[{"year":"2018","day":"31","abstract":[{"lang":"eng","text":"This document contains additional supporting evidence presented as supplemental tables. (XLSX 50Â kb)"}],"date_updated":"2023-09-13T09:01:31Z","_id":"9811","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"},{"first_name":"Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor"},{"full_name":"Ossowski, Stephan","last_name":"Ossowski","first_name":"Stephan"},{"first_name":"Martin","last_name":"Schaefer","full_name":"Schaefer, Martin"}],"oa":1,"title":"Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","publisher":"Springer Nature","month":"05","date_created":"2021-08-06T12:53:49Z","doi":"10.6084/m9.figshare.6401390.v1","department":[{"_id":"FyKo"}],"date_published":"2018-05-31T00:00:00Z","type":"research_data_reference","oa_version":"Preprint","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.6401390.v1","open_access":"1"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"279"}]},"citation":{"ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:<a href=\"https://doi.org/10.6084/m9.figshare.6401390.v1\">10.6084/m9.figshare.6401390.v1</a>","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. <a href=\"https://doi.org/10.6084/m9.figshare.6401390.v1\">https://doi.org/10.6084/m9.figshare.6401390.v1</a>.","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., &#38; Schaefer, M. (2018). Additional file 1: 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.6401390.v1\">https://doi.org/10.6084/m9.figshare.6401390.v1</a>","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.6401390.v1\">10.6084/m9.figshare.6401390.v1</a>.","mla":"Zapata, Luis, et al. <i>Additional File 1: 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.6401390.v1\">10.6084/m9.figshare.6401390.v1</a>."}},{"date_updated":"2023-09-13T09:01:31Z","abstract":[{"text":"This document contains the full list of genes with their respective significance and dN/dS values. (TXT 4499Â kb)","lang":"eng"}],"day":"31","year":"2018","author":[{"full_name":"Zapata, Luis","first_name":"Luis","last_name":"Zapata"},{"first_name":"Oriol","last_name":"Pich","full_name":"Pich, Oriol"},{"last_name":"Serrano","first_name":"Luis","full_name":"Serrano, Luis"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"last_name":"Ossowski","first_name":"Stephan","full_name":"Ossowski, Stephan"},{"first_name":"Martin","last_name":"Schaefer","full_name":"Schaefer, Martin"}],"_id":"9812","status":"public","publisher":"Springer Nature","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","oa":1,"month":"05","doi":"10.6084/m9.figshare.6401414.v1","date_created":"2021-08-06T12:58:25Z","type":"research_data_reference","oa_version":"Published Version","date_published":"2018-05-31T00:00:00Z","department":[{"_id":"FyKo"}],"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.6401414.v1","open_access":"1"}],"article_processing_charge":"No","citation":{"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.","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>","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","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>.","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>"},"related_material":{"record":[{"id":"279","status":"public","relation":"used_in_publication"}]}},{"date_created":"2021-08-06T13:04:32Z","doi":"10.25386/genetics.6148304.v1","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"date_published":"2018-04-30T00:00:00Z","oa_version":"Published Version","type":"research_data_reference","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.25386/genetics.6148304.v1"}],"related_material":{"record":[{"id":"316","status":"public","relation":"used_in_publication"}]},"citation":{"short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).","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>","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.","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>.","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>","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>.","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>."},"year":"2018","day":"30","abstract":[{"lang":"eng","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."