[{"article_processing_charge":"No","year":"2018","date_published":"2018-05-31T00:00:00Z","author":[{"full_name":"Zapata, Luis","last_name":"Zapata","first_name":"Luis"},{"first_name":"Oriol","last_name":"Pich","full_name":"Pich, Oriol"},{"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","full_name":"Ossowski, Stephan","last_name":"Ossowski"},{"first_name":"Martin","last_name":"Schaefer","full_name":"Schaefer, Martin"}],"month":"05","department":[{"_id":"FyKo"}],"title":"Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","date_updated":"2023-09-13T09:01:31Z","day":"31","date_created":"2021-08-06T12:58:25Z","_id":"9812","publisher":"Springer Nature","oa_version":"Published Version","doi":"10.6084/m9.figshare.6401414.v1","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.6401414.v1","open_access":"1"}],"related_material":{"record":[{"id":"279","status":"public","relation":"used_in_publication"}]},"abstract":[{"text":"This document contains the full list of genes with their respective significance and dN/dS values. (TXT 4499Â kb)","lang":"eng"}],"type":"research_data_reference","citation":{"chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. <a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">https://doi.org/10.6084/m9.figshare.6401414.v1</a>.","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:<a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">10.6084/m9.figshare.6401414.v1</a>","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">10.6084/m9.figshare.6401414.v1</a>.","mla":"Zapata, Luis, et al. <i>Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome</i>. Springer Nature, 2018, doi:<a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">10.6084/m9.figshare.6401414.v1</a>.","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., &#38; Schaefer, M. (2018). Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">https://doi.org/10.6084/m9.figshare.6401414.v1</a>","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."}},{"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"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"316"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.25386/genetics.6148304.v1"}],"status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"citation":{"ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Supplemental material for Bodova et al., 2018, Genetics Society of America, <a href=\"https://doi.org/10.25386/genetics.6148304.v1\">10.25386/genetics.6148304.v1</a>.","mla":"Bodova, Katarina, et al. <i>Supplemental Material for Bodova et Al., 2018</i>. Genetics Society of America, 2018, doi:<a href=\"https://doi.org/10.25386/genetics.6148304.v1\">10.25386/genetics.6148304.v1</a>.","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Supplemental material for Bodova et al., 2018. 2018. doi:<a href=\"https://doi.org/10.25386/genetics.6148304.v1\">10.25386/genetics.6148304.v1</a>","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Supplemental Material for Bodova et Al., 2018.” Genetics Society of America, 2018. <a href=\"https://doi.org/10.25386/genetics.6148304.v1\">https://doi.org/10.25386/genetics.6148304.v1</a>.","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).","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., &#38; Pickup, M. (2018). Supplemental material for Bodova et al., 2018. Genetics Society of America. <a href=\"https://doi.org/10.25386/genetics.6148304.v1\">https://doi.org/10.25386/genetics.6148304.v1</a>"},"type":"research_data_reference","title":"Supplemental material for Bodova et al., 2018","date_updated":"2025-05-28T11:57:01Z","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"month":"04","author":[{"first_name":"Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","full_name":"Bod'ová, Katarína","orcid":"0000-0002-7214-0171","last_name":"Bod'ová"},{"first_name":"Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","full_name":"Priklopil, Tadeas","last_name":"Priklopil"},{"full_name":"Field, David","orcid":"0000-0002-4014-8478","last_name":"Field","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup"}],"date_published":"2018-04-30T00:00:00Z","year":"2018","article_processing_charge":"No","doi":"10.25386/genetics.6148304.v1","oa_version":"Published Version","_id":"9813","publisher":"Genetics Society of America","date_created":"2021-08-06T13:04:32Z","day":"30"},{"status":"public","abstract":[{"lang":"eng","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."}],"related_material":{"record":[{"id":"406","status":"public","relation":"used_in_publication"}]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"chicago":"Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Implementation of the Inference Method in Matlab.” Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pone.0193049.s001\">https://doi.org/10.1371/journal.pone.0193049.s001</a>.","ama":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Implementation of the inference method in Matlab. 2018. doi:<a href=\"https://doi.org/10.1371/journal.pone.0193049.s001\">10.1371/journal.pone.0193049.s001</a>","ista":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Implementation of the inference method in Matlab, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0193049.s001\">10.1371/journal.pone.0193049.s001</a>.","mla":"Bod’Ová, Katarína, et al. <i>Implementation of the Inference Method in Matlab</i>. Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pone.0193049.s001\">10.1371/journal.pone.0193049.s001</a>.","apa":"Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., &#38; Tkačik, G. (2018). Implementation of the inference method in Matlab. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0193049.s001\">https://doi.org/10.1371/journal.pone.0193049.s001</a>","short":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, (2018).","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."},"type":"research_data_reference","month":"03","date_updated":"2023-09-15T12:06:18Z","title":"Implementation of the inference method in Matlab","department":[{"_id":"GaTk"}],"author":[{"full_name":"Bod’Ová, Katarína","last_name":"Bod’Ová","first_name":"Katarína"},{"id":"315BCD80-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","full_name":"Mitchell, Gabriel","last_name":"Mitchell"},{"last_name":"Harpaz","full_name":"Harpaz, Roy","first_name":"Roy"},{"first_name":"Elad","full_name":"Schneidman, Elad","last_name":"Schneidman"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"}],"date_published":"2018-03-07T00:00:00Z","year":"2018","article_processing_charge":"No","oa_version":"Published Version","doi":"10.1371/journal.pone.0193049.s001","date_created":"2021-08-09T07:01:24Z","day":"07","_id":"9831","publisher":"Public Library of Science"},{"oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"url":"https://doi.org/10.5061/dryad.72cg113","open_access":"1"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6095"}]},"abstract":[{"text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.","lang":"eng"}],"status":"public","type":"research_data_reference","citation":{"chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.72cg113\">https://doi.org/10.5061/dryad.72cg113</a>.","ama":"Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.72cg113\">10.5061/dryad.72cg113</a>","mla":"Faria, Rui, et al. <i>Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.72cg113\">10.5061/dryad.72cg113</a>.","ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes, Dryad, <a href=\"https://doi.org/10.5061/dryad.72cg113\">10.5061/dryad.72cg113</a>.","apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Dryad. <a href=\"https://doi.org/10.5061/dryad.72cg113\">https://doi.org/10.5061/dryad.72cg113</a>","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 <i>et al.</i>, “Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018."},"year":"2018","article_processing_charge":"No","date_published":"2018-10-09T00:00:00Z","author":[{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"last_name":"Chaube","full_name":"Chaube, Pragya","first_name":"Pragya"},{"first_name":"Hernán E.","full_name":"Morales, Hernán E.","last_name":"Morales"},{"first_name":"Tomas","full_name":"Larsson, Tomas","last_name":"Larsson"},{"full_name":"Lemmon, Alan R.","last_name":"Lemmon","first_name":"Alan R."},{"last_name":"Lemmon","full_name":"Lemmon, Emily M.","first_name":"Emily M."