTA:9949","short":"B. Vicoso, (2021).","ieee":"B. Vicoso, “Data from Hyulmans et al 2021, ‘Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2021.","mla":"Vicoso, Beatriz. Data from Hyulmans et Al 2021, “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9949.","ista":"Vicoso B. 2021. Data from Hyulmans et al 2021, ‘Transitions to asexuality and evolution of gene expression in Artemia brine shrimp’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9949.","chicago":"Vicoso, Beatriz. “Data from Hyulmans et Al 2021, ‘Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9949."},"date_updated":"2024-02-21T12:40:30Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data","status":"public","_id":"9949","date_created":"2021-08-21T13:44:22Z","doi":"10.15479/AT:ISTA:9949","related_material":{"record":[{"relation":"used_in_publication","id":"10166","status":"public"}]},"date_published":"2021-08-24T00:00:00Z","year":"2021","has_accepted_license":"1","file":[{"content_type":"application/zip","relation":"main_file","access_level":"open_access","success":1,"checksum":"90461837eed66beac6fa302993cf0ca9","file_id":"9950","file_size":139188306,"date_updated":"2021-08-21T13:43:59Z","creator":"bvicoso","file_name":"Data.zip","date_created":"2021-08-21T13:43:59Z"}],"day":"24","oa":1,"publisher":"Institute of Science and Technology Austria","month":"08","oa_version":"None"},{"date_created":"2023-05-23T16:48:27Z","date_published":"2020-09-22T00:00:00Z","related_material":{"record":[{"id":"8708","status":"public","relation":"used_in_publication"}]},"doi":"10.5061/DRYAD.R4XGXD29N","year":"2020","day":"22","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.r4xgxd29n"}],"publisher":"Dryad","month":"09","abstract":[{"lang":"eng","text":"The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study \"replicated\" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact."}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"full_name":"Simon, Alexis","last_name":"Simon","first_name":"Alexis"},{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse"},{"first_name":"Tahani","full_name":"El Ayari, Tahani","last_name":"El Ayari"},{"full_name":"Liautard-Haag, Cathy","last_name":"Liautard-Haag","first_name":"Cathy"},{"full_name":"Strelkov, Petr","last_name":"Strelkov","first_name":"Petr"},{"first_name":"John","full_name":"Welch, John","last_name":"Welch"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"}],"title":"How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels","department":[{"_id":"NiBa"}],"citation":{"ieee":"A. Simon et al., “How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels.” Dryad, 2020.","short":"A. Simon, C. Fraisse, T. El Ayari, C. Liautard-Haag, P. Strelkov, J. Welch, N. Bierne, (2020).","apa":"Simon, A., Fraisse, C., El Ayari, T., Liautard-Haag, C., Strelkov, P., Welch, J., & Bierne, N. (2020). How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. Dryad. https://doi.org/10.5061/DRYAD.R4XGXD29N","ama":"Simon A, Fraisse C, El Ayari T, et al. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. 2020. doi:10.5061/DRYAD.R4XGXD29N","mla":"Simon, Alexis, et al. How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels. Dryad, 2020, doi:10.5061/DRYAD.R4XGXD29N.","ista":"Simon A, Fraisse C, El Ayari T, Liautard-Haag C, Strelkov P, Welch J, Bierne N. 2020. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels, Dryad, 10.5061/DRYAD.R4XGXD29N.","chicago":"Simon, Alexis, Christelle Fraisse, Tahani El Ayari, Cathy Liautard-Haag, Petr Strelkov, John Welch, and Nicolas Bierne. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Dryad, 2020. https://doi.org/10.5061/DRYAD.R4XGXD29N."},"date_updated":"2023-08-04T11:04:11Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"tmp":{"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)","short":"CC0 (1.0)"},"type":"research_data_reference","status":"public","_id":"13073"},{"abstract":[{"text":"Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale, and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene-flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.q2bvq83hd"}],"oa":1,"publisher":"Dryad","month":"10","year":"2020","day":"19","date_created":"2023-05-23T16:30:20Z","doi":"10.5061/DRYAD.Q2BVQ83HD","date_published":"2020-10-19T00:00:00Z","related_material":{"record":[{"id":"8928","status":"public","relation":"used_in_publication"}],"link":[{"url":"https://github.com/starnoux/arnoux_et_al_2019","relation":"software"}]},"_id":"13065","tmp":{"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)","short":"CC0 (1.0)"},"type":"research_data_reference","status":"public","date_updated":"2023-08-04T11:19:26Z","citation":{"chicago":"Arnoux, Stephanie, Christelle Fraisse, and Christopher Sauvage. “VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Dryad, 2020. https://doi.org/10.5061/DRYAD.Q2BVQ83HD.","ista":"Arnoux S, Fraisse C, Sauvage C. 2020. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species, Dryad, 10.5061/DRYAD.Q2BVQ83HD.","mla":"Arnoux, Stephanie, et al. VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species. Dryad, 2020, doi:10.5061/DRYAD.Q2BVQ83HD.","ama":"Arnoux S, Fraisse C, Sauvage C. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. 2020. doi:10.5061/DRYAD.Q2BVQ83HD","apa":"Arnoux, S., Fraisse, C., & Sauvage, C. (2020). VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. Dryad. https://doi.org/10.5061/DRYAD.Q2BVQ83HD","ieee":"S. Arnoux, C. Fraisse, and C. Sauvage, “VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species.” Dryad, 2020.","short":"S. Arnoux, C. Fraisse, C. Sauvage, (2020)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"article_processing_charge":"No","author":[{"full_name":"Arnoux, Stephanie","last_name":"Arnoux","first_name":"Stephanie"},{"last_name":"Fraisse","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christopher","full_name":"Sauvage, Christopher","last_name":"Sauvage"}],"title":"VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species","department":[{"_id":"NiBa"}]},{"year":"2020","day":"08","date_created":"2021-08-11T13:16:03Z","date_published":"2020-01-08T00:00:00Z","doi":"10.1021/acs.nanolett.9b04445.s002","related_material":{"record":[{"id":"7166","status":"public","relation":"used_in_publication"}]},"abstract":[{"lang":"eng","text":"Data obtained from the fine-grained simulations used in Figures 2-5, data obtained from the coarse-grained numerical calculations used in Figure 6, and a sample script for the fine-grained simulation as a Jupyter notebook (ZIP)"}],"oa_version":"Published Version","publisher":"American Chemical Society ","month":"01","citation":{"chicago":"Ucar, Mehmet C, and Reinhard Lipowsky. “MURL_Dataz.” American Chemical Society , 2020. https://doi.org/10.1021/acs.nanolett.9b04445.s002.","ista":"Ucar MC, Lipowsky R. 2020. MURL_Dataz, American Chemical Society , 10.1021/acs.nanolett.9b04445.s002.","mla":"Ucar, Mehmet C., and Reinhard Lipowsky. MURL_Dataz. American Chemical Society , 2020, doi:10.1021/acs.nanolett.9b04445.s002.","ama":"Ucar MC, Lipowsky R. MURL_Dataz. 2020. doi:10.1021/acs.nanolett.9b04445.s002","apa":"Ucar, M. C., & Lipowsky, R. (2020). MURL_Dataz. American Chemical Society . https://doi.org/10.1021/acs.nanolett.9b04445.s002","short":"M.C. Ucar, R. Lipowsky, (2020).","ieee":"M. C. Ucar and R. Lipowsky, “MURL_Dataz.” American Chemical Society , 2020."},"date_updated":"2023-08-17T14:07:52Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"last_name":"Ucar","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425"},{"first_name":"Reinhard","full_name":"Lipowsky, Reinhard","last_name":"Lipowsky"}],"department":[{"_id":"EdHa"}],"title":"MURL_Dataz","_id":"9885","type":"research_data_reference","status":"public"},{"publisher":"Public Library of Science","month":"02","oa_version":"Published Version","doi":"10.1371/journal.pcbi.1007642.s003","related_material":{"record":[{"relation":"research_data","id":"7569","status":"public"}]},"date_published":"2020-02-25T00:00:00Z","date_created":"2021-08-06T07:24:37Z","year":"2020","day":"25","type":"research_data_reference","status":"public","_id":"9779","author":[{"orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","last_name":"Grah","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok"},{"first_name":"Tamar","full_name":"Friedlander, Tamar","last_name":"Friedlander"}],"article_processing_charge":"No","department":[{"_id":"GaTk"}],"title":"Distribution of crosstalk values","citation":{"ista":"Grah R, Friedlander T. 2020. Distribution of crosstalk values, Public Library of Science, 10.1371/journal.pcbi.1007642.s003.","chicago":"Grah, Rok, and Tamar Friedlander. “Distribution of Crosstalk Values.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s003.","ama":"Grah R, Friedlander T. Distribution of crosstalk values. 2020. doi:10.1371/journal.pcbi.1007642.s003","apa":"Grah, R., & Friedlander, T. (2020). Distribution of crosstalk values. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s003","ieee":"R. Grah and T. Friedlander, “Distribution of crosstalk values.” Public Library of Science, 2020.","short":"R. Grah, T. Friedlander, (2020).","mla":"Grah, Rok, and Tamar Friedlander. Distribution of Crosstalk Values. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s003."},"date_updated":"2023-08-18T06:47:47Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"title":"Supporting information","department":[{"_id":"GaTk"}],"author":[{"last_name":"Grah","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok"},{"first_name":"Tamar","last_name":"Friedlander","full_name":"Friedlander, Tamar"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-18T06:47:47Z","citation":{"mla":"Grah, Rok, and Tamar Friedlander. Supporting Information. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s001.","ama":"Grah R, Friedlander T. Supporting information. 2020. doi:10.1371/journal.pcbi.1007642.s001","apa":"Grah, R., & Friedlander, T. (2020). Supporting information. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s001","ieee":"R. Grah and T. Friedlander, “Supporting information.” Public Library of Science, 2020.","short":"R. Grah, T. Friedlander, (2020).","chicago":"Grah, Rok, and Tamar Friedlander. “Supporting Information.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s001.","ista":"Grah R, Friedlander T. 2020. Supporting information, Public Library of Science, 10.1371/journal.pcbi.1007642.s001."},"status":"public","type":"research_data_reference","_id":"9776","doi":"10.1371/journal.pcbi.1007642.s001","related_material":{"record":[{"relation":"used_in_publication","id":"7569","status":"public"}]},"date_published":"2020-02-25T00:00:00Z","date_created":"2021-08-06T07:15:04Z","day":"25","year":"2020","month":"02","publisher":"Public Library of Science","oa_version":"Published Version"},{"citation":{"ista":"Hartstein M, Hsu Y-T, Modic KA, Porras J, Loew T, Le Tacon M, Zuo H, Wang J, Zhu Z, Chan M, McDonald R, Lonzarich G, Keimer B, Sebastian S, Harrison N. 2020. Accompanying dataset for ‘Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors’, Apollo - University of Cambridge, 10.17863/cam.50169.","chicago":"Hartstein, Mate, Yu-Te Hsu, Kimberly A Modic, Juan Porras, Toshinao Loew, Matthieu Le Tacon, Huakun Zuo, et al. “Accompanying Dataset for ‘Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.’” Apollo - University of Cambridge, 2020. https://doi.org/10.17863/cam.50169.","apa":"Hartstein, M., Hsu, Y.-T., Modic, K. A., Porras, J., Loew, T., Le Tacon, M., … Harrison, N. (2020). Accompanying dataset for “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.” Apollo - University of Cambridge. https://doi.org/10.17863/cam.50169","ama":"Hartstein M, Hsu Y-T, Modic KA, et al. Accompanying dataset for “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.” 2020. doi:10.17863/cam.50169","ieee":"M. Hartstein et al., “Accompanying dataset for ‘Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.’” Apollo - University of Cambridge, 2020.","short":"M. Hartstein, Y.-T. Hsu, K.A. Modic, J. Porras, T. Loew, M. Le Tacon, H. Zuo, J. Wang, Z. Zhu, M. Chan, R. McDonald, G. Lonzarich, B. Keimer, S. Sebastian, N. Harrison, (2020).","mla":"Hartstein, Mate, et al. Accompanying Dataset for “Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.” Apollo - University of Cambridge, 2020, doi:10.17863/cam.50169."},"date_updated":"2023-08-21T07:06:48Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"first_name":"Mate","full_name":"Hartstein, Mate","last_name":"Hartstein"},{"last_name":"Hsu","full_name":"Hsu, Yu-Te","first_name":"Yu-Te"},{"orcid":"0000-0001-9760-3147","full_name":"Modic, Kimberly A","last_name":"Modic","first_name":"Kimberly A","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425"},{"first_name":"Juan","full_name":"Porras, Juan","last_name":"Porras"},{"last_name":"Loew","full_name":"Loew, Toshinao","first_name":"Toshinao"},{"first_name":"Matthieu","last_name":"Le Tacon","full_name":"Le Tacon, Matthieu"},{"first_name":"Huakun","last_name":"Zuo","full_name":"Zuo, Huakun"},{"first_name":"Jinhua","full_name":"Wang, Jinhua","last_name":"Wang"},{"first_name":"Zengwei","full_name":"Zhu, Zengwei","last_name":"Zhu"},{"first_name":"Mun","last_name":"Chan","full_name":"Chan, Mun"},{"first_name":"Ross","last_name":"McDonald","full_name":"McDonald, Ross"},{"last_name":"Lonzarich","full_name":"Lonzarich, Gilbert","first_name":"Gilbert"},{"full_name":"Keimer, Bernhard","last_name":"Keimer","first_name":"Bernhard"},{"full_name":"Sebastian, Suchitra","last_name":"Sebastian","first_name":"Suchitra"},{"first_name":"Neil","full_name":"Harrison, Neil","last_name":"Harrison"}],"title":"Accompanying dataset for 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors'","department":[{"_id":"KiMo"}],"_id":"9708","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","status":"public","year":"2020","has_accepted_license":"1","day":"29","date_created":"2021-07-23T10:00:35Z","doi":"10.17863/cam.50169","date_published":"2020-05-29T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7942"}]},"abstract":[{"text":"This research data supports 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors'. A Readme file for plotting each figure is provided.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.17863/CAM.50169"}],"oa":1,"publisher":"Apollo - University of Cambridge","month":"05"},{"status":"public","type":"research_data_reference","tmp":{"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)","short":"CC0 (1.0)"},"_id":"8809","department":[{"_id":"NiBa"}],"title":"Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina","author":[{"last_name":"Perini","full_name":"Perini, Samuel","first_name":"Samuel"},{"first_name":"Marina","last_name":"Rafajlovic","full_name":"Rafajlovic, Marina"},{"last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"first_name":"Roger","full_name":"Butlin, Roger","last_name":"Butlin"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-22T07:13:37Z","citation":{"short":"S. Perini, M. Rafajlovic, A.M. Westram, K. Johannesson, R. Butlin, (2020).","ieee":"S. Perini, M. Rafajlovic, A. M. Westram, K. Johannesson, and R. Butlin, “Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina.” Dryad, 2020.","apa":"Perini, S., Rafajlovic, M., Westram, A. M., Johannesson, K., & Butlin, R. (2020). Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. Dryad. https://doi.org/10.5061/dryad.qrfj6q5cn","ama":"Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. 2020. doi:10.5061/dryad.qrfj6q5cn","mla":"Perini, Samuel, et al. Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina. Dryad, 2020, doi:10.5061/dryad.qrfj6q5cn.","ista":"Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. 2020. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina, Dryad, 10.5061/dryad.qrfj6q5cn.","chicago":"Perini, Samuel, Marina Rafajlovic, Anja M Westram, Kerstin Johannesson, and Roger Butlin. “Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina.” Dryad, 2020. https://doi.org/10.5061/dryad.qrfj6q5cn."},"month":"07","publisher":"Dryad","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.qrfj6q5cn"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple-effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size-assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively-sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment."}],"date_published":"2020-07-01T00:00:00Z","related_material":{"record":[{"status":"public","id":"7995","relation":"used_in_publication"}]},"doi":"10.5061/dryad.qrfj6q5cn","date_created":"2020-11-25T11:07:25Z","day":"01","has_accepted_license":"1","year":"2020"},{"_id":"9326","status":"public","type":"research_data_reference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"C. Gupta, U. Khaniya, C. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020).","ieee":"C. Gupta et al., “Charge transfer and chemo-mechanical coupling in respiratory complex I.” American Chemical Society, 2020.","ama":"Gupta C, Khaniya U, Chan C, et al. Charge transfer and chemo-mechanical coupling in respiratory complex I. 2020. doi:10.1021/jacs.9b13450.s002","apa":"Gupta, C., Khaniya, U., Chan, C., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Charge transfer and chemo-mechanical coupling in respiratory complex I. American Chemical Society. https://doi.org/10.1021/jacs.9b13450.s002","mla":"Gupta, Chitrak, et al. Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I. American Chemical Society, 2020, doi:10.1021/jacs.9b13450.s002.","ista":"Gupta C, Khaniya U, Chan C, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Charge transfer and chemo-mechanical coupling in respiratory complex I, American Chemical Society, 10.1021/jacs.9b13450.s002.","chicago":"Gupta, Chitrak, Umesh Khaniya, Chun Chan, Francois Dehez, Mrinal Shekhar, M. R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I.” American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450.s002."},"date_updated":"2023-08-22T07:49:37Z","department":[{"_id":"LeSa"}],"title":"Charge transfer and chemo-mechanical coupling in respiratory complex I","author":[{"first_name":"Chitrak","last_name":"Gupta","full_name":"Gupta, Chitrak"},{"last_name":"Khaniya","full_name":"Khaniya, Umesh","first_name":"Umesh"},{"last_name":"Chan","full_name":"Chan, Chun","first_name":"Chun"},{"first_name":"Francois","last_name":"Dehez","full_name":"Dehez, Francois"},{"first_name":"Mrinal","last_name":"Shekhar","full_name":"Shekhar, Mrinal"},{"first_name":"M. R.","last_name":"Gunner","full_name":"Gunner, M. R."},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","last_name":"Sazanov","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989"},{"first_name":"Christophe","last_name":"Chipot","full_name":"Chipot, Christophe"},{"last_name":"Singharoy","full_name":"Singharoy, Abhishek","first_name":"Abhishek"}],"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The mitochondrial respiratory chain, formed by five protein complexes, utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains, however, fragmentary due to bottlenecks in understanding redox-driven conformational transitions and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons from NADH. Here, employing the latest crystal structure of T. thermophilus complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron–sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which allosterically couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol forma design essential for menaquinol release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup of the former furnishes stronger binding interactions with the pocket, favoring menaquinone for charge transport in T. thermophilus. Our computations are consistent with experimentally validated mutations and hierarchize the key residues into three functional classes, identifying new mutation targets. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the transmembrane subunits are found to be responsible for proton pumping. Put together, the simulations reveal the molecular design principles linking redox reactions to quinone turnover to proton translocation in complex I."}],"month":"05","publisher":"American Chemical Society","oa":1,"main_file_link":[{"open_access":"1"}],"day":"20","year":"2020","doi":"10.1021/jacs.9b13450.s002","date_published":"2020-05-20T00:00:00Z","related_material":{"record":[{"id":"8040","status":"public","relation":"used_in_publication"}]},"date_created":"2021-04-14T12:05:20Z"},{"publisher":"American Chemical Society ","month":"05","abstract":[{"text":"Additional analyses of the trajectories","lang":"eng"}],"oa_version":"Published Version","date_created":"2021-07-23T12:02:39Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8040"}]},"doi":"10.1021/jacs.9b13450.s001","date_published":"2020-05-20T00:00:00Z","year":"2020","day":"20","type":"research_data_reference","status":"public","_id":"9713","article_processing_charge":"No","author":[{"first_name":"Chitrak","last_name":"Gupta","full_name":"Gupta, Chitrak"},{"last_name":"Khaniya","full_name":"Khaniya, Umesh","first_name":"Umesh"},{"first_name":"Chun Kit","last_name":"Chan","full_name":"Chan, Chun Kit"},{"first_name":"Francois","last_name":"Dehez","full_name":"Dehez, Francois"},{"full_name":"Shekhar, Mrinal","last_name":"Shekhar","first_name":"Mrinal"},{"first_name":"M.R.","last_name":"Gunner","full_name":"Gunner, M.R."},{"first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A"},{"first_name":"Christophe","last_name":"Chipot","full_name":"Chipot, Christophe"},{"last_name":"Singharoy","full_name":"Singharoy, Abhishek","first_name":"Abhishek"}],"department":[{"_id":"LeSa"}],"title":"Supporting information","date_updated":"2023-08-22T07:49:38Z","citation":{"mla":"Gupta, Chitrak, et al. Supporting Information. American Chemical Society , 2020, doi:10.1021/jacs.9b13450.s001.","ama":"Gupta C, Khaniya U, Chan CK, et al. Supporting information. 2020. doi:10.1021/jacs.9b13450.s001","apa":"Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Supporting information. American Chemical Society . https://doi.org/10.1021/jacs.9b13450.s001","short":"C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020).","ieee":"C. Gupta et al., “Supporting information.” American Chemical Society , 2020.","chicago":"Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar, M.R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Supporting Information.” American Chemical Society , 2020. https://doi.org/10.1021/jacs.9b13450.s001.","ista":"Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Supporting information, American Chemical Society , 10.1021/jacs.9b13450.s001."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"type":"research_data_reference","status":"public","_id":"9878","article_processing_charge":"No","author":[{"first_name":"Chitrak","last_name":"Gupta","full_name":"Gupta, Chitrak"},{"first_name":"Umesh","last_name":"Khaniya","full_name":"Khaniya, Umesh"},{"last_name":"Chan","full_name":"Chan, Chun Kit","first_name":"Chun Kit"},{"full_name":"Dehez, Francois","last_name":"Dehez","first_name":"Francois"},{"last_name":"Shekhar","full_name":"Shekhar, Mrinal","first_name":"Mrinal"},{"full_name":"Gunner, M.R.","last_name":"Gunner","first_name":"M.R."},{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chipot, Christophe","last_name":"Chipot","first_name":"Christophe"},{"first_name":"Abhishek","full_name":"Singharoy, Abhishek","last_name":"Singharoy"}],"department":[{"_id":"LeSa"}],"title":"Movies","date_updated":"2023-08-22T07:49:38Z","citation":{"ama":"Gupta C, Khaniya U, Chan CK, et al. Movies. 2020. doi:10.1021/jacs.9b13450.s002","apa":"Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Movies. American Chemical Society. https://doi.org/10.1021/jacs.9b13450.s002","short":"C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020).","ieee":"C. Gupta et al., “Movies.” American Chemical Society, 2020.","mla":"Gupta, Chitrak, et al. Movies. American Chemical Society, 2020, doi:10.1021/jacs.9b13450.s002.","ista":"Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Movies, American Chemical Society, 10.1021/jacs.9b13450.s002.","chicago":"Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar, M.R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Movies.” American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450.s002."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"American Chemical Society","month":"05","oa_version":"Published Version","date_created":"2021-08-11T09:18:54Z","date_published":"2020-05-20T00:00:00Z","doi":"10.1021/jacs.9b13450.s002","related_material":{"record":[{"id":"8040","status":"public","relation":"used_in_publication"}]},"year":"2020","day":"20"},{"has_accepted_license":"1","year":"2020","day":"09","date_published":"2020-07-09T00:00:00Z","related_material":{"record":[{"status":"public","id":"8133","relation":"used_in_publication"}]},"doi":"10.6084/m9.figshare.12629697.v1","date_created":"2021-07-23T08:59:15Z","abstract":[{"lang":"eng","text":"Additional file 2: Supplementary Tables. The association of pre-adjusted protein levels with biological and technical covariates. Protein levels were adjusted for age, sex, array plate and four genetic principal components (population structure) prior to analyses. Significant associations are emboldened. (Table S1). pQTLs associated with inflammatory biomarker levels from Bayesian penalised regression model (Posterior Inclusion Probability > 95%). (Table S2). All pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S3). Summary of lambda values relating to ordinary least squares GWAS and EWAS performed on inflammatory protein levels (n = 70) in Lothian Birth Cohort 1936 study. (Table S4). Conditionally significant pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S5). Comparison of variance explained by ordinary least squares and Bayesian penalised regression models for concordantly identified SNPs. (Table S6). Estimate of heritability for blood protein levels as well as proportion of variance explained attributable to different prior mixtures. (Table S7). Comparison of heritability estimates from Ahsan et al. (maximum likelihood) and Hillary et al. (Bayesian penalised regression). (Table S8). List of concordant SNPs identified by linear model and Bayesian penalised regression and whether they have been previously identified as eQTLs. (Table S9). Bayesian tests of colocalisation for cis pQTLs and cis eQTLs. (Table S10). Sherlock algorithm: Genes whose expression are putatively associated with circulating inflammatory proteins that harbour pQTLs. (Table S11). CpGs associated with inflammatory protein biomarkers as identified by Bayesian model (Bayesian model; Posterior Inclusion Probability > 95%). (Table S12). CpGs associated with inflammatory protein biomarkers as identified by linear model (limma) at P < 5.14 × 10− 10. (Table S13). CpGs associated with inflammatory protein biomarkers as identified by mixed linear model (OSCA) at P < 5.14 × 10− 10. (Table S14). Estimate of variance explained for blood protein levels by DNA methylation as well as proportion of explained attributable to different prior mixtures - BayesR+. (Table S15). Comparison of variance in protein levels explained by genome-wide DNA methylation data by mixed linear model (OSCA) and Bayesian penalised regression model (BayesR+). (Table S16). Variance in circulating inflammatory protein biomarker levels explained by common genetic and methylation data (joint and conditional estimates from BayesR+). Ordered by combined variance explained by genetic and epigenetic data - smallest to largest. Significant results from t-tests comparing distributions for variance explained by methylation or genetics alone versus combined estimate are emboldened. (Table S17). Genetic and epigenetic factors identified by BayesR+ when conditioning on all SNPs and CpGs together. (Table S18). Mendelian Randomisation analyses to assess whether proteins with concordantly identified genetic signals are causally associated with Alzheimer’s disease risk. (Table S19)."}],"oa_version":"Published Version","publisher":"Springer Nature","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.12629697.v1"}],"oa":1,"month":"07","other_data_license":"CC0 + CC BY (4.0)","citation":{"chicago":"Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel L. McCartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Additional File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” Springer Nature, 2020. https://doi.org/10.6084/m9.figshare.12629697.v1.","ista":"Hillary RF, Trejo-Banos D, Kousathanas A, McCartney DL, Harris SE, Stevenson AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob EM, Wray NR, McRae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults, Springer Nature, 10.6084/m9.figshare.12629697.v1.","mla":"Hillary, Robert F., et al. Additional File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults. Springer Nature, 2020, doi:10.6084/m9.figshare.12629697.v1.","ieee":"R. F. Hillary et al., “Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults.” Springer Nature, 2020.","short":"R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. McCartney, S.E. Harris, A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie, K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. McRae, P.M. Visscher, I.J. Deary, M.R. Robinson, R.E. Marioni, (2020).","apa":"Hillary, R. F., Trejo-Banos, D., Kousathanas, A., McCartney, D. L., Harris, S. E., Stevenson, A. J., … Marioni, R. E. (2020). Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Springer Nature. https://doi.org/10.6084/m9.figshare.12629697.v1","ama":"Hillary RF, Trejo-Banos D, Kousathanas A, et al. Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. 2020. doi:10.6084/m9.figshare.12629697.v1"},"date_updated":"2023-08-22T07:55:36Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Robert F.","last_name":"Hillary","full_name":"Hillary, Robert F."},{"first_name":"Daniel","full_name":"Trejo-Banos, Daniel","last_name":"Trejo-Banos"},{"first_name":"Athanasios","last_name":"Kousathanas","full_name":"Kousathanas, Athanasios"},{"last_name":"McCartney","full_name":"McCartney, Daniel L.","first_name":"Daniel L."},{"first_name":"Sarah E.","full_name":"Harris, Sarah E.","last_name":"Harris"},{"last_name":"Stevenson","full_name":"Stevenson, Anna J.","first_name":"Anna J."},{"first_name":"Marion","full_name":"Patxot, Marion","last_name":"Patxot"},{"last_name":"Ojavee","full_name":"Ojavee, Sven Erik","first_name":"Sven Erik"},{"first_name":"Qian","last_name":"Zhang","full_name":"Zhang, Qian"},{"last_name":"Liewald","full_name":"Liewald, David C.","first_name":"David C."},{"full_name":"Ritchie, Craig W.","last_name":"Ritchie","first_name":"Craig W."},{"first_name":"Kathryn L.","last_name":"Evans","full_name":"Evans, Kathryn L."},{"full_name":"Tucker-Drob, Elliot M.","last_name":"Tucker-Drob","first_name":"Elliot M."},{"last_name":"Wray","full_name":"Wray, Naomi R.","first_name":"Naomi R."},{"full_name":"McRae, Allan F. ","last_name":"McRae","first_name":"Allan F. "},{"first_name":"Peter M.","last_name":"Visscher","full_name":"Visscher, Peter M."},{"full_name":"Deary, Ian J.","last_name":"Deary","first_name":"Ian J."},{"last_name":"Robinson","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"full_name":"Marioni, Riccardo E. ","last_name":"Marioni","first_name":"Riccardo E. "}],"article_processing_charge":"No","title":"Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults","department":[{"_id":"MaRo"}],"_id":"9706","type":"research_data_reference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"citation":{"ista":"Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface, Zenodo, 10.5281/ZENODO.3961561.","chicago":"Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.3961561.","apa":"Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Zenodo. https://doi.org/10.5281/ZENODO.3961561","ama":"Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. 2020. doi:10.5281/ZENODO.3961561","ieee":"G. M. Arnold et al., “Converting microwave and telecom photons with a silicon photonic nanomechanical interface.” Zenodo, 2020.","short":"G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, (2020).","mla":"Arnold, Georg M., et al. Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface. Zenodo, 2020, doi:10.5281/ZENODO.3961561."},"date_updated":"2023-08-22T09:27:11Z","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"3770C838-F248-11E8-B48F-1D18A9856A87","first_name":"Georg M","last_name":"Arnold","full_name":"Arnold, Georg M","orcid":"0000-0003-1397-7876"},{"full_name":"Wulf, Matthias","orcid":"0000-0001-6613-1378","last_name":"Wulf","id":"45598606-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir"},{"last_name":"Redchenko","full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena"},{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","first_name":"Alfredo R","last_name":"Rueda Sanchez","full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860"},{"last_name":"Hease","orcid":"0000-0001-9868-2166","full_name":"Hease, William J","first_name":"William J","id":"29705398-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hassani","full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","first_name":"Farid"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"}],"article_processing_charge":"No","title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface","department":[{"_id":"JoFi"}],"_id":"13056","type":"research_data_reference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","year":"2020","day":"27","doi":"10.5281/ZENODO.3961561","date_published":"2020-07-27T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"8529","status":"public"}]},"date_created":"2023-05-23T13:37:41Z","abstract":[{"text":"This datasets comprises all data shown in plots of the submitted article \"Converting microwave and telecom photons with a silicon photonic nanomechanical interface\". 