}],"date_updated":"2025-05-28T11:57:01Z","_id":"9813","author":[{"first_name":"Katarína","orcid":"0000-0002-7214-0171","last_name":"Bod'ová","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","full_name":"Bod'ová, Katarína"},{"full_name":"Priklopil, Tadeas","first_name":"Tadeas","last_name":"Priklopil","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Field, David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H"},{"first_name":"Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","full_name":"Pickup, Melinda"}],"oa":1,"title":"Supplemental material for Bodova et al., 2018","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Genetics Society of America","status":"public","month":"04"},{"abstract":[{"text":"Implementation of the inference method in Matlab, including three applications of the method: The first one for the model of ant motion, the second one for bacterial chemotaxis, and the third one for the motion of fish.","lang":"eng"}],"date_updated":"2023-09-15T12:06:18Z","year":"2018","day":"07","author":[{"last_name":"Bod’Ová","first_name":"Katarína","full_name":"Bod’Ová, Katarína"},{"first_name":"Gabriel","last_name":"Mitchell","id":"315BCD80-F248-11E8-B48F-1D18A9856A87","full_name":"Mitchell, Gabriel"},{"first_name":"Roy","last_name":"Harpaz","full_name":"Harpaz, Roy"},{"full_name":"Schneidman, Elad","first_name":"Elad","last_name":"Schneidman"},{"full_name":"Tkačik, Gašper","first_name":"Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"_id":"9831","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","publisher":"Public Library of Science","title":"Implementation of the inference method in Matlab","month":"03","doi":"10.1371/journal.pone.0193049.s001","date_created":"2021-08-09T07:01:24Z","type":"research_data_reference","oa_version":"Published Version","department":[{"_id":"GaTk"}],"date_published":"2018-03-07T00:00:00Z","article_processing_charge":"No","citation":{"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>","ieee":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Implementation of the inference method in Matlab.” Public Library of Science, 2018.","short":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, (2018).","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>.","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>"},"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"406"}]}},{"author":[{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"last_name":"Chaube","first_name":"Pragya","full_name":"Chaube, Pragya"},{"full_name":"Morales, Hernán E.","last_name":"Morales","first_name":"Hernán E."},{"full_name":"Larsson, Tomas","last_name":"Larsson","first_name":"Tomas"},{"full_name":"Lemmon, Alan R.","last_name":"Lemmon","first_name":"Alan R."},{"full_name":"Lemmon, Emily M.","last_name":"Lemmon","first_name":"Emily M."},{"full_name":"Rafajlović, Marina","last_name":"Rafajlović","first_name":"Marina"},{"full_name":"Panova, Marina","last_name":"Panova","first_name":"Marina"},{"full_name":"Ravinet, Mark","first_name":"Mark","last_name":"Ravinet"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"_id":"9837","abstract":[{"lang":"eng","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."}],"date_updated":"2023-08-24T14:50:26Z","year":"2018","day":"09","month":"10","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","publisher":"Dryad","oa":1,"title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","oa_version":"Published Version","type":"research_data_reference","department":[{"_id":"NiBa"}],"date_published":"2018-10-09T00:00:00Z","doi":"10.5061/dryad.72cg113","date_created":"2021-08-09T12:46:39Z","citation":{"short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, (2018).","ieee":"R. Faria <i>et al.</i>, “Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.","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>","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>.","ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes, Dryad, <a href=\"https://doi.org/10.5061/dryad.72cg113\">10.5061/dryad.72cg113</a>.","mla":"Faria, Rui, et al. <i>Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.72cg113\">10.5061/dryad.72cg113</a>.","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>"},"related_material":{"record":[{"id":"6095","relation":"used_in_publication","status":"public"}]},"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.72cg113"}]},{"citation":{"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>.","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>.","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>","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>","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)."