},{"full_name":"Rafajlović, Marina","last_name":"Rafajlović","first_name":"Marina"},{"full_name":"Panova, Marina","last_name":"Panova","first_name":"Marina"},{"last_name":"Ravinet","full_name":"Ravinet, Mark","first_name":"Mark"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"department":[{"_id":"NiBa"}],"date_updated":"2023-08-24T14:50:26Z","title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","month":"10","publisher":"Dryad","_id":"9837","day":"09","date_created":"2021-08-09T12:46:39Z","doi":"10.5061/dryad.72cg113","oa_version":"Published Version"},{"_id":"9838","publisher":"Dryad","date_created":"2021-08-09T12:54:35Z","day":"14","doi":"10.5061/dryad.f1s76f2","oa_version":"Published Version","date_published":"2018-06-14T00:00:00Z","author":[{"first_name":"Marketa","full_name":"Kaucka, Marketa","last_name":"Kaucka"},{"first_name":"Julian","full_name":"Petersen, Julian","last_name":"Petersen"},{"last_name":"Tesarova","full_name":"Tesarova, Marketa","first_name":"Marketa"},{"full_name":"Szarowska, Bara","last_name":"Szarowska","first_name":"Bara"},{"first_name":"Maria Eleni","full_name":"Kastriti, Maria Eleni","last_name":"Kastriti"},{"last_name":"Xie","full_name":"Xie, Meng","first_name":"Meng"},{"last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Karl","full_name":"Annusver, Karl","last_name":"Annusver"},{"first_name":"Maria","full_name":"Kasper, Maria","last_name":"Kasper"},{"full_name":"Symmons, Orsolya","last_name":"Symmons","first_name":"Orsolya"},{"first_name":"Leslie","last_name":"Pan","full_name":"Pan, Leslie"},{"last_name":"Spitz","full_name":"Spitz, Francois","first_name":"Francois"},{"first_name":"Jozef","last_name":"Kaiser","full_name":"Kaiser, Jozef"},{"last_name":"Hovorakova","full_name":"Hovorakova, Maria","first_name":"Maria"},{"last_name":"Zikmund","full_name":"Zikmund, Tomas","first_name":"Tomas"},{"first_name":"Kazunori","full_name":"Sunadome, Kazunori","last_name":"Sunadome"},{"first_name":"Michael P","full_name":"Matise, Michael P","last_name":"Matise"},{"first_name":"Hui","full_name":"Wang, Hui","last_name":"Wang"},{"full_name":"Marklund, Ulrika","last_name":"Marklund","first_name":"Ulrika"},{"first_name":"Hind","full_name":"Abdo, Hind","last_name":"Abdo"},{"first_name":"Patrik","full_name":"Ernfors, Patrik","last_name":"Ernfors"},{"last_name":"Maire","full_name":"Maire, Pascal","first_name":"Pascal"},{"full_name":"Wurmser, Maud","last_name":"Wurmser","first_name":"Maud"},{"last_name":"Chagin","full_name":"Chagin, Andrei S","first_name":"Andrei S"},{"first_name":"Kaj","full_name":"Fried, Kaj","last_name":"Fried"},{"first_name":"Igor","full_name":"Adameyko, Igor","last_name":"Adameyko"}],"year":"2018","article_processing_charge":"No","title":"Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","date_updated":"2023-09-18T09:29:07Z","department":[{"_id":"AnKi"}],"month":"06","type":"research_data_reference","citation":{"mla":"Kaucka, Marketa, et al. <i>Data from: Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.f1s76f2\">10.5061/dryad.f1s76f2</a>.","ista":"Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti ME, Xie M, Kicheva A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser M, Chagin AS, Fried K, Adameyko I. 2018. Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage, Dryad, <a href=\"https://doi.org/10.5061/dryad.f1s76f2\">10.5061/dryad.f1s76f2</a>.","ama":"Kaucka M, Petersen J, Tesarova M, et al. Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.f1s76f2\">10.5061/dryad.f1s76f2</a>","chicago":"Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Eleni Kastriti, Meng Xie, Anna Kicheva, et al. “Data from: Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.f1s76f2\">https://doi.org/10.5061/dryad.f1s76f2</a>.","ieee":"M. Kaucka <i>et al.</i>, “Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage.” Dryad, 2018.","short":"M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M.E. Kastriti, M. Xie, A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, (2018).","apa":"Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M. E., Xie, M., … Adameyko, I. (2018). Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. Dryad. <a href=\"https://doi.org/10.5061/dryad.f1s76f2\">https://doi.org/10.5061/dryad.f1s76f2</a>"},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"abstract":[{"text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.f1s76f2"}],"related_material":{"record":[{"id":"162","relation":"used_in_publication","status":"public"}]},"status":"public"},{"status":"public","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"423"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.42n44"}],"abstract":[{"lang":"eng","text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity."}],"oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","citation":{"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.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., &#38; Bollback, J. P. (2018). Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. Dryad. <a href=\"https://doi.org/10.5061/dryad.42n44\">https://doi.org/10.5061/dryad.42n44</a>","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations, Dryad, <a href=\"https://doi.org/10.5061/dryad.42n44\">10.5061/dryad.42n44</a>.","mla":"Payne, Pavel, et al. <i>Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.42n44\">10.5061/dryad.42n44</a>.","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.42n44\">https://doi.org/10.5061/dryad.42n44</a>.","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.42n44\">10.5061/dryad.42n44</a>"},"month":"03","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"title":"Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations","date_updated":"2023-09-11T12:49:17Z","article_processing_charge":"No","year":"2018","author":[{"last_name":"Payne","orcid":"0000-0002-2711-9453","full_name":"Payne, Pavel","id":"35F78294-F248-11E8-B48F-1D18A9856A87","first_name":"Pavel"},{"full_name":"Geyrhofer, Lukas","last_name":"Geyrhofer","first_name":"Lukas"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"last_name":"Bollback","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P"}],"date_published":"2018-03-12T00:00:00Z","oa_version":"Published Version","doi":"10.5061/dryad.42n44","day":"12","date_created":"2021-08-09T13:10:02Z","publisher":"Dryad","_id":"9840"},{"citation":{"ieee":"M. C. Harrison <i>et al.</i>, “Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality.” Dryad, 2018.","short":"M.C. Harrison, E. Jongepier, H.M. Robertson, N. Arning, T. Bitard-Feildel, H. Chao, C.P. Childers, H. Dinh, H. Doddapaneni, S. Dugan, J. Gowin, C. Greiner, Y. Han, H. Hu, D.S.T. Hughes, A.K. Huylmans, C. Kemena, L.P.M. Kremer, S.L. Lee, A. Lopez-Ezquerra, L. Mallet, J.M. Monroy-Kuhn, A. Moser, S.C. Murali, D.M. Muzny, S. Otani, M.-D. Piulachs, M. Poelchau, J. Qu, F. Schaub, A. Wada-Katsumata, K.C. Worley, Q. Xie, G. Ylla, M. Poulsen, R.A. Gibbs, C. Schal, S. Richards, X. Belles, J. Korb, E. Bornberg-Bauer, (2018).","apa":"Harrison, M. C., Jongepier, E., Robertson, H. M., Arning, N., Bitard-Feildel, T., Chao, H., … Bornberg-Bauer, E. (2018). Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality. Dryad. <a href=\"https://doi.org/10.5061/dryad.51d4r\">https://doi.org/10.5061/dryad.51d4r</a>","ista":"Harrison MC, Jongepier E, Robertson HM, Arning N, Bitard-Feildel T, Chao H, Childers CP, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu H, Hughes DST, Huylmans AK, Kemena C, Kremer LPM, Lee SL, Lopez-Ezquerra A, Mallet L, Monroy-Kuhn JM, Moser A, Murali SC, Muzny DM, Otani S, Piulachs M-D, Poelchau M, Qu J, Schaub F, Wada-Katsumata A, Worley KC, Xie Q, Ylla G, Poulsen M, Gibbs RA, Schal C, Richards S, Belles X, Korb J, Bornberg-Bauer E. 2018. Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality, Dryad, <a href=\"https://doi.org/10.5061/dryad.51d4r\">10.5061/dryad.51d4r</a>.","mla":"Harrison, Mark C., et al. <i>Data from: Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.51d4r\">10.5061/dryad.51d4r</a>.","chicago":"Harrison, Mark C., Evelien Jongepier, Hugh M. Robertson, Nicolas Arning, Tristan Bitard-Feildel, Hsu Chao, Christopher P. Childers, et al. “Data from: Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.51d4r\">https://doi.org/10.5061/dryad.51d4r</a>.","ama":"Harrison MC, Jongepier E, Robertson HM, et al. Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.51d4r\">10.5061/dryad.51d4r</a>"},"type":"research_data_reference","abstract":[{"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.","lang":"eng"}],"related_material":{"record":[{"id":"448","relation":"used_in_publication","status":"public"}]},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.51d4r","open_access":"1"}],"status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"doi":"10.5061/dryad.51d4r","oa_version":"Published Version","_id":"9841","publisher":"Dryad","date_created":"2021-08-09T13:13:48Z","day":"12","date_updated":"2023-09-11T14:10:56Z","title":"Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality","department":[{"_id":"BeVi"}],"month":"12","author":[{"full_name":"Harrison, Mark C.","last_name":"Harrison","first_name":"Mark C."},{"last_name":"Jongepier","full_name":"Jongepier, Evelien","first_name":"Evelien"},{"last_name":"Robertson","full_name":"Robertson, Hugh M.","first_name":"Hugh M."},{"last_name":"Arning","full_name":"Arning, Nicolas","first_name":"Nicolas"},{"full_name":"Bitard-Feildel, Tristan","last_name":"Bitard-Feildel","first_name":"Tristan"},{"full_name":"Chao, Hsu","last_name":"Chao","first_name":"Hsu"},{"first_name":"Christopher P.","last_name":"Childers","full_name":"Childers, Christopher P."},{"last_name":"Dinh","full_name":"Dinh, Huyen","first_name":"Huyen"},{"first_name":"Harshavardhan","last_name":"Doddapaneni","full_name":"Doddapaneni, Harshavardhan"},{"first_name":"Shannon","full_name":"Dugan, Shannon","last_name":"Dugan"},{"full_name":"Gowin, Johannes","last_name":"Gowin","first_name":"Johannes"},{"last_name":"Greiner","full_name":"Greiner, Carolin","first_name":"Carolin"},{"first_name":"Yi","full_name":"Han, Yi","last_name":"Han"},{"first_name":"Haofu","full_name":"Hu, Haofu","last_name":"Hu"},{"first_name":"Daniel S. T.","last_name":"Hughes","full_name":"Hughes, Daniel S. T."},{"orcid":"0000-0001-8871-4961","full_name":"Huylmans, Ann K","last_name":"Huylmans","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.","full_name":"Kremer, Lukas P. M.","last_name":"Kremer"},{"last_name":"Lee","full_name":"Lee, Sandra L.","first_name":"Sandra L."