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Surpassing the resistance quantum with a geometric superinductor. Zenodo. https://doi.org/10.5281/ZENODO.4052882","chicago":"Peruzzo, Matilda, Andrea Trioni, Farid Hassani, Martin Zemlicka, and Johannes M Fink. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.4052882.","ista":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. 2020. 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Additional raw data are available from the corresponding author on reasonable request."}],"oa_version":"Published Version","date_created":"2023-05-23T16:44:11Z","related_material":{"record":[{"id":"9114","status":"public","relation":"used_in_publication"}]},"date_published":"2020-11-10T00:00:00Z","doi":"10.5281/ZENODO.4266025","year":"2020","day":"10","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","status":"public","_id":"13071","article_processing_charge":"No","author":[{"last_name":"Hease","orcid":"0000-0001-9868-2166","full_name":"Hease, William J","first_name":"William J","id":"29705398-F248-11E8-B48F-1D18A9856A87"},{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","first_name":"Alfredo R","last_name":"Rueda Sanchez","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R"},{"full_name":"Sahu, Rishabh","orcid":"0000-0001-6264-2162","last_name":"Sahu","first_name":"Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87","full_name":"Wulf, Matthias","orcid":"0000-0001-6613-1378","last_name":"Wulf"},{"last_name":"Arnold","orcid":"0000-0003-1397-7876","full_name":"Arnold, Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","first_name":"Georg M"},{"first_name":"Harald","full_name":"Schwefel, Harald","last_name":"Schwefel"},{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"}],"title":"Bidirectional electro-optic wavelength conversion in the quantum ground state","department":[{"_id":"JoFi"}],"citation":{"chicago":"Hease, William J, Alfredo R Rueda Sanchez, Rishabh Sahu, Matthias Wulf, Georg M Arnold, Harald Schwefel, and Johannes M Fink. “Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.4266025.","ista":"Hease WJ, Rueda Sanchez AR, Sahu R, Wulf M, Arnold GM, Schwefel H, Fink JM. 2020. 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Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations."}],"month":"10","publisher":"Royal Society of London","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.7957469.v1"}],"oa":1,"day":"15","year":"2020","doi":"10.6084/m9.figshare.7957469.v1","related_material":{"record":[{"status":"public","id":"6467","relation":"used_in_publication"}]},"date_published":"2020-10-15T00:00:00Z","date_created":"2021-08-06T11:26:57Z","_id":"9799","status":"public","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-25T10:34:41Z","citation":{"mla":"Fraisse, Christelle, and John J. Welch. Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes. 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We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations."}],"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.7957472.v1","open_access":"1"}],"oa":1,"publisher":"Royal Society of London","month":"10","year":"2020","day":"15","date_created":"2021-08-06T11:18:15Z","doi":"10.6084/m9.figshare.7957472.v1","date_published":"2020-10-15T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"6467","status":"public"}]},"_id":"9798","type":"research_data_reference","status":"public","citation":{"short":"C. Fraisse, J.J. Welch, (2020).","ieee":"C. Fraisse and J. J. Welch, “Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes.” Royal Society of London, 2020.","ama":"Fraisse C, Welch JJ. 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Whilst multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defenses of ants – their social immunity – influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different-species coinfections. Here, it decreased overall pathogen sporulation success, whilst simultaneously increasing co-sporulation on individual cadavers and maintaining a higher pathogen diversity at the community-level. Mathematical modeling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast-germinating, thus less grooming-sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host- and population-level."}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"full_name":"Milutinovic, Barbara","orcid":"0000-0002-8214-4758","last_name":"Milutinovic","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara"},{"last_name":"Stock","full_name":"Stock, Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam"},{"last_name":"Grasse","full_name":"Grasse, Anna V","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Elisabeth","id":"31757262-F248-11E8-B48F-1D18A9856A87","last_name":"Naderlinger","full_name":"Naderlinger, Elisabeth"},{"orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","last_name":"Hilbe","first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"}],"department":[{"_id":"SyCr"},{"_id":"KrCh"}],"title":"Social immunity modulates competition between coinfecting pathogens","citation":{"apa":"Milutinovic, B., Stock, M., Grasse, A. 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Social immunity modulates competition between coinfecting pathogens, Dryad, 10.5061/DRYAD.CRJDFN318.","chicago":"Milutinovic, Barbara, Miriam Stock, Anna V Grasse, Elisabeth Naderlinger, Christian Hilbe, and Sylvia Cremer. “Social Immunity Modulates Competition between Coinfecting Pathogens.” Dryad, 2020. https://doi.org/10.5061/DRYAD.CRJDFN318."},"date_updated":"2023-09-05T16:04:48Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"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)","short":"CC0 (1.0)"},"type":"research_data_reference","status":"public","_id":"13060"},{"oa_version":"Published Version","abstract":[{"text":"PADREV : 4,4'-dimethoxy[1,1'-biphenyl]-2,2',5,5'-tetrol\r\nSpace Group: C 2 (5), Cell: a 24.488(16)Å b 5.981(4)Å c 3.911(3)Å, α 90° β 91.47(3)° γ 90°","lang":"eng"}],"month":"03","publisher":"CCDC","oa":1,"main_file_link":[{"url":"https://dx.doi.org/10.5517/ccdc.csd.cc24vsrk","open_access":"1"}],"day":"22","year":"2020","date_published":"2020-03-22T00:00:00Z","doi":"10.5517/ccdc.csd.cc24vsrk","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8329"}]},"date_created":"2021-08-06T07:41:07Z","_id":"9780","status":"public","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-05T16:03:47Z","citation":{"ama":"Schlemmer W, Nothdurft P, Petzold A, et al. 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Aggarwal, et. al. \r\nThe measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html).\r\n"}],"oa_version":"Published Version"},{"abstract":[{"text":"Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by \"translation bottlenecks\": points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of \"continuous epistasis\" in bacterial physiology.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"07","has_accepted_license":"1","year":"2020","file":[{"content_type":"application/zip","relation":"main_file","access_level":"open_access","checksum":"5c321dbbb6d4b3c85da786fd3ebbdc98","file_id":"8098","file_size":255770756,"date_updated":"2020-07-14T12:48:09Z","creator":"bkavcic","file_name":"natComm_2020_scripts.zip","date_created":"2020-07-06T20:38:27Z"}],"day":"15","doi":"10.15479/AT:ISTA:8097","date_published":"2020-07-15T00:00:00Z","contributor":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","contributor_type":"research_group","first_name":"Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik"},{"last_name":"Bollenbach","first_name":"Tobias","contributor_type":"research_group","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2020-07-06T20:40:19Z","_id":"8097","type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"date_updated":"2024-02-21T12:40:51Z","citation":{"chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8097.","ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8097.","mla":"Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8097.","ama":"Kavcic B. Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.” 2020. doi:10.15479/AT:ISTA:8097","apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8097","ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics.’” Institute of Science and Technology Austria, 2020.","short":"B. Kavcic, (2020)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","first_name":"Bor"}],"article_processing_charge":"No","department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:48:09Z","title":"Analysis scripts and research data for the paper \"Mechanisms of drug interactions between translation-inhibiting antibiotics\""},{"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data","_id":"8254","title":"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)","file_date_updated":"2020-08-18T08:03:23Z","department":[{"_id":"NiBa"}],"article_processing_charge":"No","author":[{"orcid":"0000-0003-1771-714X","full_name":"Arathoon, Louise S","last_name":"Arathoon","first_name":"Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"citation":{"ieee":"L. S. Arathoon, “Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus).” Institute of Science and Technology Austria, 2020.","short":"L.S. Arathoon, (2020).","ama":"Arathoon LS. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). 2020. doi:10.15479/AT:ISTA:8254","apa":"Arathoon, L. S. (2020). Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8254","mla":"Arathoon, Louise S. Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus). Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8254.","ista":"Arathoon LS. 2020. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus), Institute of Science and Technology Austria, 10.15479/AT:ISTA:8254.","chicago":"Arathoon, Louise S. “Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus).” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8254."},"date_updated":"2024-02-21T12:41:09Z","month":"08","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Here are the research data underlying the publication \"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)\". Further information are summed up in the README document.\r\nThe files for this record have been updated and are now found in the linked DOI https://doi.org/10.15479/AT:ISTA:9192."}],"contributor":[{"contributor_type":"data_collector","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S","last_name":"Arathoon"},{"first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Surendranadh"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"contributor_type":"project_member","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","orcid":"0000-0002-4014-8478","last_name":"Field"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup"},{"first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Baskett"}],"date_created":"2020-08-12T12:49:23Z","doi":"10.15479/AT:ISTA:8254","related_material":{"record":[{"relation":"later_version","id":"11321","status":"public"},{"id":"9192","status":"public","relation":"later_version"}]},"date_published":"2020-08-18T00:00:00Z","day":"18","file":[{"creator":"dernst","date_updated":"2020-08-18T08:03:23Z","file_size":5778420,"date_created":"2020-08-18T08:03:23Z","file_name":"Data_Rcode_MathematicaNB.zip","access_level":"open_access","relation":"main_file","content_type":"application/x-zip-compressed","file_id":"8280","checksum":"4f1382ed4384751b6013398c11557bf6","success":1}],"year":"2020","has_accepted_license":"1"},{"_id":"8930","type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"date_updated":"2024-02-21T12:41:42Z","citation":{"mla":"Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Minimal Biophysical Model of Combined Antibiotic Action.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8930.","ama":"Kavcic B. Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” 2020. doi:10.15479/AT:ISTA:8930","apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8930","short":"B. Kavcic, (2020).","ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action.’” Institute of Science and Technology Austria, 2020.","chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Minimal Biophysical Model of Combined Antibiotic Action.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8930.","ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8930."},"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"350F91D2-F248-11E8-B48F-1D18A9856A87","first_name":"Bor","full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X","last_name":"Kavcic"}],"article_processing_charge":"No","file_date_updated":"2020-12-09T15:00:19Z","title":"Analysis scripts and research data for the paper \"Minimal biophysical model of combined antibiotic action\"","department":[{"_id":"GaTk"}],"abstract":[{"text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.","lang":"eng"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"12","has_accepted_license":"1","year":"2020","file":[{"creator":"bkavcic","file_size":315494370,"date_updated":"2020-12-09T15:00:19Z","file_name":"PLoSCompBiol2020_datarep.zip","date_created":"2020-12-09T15:00:19Z","relation":"main_file","access_level":"open_access","content_type":"application/zip","success":1,"file_id":"8932","checksum":"60a818edeffaa7da1ebf5f8fbea9ba18"}],"day":"10","doi":"10.15479/AT:ISTA:8930","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8997"}]},"date_published":"2020-12-10T00:00:00Z","contributor":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","contributor_type":"supervisor","last_name":"Tkačik","orcid":"0000-0002-6699-1455"},{"last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","contributor_type":"supervisor"}],"date_created":"2020-12-09T15:04:02Z"},{"publisher":"Institute of Science and Technology Austria","oa":1,"month":"12","abstract":[{"text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks.","lang":"eng"}],"oa_version":"Published Version","doi":"10.15479/AT:ISTA:8951","date_published":"2020-12-21T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"9283"}]},"contributor":[{"last_name":"Nagy-Staron","first_name":"Anna A","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Kathrin","last_name":"Tomasek"},{"contributor_type":"project_member","first_name":"Caroline","last_name":"Caruso Carter"},{"first_name":"Elisabeth","contributor_type":"project_member","last_name":"Sonnleitner"},{"id":"350F91D2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Bor","last_name":"Kavcic","orcid":"0000-0001-6041-254X"},{"first_name":"Tiago","contributor_type":"project_member","last_name":"Paixão"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","contributor_type":"project_manager","orcid":"0000-0001-6220-2052","last_name":"Guet"}],"date_created":"2020-12-20T10:00:26Z","has_accepted_license":"1","year":"2020","day":"21","file":[{"content_type":"text/plain","relation":"main_file","access_level":"open_access","success":1,"checksum":"f57862aeee1690c7effd2b1117d40ed1","file_id":"8952","file_size":523,"date_updated":"2020-12-20T09:52:52Z","creator":"bkavcic","file_name":"readme.txt","date_created":"2020-12-20T09:52:52Z"},{"checksum":"f2c6d5232ec6d551b6993991e8689e9f","file_id":"8954","success":1,"content_type":"application/octet-stream","access_level":"open_access","relation":"main_file","date_created":"2020-12-20T22:01:44Z","file_name":"GRNs Research depository.gb","date_updated":"2020-12-20T22:01:44Z","file_size":379228,"creator":"bkavcic"}],"type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Gene regulatory networks","Gene expression","Escherichia coli","Synthetic Biology"],"_id":"8951","author":[{"orcid":"0000-0002-1391-8377","full_name":"Nagy-Staron, Anna A","last_name":"Nagy-Staron","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","first_name":"Anna A"}],"article_processing_charge":"No","file_date_updated":"2020-12-20T22:01:44Z","title":"Sequences of gene regulatory network permutations for the article \"Local genetic context shapes the function of a gene regulatory network\"","department":[{"_id":"CaGu"}],"citation":{"mla":"Nagy-Staron, Anna A. Sequences of Gene Regulatory Network Permutations for the Article “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8951.","short":"A.A. Nagy-Staron, (2020).","ieee":"A. A. Nagy-Staron, “Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network.’” Institute of Science and Technology Austria, 2020.","ama":"Nagy-Staron AA. Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” 2020. doi:10.15479/AT:ISTA:8951","apa":"Nagy-Staron, A. A. (2020). Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8951","chicago":"Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory Network.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8951.","ista":"Nagy-Staron AA. 2020. Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8951."},"date_updated":"2024-02-21T12:41:57Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"_id":"7383","status":"public","keyword":["Matlab scripts","analysis of microfluidics","mathematical model"],"type":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Grah R. 2020. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7383.","chicago":"Grah, Rok. “Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7383.","ieee":"R. Grah, “Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation.” Institute of Science and Technology Austria, 2020.","short":"R. Grah, (2020).","apa":"Grah, R. (2020). Matlab scripts 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:7383","ama":"Grah R. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. 2020. doi:10.15479/AT:ISTA:7383","mla":"Grah, Rok. Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7383."},"date_updated":"2024-02-21T12:42:31Z","title":"Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:47:57Z","author":[{"id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok","last_name":"Grah","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok"}],"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"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. 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Supplementary Data for “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7689.","apa":"Katsaros, G. (2020). Supplementary data for “Zero field splitting of heavy-hole states in quantum dots.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7689","ama":"Katsaros G. Supplementary data for “Zero field splitting of heavy-hole states in quantum dots.” 2020. doi:10.15479/AT:ISTA:7689","ieee":"G. Katsaros, “Supplementary data for ‘Zero field splitting of heavy-hole states in quantum dots.’” Institute of Science and Technology Austria, 2020.","short":"G. Katsaros, (2020).","chicago":"Katsaros, Georgios. “Supplementary Data for ‘Zero Field Splitting of Heavy-Hole States in Quantum Dots.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7689.","ista":"Katsaros G. 2020. Supplementary data for ‘Zero field splitting of heavy-hole states in quantum dots’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7689."},"date_updated":"2024-02-21T12:44:02Z","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data","tmp":{"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)","short":"CC0 (1.0)"},"status":"public","project":[{"grant_number":"862046","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","call_identifier":"H2020","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E"},{"call_identifier":"FWF","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","name":"Towards scalable hut wire quantum devices","grant_number":"P32235"}],"_id":"7689","related_material":{"record":[{"id":"8203","status":"public","relation":"used_in_publication"}]},"doi":"10.15479/AT:ISTA:7689","date_published":"2020-05-01T00:00:00Z","contributor":[{"last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","contributor_type":"contact_person","first_name":"Georgios"}],"ec_funded":1,"date_created":"2020-05-01T15:14:46Z","has_accepted_license":"1","year":"2020","file":[{"content_type":"application/x-zip-compressed","relation":"main_file","access_level":"open_access","file_id":"7786","checksum":"d23c0cb9e2d19e14e2f902b88b97c05d","file_size":5514403,"date_updated":"2020-07-14T12:48:02Z","creator":"gkatsaro","file_name":"DOI_ZeroFieldSplitting.zip","date_created":"2020-05-01T15:13:28Z"}],"day":"01","publisher":"Institute of Science and Technology Austria","oa":1,"month":"05","abstract":[{"text":"These are the supplementary research data to the publication \"Zero field splitting of heavy-hole states in quantum dots\". All matrix files have the same format. Within each column the bias voltage is changed. Each column corresponds to either a different gate voltage or magnetic field. The voltage values are given in mV, the current values in pA. Find a specific description in the included Readme file.\r\n","lang":"eng"}],"oa_version":"Published Version"},{"citation":{"mla":"Guseinov, Ruslan. Supplementary Data for “Computational Design of Cold Bent Glass Façades.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8761.","ama":"Guseinov R. Supplementary data for “Computational design of cold bent glass façades.” 2020. doi:10.15479/AT:ISTA:8761","apa":"Guseinov, R. (2020). Supplementary data for “Computational design of cold bent glass façades.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8761","short":"R. Guseinov, (2020).","ieee":"R. 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Optogenetic alteration of hippocampal network activity, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8563.","mla":"Csicsvari, Jozsef L., et al. Optogenetic Alteration of Hippocampal Network Activity. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8563.","ieee":"J. L. Csicsvari, I. Gridchyn, and P. Schönenberger, “Optogenetic alteration of hippocampal network activity.” Institute of Science and Technology Austria, 2020.","short":"J.L. Csicsvari, I. Gridchyn, P. Schönenberger, (2020).","apa":"Csicsvari, J. L., Gridchyn, I., & Schönenberger, P. (2020). Optogenetic alteration of hippocampal network activity. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8563","ama":"Csicsvari JL, Gridchyn I, Schönenberger P. Optogenetic alteration of hippocampal network activity. 2020. doi:10.15479/AT:ISTA:8563"},"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari"},{"first_name":"Igor","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","full_name":"Gridchyn, Igor","orcid":"0000-0002-1807-1929","last_name":"Gridchyn"},{"last_name":"Schönenberger","full_name":"Schönenberger, Philipp","first_name":"Philipp","id":"3B9D816C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Optogenetic alteration of hippocampal network activity","department":[{"_id":"JoCs"}],"file_date_updated":"2020-10-19T10:12:29Z","_id":"8563","type":"research_data","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","has_accepted_license":"1","year":"2020","day":"19","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/x-compressed","file_id":"8564","checksum":"a16098a6d172f9c42ab5af5f6991668c","success":1,"creator":"jozsef","date_updated":"2020-09-23T14:36:17Z","file_size":145243906,"date_created":"2020-09-23T14:36:17Z","file_name":"upload.tgz"},{"file_name":"redme.docx","date_created":"2020-10-19T10:12:29Z","file_size":11648,"date_updated":"2020-10-19T10:12:29Z","creator":"jozsef","success":1,"file_id":"8675","checksum":"0bfc54b7e14c0694cd081617318ba606","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"main_file","access_level":"open_access"}],"related_material":{"record":[{"id":"8740","status":"public","relation":"used_in_publication"}]},"date_published":"2020-10-19T00:00:00Z","doi":"10.15479/AT:ISTA:8563","date_created":"2020-09-23T14:39:54Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","contributor":[{"orcid":"0000-0002-5193-4036","last_name":"Csicsvari","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_leader"}],"abstract":[{"lang":"eng","text":"Supplementary data provided for the provided for the publication:\r\nIgor Gridchyn , Philipp Schoenenberger , Joseph O'Neill , Jozsef Csicsvari (2020) Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. Elife."}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"10"},{"oa":1,"publisher":"Institute of Science and Technology Austria","month":"12","abstract":[{"text":"Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications.","lang":"eng"}],"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","date_created":"2023-11-22T15:00:57Z","contributor":[{"orcid":"0000-0001-7149-769X","last_name":"Fäßler","first_name":"Florian","contributor_type":"researcher","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zens","first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher"},{"last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher"},{"last_name":"Schur","orcid":"0000-0003-4790-8078","contributor_type":"researcher","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"}],"date_published":"2020-12-01T00:00:00Z","doi":"10.15479/AT:ISTA:14592","related_material":{"record":[{"status":"public","id":"8586","relation":"research_data"}]},"year":"2020","has_accepted_license":"1","day":"01","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/zip","file_id":"14593","checksum":"0108616e2a59e51879ea51299a29b091","success":1,"creator":"fschur","date_updated":"2023-11-22T14:58:44Z","file_size":49297,"date_created":"2023-11-22T14:58:44Z","file_name":"3Dprint-files_download_v2.zip"},{"file_name":"readme.txt","date_created":"2023-12-01T10:39:59Z","creator":"cchlebak","file_size":641,"date_updated":"2023-12-01T10:39:59Z","success":1,"file_id":"14637","checksum":"4c66ddedee4d01c1c4a7978208350cfc","relation":"main_file","access_level":"open_access","content_type":"text/plain"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"research_data","status":"public","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"_id":"14592","article_processing_charge":"No","author":[{"orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"}],"file_date_updated":"2023-12-01T10:39:59Z","department":[{"_id":"FlSc"}],"title":"STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","citation":{"ista":"Schur FK. 2020. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14592.","chicago":"Schur, Florian KM. “STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:14592.","apa":"Schur, F. K. (2020). STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14592","ama":"Schur FK. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. 2020. doi:10.15479/AT:ISTA:14592","short":"F.K. Schur, (2020).","ieee":"F. K. Schur, “STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy.” Institute of Science and Technology Austria, 2020.","mla":"Schur, Florian KM. STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:14592."},"date_updated":"2024-02-21T12:44:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"]},{"oa":1,"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9411761.v1","open_access":"1"}],"publisher":"Springer Nature","month":"08","abstract":[{"lang":"eng","text":"Additional file 1: Table S1. Kinetics of MDA-MB-231 cell growth in either the presence or absence of 100Â mg/L glyphosate. Cell counts are given at day-1 of seeding flasks and following 6-days of continuous culture. Note: no differences in cell numbers were observed between negative control and glyphosate treated cultures."}],"oa_version":"Published Version","date_created":"2021-08-06T08:14:05Z","date_published":"2019-08-09T00:00:00Z","doi":"10.6084/m9.figshare.9411761.v1","related_material":{"record":[{"relation":"used_in_publication","id":"6819","status":"public"}]},"year":"2019","day":"09","type":"research_data_reference","status":"public","_id":"9784","article_processing_charge":"No","author":[{"last_name":"Antoniou","full_name":"Antoniou, Michael N.","first_name":"Michael N."},{"id":"2A103192-F248-11E8-B48F-1D18A9856A87","first_name":"Armel","full_name":"Nicolas, Armel","last_name":"Nicolas"},{"first_name":"Robin","last_name":"Mesnage","full_name":"Mesnage, Robin"},{"full_name":"Biserni, Martina","last_name":"Biserni","first_name":"Martina"},{"first_name":"Francesco V.","last_name":"Rao","full_name":"Rao, Francesco V."},{"last_name":"Martin","full_name":"Martin, Cristina Vazquez","first_name":"Cristina Vazquez"}],"department":[{"_id":"LifeSc"}],"title":"MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells","citation":{"chicago":"Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco V. Rao, and Cristina Vazquez Martin. “MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9411761.v1.","ista":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells, Springer Nature, 10.6084/m9.figshare.9411761.v1.","mla":"Antoniou, Michael N., et al. MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells. Springer Nature, 2019, doi:10.6084/m9.figshare.9411761.v1.","apa":"Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin, C. V. (2019). MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. Springer Nature. https://doi.org/10.6084/m9.figshare.9411761.v1","ama":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. 2019. doi:10.6084/m9.figshare.9411761.v1","short":"M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin, (2019).","ieee":"M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin, “MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells.” Springer Nature, 2019."},"date_updated":"2023-02-23T12:52:29Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"status":"public","type":"research_data_reference","_id":"9839","title":"Data from: Is the sky the limit? On the expansion threshold of a species' range","department":[{"_id":"NiBa"}],"article_processing_charge":"No","author":[{"first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0951-3112","full_name":"Polechova, Jitka","last_name":"Polechova"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"mla":"Polechova, Jitka. Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range. Dryad, 2019, doi:10.5061/dryad.5vv37.","ama":"Polechova J. Data from: Is the sky the limit? On the expansion threshold of a species’ range. 2019. doi:10.5061/dryad.5vv37","apa":"Polechova, J. (2019). Data from: Is the sky the limit? On the expansion threshold of a species’ range. Dryad. https://doi.org/10.5061/dryad.5vv37","short":"J. Polechova, (2019).","ieee":"J. Polechova, “Data from: Is the sky the limit? On the expansion threshold of a species’ range.” Dryad, 2019.","chicago":"Polechova, Jitka. “Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” Dryad, 2019. https://doi.org/10.5061/dryad.5vv37.","ista":"Polechova J. 2019. Data from: Is the sky the limit? On the expansion threshold of a species’ range, Dryad, 10.5061/dryad.5vv37."},"date_updated":"2023-02-23T11:14:30Z","month":"06","main_file_link":[{"url":"https://doi.org/10.5061/dryad.5vv37","open_access":"1"}],"oa":1,"publisher":"Dryad","oa_version":"Published Version","abstract":[{"text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range.","lang":"eng"}],"date_created":"2021-08-09T13:07:28Z","related_material":{"record":[{"id":"315","status":"public","relation":"used_in_publication"}]},"date_published":"2019-06-22T00:00:00Z","doi":"10.5061/dryad.5vv37","day":"22","year":"2019"},{"year":"2019","day":"19","date_created":"2021-07-27T09:51:46Z","doi":"10.1021/acs.nanolett.9b04445.s001","date_published":"2019-12-19T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"7166","status":"public"}]},"abstract":[{"lang":"eng","text":"A detailed description of the two stochastic models, table of parameters, supplementary data for Figures 4 and 5, parameter dependence of the results, and an analysis on motors with different force–velocity functions (PDF)"}],"oa_version":"Published Version","publisher":"American Chemical Society ","month":"12","date_updated":"2023-08-17T14:07:52Z","citation":{"apa":"Ucar, M. C., & Lipowsky, R. (2019). Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. American Chemical Society . https://doi.org/10.1021/acs.nanolett.9b04445.s001","ama":"Ucar MC, Lipowsky R. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. 2019. doi:10.1021/acs.nanolett.9b04445.s001","short":"M.C. Ucar, R. Lipowsky, (2019).","ieee":"M. C. Ucar and R. Lipowsky, “Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding.” American Chemical Society , 2019.","mla":"Ucar, Mehmet C., and Reinhard Lipowsky. Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding. American Chemical Society , 2019, doi:10.1021/acs.nanolett.9b04445.s001.","ista":"Ucar MC, Lipowsky R. 2019. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding, American Chemical Society , 10.1021/acs.nanolett.9b04445.s001.","chicago":"Ucar, Mehmet C, and Reinhard Lipowsky. “Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.” American Chemical Society , 2019. https://doi.org/10.1021/acs.nanolett.9b04445.s001."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","last_name":"Ucar","full_name":"Ucar, Mehmet C","orcid":"0000-0003-0506-4217"},{"first_name":"Reinhard","full_name":"Lipowsky, Reinhard","last_name":"Lipowsky"}],"title":"Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding","department":[{"_id":"EdHa"}],"_id":"9726","type":"research_data_reference","status":"public"},{"type":"research_data_reference","status":"public","_id":"9801","author":[{"full_name":"Merrill, Richard M.","last_name":"Merrill","first_name":"Richard M."},{"first_name":"Pasi","last_name":"Rastas","full_name":"Rastas, Pasi"},{"first_name":"Simon H.","last_name":"Martin","full_name":"Martin, Simon H."},{"id":"386D7308-F248-11E8-B48F-1D18A9856A87","first_name":"Maria C","full_name":"Melo Hurtado, Maria C","last_name":"Melo Hurtado"},{"first_name":"Sarah","last_name":"Barker","full_name":"Barker, Sarah"},{"first_name":"John","last_name":"Davey","full_name":"Davey, John"},{"last_name":"Mcmillan","full_name":"Mcmillan, W. Owen","first_name":"W. Owen"},{"full_name":"Jiggins, Chris D.","last_name":"Jiggins","first_name":"Chris D."}],"article_processing_charge":"No","department":[{"_id":"NiBa"}],"title":"Raw behavioral data","citation":{"chicago":"Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado, Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Raw Behavioral Data.