},"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"162"}]},"article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.5061/dryad.f1s76f2","open_access":"1"}],"oa_version":"Published Version","type":"research_data_reference","department":[{"_id":"AnKi"}],"date_published":"2018-06-14T00:00:00Z","doi":"10.5061/dryad.f1s76f2","date_created":"2021-08-09T12:54:35Z","month":"06","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","publisher":"Dryad","oa":1,"title":"Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","author":[{"last_name":"Kaucka","first_name":"Marketa","full_name":"Kaucka, Marketa"},{"last_name":"Petersen","first_name":"Julian","full_name":"Petersen, Julian"},{"full_name":"Tesarova, Marketa","last_name":"Tesarova","first_name":"Marketa"},{"full_name":"Szarowska, Bara","last_name":"Szarowska","first_name":"Bara"},{"first_name":"Maria Eleni","last_name":"Kastriti","full_name":"Kastriti, Maria Eleni"},{"full_name":"Xie, Meng","last_name":"Xie","first_name":"Meng"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","orcid":"0000-0003-4509-4998","first_name":"Anna","full_name":"Kicheva, Anna"},{"full_name":"Annusver, Karl","last_name":"Annusver","first_name":"Karl"},{"last_name":"Kasper","first_name":"Maria","full_name":"Kasper, Maria"},{"first_name":"Orsolya","last_name":"Symmons","full_name":"Symmons, Orsolya"},{"full_name":"Pan, Leslie","first_name":"Leslie","last_name":"Pan"},{"first_name":"Francois","last_name":"Spitz","full_name":"Spitz, Francois"},{"full_name":"Kaiser, Jozef","last_name":"Kaiser","first_name":"Jozef"},{"full_name":"Hovorakova, Maria","first_name":"Maria","last_name":"Hovorakova"},{"full_name":"Zikmund, Tomas","first_name":"Tomas","last_name":"Zikmund"},{"last_name":"Sunadome","first_name":"Kazunori","full_name":"Sunadome, Kazunori"},{"full_name":"Matise, Michael P","last_name":"Matise","first_name":"Michael P"},{"first_name":"Hui","last_name":"Wang","full_name":"Wang, Hui"},{"full_name":"Marklund, Ulrika","last_name":"Marklund","first_name":"Ulrika"},{"last_name":"Abdo","first_name":"Hind","full_name":"Abdo, Hind"},{"full_name":"Ernfors, Patrik","first_name":"Patrik","last_name":"Ernfors"},{"first_name":"Pascal","last_name":"Maire","full_name":"Maire, Pascal"},{"full_name":"Wurmser, Maud","first_name":"Maud","last_name":"Wurmser"},{"first_name":"Andrei S","last_name":"Chagin","full_name":"Chagin, Andrei S"},{"full_name":"Fried, Kaj","last_name":"Fried","first_name":"Kaj"},{"full_name":"Adameyko, Igor","first_name":"Igor","last_name":"Adameyko"}],"_id":"9838","abstract":[{"lang":"eng","text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts."}],"date_updated":"2023-09-18T09:29:07Z","year":"2018","day":"14"},{"type":"research_data_reference","oa_version":"Published Version","date_published":"2018-03-12T00:00:00Z","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"doi":"10.5061/dryad.42n44","date_created":"2021-08-09T13:10:02Z","citation":{"short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).","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>","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.","mla":"Payne, Pavel, et al. <i>Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.42n44\">10.5061/dryad.42n44</a>.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., &#38; Bollback, J. P. (2018). Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. Dryad. <a href=\"https://doi.org/10.5061/dryad.42n44\">https://doi.org/10.5061/dryad.42n44</a>","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>.","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>."},"related_material":{"record":[{"id":"423","relation":"used_in_publication","status":"public"}]},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.42n44","open_access":"1"}],"article_processing_charge":"No","author":[{"last_name":"Payne","id":"35F78294-F248-11E8-B48F-1D18A9856A87","first_name":"Pavel","orcid":"0000-0002-2711-9453","full_name":"Payne, Pavel"},{"full_name":"Geyrhofer, Lukas","first_name":"Lukas","last_name":"Geyrhofer"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","full_name":"Bollback, Jonathan P"}],"_id":"9840","date_updated":"2023-09-11T12:49:17Z","abstract":[{"text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity.","lang":"eng"}],"day":"12","year":"2018","month":"03","status":"public","publisher":"Dryad","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations","oa":1},{"citation":{"ieee":"M. C. Harrison <i>et al.</i>, “Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality.” Dryad, 2018.","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>","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>."