},{"first_name":"Alberto","last_name":"Lopez-Ezquerra","full_name":"Lopez-Ezquerra, Alberto"},{"first_name":"Ludovic","last_name":"Mallet","full_name":"Mallet, Ludovic"},{"full_name":"Monroy-Kuhn, Jose M.","last_name":"Monroy-Kuhn","first_name":"Jose M."},{"first_name":"Annabell","full_name":"Moser, Annabell","last_name":"Moser"},{"full_name":"Murali, Shwetha C.","last_name":"Murali","first_name":"Shwetha C."},{"first_name":"Donna M.","last_name":"Muzny","full_name":"Muzny, Donna M."},{"last_name":"Otani","full_name":"Otani, Saria","first_name":"Saria"},{"first_name":"Maria-Dolors","last_name":"Piulachs","full_name":"Piulachs, Maria-Dolors"},{"last_name":"Poelchau","full_name":"Poelchau, Monica","first_name":"Monica"},{"last_name":"Qu","full_name":"Qu, Jiaxin","first_name":"Jiaxin"},{"last_name":"Schaub","full_name":"Schaub, Florentine","first_name":"Florentine"},{"first_name":"Ayako","last_name":"Wada-Katsumata","full_name":"Wada-Katsumata, Ayako"},{"first_name":"Kim C.","last_name":"Worley","full_name":"Worley, Kim C."},{"first_name":"Qiaolin","last_name":"Xie","full_name":"Xie, Qiaolin"},{"last_name":"Ylla","full_name":"Ylla, Guillem","first_name":"Guillem"},{"first_name":"Michael","full_name":"Poulsen, Michael","last_name":"Poulsen"},{"full_name":"Gibbs, Richard A.","last_name":"Gibbs","first_name":"Richard A."},{"first_name":"Coby","full_name":"Schal, Coby","last_name":"Schal"},{"first_name":"Stephen","full_name":"Richards, Stephen","last_name":"Richards"},{"full_name":"Belles, Xavier","last_name":"Belles","first_name":"Xavier"},{"last_name":"Korb","full_name":"Korb, Judith","first_name":"Judith"},{"first_name":"Erich","full_name":"Bornberg-Bauer, Erich","last_name":"Bornberg-Bauer"}],"date_published":"2018-12-12T00:00:00Z","article_processing_charge":"No","year":"2018"},{"date_published":"2018-12-13T00:00:00Z","article_processing_charge":"Yes","month":"12","date_updated":"2023-09-19T15:08:53Z","title":"Are assortative mating and genital divergence driven by reinforcement?","date_created":"2021-08-16T07:30:00Z","external_id":{"isi":["000452990000002"],"pmid":["30564439"]},"_id":"9915","page":"557-566","file_date_updated":"2021-08-16T07:37:28Z","publication":"Evolution Letters","issue":"6","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"The authors express a special thanks to Dr Richard Willan at the Museum and Art Gallery of the Northern Territory for guidance and support in the field, and to Carole Smadja for reading and commenting on the manuscript. The authors thank the Government of Western Australia Department of Parks and Wildlife (license no. 009254) and Fishery Research Division (exemption no. 2262) for assistance with permits. Khalid Belkhir modified the coalescent sampler msnsam for the specific needs of this project and Martin Hirsch helped to set up the ABC pipeline and to modify the summary statistic calculator mscalc. The authors are grateful to the Crafoord Foundation for supporting this project. R.K.B., A.M.W., and L.D. were supported by grants from the Natural Environment Research Council, R.K.B. and A.M.W. were also supported by the European Research Council and R.K.B. and L.D. by the Leverhulme Trust. M.M.R. was supported by Consejo Nacional de Ciencia y Tecnología and Secretaría de Educación Pública, Mexico. G.B. was supported by the Centre for Animal Movement Research (CAnMove) financed by a Linnaeus grant (No. 349-2007-8690) from the Swedish Research Council and Lund University.","oa":1,"intvolume":"         2","volume":2,"related_material":{"record":[{"status":"public","relation":"research_data","id":"9929"}]},"isi":1,"author":[{"first_name":"Johan","last_name":"Hollander","full_name":"Hollander, Johan"},{"full_name":"Montaño-Rendón, Mauricio","last_name":"Montaño-Rendón","first_name":"Mauricio"},{"last_name":"Bianco","full_name":"Bianco, Giuseppe","first_name":"Giuseppe"},{"first_name":"Xi","full_name":"Yang, Xi","last_name":"Yang"},{"last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"first_name":"Ludovic","full_name":"Duvaux, Ludovic","last_name":"Duvaux"},{"full_name":"Reid, David G.","last_name":"Reid","first_name":"David G."},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."}],"year":"2018","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"BeVi"}],"publication_identifier":{"eissn":["2056-3744"],"issn":[" 2056-3744"]},"day":"13","publisher":"Wiley","oa_version":"Published Version","doi":"10.1002/evl3.85","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","pmid":1,"has_accepted_license":"1","publication_status":"published","abstract":[{"text":"The evolution of assortative mating is a key part of the speciation process. Stronger assortment, or greater divergence in mating traits, between species pairs with overlapping ranges is commonly observed, but possible causes of this pattern of reproductive character displacement are difficult to distinguish. We use a multidisciplinary approach to provide a rare example where it is possible to distinguish among hypotheses concerning the evolution of reproductive character displacement. We build on an earlier comparative analysis that illustrated a strong pattern of greater divergence in penis form between pairs of sister species with overlapping ranges than between allopatric sister-species pairs, in a large clade of marine gastropods (Littorinidae). We investigate both assortative mating and divergence in male genitalia in one of the sister-species pairs, discriminating among three contrasting processes each of which can generate a pattern of reproductive character displacement: reinforcement, reproductive interference and the Templeton effect. We demonstrate reproductive character displacement in assortative mating, but not in genital form between this pair of sister species and use demographic models to distinguish among the different processes. Our results support a model with no gene flow since secondary contact and thus favor reproductive interference as the cause of reproductive character displacement for mate choice, rather than reinforcement. High gene flow within species argues against the Templeton effect. Secondary contact appears to have had little impact on genital divergence.","lang":"eng"}],"article_type":"letter_note","ddc":["570"],"citation":{"chicago":"Hollander, Johan, Mauricio Montaño-Rendón, Giuseppe Bianco, Xi Yang, Anja M Westram, Ludovic Duvaux, David G. Reid, and Roger K. Butlin. “Are Assortative Mating and Genital Divergence Driven by Reinforcement?” <i>Evolution Letters</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/evl3.85\">https://doi.org/10.1002/evl3.85</a>.","ama":"Hollander J, Montaño-Rendón M, Bianco G, et al. Are assortative mating and genital divergence driven by reinforcement? <i>Evolution Letters</i>. 2018;2(6):557-566. doi:<a href=\"https://doi.org/10.1002/evl3.85\">10.1002/evl3.85</a>","mla":"Hollander, Johan, et al. “Are Assortative Mating and Genital Divergence Driven by Reinforcement?” <i>Evolution Letters</i>, vol. 2, no. 6, Wiley, 2018, pp. 557–66, doi:<a href=\"https://doi.org/10.1002/evl3.85\">10.1002/evl3.85</a>.","ista":"Hollander J, Montaño-Rendón M, Bianco G, Yang X, Westram AM, Duvaux L, Reid DG, Butlin RK. 2018. Are assortative mating and genital divergence driven by reinforcement? Evolution Letters. 2(6), 557–566.","short":"J. Hollander, M. Montaño-Rendón, G. Bianco, X. Yang, A.M. Westram, L. Duvaux, D.G. Reid, R.K. Butlin, Evolution Letters 2 (2018) 557–566.","apa":"Hollander, J., Montaño-Rendón, M., Bianco, G., Yang, X., Westram, A. M., Duvaux, L., … Butlin, R. K. (2018). Are assortative mating and genital divergence driven by reinforcement? <i>Evolution Letters</i>. Wiley. <a href=\"https://doi.org/10.1002/evl3.85\">https://doi.org/10.1002/evl3.85</a>","ieee":"J. Hollander <i>et al.</i>, “Are assortative mating and genital divergence driven by reinforcement?,” <i>Evolution Letters</i>, vol. 2, no. 6. Wiley, pp. 557–566, 2018."},"type":"journal_article","file":[{"file_name":"2018_EvolutionLetters_Hollander.pdf","access_level":"open_access","success":1,"relation":"main_file","checksum":"997a78ac41c809975ca69cbdea441f88","file_size":584606,"date_updated":"2021-08-16T07:37:28Z","content_type":"application/pdf","creator":"asandaue","date_created":"2021-08-16T07:37:28Z","file_id":"9916"}]},{"author":[{"last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"first_name":"Marina","full_name":"Rafajlović, Marina","last_name":"Rafajlović"},{"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"},{"first_name":"Marina","full_name":"Panova, Marina","last_name":"Panova"},{"first_name":"Mark","full_name":"Ravinet, Mark","last_name":"Ravinet"},{"last_name":"Blomberg","full_name":"Blomberg, Anders","first_name":"Anders"},{"first_name":"Bernhard","last_name":"Mehlig","full_name":"Mehlig, Bernhard"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"last_name":"Butlin","full_name":"Butlin, Roger","first_name":"Roger"}],"isi":1,"year":"2018","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"BeVi"}],"publication_identifier":{"eissn":["2056-3744"],"issn":["2056-3744"]},"day":"20","publisher":"Wiley","oa_version":"Published Version","doi":"10.1002/evl3.74","quality_controlled":"1","language":[{"iso":"eng"}],"has_accepted_license":"1","pmid":1,"status":"public","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 emphasizes 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."}],"publication_status":"published","article_type":"letter_note","ddc":["570"],"citation":{"ieee":"A. M. Westram <i>et al.