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pbio.2005902.s006.","ista":"Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan WO, Jiggins CD. 2019. Raw behavioral data, Public Library of Science, 10.1371/journal.pbio.2005902.s006.","mla":"Merrill, Richard M., et al. Raw Behavioral Data. Public Library of Science, 2019, doi:10.1371/journal.pbio.2005902.s006.","apa":"Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S., Davey, J., … Jiggins, C. D. (2019). Raw behavioral data. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005902.s006","ama":"Merrill RM, Rastas P, Martin SH, et al. Raw behavioral data. 2019. doi:10.1371/journal.pbio.2005902.s006","ieee":"R. M. Merrill et al., “Raw behavioral data.” Public Library of Science, 2019.","short":"R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey, W.O. Mcmillan, C.D. Jiggins, (2019)."},"date_updated":"2023-08-24T14:46:23Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","month":"02","oa_version":"Published Version","date_published":"2019-02-07T00:00:00Z","related_material":{"record":[{"id":"6022","status":"public","relation":"used_in_publication"}]},"doi":"10.1371/journal.pbio.2005902.s006","date_created":"2021-08-06T11:34:56Z","year":"2019","day":"07"},{"year":"2019","day":"05","date_created":"2021-08-06T12:06:40Z","date_published":"2019-02-05T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6105"}]},"doi":"10.5061/dryad.9kj41f0","abstract":[{"text":"1. Hosts can alter their strategy towards pathogens during their lifetime, i.e., they can show phenotypic plasticity in immunity or life history. Immune priming is one such example, where a previous encounter with a pathogen confers enhanced protection upon secondary challenge, resulting in reduced pathogen load (i.e. resistance) and improved host survival. However, an initial encounter might also enhance tolerance, particularly to less virulent opportunistic pathogens that establish persistent infections. In this scenario, individuals are better able to reduce the negative fitness consequences that result from a high pathogen load. Finally, previous exposure may also lead to life history adjustments, such as terminal investment into reproduction. 2. Using different Drosophila melanogaster host genotypes and two bacterial pathogens, Lactococcus lactis and Pseudomonas entomophila, we tested if previous exposure results in resistance or tolerance and whether it modifies immune gene expression during an acute-phase infection (one day post-challenge). We then asked if previous pathogen exposure affects chronic-phase pathogen persistence and longer-term survival (28 days post-challenge). 3. We predicted that previous exposure would increase host resistance to an early stage bacterial infection while it might come at a cost to host fecundity tolerance. We reasoned that resistance would be due in part to stronger immune gene expression after challenge. We expected that previous exposure would improve long-term survival, that it would reduce infection persistence, and we expected to find genetic variation in these responses. 4. We found that previous exposure to P. entomophila weakened host resistance to a second infection independent of genotype and had no effect on immune gene expression. Fecundity tolerance showed genotypic variation but was not influenced by previous exposure. However, L. lactis persisted as a chronic infection, whereas survivors cleared the more pathogenic P. entomophila infection. 5. To our knowledge, this is the first study that addresses host tolerance to bacteria in relation to previous exposure, taking a multi-faceted approach to address the topic. Our results suggest that previous exposure comes with transient costs to resistance during the early stage of infection in this host-pathogen system and that infection persistence may be bacterium-specific.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.9kj41f0"}],"oa":1,"publisher":"Dryad","month":"02","citation":{"ista":"Kutzer M, Kurtz J, Armitage SAO. 2019. Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance, Dryad, 10.5061/dryad.9kj41f0.","chicago":"Kutzer, Megan, Joachim Kurtz, and Sophie A.O. Armitage. “Data from: A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance.” Dryad, 2019. https://doi.org/10.5061/dryad.9kj41f0.","short":"M. Kutzer, J. Kurtz, S.A.O. Armitage, (2019).","ieee":"M. Kutzer, J. Kurtz, and S. A. O. Armitage, “Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance.” Dryad, 2019.","apa":"Kutzer, M., Kurtz, J., & Armitage, S. A. O. (2019). Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. Dryad. https://doi.org/10.5061/dryad.9kj41f0","ama":"Kutzer M, Kurtz J, Armitage SAO. Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. 2019. doi:10.5061/dryad.9kj41f0","mla":"Kutzer, Megan, et al. Data from: A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance. Dryad, 2019, doi:10.5061/dryad.9kj41f0."},"date_updated":"2023-08-25T08:04:52Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"last_name":"Kutzer","full_name":"Kutzer, Megan","orcid":"0000-0002-8696-6978","id":"29D0B332-F248-11E8-B48F-1D18A9856A87","first_name":"Megan"},{"first_name":"Joachim","full_name":"Kurtz, Joachim","last_name":"Kurtz"},{"last_name":"Armitage","full_name":"Armitage, Sophie A.O.","first_name":"Sophie A.O."}],"title":"Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance","department":[{"_id":"SyCr"}],"_id":"9806","type":"research_data_reference","status":"public"},{"day":"10","year":"2019","date_created":"2021-08-06T08:50:15Z","doi":"10.1371/journal.pgen.1008079.s011","date_published":"2019-04-10T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6419"}]},"oa_version":"Published Version","month":"04","publisher":"Public Library of Science","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-25T10:30:36Z","citation":{"short":"V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, (2019).","ieee":"V. Pokusaeva et al., “A statistical summary of segment libraries and sequencing results.” Public Library of Science, 2019.","apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). A statistical summary of segment libraries and sequencing results. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s011","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment libraries and sequencing results. 2019. doi:10.1371/journal.pgen.1008079.s011","mla":"Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011.","ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. A statistical summary of segment libraries and sequencing results, Public Library of Science, 10.1371/journal.pgen.1008079.s011.","chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A Statistical Summary of Segment Libraries and Sequencing Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s011."},"title":"A statistical summary of segment libraries and sequencing results","department":[{"_id":"FyKo"}],"article_processing_charge":"No","author":[{"last_name":"Pokusaeva","orcid":"0000-0001-7660-444X","full_name":"Pokusaeva, Victoria","first_name":"Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dinara R.","last_name":"Usmanova","full_name":"Usmanova, Dinara R."},{"first_name":"Ekaterina V.","full_name":"Putintseva, Ekaterina V.","last_name":"Putintseva"},{"last_name":"Espinar","full_name":"Espinar, Lorena","first_name":"Lorena"},{"last_name":"Sarkisyan","full_name":"Sarkisyan, Karen","orcid":"0000-0002-5375-6341","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","first_name":"Karen"},{"full_name":"Mishin, Alexander S.","last_name":"Mishin","first_name":"Alexander S."},{"full_name":"Bogatyreva, Natalya S.","last_name":"Bogatyreva","first_name":"Natalya S."},{"last_name":"Ivankov","full_name":"Ivankov, Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","first_name":"Dmitry"},{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","last_name":"Akopyan"},{"first_name":"Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","last_name":"Avvakumov","full_name":"Avvakumov, Sergey"},{"full_name":"Povolotskaya, Inna S.","last_name":"Povolotskaya","first_name":"Inna S."},{"last_name":"Filion","full_name":"Filion, Guillaume J.","first_name":"Guillaume J."},{"first_name":"Lucas B.","full_name":"Carey, Lucas B.","last_name":"Carey"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov"}],"_id":"9790","status":"public","type":"research_data_reference"},{"oa_version":"Published Version","publisher":"Public Library of Science","month":"04","year":"2019","day":"10","doi":"10.1371/journal.pgen.1008079.s011","date_published":"2019-04-10T00:00:00Z","related_material":{"record":[{"id":"6419","status":"public","relation":"used_in_publication"}]},"date_created":"2021-08-06T11:08:20Z","_id":"9797","type":"research_data_reference","status":"public","citation":{"ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment libraries and sequencing results. 2019. doi:10.1371/journal.pgen.1008079.s011","apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). A statistical summary of segment libraries and sequencing results. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s011","ieee":"V. Pokusaeva et al., “A statistical summary of segment libraries and sequencing results.” Public Library of Science, 2019.","short":"V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, (2019).","mla":"Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011.","ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. A statistical summary of segment libraries and sequencing results, Public Library of Science, 10.1371/journal.pgen.1008079.s011.","chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A Statistical Summary of Segment Libraries and Sequencing Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s011."},"date_updated":"2023-08-25T10:30:36Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"id":"3184041C-F248-11E8-B48F-1D18A9856A87","first_name":"Victoria","last_name":"Pokusaeva","orcid":"0000-0001-7660-444X","full_name":"Pokusaeva, Victoria"},{"first_name":"Dinara R.","last_name":"Usmanova","full_name":"Usmanova, Dinara R."},{"first_name":"Ekaterina V.","full_name":"Putintseva, Ekaterina V.","last_name":"Putintseva"},{"first_name":"Lorena","last_name":"Espinar","full_name":"Espinar, Lorena"},{"first_name":"Karen","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5375-6341","full_name":"Sarkisyan, Karen","last_name":"Sarkisyan"},{"first_name":"Alexander S.","last_name":"Mishin","full_name":"Mishin, Alexander S."},{"last_name":"Bogatyreva","full_name":"Bogatyreva, Natalya S.","first_name":"Natalya S."},{"first_name":"Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","last_name":"Ivankov","full_name":"Ivankov, Dmitry"},{"first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X"},{"last_name":"Povolotskaya","full_name":"Povolotskaya, Inna S.","first_name":"Inna S."},{"full_name":"Filion, Guillaume J.","last_name":"Filion","first_name":"Guillaume J."},{"full_name":"Carey, Lucas B.","last_name":"Carey","first_name":"Lucas B."},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"}],"article_processing_charge":"No","department":[{"_id":"FyKo"}],"title":"A statistical summary of segment libraries and sequencing results"},{"date_created":"2021-08-06T08:38:50Z","related_material":{"record":[{"status":"public","id":"6419","relation":"used_in_publication"}]},"date_published":"2019-04-10T00:00:00Z","doi":"10.1371/journal.pgen.1008079.s010","day":"10","year":"2019","month":"04","publisher":"Public Library of Science","oa_version":"Published Version","department":[{"_id":"FyKo"}],"title":"Multiple alignment of His3 orthologues","article_processing_charge":"No","author":[{"full_name":"Pokusaeva, Victoria","orcid":"0000-0001-7660-444X","last_name":"Pokusaeva","first_name":"Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Usmanova, Dinara R.","last_name":"Usmanova","first_name":"Dinara R."},{"last_name":"Putintseva","full_name":"Putintseva, Ekaterina V.","first_name":"Ekaterina V."},{"last_name":"Espinar","full_name":"Espinar, Lorena","first_name":"Lorena"},{"id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","full_name":"Sarkisyan, Karen","orcid":"0000-0002-5375-6341","last_name":"Sarkisyan"},{"first_name":"Alexander S.","last_name":"Mishin","full_name":"Mishin, Alexander S."},{"last_name":"Bogatyreva","full_name":"Bogatyreva, Natalya S.","first_name":"Natalya S."},{"first_name":"Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","last_name":"Ivankov","full_name":"Ivankov, Dmitry"},{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","last_name":"Akopyan"},{"full_name":"Avvakumov, Sergey","last_name":"Avvakumov","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","first_name":"Sergey"},{"first_name":"Inna S.","full_name":"Povolotskaya, Inna S.","last_name":"Povolotskaya"},{"first_name":"Guillaume J.","last_name":"Filion","full_name":"Filion, Guillaume J."},{"first_name":"Lucas B.","last_name":"Carey","full_name":"Carey, Lucas B."},{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “Multiple Alignment of His3 Orthologues.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s010.","ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. Multiple alignment of His3 orthologues, Public Library of Science, 10.1371/journal.pgen.1008079.s010.","mla":"Pokusaeva, Victoria, et al. Multiple Alignment of His3 Orthologues. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s010.","ieee":"V. Pokusaeva et al., “Multiple alignment of His3 orthologues.” Public Library of Science, 2019.","short":"V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, (2019).","apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). Multiple alignment of His3 orthologues. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s010","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. Multiple alignment of His3 orthologues. 2019. doi:10.1371/journal.pgen.1008079.s010"},"date_updated":"2023-08-25T10:30:36Z","status":"public","type":"research_data_reference","_id":"9789"},{"_id":"9804","status":"public","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-29T06:41:51Z","citation":{"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.","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.","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).","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","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","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."},"department":[{"_id":"NiBa"}],"title":"Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","article_processing_charge":"No","author":[{"last_name":"Castro","full_name":"Castro, João Pl","first_name":"João Pl"},{"first_name":"Michelle N.","last_name":"Yancoskie","full_name":"Yancoskie, Michelle N."},{"first_name":"Marta","last_name":"Marchini","full_name":"Marchini, Marta"},{"id":"43FE426A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefanie","orcid":"0000-0002-9849-498X","full_name":"Belohlavy, Stefanie","last_name":"Belohlavy"},{"last_name":"Hiramatsu","full_name":"Hiramatsu, Layla","first_name":"Layla"},{"last_name":"Kučka","full_name":"Kučka, Marek","first_name":"Marek"},{"first_name":"William H.","last_name":"Beluch","full_name":"Beluch, William H."},{"last_name":"Naumann","full_name":"Naumann, Ronald","first_name":"Ronald"},{"first_name":"Isabella","last_name":"Skuplik","full_name":"Skuplik, Isabella"},{"full_name":"Cobb, John","last_name":"Cobb","first_name":"John"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"last_name":"Rolian","full_name":"Rolian, Campbell","first_name":"Campbell"},{"last_name":"Chan","full_name":"Chan, Yingguang Frank","first_name":"Yingguang Frank"}],"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"month":"06","main_file_link":[{"url":"https://doi.org/10.5061/dryad.0q2h6tk","open_access":"1"}],"oa":1,"publisher":"Dryad","day":"06","year":"2019","date_created":"2021-08-06T11:52:54Z","related_material":{"record":[{"relation":"used_in_publication","id":"6713","status":"public"}]},"doi":"10.5061/dryad.0q2h6tk","date_published":"2019-06-06T00:00:00Z"},{"doi":"10.5061/dryad.8tp0900","related_material":{"record":[{"status":"public","id":"6680","relation":"used_in_publication"}]},"date_published":"2019-07-16T00:00:00Z","date_created":"2021-08-06T11:45:11Z","day":"16","year":"2019","month":"07","publisher":"Dryad","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.8tp0900"}],"oa_version":"Published Version","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"}],"title":"Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat","department":[{"_id":"NiBa"}],"author":[{"first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","full_name":"Sachdeva, Himani"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"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).","ieee":"H. Sachdeva, “Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat.” Dryad, 2019.","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","ama":"Sachdeva H. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. 2019. doi:10.5061/dryad.8tp0900","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.","ista":"Sachdeva H. 2019. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat, Dryad, 10.5061/dryad.8tp0900."},"date_updated":"2023-08-29T06:43:57Z","status":"public","type":"research_data_reference","_id":"9802"},{"article_processing_charge":"No","author":[{"orcid":"0000-0003-1615-3282","full_name":"Ruess, Jakob","last_name":"Ruess","first_name":"Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87"},{"id":"4569785E-F248-11E8-B48F-1D18A9856A87","first_name":"Maros","last_name":"Pleska","full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet"},{"orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"title":"Supporting text and results","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"citation":{"ieee":"J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Supporting text and results.” Public Library of Science, 2019.","short":"J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, (2019).","apa":"Ruess, J., Pleska, M., Guet, C. C., & Tkačik, G. (2019). Supporting text and results. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007168.s001","ama":"Ruess J, Pleska M, Guet CC, Tkačik G. Supporting text and results. 2019. doi:10.1371/journal.pcbi.1007168.s001","mla":"Ruess, Jakob, et al. Supporting Text and Results. Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007168.s001.","ista":"Ruess J, Pleska M, Guet CC, Tkačik G. 2019. Supporting text and results, Public Library of Science, 10.1371/journal.pcbi.1007168.s001.","chicago":"Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Supporting Text and Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007168.s001."},"date_updated":"2023-08-29T07:10:05Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9786","date_created":"2021-08-06T08:23:43Z","doi":"10.1371/journal.pcbi.1007168.s001","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6784"}]},"date_published":"2019-07-02T00:00:00Z","year":"2019","day":"02","publisher":"Public Library of Science","month":"07","oa_version":"Published Version"},{"date_published":"2019-07-22T00:00:00Z","related_material":{"record":[{"id":"14058","status":"public","relation":"used_in_publication"},{"relation":"used_in_publication","status":"public","id":"6831"}]},"doi":"10.5061/dryad.n1701c9","date_created":"2021-08-06T11:48:42Z","day":"22","year":"2019","month":"07","publisher":"Dryad","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.n1701c9"}],"oa_version":"Published Version","abstract":[{"text":"Understanding the mechanisms causing phenotypic differences between females and males has long fascinated evolutionary biologists. An extensive literature exists on animal sexual dimorphism but less is known about sex differences in plants, particularly the extent of geographical variation in sexual dimorphism and its life-cycle dynamics. Here, we investigate patterns of genetically-based sexual dimorphism in vegetative and reproductive traits of a wind-pollinated dioecious plant, Rumex hastatulus, across three life-cycle stages using open-pollinated families from 30 populations spanning the geographic range and chromosomal variation (XY and XY1Y2) of the species. The direction and degree of sexual dimorphism was highly variable among populations and life-cycle stages. Sex-specific differences in reproductive function explained a significant amount of temporal change in sexual dimorphism. For several traits, geographical variation in sexual dimorphism was associated with bioclimatic parameters, likely due to the differential responses of the sexes to climate. We found no systematic differences in sexual dimorphism between chromosome races. Sex-specific trait differences in dioecious plants largely result from a balance between sexual and natural selection on resource allocation. Our results indicate that abiotic factors associated with geographical context also play a role in modifying sexual dimorphism during the plant life cycle.","lang":"eng"}],"title":"Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"author":[{"full_name":"Puixeu Sala, Gemma","orcid":"0000-0001-8330-1754","last_name":"Puixeu Sala","first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","last_name":"Pickup","orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda"},{"full_name":"Field, David","last_name":"Field","first_name":"David"},{"full_name":"Barrett, Spencer C.H.","last_name":"Barrett","first_name":"Spencer C.H."}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"chicago":"Puixeu Sala, Gemma, Melinda Pickup, David Field, and Spencer C.H. Barrett. “Data from: Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” Dryad, 2019. https://doi.org/10.5061/dryad.n1701c9.","ista":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. 2019. Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics, Dryad, 10.5061/dryad.n1701c9.","mla":"Puixeu Sala, Gemma, et al. Data from: Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics. Dryad, 2019, doi:10.5061/dryad.n1701c9.","ama":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics. 2019. doi:10.5061/dryad.n1701c9","apa":"Puixeu Sala, G., Pickup, M., Field, D., & Barrett, S. C. H. (2019). 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Sigalova et al., “Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 5 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808886.v1.","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. 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(CSV 3 kb)","lang":"eng"}],"oa_version":"Published Version"},{"publisher":"Dryad","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.tb2rbnzwk","open_access":"1"}],"month":"12","abstract":[{"text":"Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the \"Crab\" and \"Wave\" ecotypes of the snail Littorina saxatilis divergent selection forms strong barriers to gene flow, while the role of postzygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Postzygotic barriers might include genetic incompatibilities (e.g. Dobzhansky-Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1011 embryos (mean 130±123) and abortion rates varied between 0 and100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterised female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant postzygotic barriers contributing to ecotype divergence and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females.","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"id":"7205","status":"public","relation":"used_in_publication"}]},"date_published":"2019-12-02T00:00:00Z","doi":"10.5061/DRYAD.TB2RBNZWK","date_created":"2023-05-23T16:36:27Z","year":"2019","day":"02","type":"research_data_reference","tmp":{"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)","short":"CC0 (1.0)"},"status":"public","_id":"13067","author":[{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"first_name":"Zuzanna","full_name":"Zagrodzka, Zuzanna","last_name":"Zagrodzka"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"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":"Roger","full_name":"Butlin, Roger","last_name":"Butlin"}],"article_processing_charge":"No","department":[{"_id":"NiBa"}],"title":"Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?","date_updated":"2023-09-06T14:48:57Z","citation":{"mla":"Johannesson, Kerstin, et al. 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Butlin, “Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?” Dryad, 2019.","chicago":"Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger Butlin. “Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes?” Dryad, 2019. https://doi.org/10.5061/DRYAD.TB2RBNZWK.","ista":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. 2019. 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(2018) report on a 25‐year long study of the mosquitoes Anopheles gambiae (Figure 1) and Anopheles coluzzi in Mali, based on genotypes at 15 single‐nucleotide polymorphism (SNP). The species are usually reproductively isolated from each other, but in 2002 and 2006, bursts of hybridization were observed, when F1 hybrids became abundant. Alleles backcrossed from A. gambiae into A. coluzzi, but after the first event, these declined over the following years. In contrast, after 2006, an insecticide resistance allele that had established in A. gambiae spread into A. coluzzi, and rose to high frequency there, over 6 years (~75 generations). Whole genome sequences of 74 individuals showed that A. gambiae SNP from across the genome had become common in the A. coluzzi population, but that most of these were clustered in 34 genes around the resistance locus. A new set of SNP from 25 of these genes were assayed over time; over the 4 years since near‐fixation of the resistance allele; some remained common, whereas others declined. What do these patterns tell us about this introgression event?","lang":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"department":[{"_id":"NiBa"}],"title":"Data from: The consequences of an introgression event","citation":{"apa":"Barton, N. H. (2019). Data from: The consequences of an introgression event. Dryad. https://doi.org/10.5061/dryad.2kb6fh4","ama":"Barton NH. Data from: The consequences of an introgression event. 2019. doi:10.5061/dryad.2kb6fh4","short":"N.H. Barton, (2019).","ieee":"N. H. Barton, “Data from: The consequences of an introgression event.” Dryad, 2019.","mla":"Barton, Nicholas H. Data from: The Consequences of an Introgression Event. Dryad, 2019, doi:10.5061/dryad.2kb6fh4.","ista":"Barton NH. 2019. Data from: The consequences of an introgression event, Dryad, 10.5061/dryad.2kb6fh4.","chicago":"Barton, Nicholas H. “Data from: The Consequences of an Introgression Event.” Dryad, 2019. https://doi.org/10.5061/dryad.2kb6fh4."},"date_updated":"2023-09-19T10:06:07Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9805"},{"day":"13","file":[{"creator":"itomanek","file_size":2456192500,"date_updated":"2020-07-14T12:47:47Z","file_name":"D8_S35_R2_001.fastq","date_created":"2019-11-13T08:52:21Z","title":"Locus1_amplified","relation":"main_file","access_level":"open_access","content_type":"application/octet-stream","description":"Illumina whole genome sequence data for Locus 1 - amplified.","file_id":"7017","checksum":"72441055043eda4cbf1398a422e2c118"},{"file_name":"IT028_S11_R2_001.fastq","title":"Locus1_ancestral","date_created":"2019-11-13T08:52:59Z","file_size":2833452234,"date_updated":"2020-07-14T12:47:47Z","creator":"itomanek","file_id":"7018","checksum":"a4ac50bf655d9c751f0305ade5c2ee16","description":"Illumina whole genome sequence data for Locus 1 - 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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."}],"month":"11","oa":1,"publisher":"Institute of Science and Technology Austria","ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","short":"I. Tomanek, (2019).","apa":"Tomanek, I. 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Supplementary data for ‘Programming temporal morphing of self-actuated shells’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7154.","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.","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","ama":"Guseinov R. Supplementary data for “Programming temporal morphing of self-actuated shells.” 2019. doi: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.","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."}},{"article_processing_charge":"No","author":[{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:47:17Z","title":"Supplementary data for \"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome\" (Huylman, Toups et al., 2019). ","date_updated":"2024-02-21T12:45:42Z","citation":{"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.","short":"B. Vicoso, (2019).","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","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data","status":"public","_id":"6060","date_created":"2019-02-28T10:55:15Z","date_published":"2019-02-28T00:00:00Z","doi":"10.15479/AT:ISTA:6060","related_material":{"record":[{"status":"public","id":"6418","relation":"research_paper"}]},"year":"2019","has_accepted_license":"1","file":[{"content_type":"application/zip","access_level":"open_access","relation":"main_file","checksum":"a338a622d728af0e3199cb07e6dd64d3","file_id":"6061","date_updated":"2020-07-14T12:47:17Z","file_size":36646050,"creator":"bvicoso","date_created":"2019-02-28T10:54:27Z","file_name":"SupData.zip"}],"day":"28","oa":1,"publisher":"Institute of Science and Technology Austria","month":"02","oa_version":"Published Version"},{"_id":"6074","type":"research_data","status":"public","citation":{"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.","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.","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","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","short":"C. Dotter, G. Novarino, (2019).","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.","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."},"date_updated":"2024-02-21T13:41:01Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Dotter, Christoph","orcid":"0000-0002-9033-9096","last_name":"Dotter"},{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino"}],"file_date_updated":"2020-07-14T12:47:18Z","title":"Supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\"","department":[{"_id":"GaNo"}],"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."}],"oa_version":"Published Version","oa":1,"publisher":"Institute of Science and Technology Austria","month":"01","year":"2019","has_accepted_license":"1","day":"09","file":[{"checksum":"bc1b285edca9e98a2c63d153c79bb75b","file_id":"6084","access_level":"open_access","relation":"supplementary_material","content_type":"application/zip","date_created":"2019-03-07T13:37:19Z","file_name":"Setd5_paper.zip","creator":"dernst","date_updated":"2020-07-14T12:47:18Z","file_size":33202743}],"date_created":"2019-03-07T13:32:35Z","related_material":{"record":[{"relation":"research_paper","id":"3","status":"public"}]},"doi":"10.15479/AT:ISTA:6074","date_published":"2019-01-09T00:00:00Z"},{"month":"03","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Open the files in Jupyter Notebook (reccomended https://www.anaconda.com/distribution/#download-section with Python 3.7)."}],"related_material":{"record":[{"relation":"research_paper","status":"public","id":"6194"}]},"date_published":"2019-03-29T00:00:00Z","doi":"10.15479/AT:ISTA:6062","date_created":"2019-03-04T14:20:58Z","license":"https://creativecommons.org/licenses/by-sa/4.0/","day":"29","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/zip","file_id":"6068","checksum":"48e7b9a02939b763417733239522a236","creator":"mnardin","date_updated":"2020-07-14T12:47:18Z","file_size":37002186,"date_created":"2019-03-05T09:29:37Z","title":"Data for the paper \"The Entorhinal Cognitive Map is Attracted to Goals\"","file_name":"Online_data.zip"}],"has_accepted_license":"1","year":"2019","status":"public","type":"research_data","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"_id":"6062","file_date_updated":"2020-07-14T12:47:18Z","title":"Supplementary Code and Data for the paper \"The Entorhinal Cognitive Map is Attracted to Goals\"","department":[{"_id":"JoCs"}],"author":[{"orcid":"0000-0001-8849-6570","full_name":"Nardin, Michele","last_name":"Nardin","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","first_name":"Michele"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:46:04Z","citation":{"mla":"Nardin, Michele. Supplementary Code and Data for the Paper “The Entorhinal Cognitive Map Is Attracted to Goals.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6062.","ieee":"M. Nardin, “Supplementary Code and Data for the paper ‘The Entorhinal Cognitive Map is Attracted to Goals.’” Institute of Science and Technology Austria, 2019.","short":"M. Nardin, (2019).","ama":"Nardin M. Supplementary Code and Data for the paper “The Entorhinal Cognitive Map is Attracted to Goals.” 2019. doi:10.15479/AT:ISTA:6062","apa":"Nardin, M. (2019). Supplementary Code and Data for the paper “The Entorhinal Cognitive Map is Attracted to Goals.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6062","chicago":"Nardin, Michele. “Supplementary Code and Data for the Paper ‘The Entorhinal Cognitive Map Is Attracted to Goals.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6062.","ista":"Nardin M. 2019. Supplementary Code and Data for the paper ‘The Entorhinal Cognitive Map is Attracted to Goals’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:6062."