},"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"448"}]},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.51d4r","open_access":"1"}],"article_processing_charge":"No","type":"research_data_reference","oa_version":"Published Version","date_published":"2018-12-12T00:00:00Z","department":[{"_id":"BeVi"}],"doi":"10.5061/dryad.51d4r","date_created":"2021-08-09T13:13:48Z","month":"12","status":"public","publisher":"Dryad","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality","oa":1,"author":[{"last_name":"Harrison","first_name":"Mark C.","full_name":"Harrison, Mark C."},{"full_name":"Jongepier, Evelien","last_name":"Jongepier","first_name":"Evelien"},{"last_name":"Robertson","first_name":"Hugh M.","full_name":"Robertson, Hugh M."},{"full_name":"Arning, Nicolas","last_name":"Arning","first_name":"Nicolas"},{"full_name":"Bitard-Feildel, Tristan","last_name":"Bitard-Feildel","first_name":"Tristan"},{"first_name":"Hsu","last_name":"Chao","full_name":"Chao, Hsu"},{"first_name":"Christopher P.","last_name":"Childers","full_name":"Childers, Christopher P."},{"full_name":"Dinh, Huyen","first_name":"Huyen","last_name":"Dinh"},{"last_name":"Doddapaneni","first_name":"Harshavardhan","full_name":"Doddapaneni, Harshavardhan"},{"first_name":"Shannon","last_name":"Dugan","full_name":"Dugan, Shannon"},{"first_name":"Johannes","last_name":"Gowin","full_name":"Gowin, Johannes"},{"last_name":"Greiner","first_name":"Carolin","full_name":"Greiner, Carolin"},{"first_name":"Yi","last_name":"Han","full_name":"Han, Yi"},{"last_name":"Hu","first_name":"Haofu","full_name":"Hu, Haofu"},{"last_name":"Hughes","first_name":"Daniel S. T.","full_name":"Hughes, Daniel S. T."},{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans","orcid":"0000-0001-8871-4961","first_name":"Ann K","full_name":"Huylmans, Ann K"},{"full_name":"Kemena, Carsten","first_name":"Carsten","last_name":"Kemena"},{"full_name":"Kremer, Lukas P. M.","first_name":"Lukas P. M.","last_name":"Kremer"},{"full_name":"Lee, Sandra L.","last_name":"Lee","first_name":"Sandra L."},{"full_name":"Lopez-Ezquerra, Alberto","first_name":"Alberto","last_name":"Lopez-Ezquerra"},{"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","last_name":"Moser","full_name":"Moser, Annabell"},{"full_name":"Murali, Shwetha C.","first_name":"Shwetha C.","last_name":"Murali"},{"last_name":"Muzny","first_name":"Donna M.","full_name":"Muzny, Donna M."},{"full_name":"Otani, Saria","last_name":"Otani","first_name":"Saria"},{"first_name":"Maria-Dolors","last_name":"Piulachs","full_name":"Piulachs, Maria-Dolors"},{"full_name":"Poelchau, Monica","first_name":"Monica","last_name":"Poelchau"},{"full_name":"Qu, Jiaxin","first_name":"Jiaxin","last_name":"Qu"},{"last_name":"Schaub","first_name":"Florentine","full_name":"Schaub, Florentine"},{"full_name":"Wada-Katsumata, Ayako","first_name":"Ayako","last_name":"Wada-Katsumata"},{"full_name":"Worley, Kim C.","last_name":"Worley","first_name":"Kim C."},{"full_name":"Xie, Qiaolin","first_name":"Qiaolin","last_name":"Xie"},{"full_name":"Ylla, Guillem","first_name":"Guillem","last_name":"Ylla"},{"last_name":"Poulsen","first_name":"Michael","full_name":"Poulsen, Michael"},{"last_name":"Gibbs","first_name":"Richard A.","full_name":"Gibbs, Richard A."},{"full_name":"Schal, Coby","last_name":"Schal","first_name":"Coby"},{"full_name":"Richards, Stephen","last_name":"Richards","first_name":"Stephen"},{"last_name":"Belles","first_name":"Xavier","full_name":"Belles, Xavier"},{"full_name":"Korb, Judith","last_name":"Korb","first_name":"Judith"},{"full_name":"Bornberg-Bauer, Erich","last_name":"Bornberg-Bauer","first_name":"Erich"}],"_id":"9841","date_updated":"2023-09-11T14:10:56Z","abstract":[{"lang":"eng","text":"Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity."}],"day":"12","year":"2018"},{"pmid":1,"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.","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"13","author":[{"full_name":"Hollander, Johan","first_name":"Johan","last_name":"Hollander"},{"first_name":"Mauricio","last_name":"Montaño-Rendón","full_name":"Montaño-Rendón, Mauricio"},{"full_name":"Bianco, Giuseppe","last_name":"Bianco","first_name":"Giuseppe"},{"first_name":"Xi","last_name":"Yang","full_name":"Yang, Xi"},{"orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"last_name":"Duvaux","first_name":"Ludovic","full_name":"Duvaux, Ludovic"},{"full_name":"Reid, David G.","last_name":"Reid","first_name":"David G."},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."