</i>, “Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow,” <i>Evolution Letters</i>, vol. 2, no. 4. Wiley, pp. 297–309, 2018.","apa":"Westram, A. M., Rafajlović, M., Chaube, P., Faria, R., Larsson, T., Panova, M., … Butlin, R. (2018). Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow. <i>Evolution Letters</i>. Wiley. <a href=\"https://doi.org/10.1002/evl3.74\">https://doi.org/10.1002/evl3.74</a>","short":"A.M. Westram, M. Rafajlović, P. Chaube, R. Faria, T. Larsson, M. Panova, M. Ravinet, A. Blomberg, B. Mehlig, K. Johannesson, R. Butlin, Evolution Letters 2 (2018) 297–309.","ista":"Westram AM, Rafajlović M, Chaube P, Faria R, Larsson T, Panova M, Ravinet M, Blomberg A, Mehlig B, Johannesson K, Butlin R. 2018. Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow. Evolution Letters. 2(4), 297–309.","mla":"Westram, Anja M., et al. “Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow.” <i>Evolution Letters</i>, vol. 2, no. 4, Wiley, 2018, pp. 297–309, doi:<a href=\"https://doi.org/10.1002/evl3.74\">10.1002/evl3.74</a>.","chicago":"Westram, Anja M, Marina Rafajlović, Pragya Chaube, Rui Faria, Tomas Larsson, Marina Panova, Mark Ravinet, et al. “Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow.” <i>Evolution Letters</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/evl3.74\">https://doi.org/10.1002/evl3.74</a>.","ama":"Westram AM, Rafajlović M, Chaube P, et al. Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow. <i>Evolution Letters</i>. 2018;2(4):297-309. doi:<a href=\"https://doi.org/10.1002/evl3.74\">10.1002/evl3.74</a>"},"type":"journal_article","file":[{"content_type":"application/pdf","date_updated":"2021-08-16T07:48:03Z","file_size":764299,"relation":"main_file","checksum":"8524e72507d521416be3f8ccfcd5e3f5","success":1,"access_level":"open_access","file_name":"2018_EvolutionLetters_Westram.pdf","file_id":"9918","date_created":"2021-08-16T07:48:03Z","creator":"asandaue"}],"date_published":"2018-08-20T00:00:00Z","article_processing_charge":"Yes","month":"08","title":"Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow","date_updated":"2023-09-19T15:08:25Z","date_created":"2021-08-16T07:45:38Z","external_id":{"pmid":["30283683"],"isi":["000446774400004"]},"_id":"9917","page":"297-309","file_date_updated":"2021-08-16T07:48:03Z","publication":"Evolution Letters","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"We are very grateful to people who helped with fieldwork, snail processing, and DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise Liabot and Irena Senčić. We would also like to thank Magnus Alm Rosenblad and Mats Töpel for their contribution to assembling the Littorina saxatilis genome, Carl André, Pasi Rastas, and Romain Villoutreix for discussion, and two anonymous reviewers for their helpful comments on the manuscript. We are grateful to RapidGenomics for library preparation and sequencing. We thank the Natural Environment Research Council, the European Research Council and the Swedish Research Councils VR and Formas (Linnaeus grant to the Centre for Marine Evolutionary Biology and Tage Erlander Guest Professorship) for funding. P.C. was funded by the University of Sheffield Vice-chancellor's India scholarship. R.F. is funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 706376. M. Raf. was supported by the Adlerbert Research Foundation.","issue":"4","intvolume":"         2","oa":1,"volume":2,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9930"}]}},{"citation":{"short":"J. Hollander, M. Montaño-Rendón, G. Bianco, X. Yang, A.M. Westram, L. Duvaux, D.G. Reid, R.K. Butlin, (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. <a href=\"https://doi.org/10.5061/dryad.51sd2p5\">https://doi.org/10.5061/dryad.51sd2p5</a>","ieee":"J. Hollander <i>et al.</i>, “Data from: Are assortative mating and genital divergence driven by reinforcement?” Dryad, 2018.","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. <a href=\"https://doi.org/10.5061/dryad.51sd2p5\">https://doi.org/10.5061/dryad.51sd2p5</a>.","ama":"Hollander J, Montaño-Rendón M, Bianco G, et al. Data from: Are assortative mating and genital divergence driven by reinforcement? 2018. doi:<a href=\"https://doi.org/10.5061/dryad.51sd2p5\">10.5061/dryad.51sd2p5</a>","mla":"Hollander, Johan, et al. <i>Data from: Are Assortative Mating and Genital Divergence Driven by Reinforcement?</i> Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.51sd2p5\">10.5061/dryad.51sd2p5</a>.","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, <a href=\"https://doi.org/10.5061/dryad.51sd2p5\">10.5061/dryad.51sd2p5</a>."},"type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"abstract":[{"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. Secondary contact appears to have had little impact on genital divergence.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.5061/dryad.51sd2p5","open_access":"1"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"9915"}]},"status":"public","publisher":"Dryad","_id":"9929","date_created":"2021-08-17T08:51:06Z","day":"17","doi":"10.5061/dryad.51sd2p5","oa_version":"Published Version","date_published":"2018-10-17T00:00:00Z","author":[{"full_name":"Hollander, Johan","last_name":"Hollander","first_name":"Johan"},{"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","full_name":"Yang, Xi","last_name":"Yang"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram"},{"first_name":"Ludovic","full_name":"Duvaux, Ludovic","last_name":"Duvaux"},{"full_name":"Reid, David G.","last_name":"Reid","first_name":"David G."},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"}],"year":"2018","article_processing_charge":"No","date_updated":"2023-09-19T15:08:53Z","title":"Data from: Are assortative mating and genital divergence driven by reinforcement?","department":[{"_id":"BeVi"}],"month":"10"},{"citation":{"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. <a href=\"https://doi.org/10.5061/dryad.bp25b65\">https://doi.org/10.5061/dryad.bp25b65</a>","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).","ieee":"A. M. Westram <i>et al.</i>, “Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow.” Dryad, 2018.","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. <a href=\"https://doi.org/10.5061/dryad.bp25b65\">https://doi.org/10.5061/dryad.bp25b65</a>.","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:<a href=\"https://doi.org/10.5061/dryad.bp25b65\">10.5061/dryad.bp25b65</a>","mla":"Westram, Anja M., et al. <i>Data from: Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.bp25b65\">10.5061/dryad.bp25b65</a>.","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, <a href=\"https://doi.org/10.5061/dryad.bp25b65\">10.5061/dryad.bp25b65</a>."},"type":"research_data_reference","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.bp25b65"}],"related_material":{"record":[{"id":"9917","relation":"used_in_publication","status":"public"}]},"abstract":[{"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.","lang":"eng"}],"status":"public","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","doi":"10.5061/dryad.bp25b65","oa_version":"Published Version","publisher":"Dryad","_id":"9930","day":"23","date_created":"2021-08-17T08:58:47Z","department":[{"_id":"BeVi"}],"title":"Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow","date_updated":"2023-09-19T15:08:24Z","month":"07","year":"2018","article_processing_charge":"No","author":[{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969"},{"first_name":"Marina","full_name":"Rafajlović, Marina","last_name":"Rafajlović"},{"first_name":"Pragya","last_name":"Chaube","full_name":"Chaube, Pragya"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"first_name":"Tomas","full_name":"Larsson, Tomas","last_name":"Larsson"},{"last_name":"Panova","full_name":"Panova, Marina","first_name":"Marina"},{"first_name":"Mark","full_name":"Ravinet, Mark","last_name":"Ravinet"},{"first_name":"Anders","last_name":"Blomberg","full_name":"Blomberg, Anders"},{"first_name":"Bernhard","full_name":"Mehlig, Bernhard","last_name":"Mehlig"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"last_name":"Butlin","full_name":"Butlin, Roger","first_name":"Roger"}],"date_published":"2018-07-23T00:00:00Z"},{"department":[{"_id":"VlKo"}],"publication_identifier":{"eissn":["2211-2766"],"issn":["2211-2758"],"eisbn":["9783319747729"],"isbn":["9783319747712"]},"year":"2018","author":[{"full_name":"Kazda, Alexandr","last_name":"Kazda","first_name":"Alexandr","id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kozik, Marcin","last_name":"Kozik","first_name":"Marcin"},{"full_name":"McKenzie, Ralph","last_name":"McKenzie","first_name":"Ralph"},{"full_name":"Moore, Matthew","last_name":"Moore","first_name":"Matthew"}],"editor":[{"last_name":"Czelakowski","full_name":"Czelakowski, J","first_name":"J"}],"doi":"10.1007/978-3-319-74772-9_7","oa_version":"Preprint","arxiv":1,"publisher":"Springer Nature","series_title":"OCTR","day":"21","publication_status":"published","abstract":[{"text":"We prove that every congruence distributive variety has directed Jónsson terms, and every congruence modular variety has directed Gumm terms. The directed terms we construct witness every case of absorption witnessed by the original Jónsson or Gumm terms. This result is equivalent to a pair of claims about absorption for admissible preorders in congruence distributive and congruence modular varieties, respectively. For finite algebras, these absorption theorems have already seen significant applications, but until now, it was not clear if the theorems hold for general algebras as well. Our method also yields a novel proof of a result by P. Lipparini about the existence of a chain of terms (which we call Pixley terms) in varieties that are at the same time congruence distributive and k-permutable for some k.","lang":"eng"}],"status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","citation":{"short":"A. Kazda, M. Kozik, R. McKenzie, M. Moore, in:, J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, Springer Nature, Cham, 2018, pp. 203–220.","apa":"Kazda, A., Kozik, M., McKenzie, R., &#38; Moore, M. (2018). Absorption and directed Jónsson terms. In J. Czelakowski (Ed.), <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i> (Vol. 16, pp. 203–220). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-74772-9_7\">https://doi.org/10.1007/978-3-319-74772-9_7</a>","ieee":"A. Kazda, M. Kozik, R. McKenzie, and M. Moore, “Absorption and directed Jónsson terms,” in <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i>, vol. 16, J. Czelakowski, Ed. Cham: Springer Nature, 2018, pp. 203–220.","ama":"Kazda A, Kozik M, McKenzie R, Moore M. Absorption and directed Jónsson terms. In: Czelakowski J, ed. <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i>. Vol 16. OCTR. Cham: Springer Nature; 2018:203-220. doi:<a href=\"https://doi.org/10.1007/978-3-319-74772-9_7\">10.1007/978-3-319-74772-9_7</a>","chicago":"Kazda, Alexandr, Marcin Kozik, Ralph McKenzie, and Matthew Moore. “Absorption and Directed Jónsson Terms.” In <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i>, edited by J Czelakowski, 16:203–20. OCTR. Cham: Springer Nature, 2018. <a href=\"https://doi.org/10.1007/978-3-319-74772-9_7\">https://doi.org/10.1007/978-3-319-74772-9_7</a>.","ista":"Kazda A, Kozik M, McKenzie R, Moore M. 2018.Absorption and directed Jónsson terms. In: Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science. vol. 16, 203–220.","mla":"Kazda, Alexandr, et al. “Absorption and Directed Jónsson Terms.” <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i>, edited by J Czelakowski, vol. 16, Springer Nature, 2018, pp. 203–20, doi:<a href=\"https://doi.org/10.1007/978-3-319-74772-9_7\">10.1007/978-3-319-74772-9_7</a>."},"type":"book_chapter","title":"Absorption and directed Jónsson terms","date_updated":"2023-09-05T15:37:18Z","month":"03","article_processing_charge":"No","date_published":"2018-03-21T00:00:00Z","publication":"Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science","page":"203-220","_id":"10864","external_id":{"arxiv":["1502.01072"]},"date_created":"2022-03-18T10:30:32Z","main_file_link":[{"url":"https://arxiv.org/abs/1502.01072","open_access":"1"}],"volume":16,"place":"Cham","oa":1,"intvolume":"        16","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"The second author was supported by National Science Center grant DEC-2011-/01/B/ST6/01006.","scopus_import":"1"},{"quality_controlled":"1","language":[{"iso":"eng"}],"pmid":1,"status":"public","publication_status":"published","abstract":[{"text":"Acquisition of evolutionary novelties is a fundamental process for adapting to the external environment and invading new niches and results in the diversification of life, which we can see in the world today. How such novel phenotypic traits are acquired in the course of evolution and are built up in developing embryos has been a central question in biology. Whole-genome duplication (WGD) is a process of genome doubling that supplies raw genetic materials and increases genome complexity. Recently, it has been gradually revealed that WGD and subsequent fate changes of duplicated genes can facilitate phenotypic evolution. Here, we review the current understanding of the relationship between WGD and the acquisition of evolutionary novelties. We show some examples of this link and discuss how WGD and subsequent duplicated genes can facilitate phenotypic evolution as well as when such genomic doubling can be advantageous for adaptation.","lang":"eng"}],"article_type":"original","type":"journal_article","citation":{"ama":"Yuuta M, Koshiba-Takeuchi K. Significance of whole-genome duplications on the emergence of evolutionary novelties. <i>Briefings in Functional Genomics</i>. 2018;17(5):329-338. doi:<a href=\"https://doi.org/10.1093/bfgp/ely007\">10.1093/bfgp/ely007</a>","chicago":"Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome Duplications on the Emergence of Evolutionary Novelties.” <i>Briefings in Functional Genomics</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/bfgp/ely007\">https://doi.org/10.1093/bfgp/ely007</a>.","mla":"Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome Duplications on the Emergence of Evolutionary Novelties.” <i>Briefings in Functional Genomics</i>, vol. 17, no. 5, Oxford University Press, 2018, pp. 329–38, doi:<a href=\"https://doi.org/10.1093/bfgp/ely007\">10.1093/bfgp/ely007</a>.","ista":"Yuuta M, Koshiba-Takeuchi K. 2018. Significance of whole-genome duplications on the emergence of evolutionary novelties. Briefings in Functional Genomics. 17(5), 329–338.","short":"M. Yuuta, K. Koshiba-Takeuchi, Briefings in Functional Genomics 17 (2018) 329–338.","apa":"Yuuta, M., &#38; Koshiba-Takeuchi, K. (2018). Significance of whole-genome duplications on the emergence of evolutionary novelties. <i>Briefings in Functional Genomics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bfgp/ely007\">https://doi.org/10.1093/bfgp/ely007</a>","ieee":"M. Yuuta and K. Koshiba-Takeuchi, “Significance of whole-genome duplications on the emergence of evolutionary novelties,” <i>Briefings in Functional Genomics</i>, vol. 17, no. 5. Oxford University Press, pp. 329–338, 2018."},"author":[{"last_name":"Yuuta","full_name":"Yuuta, Moriyama","orcid":"0000-0002-2853-8051","id":"4968E7C8-F248-11E8-B48F-1D18A9856A87","first_name":"Moriyama"},{"first_name":"Kazuko","last_name":"Koshiba-Takeuchi","full_name":"Koshiba-Takeuchi, Kazuko"}],"isi":1,"year":"2018","publication_identifier":{"eissn":["2041-2657"],"issn":["2041-2649"]},"department":[{"_id":"CaHe"}],"day":"01","publisher":"Oxford University Press","oa_version":"Published Version","doi":"10.1093/bfgp/ely007","acknowledgement":"This work was supported by JSPS overseas research fellowships (Y.M.) and SENSHIN Medical Research Foundation (K.K.T.).","issue":"5","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"intvolume":"        17","volume":17,"main_file_link":[{"url":"https://doi.org/10.1093/bfgp/ely007","open_access":"1"}],"scopus_import":"1","date_published":"2018-09-01T00:00:00Z","article_processing_charge":"No","keyword":["Genetics","Molecular Biology","Biochemistry","General Medicine"],"month":"09","date_updated":"2023-09-19T15:11:22Z","title":"Significance of whole-genome duplications on the emergence of evolutionary novelties","date_created":"2022-03-18T12:40:35Z","external_id":{"pmid":["29579140"],"isi":["000456054400004"]},"_id":"10880","page":"329-338","publication":"Briefings in Functional Genomics"},{"quality_controlled":"1","publication_status":"published","abstract":[{"text":"Strigolactones (SLs) are a relatively recent addition to the list of plant hormones that control different aspects of plant development. SL signalling is perceived by an α/β hydrolase, DWARF 14 (D14). A close homolog of D14, KARRIKIN INSENSTIVE2 (KAI2), is involved in perception of an uncharacterized molecule called karrikin (KAR). Recent studies in Arabidopsis identified the SUPPRESSOR OF MAX2 1 (SMAX1) and SMAX1-LIKE 7 (SMXL7) to be potential SCF–MAX2 complex-mediated proteasome targets of KAI2 and D14, respectively. Genetic studies on SMXL7 and SMAX1 demonstrated distinct developmental roles for each, but very little is known about these repressors in terms of their sequence features. In this study, we performed an extensive comparative analysis of SMXLs and determined their phylogenetic and evolutionary history in the plant lineage. Our results show that SMXL family members can be sub-divided into four distinct phylogenetic clades/classes, with an ancient SMAX1. Further, we identified the clade-specific motifs that have evolved and that might act as determinants of SL-KAR signalling specificity. These specificities resulted from functional diversities among the clades. Our results suggest that a gradual co-evolution of SMXL members with their upstream receptors D14/KAI2 provided an increased specificity to both the SL perception and response in land plants.","lang":"eng"}],"pmid":1,"status":"public","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","citation":{"apa":"Moturu, T. R., Thula, S., Singh, R. K., Nodzyński, T., Vařeková, R. S., Friml, J., &#38; Simon, S. (2018). Molecular evolution and diversification of the SMXL gene family. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/ery097\">https://doi.org/10.1093/jxb/ery097</a>","short":"T.R. Moturu, S. Thula, R.K. Singh, T. Nodzyński, R.S. Vařeková, J. Friml, S. Simon, Journal of Experimental Botany 69 (2018) 2367–2378.","ieee":"T. R. Moturu <i>et al.</i>, “Molecular evolution and diversification of the SMXL gene family,” <i>Journal of Experimental Botany</i>, vol. 69, no. 9. Oxford University Press, pp. 2367–2378, 2018.","chicago":"Moturu, Taraka Ramji, Sravankumar Thula, Ravi Kumar Singh, Tomasz Nodzyński, Radka Svobodová Vařeková, Jiří Friml, and Sibu Simon. “Molecular Evolution and Diversification of the SMXL Gene Family.