}},{"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"}],"oa_version":"Published Version","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.72cg113","open_access":"1"}],"publisher":"Dryad","month":"10","year":"2018","day":"09","date_created":"2021-08-09T12:46:39Z","related_material":{"record":[{"relation":"used_in_publication","id":"6095","status":"public"}]},"doi":"10.5061/dryad.72cg113","date_published":"2018-10-09T00:00:00Z","_id":"9837","type":"research_data_reference","status":"public","date_updated":"2023-08-24T14:50:26Z","citation":{"ama":"Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:10.5061/dryad.72cg113","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. https://doi.org/10.5061/dryad.72cg113","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).","ieee":"R. Faria et al., “Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.","mla":"Faria, Rui, et al. Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes. Dryad, 2018, doi:10.5061/dryad.72cg113.","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, 10.5061/dryad.72cg113.","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. https://doi.org/10.5061/dryad.72cg113."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"first_name":"Pragya","full_name":"Chaube, Pragya","last_name":"Chaube"},{"first_name":"Hernán E.","last_name":"Morales","full_name":"Morales, Hernán E."},{"first_name":"Tomas","full_name":"Larsson, Tomas","last_name":"Larsson"},{"full_name":"Lemmon, Alan R.","last_name":"Lemmon","first_name":"Alan R."},{"full_name":"Lemmon, Emily M.","last_name":"Lemmon","first_name":"Emily M."},{"first_name":"Marina","full_name":"Rafajlović, Marina","last_name":"Rafajlović"},{"last_name":"Panova","full_name":"Panova, Marina","first_name":"Marina"},{"first_name":"Mark","full_name":"Ravinet, Mark","last_name":"Ravinet"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","department":[{"_id":"NiBa"}]},{"article_processing_charge":"No","author":[{"first_name":"Edgar","full_name":"Garriga, Edgar","last_name":"Garriga"},{"last_name":"di Tommaso","full_name":"di Tommaso, Paolo","first_name":"Paolo"},{"first_name":"Cedrik","full_name":"Magis, Cedrik","last_name":"Magis"},{"full_name":"Erb, Ionas","last_name":"Erb","first_name":"Ionas"},{"first_name":"Leila","last_name":"Mansouri","full_name":"Mansouri, Leila"},{"full_name":"Baltzis, Athanasios","last_name":"Baltzis","first_name":"Athanasios"},{"full_name":"Laayouni, Hafid","last_name":"Laayouni","first_name":"Hafid"},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Evan","full_name":"Floden, Evan","last_name":"Floden"},{"first_name":"Cedric","full_name":"Notredame, Cedric","last_name":"Notredame"}],"department":[{"_id":"FyKo"}],"title":"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method","date_updated":"2023-09-06T14:32:51Z","citation":{"ieee":"E. Garriga et al., “Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method.” Zenodo, 2018.","short":"E. Garriga, P. di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, (2018).","apa":"Garriga, E., di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2018). Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. Zenodo. https://doi.org/10.5281/ZENODO.2025846","ama":"Garriga E, di Tommaso P, Magis C, et al. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. 2018. doi:10.5281/ZENODO.2025846","mla":"Garriga, Edgar, et al. Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method. Zenodo, 2018, doi:10.5281/ZENODO.2025846.","ista":"Garriga E, di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2018. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method, Zenodo, 10.5281/ZENODO.2025846.","chicago":"Garriga, Edgar, Paolo di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Zenodo, 2018. https://doi.org/10.5281/ZENODO.2025846."},"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","status":"public","_id":"13059","date_created":"2023-05-23T16:08:20Z","doi":"10.5281/ZENODO.2025846","date_published":"2018-12-07T00:00:00Z","related_material":{"record":[{"status":"public","id":"7181","relation":"used_in_publication"}]},"year":"2018","day":"07","oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.3271452","open_access":"1"}],"publisher":"Zenodo","month":"12","abstract":[{"text":"This dataset contains a GitHub repository containing all the data, analysis, Nextflow workflows and Jupyter notebooks to replicate the manuscript titled \"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method\".\r\nIt also contains the Multiple Sequence Alignments (MSAs) generated and well as the main figures and tables from the manuscript.\r\nThe repository is also available at GitHub (https://github.com/cbcrg/dpa-analysis) release `v1.2`.\r\nFor details on how to use the regressive alignment algorithm, see the T-Coffee software suite (https://github.com/cbcrg/tcoffee).","lang":"eng"}],"oa_version":"Published Version"},{"date_created":"2021-08-09T13:10:02Z","date_published":"2018-03-12T00:00:00Z","related_material":{"record":[{"status":"public","id":"423","relation":"used_in_publication"}]},"doi":"10.5061/dryad.42n44","day":"12","year":"2018","month":"03","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.42n44"}],"oa":1,"publisher":"Dryad","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"title":"Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"article_processing_charge":"No","author":[{"id":"35F78294-F248-11E8-B48F-1D18A9856A87","first_name":"Pavel","full_name":"Payne, Pavel","orcid":"0000-0002-2711-9453","last_name":"Payne"},{"last_name":"Geyrhofer","full_name":"Geyrhofer, Lukas","first_name":"Lukas"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","last_name":"Bollback"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-11T12:49:17Z","citation":{"ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations, Dryad, 10.5061/dryad.42n44.","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. https://doi.org/10.5061/dryad.42n44.","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. 2018. doi:10.5061/dryad.42n44","apa":"Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. Dryad. https://doi.org/10.5061/dryad.42n44","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.","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).","mla":"Payne, Pavel, et al. Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations. Dryad, 2018, doi:10.5061/dryad.42n44."},"status":"public","type":"research_data_reference","_id":"9840"},{"doi":"10.25386/genetics.6148304.v1","related_material":{"record":[{"id":"316","status":"public","relation":"used_in_publication"}]},"date_published":"2018-04-30T00:00:00Z","date_created":"2021-08-06T13:04:32Z","year":"2018","day":"30","publisher":"Genetics Society of America","oa":1,"main_file_link":[{"url":"https://doi.org/10.25386/genetics.6148304.v1","open_access":"1"}],"month":"04","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"}],"oa_version":"Published Version","author":[{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarína","last_name":"Bod'ová","orcid":"0000-0002-7214-0171","full_name":"Bod'ová, Katarína"},{"id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","first_name":"Tadeas","full_name":"Priklopil, Tadeas","last_name":"Priklopil"},{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David","orcid":"0000-0002-4014-8478","last_name":"Field"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"last_name":"Pickup","orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Supplemental material for Bodova et al., 2018","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"citation":{"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. https://doi.org/10.25386/genetics.6148304.v1.","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Supplemental material for Bodova et al., 2018, Genetics Society of America, 10.25386/genetics.6148304.v1.","mla":"Bodova, Katarina, et al. Supplemental Material for Bodova et Al., 2018. Genetics Society of America, 2018, doi:10.25386/genetics.6148304.v1.","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018). Supplemental material for Bodova et al., 2018. Genetics Society of America. https://doi.org/10.25386/genetics.6148304.v1","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Supplemental material for Bodova et al., 2018. 2018. doi:10.25386/genetics.6148304.v1","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.","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018)."},"date_updated":"2023-09-11T13:57:42Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9813"},{"department":[{"_id":"BeVi"}],"title":"Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality","author":[{"full_name":"Harrison, Mark C.","last_name":"Harrison","first_name":"Mark C."},{"first_name":"Evelien","full_name":"Jongepier, Evelien","last_name":"Jongepier"},{"first_name":"Hugh M.","last_name":"Robertson","full_name":"Robertson, Hugh M."},{"first_name":"Nicolas","last_name":"Arning","full_name":"Arning, Nicolas"},{"first_name":"Tristan","last_name":"Bitard-Feildel","full_name":"Bitard-Feildel, Tristan"},{"full_name":"Chao, Hsu","last_name":"Chao","first_name":"Hsu"},{"last_name":"Childers","full_name":"Childers, Christopher P.","first_name":"Christopher P."},{"first_name":"Huyen","full_name":"Dinh, Huyen","last_name":"Dinh"},{"last_name":"Doddapaneni","full_name":"Doddapaneni, Harshavardhan","first_name":"Harshavardhan"},{"first_name":"Shannon","last_name":"Dugan","full_name":"Dugan, Shannon"},{"full_name":"Gowin, Johannes","last_name":"Gowin","first_name":"Johannes"},{"first_name":"Carolin","last_name":"Greiner","full_name":"Greiner, Carolin"},{"full_name":"Han, Yi","last_name":"Han","first_name":"Yi"},{"first_name":"Haofu","last_name":"Hu","full_name":"Hu, Haofu"},{"first_name":"Daniel S. T.","full_name":"Hughes, Daniel S. T.","last_name":"Hughes"},{"last_name":"Huylmans","full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K"},{"last_name":"Kemena","full_name":"Kemena, Carsten","first_name":"Carsten"},{"first_name":"Lukas P. M.","last_name":"Kremer","full_name":"Kremer, Lukas P. M."},{"full_name":"Lee, Sandra L.","last_name":"Lee","first_name":"Sandra L."},{"last_name":"Lopez-Ezquerra","full_name":"Lopez-Ezquerra, Alberto","first_name":"Alberto"},{"full_name":"Mallet, Ludovic","last_name":"Mallet","first_name":"Ludovic"},{"first_name":"Jose M.","full_name":"Monroy-Kuhn, Jose M.","last_name":"Monroy-Kuhn"},{"last_name":"Moser","full_name":"Moser, Annabell","first_name":"Annabell"},{"first_name":"Shwetha C.","last_name":"Murali","full_name":"Murali, Shwetha C."},{"first_name":"Donna M.","full_name":"Muzny, Donna M.","last_name":"Muzny"},{"first_name":"Saria","last_name":"Otani","full_name":"Otani, Saria"},{"last_name":"Piulachs","full_name":"Piulachs, Maria-Dolors","first_name":"Maria-Dolors"},{"last_name":"Poelchau","full_name":"Poelchau, Monica","first_name":"Monica"},{"first_name":"Jiaxin","last_name":"Qu","full_name":"Qu, Jiaxin"},{"first_name":"Florentine","last_name":"Schaub","full_name":"Schaub, Florentine"},{"first_name":"Ayako","last_name":"Wada-Katsumata","full_name":"Wada-Katsumata, Ayako"},{"full_name":"Worley, Kim C.","last_name":"Worley","first_name":"Kim C."},{"first_name":"Qiaolin","last_name":"Xie","full_name":"Xie, Qiaolin"},{"first_name":"Guillem","last_name":"Ylla","full_name":"Ylla, Guillem"},{"full_name":"Poulsen, Michael","last_name":"Poulsen","first_name":"Michael"},{"first_name":"Richard A.","full_name":"Gibbs, Richard A.","last_name":"Gibbs"},{"full_name":"Schal, Coby","last_name":"Schal","first_name":"Coby"},{"first_name":"Stephen","full_name":"Richards, Stephen","last_name":"Richards"},{"first_name":"Xavier","last_name":"Belles","full_name":"Belles, Xavier"},{"last_name":"Korb","full_name":"Korb, Judith","first_name":"Judith"},{"first_name":"Erich","last_name":"Bornberg-Bauer","full_name":"Bornberg-Bauer, Erich"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"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, 10.5061/dryad.51d4r.","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. https://doi.org/10.5061/dryad.51d4r.","ama":"Harrison MC, Jongepier E, Robertson HM, et al. Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality. 2018. doi:10.5061/dryad.51d4r","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. https://doi.org/10.5061/dryad.51d4r","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).","ieee":"M. C. Harrison et al., “Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality.” Dryad, 2018.","mla":"Harrison, Mark C., et al. Data from: Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality. Dryad, 2018, doi:10.5061/dryad.51d4r."},"date_updated":"2023-09-11T14:10:56Z","status":"public","type":"research_data_reference","_id":"9841","doi":"10.5061/dryad.51d4r","related_material":{"record":[{"id":"448","status":"public","relation":"used_in_publication"}]},"date_published":"2018-12-12T00:00:00Z","date_created":"2021-08-09T13:13:48Z","day":"12","year":"2018","month":"12","publisher":"Dryad","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.51d4r"}],"oa":1,"oa_version":"Published Version","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."}]},{"month":"08","publisher":"Public Library of Science","oa_version":"Published Version","doi":"10.1371/journal.pbio.2005971.s008","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"82"}]},"date_published":"2018-08-16T00:00:00Z","date_created":"2021-08-06T12:43:44Z","day":"16","year":"2018","status":"public","type":"research_data_reference","_id":"9810","department":[{"_id":"CaGu"}],"title":"Numerical data used in figures","author":[{"first_name":"Waqas","full_name":"Chaudhry, Waqas","last_name":"Chaudhry"},{"last_name":"Pleska","full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479","id":"4569785E-F248-11E8-B48F-1D18A9856A87","first_name":"Maros"},{"first_name":"Nilang","last_name":"Shah","full_name":"Shah, Nilang"},{"first_name":"Howard","last_name":"Weiss","full_name":"Weiss, Howard"},{"first_name":"Ingrid","full_name":"Mccall, Ingrid","last_name":"Mccall"},{"first_name":"Justin","full_name":"Meyer, Justin","last_name":"Meyer"},{"last_name":"Gupta","full_name":"Gupta, Animesh","first_name":"Animesh"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet"},{"last_name":"Levin","full_name":"Levin, Bruce","first_name":"Bruce"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-13T08:45:41Z","citation":{"short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, (2018).","ieee":"W. Chaudhry et al., “Numerical data used in figures.” Public Library of Science, 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. https://doi.org/10.1371/journal.pbio.2005971.s008","ama":"Chaudhry W, Pleska M, Shah N, et al. Numerical data used in figures. 2018. doi:10.1371/journal.pbio.2005971.s008","mla":"Chaudhry, Waqas, et al. Numerical Data Used in Figures. Public Library of Science, 2018, doi:10.1371/journal.pbio.2005971.s008.","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, 10.1371/journal.pbio.2005971.s008.","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. https://doi.org/10.1371/journal.pbio.2005971.s008."}},{"_id":"9812","type":"research_data_reference","status":"public","date_updated":"2023-09-13T09:01:31Z","citation":{"apa":"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. https://doi.org/10.6084/m9.figshare.6401414.v1","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:10.6084/m9.figshare.6401414.v1","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","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.","mla":"Zapata, Luis, et al. Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401414.v1.","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, 10.6084/m9.figshare.6401414.v1.","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. https://doi.org/10.6084/m9.figshare.6401414.v1."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Zapata","full_name":"Zapata, Luis","first_name":"Luis"},{"first_name":"Oriol","full_name":"Pich, Oriol","last_name":"Pich"},{"first_name":"Luis","last_name":"Serrano","full_name":"Serrano, Luis"},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stephan","last_name":"Ossowski","full_name":"Ossowski, Stephan"},{"first_name":"Martin","full_name":"Schaefer, Martin","last_name":"Schaefer"}],"article_processing_charge":"No","department":[{"_id":"FyKo"}],"title":"Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","abstract":[{"text":"This document contains the full list of genes with their respective significance and dN/dS values. (TXT 4499Â kb)","lang":"eng"}],"oa_version":"Published Version","publisher":"Springer Nature","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.6401414.v1","open_access":"1"}],"oa":1,"month":"05","year":"2018","day":"31","doi":"10.6084/m9.figshare.6401414.v1","related_material":{"record":[{"id":"279","status":"public","relation":"used_in_publication"}]},"date_published":"2018-05-31T00:00:00Z","date_created":"2021-08-06T12:58:25Z"},{"year":"2018","day":"31","doi":"10.6084/m9.figshare.6401390.v1","date_published":"2018-05-31T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"279"}]},"date_created":"2021-08-06T12:53:49Z","abstract":[{"text":"This document contains additional supporting evidence presented as supplemental tables. (XLSX 50Â kb)","lang":"eng"}],"oa_version":"Preprint","publisher":"Springer Nature","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.6401390.v1","open_access":"1"}],"oa":1,"month":"05","citation":{"ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401390.v1.","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.6401390.v1.","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401390.v1","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401390.v1","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","mla":"Zapata, Luis, et al. Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401390.v1."},"date_updated":"2023-09-13T09:01:31Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Luis","last_name":"Zapata","full_name":"Zapata, Luis"},{"last_name":"Pich","full_name":"Pich, Oriol","first_name":"Oriol"},{"first_name":"Luis","last_name":"Serrano","full_name":"Serrano, Luis"},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stephan","last_name":"Ossowski","full_name":"Ossowski, Stephan"},{"last_name":"Schaefer","full_name":"Schaefer, Martin","first_name":"Martin"}],"article_processing_charge":"No","title":"Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","department":[{"_id":"FyKo"}],"_id":"9811","type":"research_data_reference","status":"public"},{"year":"2018","day":"03","date_created":"2021-08-06T12:26:53Z","date_published":"2018-11-03T00:00:00Z","doi":"10.6084/m9.figshare.7295339.v1","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"20"}]},"abstract":[{"lang":"eng","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)."}],"oa_version":"Published Version","oa":1,"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.7295339.v1","open_access":"1"}],"publisher":"Springer Nature","month":"11","date_updated":"2023-09-13T09:10:47Z","citation":{"apa":"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. https://doi.org/10.6084/m9.figshare.7295339.v1","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:10.6084/m9.figshare.7295339.v1","ieee":"J. Higareda Almaraz et al., “Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018.","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018).","mla":"Higareda Almaraz, Juan, et al. Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes. Springer Nature, 2018, doi:10.6084/m9.figshare.7295339.v1.","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, 10.6084/m9.figshare.7295339.v1.","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. https://doi.org/10.6084/m9.figshare.7295339.v1."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"first_name":"Juan","full_name":"Higareda Almaraz, Juan","last_name":"Higareda Almaraz"},{"last_name":"Karbiener","full_name":"Karbiener, Michael","first_name":"Michael"},{"full_name":"Giroud, Maude","last_name":"Giroud","first_name":"Maude"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Pauler","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian"},{"full_name":"Gerhalter, Teresa","last_name":"Gerhalter","first_name":"Teresa"},{"first_name":"Stephan","full_name":"Herzig, Stephan","last_name":"Herzig"},{"first_name":"Marcel","last_name":"Scheideler","full_name":"Scheideler, Marcel"}],"title":"Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","department":[{"_id":"SiHi"}],"_id":"9807","type":"research_data_reference","status":"public"},{"status":"public","type":"research_data_reference","_id":"9808","title":"Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","department":[{"_id":"SiHi"}],"article_processing_charge":"No","author":[{"full_name":"Higareda Almaraz, Juan","last_name":"Higareda Almaraz","first_name":"Juan"},{"first_name":"Michael","last_name":"Karbiener","full_name":"Karbiener, Michael"},{"first_name":"Maude","full_name":"Giroud, Maude","last_name":"Giroud"},{"first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048"},{"last_name":"Gerhalter","full_name":"Gerhalter, Teresa","first_name":"Teresa"},{"first_name":"Stephan","full_name":"Herzig, Stephan","last_name":"Herzig"},{"first_name":"Marcel","last_name":"Scheideler","full_name":"Scheideler, Marcel"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-13T09:10:47Z","citation":{"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. https://doi.org/10.6084/m9.figshare.7295369.v1.","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, 10.6084/m9.figshare.7295369.v1.","mla":"Higareda Almaraz, Juan, et al. Additional File 3: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes. Springer Nature, 2018, doi:10.6084/m9.figshare.7295369.v1.","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018).","ieee":"J. Higareda Almaraz et al., “Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018.","apa":"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. https://doi.org/10.6084/m9.figshare.7295369.v1","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:10.6084/m9.figshare.7295369.v1"},"month":"11","oa":1,"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.7295369.v1","open_access":"1"}],"publisher":"Springer Nature","oa_version":"Published Version","abstract":[{"text":"Table S4. Counts per Gene per Million Reads Mapped. (XLSX 2751 kb).","lang":"eng"}],"date_created":"2021-08-06T12:31:57Z","doi":"10.6084/m9.figshare.7295369.v1","date_published":"2018-11-03T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"20","status":"public"}]},"day":"03","year":"2018"},{"article_processing_charge":"No","author":[{"first_name":"Katarína","full_name":"Bod’Ová, Katarína","last_name":"Bod’Ová"},{"last_name":"Mitchell","full_name":"Mitchell, Gabriel","first_name":"Gabriel","id":"315BCD80-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roy","full_name":"Harpaz, Roy","last_name":"Harpaz"},{"last_name":"Schneidman","full_name":"Schneidman, Elad","first_name":"Elad"},{"last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GaTk"}],"title":"Implementation of the inference method in Matlab","date_updated":"2023-09-15T12:06:18Z","citation":{"mla":"Bod’Ová, Katarína, et al. Implementation of the Inference Method in Matlab. Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.s001.","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.","short":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, (2018).","apa":"Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018). Implementation of the inference method in Matlab. Public Library of Science. https://doi.org/10.1371/journal.pone.0193049.s001","ama":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Implementation of the inference method in Matlab. 2018. doi:10.1371/journal.pone.0193049.s001","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. https://doi.org/10.1371/journal.pone.0193049.s001.","ista":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Implementation of the inference method in Matlab, Public Library of Science, 10.1371/journal.pone.0193049.s001."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9831","date_created":"2021-08-09T07:01:24Z","date_published":"2018-03-07T00:00:00Z","doi":"10.1371/journal.pone.0193049.s001","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"406"}]},"year":"2018","day":"07","publisher":"Public Library of Science","month":"03","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"}],"oa_version":"Published Version"},{"doi":"10.5061/dryad.f1s76f2","related_material":{"record":[{"id":"162","status":"public","relation":"used_in_publication"}]},"date_published":"2018-06-14T00:00:00Z","date_created":"2021-08-09T12:54:35Z","year":"2018","day":"14","publisher":"Dryad","main_file_link":[{"url":"https://doi.org/10.5061/dryad.f1s76f2","open_access":"1"}],"oa":1,"month":"06","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","author":[{"first_name":"Marketa","last_name":"Kaucka","full_name":"Kaucka, Marketa"},{"first_name":"Julian","last_name":"Petersen","full_name":"Petersen, Julian"},{"first_name":"Marketa","full_name":"Tesarova, Marketa","last_name":"Tesarova"},{"first_name":"Bara","last_name":"Szarowska","full_name":"Szarowska, Bara"},{"full_name":"Kastriti, Maria Eleni","last_name":"Kastriti","first_name":"Maria Eleni"},{"first_name":"Meng","last_name":"Xie","full_name":"Xie, Meng"},{"orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","last_name":"Kicheva","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Karl","full_name":"Annusver, Karl","last_name":"Annusver"},{"last_name":"Kasper","full_name":"Kasper, Maria","first_name":"Maria"},{"first_name":"Orsolya","full_name":"Symmons, Orsolya","last_name":"Symmons"},{"last_name":"Pan","full_name":"Pan, Leslie","first_name":"Leslie"},{"last_name":"Spitz","full_name":"Spitz, Francois","first_name":"Francois"},{"first_name":"Jozef","full_name":"Kaiser, Jozef","last_name":"Kaiser"},{"last_name":"Hovorakova","full_name":"Hovorakova, Maria","first_name":"Maria"},{"first_name":"Tomas","last_name":"Zikmund","full_name":"Zikmund, Tomas"},{"full_name":"Sunadome, Kazunori","last_name":"Sunadome","first_name":"Kazunori"},{"full_name":"Matise, Michael P","last_name":"Matise","first_name":"Michael P"},{"first_name":"Hui","last_name":"Wang","full_name":"Wang, Hui"},{"last_name":"Marklund","full_name":"Marklund, Ulrika","first_name":"Ulrika"},{"first_name":"Hind","last_name":"Abdo","full_name":"Abdo, Hind"},{"first_name":"Patrik","full_name":"Ernfors, Patrik","last_name":"Ernfors"},{"first_name":"Pascal","last_name":"Maire","full_name":"Maire, Pascal"},{"first_name":"Maud","full_name":"Wurmser, Maud","last_name":"Wurmser"},{"first_name":"Andrei S","last_name":"Chagin","full_name":"Chagin, Andrei S"},{"full_name":"Fried, Kaj","last_name":"Fried","first_name":"Kaj"},{"full_name":"Adameyko, Igor","last_name":"Adameyko","first_name":"Igor"}],"article_processing_charge":"No","title":"Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","department":[{"_id":"AnKi"}],"citation":{"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:10.5061/dryad.f1s76f2","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. https://doi.org/10.5061/dryad.f1s76f2","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).","ieee":"M. Kaucka et al., “Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage.” Dryad, 2018.","mla":"Kaucka, Marketa, et al. Data from: Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage. Dryad, 2018, doi:10.5061/dryad.f1s76f2.","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, 10.5061/dryad.f1s76f2.","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. https://doi.org/10.5061/dryad.f1s76f2."},"date_updated":"2023-09-18T09:29:07Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9838"},{"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.bp25b65"}],"publisher":"Dryad","month":"07","abstract":[{"lang":"eng","text":"Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g. outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e. focuses on spatial patterns of allele frequency change) with system-specific simulations to identify loci inconsistent with neutral evolution. We apply this to a genome-wide SNP set from an ideally-suited study organism, the intertidal snail Littorina saxatilis, which shows primary divergence between ecotypes associated with different shore habitats. We detect many SNPs with clinal patterns, most of which are consistent with neutrality. Among non-neutral SNPs, most are located within three large putative inversions differentiating ecotypes. Many non-neutral SNPs show relatively low levels of differentiation. We discuss potential reasons for this pattern, including loose linkage to selected variants, polygenic adaptation and a component of balancing selection within populations (which may be expected for inversions). Our work is in line with theory predicting a role for inversions in divergence, and emphasises that genomic regions contributing to divergence may not always be accessible with methods purely based on allele frequency differences. These conclusions call for approaches that take spatial patterns of allele frequency change into account in other systems."}],"oa_version":"Published Version","date_created":"2021-08-17T08:58:47Z","date_published":"2018-07-23T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"9917","status":"public"}]},"doi":"10.5061/dryad.bp25b65","year":"2018","day":"23","type":"research_data_reference","status":"public","_id":"9930","article_processing_charge":"No","author":[{"last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rafajlović","full_name":"Rafajlović, Marina","first_name":"Marina"},{"full_name":"Chaube, Pragya","last_name":"Chaube","first_name":"Pragya"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"first_name":"Tomas","last_name":"Larsson","full_name":"Larsson, Tomas"},{"last_name":"Panova","full_name":"Panova, Marina","first_name":"Marina"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"},{"first_name":"Anders","full_name":"Blomberg, Anders","last_name":"Blomberg"},{"full_name":"Mehlig, Bernhard","last_name":"Mehlig","first_name":"Bernhard"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"}],"title":"Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow","department":[{"_id":"BeVi"}],"citation":{"chicago":"Westram, Anja M, Marina Rafajlović, Pragya Chaube, Rui Faria, Tomas Larsson, Marina Panova, Mark Ravinet, et al. “Data from: Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow.” Dryad, 2018. https://doi.org/10.5061/dryad.bp25b65.","ista":"Westram AM, Rafajlović M, Chaube P, Faria R, Larsson T, Panova M, Ravinet M, Blomberg A, Mehlig B, Johannesson K, Butlin R. 2018. Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow, Dryad, 10.5061/dryad.bp25b65.","mla":"Westram, Anja M., et al. Data from: Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow. Dryad, 2018, doi:10.5061/dryad.bp25b65.","apa":"Westram, A. M., Rafajlović, M., Chaube, P., Faria, R., Larsson, T., Panova, M., … Butlin, R. (2018). Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow. Dryad. https://doi.org/10.5061/dryad.bp25b65","ama":"Westram AM, Rafajlović M, Chaube P, et al. Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow. 2018. doi:10.5061/dryad.bp25b65","ieee":"A. M. Westram et al., “Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow.” Dryad, 2018.","short":"A.M. Westram, M. Rafajlović, P. Chaube, R. Faria, T. Larsson, M. Panova, M. Ravinet, A. Blomberg, B. Mehlig, K. Johannesson, R. Butlin, (2018)."},"date_updated":"2023-09-19T15:08:24Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-19T15:08:53Z","citation":{"ista":"Hollander J, Montaño-Rendón M, Bianco G, Yang X, Westram AM, Duvaux L, Reid DG, Butlin RK. 2018. Data from: Are assortative mating and genital divergence driven by reinforcement?, Dryad, 10.5061/dryad.51sd2p5.","chicago":"Hollander, Johan, Mauricio Montaño-Rendón, Giuseppe Bianco, Xi Yang, Anja M Westram, Ludovic Duvaux, David G. Reid, and Roger K. Butlin. “Data from: Are Assortative Mating and Genital Divergence Driven by Reinforcement?” Dryad, 2018. https://doi.org/10.5061/dryad.51sd2p5.","short":"J. Hollander, M. Montaño-Rendón, G. Bianco, X. Yang, A.M. Westram, L. Duvaux, D.G. Reid, R.K. Butlin, (2018).","ieee":"J. Hollander et al., “Data from: Are assortative mating and genital divergence driven by reinforcement?” Dryad, 2018.","apa":"Hollander, J., Montaño-Rendón, M., Bianco, G., Yang, X., Westram, A. M., Duvaux, L., … Butlin, R. K. (2018). Data from: Are assortative mating and genital divergence driven by reinforcement? Dryad. https://doi.org/10.5061/dryad.51sd2p5","ama":"Hollander J, Montaño-Rendón M, Bianco G, et al. Data from: Are assortative mating and genital divergence driven by reinforcement? 2018. doi:10.5061/dryad.51sd2p5","mla":"Hollander, Johan, et al. Data from: Are Assortative Mating and Genital Divergence Driven by Reinforcement? Dryad, 2018, doi:10.5061/dryad.51sd2p5."},"department":[{"_id":"BeVi"}],"title":"Data from: Are assortative mating and genital divergence driven by reinforcement?","article_processing_charge":"No","author":[{"first_name":"Johan","full_name":"Hollander, Johan","last_name":"Hollander"},{"last_name":"Montaño-Rendón","full_name":"Montaño-Rendón, Mauricio","first_name":"Mauricio"},{"last_name":"Bianco","full_name":"Bianco, Giuseppe","first_name":"Giuseppe"},{"first_name":"Xi","last_name":"Yang","full_name":"Yang, Xi"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Duvaux, Ludovic","last_name":"Duvaux","first_name":"Ludovic"},{"first_name":"David G.","last_name":"Reid","full_name":"Reid, David G."},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"}],"_id":"9929","status":"public","type":"research_data_reference","day":"17","year":"2018","date_created":"2021-08-17T08:51:06Z","doi":"10.5061/dryad.51sd2p5","date_published":"2018-10-17T00:00:00Z","related_material":{"record":[{"status":"public","id":"9915","relation":"used_in_publication"}]},"oa_version":"Published Version","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 favour 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. 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