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/jxb/ery097\">https://doi.org/10.1093/jxb/ery097</a>.","ama":"Moturu TR, Thula S, Singh RK, et al. Molecular evolution and diversification of the SMXL gene family. <i>Journal of Experimental Botany</i>. 2018;69(9):2367-2378. doi:<a href=\"https://doi.org/10.1093/jxb/ery097\">10.1093/jxb/ery097</a>","ista":"Moturu TR, Thula S, Singh RK, Nodzyński T, Vařeková RS, Friml J, Simon S. 2018. Molecular evolution and diversification of the SMXL gene family. Journal of Experimental Botany. 69(9), 2367–2378.","mla":"Moturu, Taraka Ramji, et al. “Molecular Evolution and Diversification of the SMXL Gene Family.” <i>Journal of Experimental Botany</i>, vol. 69, no. 9, Oxford University Press, 2018, pp. 2367–78, doi:<a href=\"https://doi.org/10.1093/jxb/ery097\">10.1093/jxb/ery097</a>."},"year":"2018","isi":1,"author":[{"last_name":"Moturu","full_name":"Moturu, Taraka Ramji","first_name":"Taraka Ramji"},{"first_name":"Sravankumar","last_name":"Thula","full_name":"Thula, Sravankumar"},{"full_name":"Singh, Ravi Kumar","last_name":"Singh","first_name":"Ravi Kumar"},{"first_name":"Tomasz","last_name":"Nodzyński","full_name":"Nodzyński, Tomasz"},{"first_name":"Radka Svobodová","last_name":"Vařeková","full_name":"Vařeková, Radka Svobodová"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Simon, Sibu","last_name":"Simon","first_name":"Sibu"}],"department":[{"_id":"JiFr"}],"publication_identifier":{"issn":["0022-0957"],"eissn":["1460-2431"]},"publisher":"Oxford University Press","day":"13","doi":"10.1093/jxb/ery097","oa_version":"None","intvolume":"        69","acknowledgement":"This project received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Actions and it is co-financed by the South Moravian Region under grant agreement No. 665860 (SS). Access to computing and storage facilities owned by parties and projects contributing to the national grid infrastructure, MetaCentrum, provided under the program ‘Projects of Large Infrastructure for Research, Development, and Innovations’ (LM2010005) was greatly appreciated (RSV). The project was funded by The Ministry of Education, Youth and Sports/MES of the Czech Republic under the project CEITEC 2020 (LQ1601) (TN, TRM). JF was supported by the European Research Council (project ERC-2011-StG 20101109-PSDP) and the Czech Science Foundation GAČR (GA13-40637S). We thank Dr Kamel Chibani for active discussions on the evolutionary analysis and Nandan Mysore Vardarajan for his critical comments on the manuscript. This article reflects\r\nonly the authors’ views, and the EU is not responsible for any use that may be made of the information it contains. ","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"9","volume":69,"scopus_import":"1","article_processing_charge":"No","keyword":["Plant Science","Physiology"],"date_published":"2018-04-13T00:00:00Z","ec_funded":1,"title":"Molecular evolution and diversification of the SMXL gene family","date_updated":"2025-05-07T11:12:33Z","month":"04","project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"_id":"10881","external_id":{"isi":["000430727000016"],"pmid":["29538714"]},"date_created":"2022-03-18T12:43:22Z","publication":"Journal of Experimental Botany","page":"2367-2378"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1712.08087","open_access":"1"}],"scopus_import":"1","date_published":"2018-12-17T00:00:00Z","article_processing_charge":"No","month":"12","title":"Learning intelligent dialogs for bounding box annotation","date_updated":"2023-09-19T15:11:49Z","date_created":"2022-03-18T12:45:09Z","external_id":{"isi":["000457843609036"],"arxiv":["1712.08087"]},"_id":"10882","page":"9175-9184","publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","publication_status":"published","abstract":[{"text":"We introduce Intelligent Annotation Dialogs for bounding box annotation. We train an agent to automatically choose a sequence of actions for a human annotator to produce a bounding box in a minimal amount of time. Specifically, we consider two actions: box verification [34], where the annotator verifies a box generated by an object detector, and manual box drawing. We explore two kinds of agents, one based on predicting the probability that a box will be positively verified, and the other based on reinforcement learning. We demonstrate that (1) our agents are able to learn efficient annotation strategies in several scenarios, automatically adapting to the image difficulty, the desired quality of the boxes, and the detector strength; (2) in all scenarios the resulting annotation dialogs speed up annotation compared to manual box drawing alone and box verification alone, while also outperforming any fixed combination of verification and drawing in most scenarios; (3) in a realistic scenario where the detector is iteratively re-trained, our agents evolve a series of strategies that reflect the shifting trade-off between verification and drawing as the detector grows stronger.","lang":"eng"}],"citation":{"apa":"Uijlings, J., Konyushkova, K., Lampert, C., &#38; Ferrari, V. (2018). Learning intelligent dialogs for bounding box annotation. In <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i> (pp. 9175–9184). Salt Lake City, UT, United States: IEEE. <a href=\"https://doi.org/10.1109/cvpr.2018.00956\">https://doi.org/10.1109/cvpr.2018.00956</a>","short":"J. Uijlings, K. Konyushkova, C. Lampert, V. Ferrari, in:, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 9175–9184.","ieee":"J. Uijlings, K. Konyushkova, C. Lampert, and V. Ferrari, “Learning intelligent dialogs for bounding box annotation,” in <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Salt Lake City, UT, United States, 2018, pp. 9175–9184.","chicago":"Uijlings, Jasper, Ksenia Konyushkova, Christoph Lampert, and Vittorio Ferrari. “Learning Intelligent Dialogs for Bounding Box Annotation.” In <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, 9175–84. IEEE, 2018. <a href=\"https://doi.org/10.1109/cvpr.2018.00956\">https://doi.org/10.1109/cvpr.2018.00956</a>.","ama":"Uijlings J, Konyushkova K, Lampert C, Ferrari V. Learning intelligent dialogs for bounding box annotation. In: <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. IEEE; 2018:9175-9184. doi:<a href=\"https://doi.org/10.1109/cvpr.2018.00956\">10.1109/cvpr.2018.00956</a>","ista":"Uijlings J, Konyushkova K, Lampert C, Ferrari V. 2018. Learning intelligent dialogs for bounding box annotation. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVF: Conference on Computer Vision and Pattern Recognition, 9175–9184.","mla":"Uijlings, Jasper, et al. “Learning Intelligent Dialogs for Bounding Box Annotation.” <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, IEEE, 2018, pp. 9175–84, doi:<a href=\"https://doi.org/10.1109/cvpr.2018.00956\">10.1109/cvpr.2018.00956</a>."},"type":"conference","isi":1,"author":[{"first_name":"Jasper","full_name":"Uijlings, Jasper","last_name":"Uijlings"},{"full_name":"Konyushkova, Ksenia","last_name":"Konyushkova","first_name":"Ksenia"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert"},{"full_name":"Ferrari, Vittorio","last_name":"Ferrari","first_name":"Vittorio"}],"year":"2018","conference":{"name":"CVF: Conference on Computer Vision and Pattern Recognition","location":"Salt Lake City, UT, United States","start_date":"2018-06-18","end_date":"2018-06-23"},"department":[{"_id":"ChLa"}],"publication_identifier":{"eissn":["2575-7075"],"isbn":["9781538664209"]},"day":"17","publisher":"IEEE","oa_version":"Preprint","arxiv":1,"doi":"10.1109/cvpr.2018.00956"},{"author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Dvořák","full_name":"Dvořák, Wolfgang","first_name":"Wolfgang"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"first_name":"Alexander","last_name":"Svozil","full_name":"Svozil, Alexander"}],"conference":{"name":"LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning","end_date":"2018-11-21","start_date":"2018-11-17","location":"Awassa, Ethiopia"},"year":"2018","department":[{"_id":"KrCh"}],"publication_identifier":{"issn":["2398-7340"]},"day":"23","publisher":"EasyChair","oa_version":"Published Version","arxiv":1,"doi":"10.29007/5z5k","quality_controlled":"1","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","abstract":[{"text":"Solving parity games, which are equivalent to modal μ-calculus model checking, is a central algorithmic problem in formal methods, with applications in reactive synthesis, program repair, verification of branching-time properties, etc. Besides the standard compu- tation model with the explicit representation of games, another important theoretical model of computation is that of set-based symbolic algorithms. Set-based symbolic algorithms use basic set operations and one-step predecessor operations on the implicit description of games, rather than the explicit representation. The significance of symbolic algorithms is that they provide scalable algorithms for large finite-state systems, as well as for infinite-state systems with finite quotient. Consider parity games on graphs with n vertices and parity conditions with d priorities. While there is a rich literature of explicit algorithms for parity games, the main results for set-based symbolic algorithms are as follows: (a) the basic algorithm that requires O(nd) symbolic operations and O(d) symbolic space; and (b) an improved algorithm that requires O(nd/3+1) symbolic operations and O(n) symbolic space. In this work, our contributions are as follows: (1) We present a black-box set-based symbolic algorithm based on the explicit progress measure algorithm. Two important consequences of our algorithm are as follows: (a) a set-based symbolic algorithm for parity games that requires quasi-polynomially many symbolic operations and O(n) symbolic space; and (b) any future improvement in progress measure based explicit algorithms immediately imply an efficiency improvement in our set-based symbolic algorithm for parity games. (2) We present a set-based symbolic algorithm that requires quasi-polynomially many symbolic operations and O(d · log n) symbolic space. Moreover, for the important special case of d ≤ log n, our algorithm requires only polynomially many symbolic operations and poly-logarithmic symbolic space.","lang":"eng"}],"publication_status":"published","ddc":["000"],"citation":{"chicago":"Chatterjee, Krishnendu, Wolfgang Dvořák, Monika H Henzinger, and Alexander Svozil. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” In <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i>, 57:233–53. EasyChair, 2018. <a href=\"https://doi.org/10.29007/5z5k\">https://doi.org/10.29007/5z5k</a>.","ama":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. Quasipolynomial set-based symbolic algorithms for parity games. In: <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i>. Vol 57. EasyChair; 2018:233-253. doi:<a href=\"https://doi.org/10.29007/5z5k\">10.29007/5z5k</a>","ista":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. 2018. Quasipolynomial set-based symbolic algorithms for parity games. 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning, EPiC Series in Computing, vol. 57, 233–253.","mla":"Chatterjee, Krishnendu, et al. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i>, vol. 57, EasyChair, 2018, pp. 233–53, doi:<a href=\"https://doi.org/10.29007/5z5k\">10.29007/5z5k</a>.","short":"K. Chatterjee, W. Dvořák, M.H. Henzinger, A. Svozil, in:, 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, EasyChair, 2018, pp. 233–253.","apa":"Chatterjee, K., Dvořák, W., Henzinger, M. H., &#38; Svozil, A. (2018). Quasipolynomial set-based symbolic algorithms for parity games. In <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i> (Vol. 57, pp. 233–253). Awassa, Ethiopia: EasyChair. <a href=\"https://doi.org/10.29007/5z5k\">https://doi.org/10.29007/5z5k</a>","ieee":"K. Chatterjee, W. Dvořák, M. H. Henzinger, and A. Svozil, “Quasipolynomial set-based symbolic algorithms for parity games,” in <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i>, Awassa, Ethiopia, 2018, vol. 57, pp. 233–253."},"type":"conference","file":[{"file_id":"11392","creator":"dernst","date_created":"2022-05-17T07:51:08Z","relation":"main_file","checksum":"1229aa8640bd6db610c85decf2265480","file_size":720893,"date_updated":"2022-05-17T07:51:08Z","content_type":"application/pdf","file_name":"2018_EPiCs_Chatterjee.pdf","access_level":"open_access","success":1}],"ec_funded":1,"date_published":"2018-10-23T00:00:00Z","article_processing_charge":"No","month":"10","title":"Quasipolynomial set-based symbolic algorithms for parity games","date_updated":"2022-07-29T09:24:31Z","date_created":"2022-03-18T12:46:32Z","external_id":{"arxiv":["1909.04983"]},"_id":"10883","project":[{"name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"page":"233-253","file_date_updated":"2022-05-17T07:51:08Z","publication":"22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","acknowledgement":"A. S. is fully supported by the Vienna Science and Technology Fund (WWTF) through project ICT15-003. K.C. is supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Starting grant (279307: Graph Games). For M.H the research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013) /ERC Grant Agreement no. 340506.","oa":1,"intvolume":"        57","alternative_title":["EPiC Series in Computing"],"volume":57,"scopus_import":"1"},{"quality_controlled":"1","oa":1,"intvolume":"        32","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"1","main_file_link":[{"url":"https://arxiv.org/abs/1606.01814","open_access":"1"}],"publist_id":"6284","publication_status":"published","abstract":[{"text":"A graphical model encodes conditional independence relations via the Markov properties. For an undirected graph these conditional independence relations can be represented by a simple polytope known as the graph associahedron, which can be constructed as a Minkowski sum of standard simplices. We show that there is an analogous polytope for conditional independence relations coming from a regular Gaussian model, and it can be defined using multiinformation or relative entropy. For directed acyclic graphical models we give a construction of this polytope as a Minkowski sum of matroid polytopes. Finally, we apply this geometric insight to construct a new ordering-based search algorithm for causal inference via directed acyclic graphical models. ","lang":"eng"}],"volume":32,"status":"public","language":[{"iso":"eng"}],"extern":"1","type":"journal_article","citation":{"mla":"Mohammadi, Fatemeh, et al. “Generalized Permutohedra from Probabilistic Graphical Models.” <i>SIAM Journal on Discrete Mathematics</i>, vol. 32, no. 1, SIAM, 2018, pp. 64–93, doi:<a href=\"https://doi.org/10.1137/16M107894X\">10.1137/16M107894X</a>.","ista":"Mohammadi F, Uhler C, Wang C, Yu J. 2018. Generalized permutohedra from probabilistic graphical models. SIAM Journal on Discrete Mathematics. 32(1), 64–93.","ama":"Mohammadi F, Uhler C, Wang C, Yu J. Generalized permutohedra from probabilistic graphical models. <i>SIAM Journal on Discrete Mathematics</i>. 2018;32(1):64-93. doi:<a href=\"https://doi.org/10.1137/16M107894X\">10.1137/16M107894X</a>","chicago":"Mohammadi, Fatemeh, Caroline Uhler, Charles Wang, and Josephine Yu. “Generalized Permutohedra from Probabilistic Graphical Models.” <i>SIAM Journal on Discrete Mathematics</i>. SIAM, 2018. <a href=\"https://doi.org/10.1137/16M107894X\">https://doi.org/10.1137/16M107894X</a>.","ieee":"F. Mohammadi, C. Uhler, C. Wang, and J. Yu, “Generalized permutohedra from probabilistic graphical models,” <i>SIAM Journal on Discrete Mathematics</i>, vol. 32, no. 1. SIAM, pp. 64–93, 2018.","short":"F. Mohammadi, C. Uhler, C. Wang, J. Yu, SIAM Journal on Discrete Mathematics 32 (2018) 64–93.","apa":"Mohammadi, F., Uhler, C., Wang, C., &#38; Yu, J. (2018). Generalized permutohedra from probabilistic graphical models. <i>SIAM Journal on Discrete Mathematics</i>. SIAM. <a href=\"https://doi.org/10.1137/16M107894X\">https://doi.org/10.1137/16M107894X</a>"},"year":"2018","author":[{"id":"2C29581E-F248-11E8-B48F-1D18A9856A87","first_name":"Fatemeh","last_name":"Mohammadi","full_name":"Mohammadi, Fatemeh"},{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","last_name":"Uhler","full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216"},{"first_name":"Charles","last_name":"Wang","full_name":"Wang, Charles"},{"first_name":"Josephine","last_name":"Yu","full_name":"Yu, Josephine"}],"date_published":"2018-01-01T00:00:00Z","title":"Generalized permutohedra from probabilistic graphical models","date_updated":"2021-01-12T06:48:13Z","month":"01","_id":"1092","publisher":"SIAM","day":"01","date_created":"2018-12-11T11:50:06Z","publication":"SIAM Journal on Discrete Mathematics","doi":"10.1137/16M107894X","page":"64-93","oa_version":"Preprint"},{"scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1806.10843","open_access":"1"}],"volume":270,"oa":1,"intvolume":"       270","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"185 - 214","_id":"11","project":[{"call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems"}],"external_id":{"arxiv":["1806.10843"]},"date_created":"2018-12-11T11:44:08Z","date_updated":"2021-01-12T06:48:16Z","title":"Mean-field limits of particles in interaction with quantised radiation fields","month":"10","date_published":"2018-10-27T00:00:00Z","ec_funded":1,"citation":{"chicago":"Leopold, Nikolai K, and Peter Pickl. “Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields,” 270:185–214. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-030-01602-9_9\">https://doi.org/10.1007/978-3-030-01602-9_9</a>.","ama":"Leopold NK, Pickl P. Mean-field limits of particles in interaction with quantised radiation fields. In: Vol 270. Springer; 2018:185-214. doi:<a href=\"https://doi.org/10.1007/978-3-030-01602-9_9\">10.1007/978-3-030-01602-9_9</a>","ista":"Leopold NK, Pickl P. 2018. Mean-field limits of particles in interaction with quantised radiation fields. MaLiQS: Macroscopic Limits of Quantum Systems vol. 270, 185–214.","mla":"Leopold, Nikolai K., and Peter Pickl. <i>Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields</i>. Vol. 270, Springer, 2018, pp. 185–214, doi:<a href=\"https://doi.org/10.1007/978-3-030-01602-9_9\">10.1007/978-3-030-01602-9_9</a>.","short":"N.K. Leopold, P. Pickl, in:, Springer, 2018, pp. 185–214.","apa":"Leopold, N. K., &#38; Pickl, P. (2018). Mean-field limits of particles in interaction with quantised radiation fields (Vol. 270, pp. 185–214). Presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany: Springer. <a href=\"https://doi.org/10.1007/978-3-030-01602-9_9\">https://doi.org/10.1007/978-3-030-01602-9_9</a>","ieee":"N. K. Leopold and P. Pickl, “Mean-field limits of particles in interaction with quantised radiation fields,” presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany, 2018, vol. 270, pp. 185–214."},"type":"conference","publist_id":"8045","abstract":[{"text":"We report on a novel strategy to derive mean-field limits of quantum mechanical systems in which a large number of particles weakly couple to a second-quantized radiation field. The technique combines the method of counting and the coherent state approach to study the growth of the correlations among the particles and in the radiation field. As an instructional example, we derive the Schrödinger–Klein–Gordon system of equations from the Nelson model with ultraviolet cutoff and possibly massless scalar field. In particular, we prove the convergence of the reduced density matrices (of the nonrelativistic particles and the field bosons) associated with the exact time evolution to the projectors onto the solutions of the Schrödinger–Klein–Gordon equations in trace norm. Furthermore, we derive explicit bounds on the rate of convergence of the one-particle reduced density matrix of the nonrelativistic particles in Sobolev norm.","lang":"eng"}],"publication_status":"published","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","doi":"10.1007/978-3-030-01602-9_9","oa_version":"Preprint","arxiv":1,"publisher":"Springer","day":"27","department":[{"_id":"RoSe"}],"year":"2018","conference":{"location":"Munich, Germany","start_date":"2017-03-30","end_date":"2017-04-01","name":"MaLiQS: Macroscopic Limits of Quantum Systems"},"author":[{"id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","first_name":"Nikolai K","full_name":"Leopold, Nikolai K","orcid":"0000-0002-0495-6822","last_name":"Leopold"},{"first_name":"Peter","full_name":"Pickl, Peter","last_name":"Pickl"}]},{"author":[{"full_name":"McCloskey, Asako","last_name":"McCloskey","first_name":"Asako"},{"first_name":"Arkaitz","last_name":"Ibarra","full_name":"Ibarra, Arkaitz"},{"last_name":"HETZER","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"year":"2018","publication_identifier":{"issn":["0890-9369","1549-5477"]},"publisher":"Cold Spring Harbor Laboratory","day":"18","doi":"10.1101/gad.315523.118","oa_version":"Published Version","quality_controlled":"1","publication_status":"published","abstract":[{"text":"The total number of nuclear pore complexes (NPCs) per nucleus varies greatly between different cell types and is known to change during cell differentiation and cell transformation. However, the underlying mechanisms that control how many nuclear transport channels are assembled into a given nuclear envelope remain unclear. Here, we report that depletion of the NPC basket protein Tpr, but not Nup153, dramatically increases the total NPC number in various cell types. This negative regulation of Tpr occurs via a phosphorylation cascade of extracellular signal-regulated kinase (ERK), the central kinase of the mitogen-activated protein kinase (MAPK) pathway. Tpr serves as a scaffold for ERK to phosphorylate the nucleoporin (Nup) Nup153, which is critical for early stages of NPC biogenesis. Our results reveal a critical role of the Nup Tpr in coordinating signal transduction pathways during cell proliferation and the dynamic organization of the nucleus.","lang":"eng"}],"language":[{"iso":"eng"}],"status":"public","pmid":1,"article_type":"original","type":"journal_article","citation":{"ieee":"A. McCloskey, A. Ibarra, and M. Hetzer, “Tpr regulates the total number of nuclear pore complexes per cell nucleus,” <i>Genes &#38; Development</i>, vol. 32, no. 19–20. Cold Spring Harbor Laboratory, pp. 1321–1331, 2018.","apa":"McCloskey, A., Ibarra, A., &#38; Hetzer, M. (2018). Tpr regulates the total number of nuclear pore complexes per cell nucleus. <i>Genes &#38; Development</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/gad.315523.118\">https://doi.org/10.1101/gad.315523.118</a>","short":"A. McCloskey, A. Ibarra, M. Hetzer, Genes &#38; Development 32 (2018) 1321–1331.","ista":"McCloskey A, Ibarra A, Hetzer M. 2018. Tpr regulates the total number of nuclear pore complexes per cell nucleus. Genes &#38; Development. 32(19–20), 1321–1331.","mla":"McCloskey, Asako, et al. “Tpr Regulates the Total Number of Nuclear Pore Complexes per Cell Nucleus.” <i>Genes &#38; Development</i>, vol. 32, no. 19–20, Cold Spring Harbor Laboratory, 2018, pp. 1321–31, doi:<a href=\"https://doi.org/10.1101/gad.315523.118\">10.1101/gad.315523.118</a>.","chicago":"McCloskey, Asako, Arkaitz Ibarra, and Martin Hetzer. “Tpr Regulates the Total Number of Nuclear Pore Complexes per Cell Nucleus.” <i>Genes &#38; Development</i>. Cold Spring Harbor Laboratory, 2018. <a href=\"https://doi.org/10.1101/gad.315523.118\">https://doi.org/10.1101/gad.315523.118</a>.","ama":"McCloskey A, Ibarra A, Hetzer M. Tpr regulates the total number of nuclear pore complexes per cell nucleus. <i>Genes &#38; Development</i>. 2018;32(19-20):1321-1331. doi:<a href=\"https://doi.org/10.1101/gad.315523.118\">10.1101/gad.315523.118</a>"},"date_published":"2018-09-18T00:00:00Z","article_processing_charge":"No","keyword":["Developmental Biology","Genetics"],"date_updated":"2022-07-18T08:32:32Z","title":"Tpr regulates the total number of nuclear pore complexes per cell nucleus","month":"09","_id":"11063","date_created":"2022-04-07T07:45:30Z","external_id":{"pmid":["30228202"]},"publication":"Genes & Development","page":"1321-1331","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","issue":"19-20","intvolume":"        32","oa":1,"volume":32,"main_file_link":[{"url":"https://doi.org/10.1101/gad.315523.118","open_access":"1"}],"scopus_import":"1","extern":"1"},{"publication":"Genome Biology","external_id":{"pmid":["30567591"]},"date_created":"2022-04-07T07:45:40Z","_id":"11064","month":"12","date_updated":"2022-07-18T08:32:34Z","title":"Predicting age from the transcriptome of human dermal fibroblasts","article_processing_charge":"No","date_published":"2018-12-20T00:00:00Z","extern":"1","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s13059-018-1599-6"}],"volume":19,"oa":1,"intvolume":"        19","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","article_number":"221","oa_version":"Published Version","doi":"10.1186/s13059-018-1599-6","day":"20","publisher":"BioMed Central","publication_identifier":{"issn":["1474-760X"]},"year":"2018","author":[{"full_name":"Fleischer, Jason G.","last_name":"Fleischer","first_name":"Jason G."},{"first_name":"Roberta","full_name":"Schulte, Roberta","last_name":"Schulte"},{"first_name":"Hsiao H.","last_name":"Tsai","full_name":"Tsai, Hsiao H."},{"last_name":"Tyagi","full_name":"Tyagi, Swati","first_name":"Swati"},{"last_name":"Ibarra","full_name":"Ibarra, Arkaitz","first_name":"Arkaitz"},{"first_name":"Maxim N.","full_name":"Shokhirev, Maxim N.","last_name":"Shokhirev"},{"first_name":"Ling","last_name":"Huang","full_name":"Huang, Ling"},{"full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"},{"first_name":"Saket","full_name":"Navlakha, Saket","last_name":"Navlakha"}],"type":"journal_article","citation":{"ama":"Fleischer JG, Schulte R, Tsai HH, et al. Predicting age from the transcriptome of human dermal fibroblasts. <i>Genome Biology</i>. 2018;19. doi:<a href=\"https://doi.org/10.1186/s13059-018-1599-6\">10.1186/s13059-018-1599-6</a>","chicago":"Fleischer, Jason G., Roberta Schulte, Hsiao H. Tsai, Swati Tyagi, Arkaitz Ibarra, Maxim N. Shokhirev, Ling Huang, Martin Hetzer, and Saket Navlakha. “Predicting Age from the Transcriptome of Human Dermal Fibroblasts.” <i>Genome Biology</i>. BioMed Central, 2018. <a href=\"https://doi.org/10.1186/s13059-018-1599-6\">https://doi.org/10.1186/s13059-018-1599-6</a>.","ista":"Fleischer JG, Schulte R, Tsai HH, Tyagi S, Ibarra A, Shokhirev MN, Huang L, Hetzer M, Navlakha S. 2018. Predicting age from the transcriptome of human dermal fibroblasts. Genome Biology. 19, 221.","mla":"Fleischer, Jason G., et al. “Predicting Age from the Transcriptome of Human Dermal Fibroblasts.” <i>Genome Biology</i>, vol. 19, 221, BioMed Central, 2018, doi:<a href=\"https://doi.org/10.1186/s13059-018-1599-6\">10.1186/s13059-018-1599-6</a>.","apa":"Fleischer, J. G., Schulte, R., Tsai, H. H., Tyagi, S., Ibarra, A., Shokhirev, M. N., … Navlakha, S. (2018). Predicting age from the transcriptome of human dermal fibroblasts. <i>Genome Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13059-018-1599-6\">https://doi.org/10.1186/s13059-018-1599-6</a>","short":"J.G. Fleischer, R. Schulte, H.H. Tsai, S. Tyagi, A. Ibarra, M.N. Shokhirev, L. Huang, M. Hetzer, S. Navlakha, Genome Biology 19 (2018).","ieee":"J. G. Fleischer <i>et al.</i>, “Predicting age from the transcriptome of human dermal fibroblasts,” <i>Genome Biology</i>, vol. 19. BioMed Central, 2018."},"article_type":"original","status":"public","pmid":1,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Biomarkers of aging can be used to assess the health of individuals and to study aging and age-related diseases. We generate a large dataset of genome-wide RNA-seq profiles of human dermal fibroblasts from 133 people aged 1 to 94 years old to test whether signatures of aging are encoded within the transcriptome. We develop an ensemble machine learning method that predicts age to a median error of 4 years, outperforming previous methods used to predict age. The ensemble was further validated by testing it on ten progeria patients, and our method is the only one that predicts accelerated aging in these patients."}],"publication_status":"published","quality_controlled":"1"}]