}],"isi":1,"file":[{"date_created":"2021-08-16T07:37:28Z","date_updated":"2021-08-16T07:37:28Z","file_name":"2018_EvolutionLetters_Hollander.pdf","access_level":"open_access","file_id":"9916","creator":"asandaue","checksum":"997a78ac41c809975ca69cbdea441f88","success":1,"file_size":584606,"content_type":"application/pdf","relation":"main_file"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Wiley","title":"Are assortative mating and genital divergence driven by reinforcement?","has_accepted_license":"1","publication":"Evolution Letters","page":"557-566","date_created":"2021-08-16T07:30:00Z","type":"journal_article","department":[{"_id":"BeVi"}],"language":[{"iso":"eng"}],"article_type":"letter_note","article_processing_charge":"Yes","quality_controlled":"1","volume":2,"external_id":{"pmid":["30564439"],"isi":["000452990000002"]},"related_material":{"record":[{"relation":"research_data","status":"public","id":"9929"}]},"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"}],"issue":"6","date_updated":"2023-09-19T15:08:53Z","year":"2018","_id":"9915","status":"public","publication_identifier":{"eissn":["2056-3744"],"issn":[" 2056-3744"]},"oa":1,"month":"12","doi":"10.1002/evl3.85","publication_status":"published","oa_version":"Published Version","date_published":"2018-12-13T00:00:00Z","file_date_updated":"2021-08-16T07:37:28Z","ddc":["570"],"citation":{"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>","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.","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>","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.","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>."},"intvolume":"         2"},{"month":"08","publication_identifier":{"issn":["2056-3744"],"eissn":["2056-3744"]},"oa":1,"status":"public","_id":"9917","year":"2018","date_updated":"2023-09-19T15:08:25Z","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."}],"issue":"4","citation":{"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>","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.","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.","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>.","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>.","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>"},"intvolume":"         2","ddc":["570"],"file_date_updated":"2021-08-16T07:48:03Z","date_published":"2018-08-20T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1002/evl3.74","title":"Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow","publisher":"Wiley","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_size":764299,"success":1,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","checksum":"8524e72507d521416be3f8ccfcd5e3f5","creator":"asandaue","file_id":"9918","date_created":"2021-08-16T07:48:03Z","file_name":"2018_EvolutionLetters_Westram.pdf","date_updated":"2021-08-16T07:48:03Z"}],"author":[{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"last_name":"Chaube","first_name":"Pragya","full_name":"Chaube, Pragya"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"full_name":"Larsson, Tomas","last_name":"Larsson","first_name":"Tomas"},{"last_name":"Panova","first_name":"Marina","full_name":"Panova, Marina"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"},{"full_name":"Blomberg, Anders","first_name":"Anders","last_name":"Blomberg"},{"full_name":"Mehlig, Bernhard","first_name":"Bernhard","last_name":"Mehlig"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"full_name":"Butlin, Roger","first_name":"Roger","last_name":"Butlin"}],"isi":1,"day":"20","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"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.","pmid":1,"related_material":{"record":[{"id":"9930","status":"public","relation":"research_data"}]},"external_id":{"isi":["000446774400004"],"pmid":["30283683"]},"quality_controlled":"1","volume":2,"article_type":"letter_note","article_processing_charge":"Yes","language":[{"iso":"eng"}],"department":[{"_id":"BeVi"}],"type":"journal_article","date_created":"2021-08-16T07:45:38Z","page":"297-309","publication":"Evolution Letters","has_accepted_license":"1"},{"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"9915"}]},"citation":{"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>.","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>.","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>","short":"J. Hollander, M. Montaño-Rendón, G. Bianco, X. Yang, A.M. Westram, L. Duvaux, D.G. Reid, R.K. Butlin, (2018).","ieee":"J. Hollander <i>et al.</i>, “Data from: Are assortative mating and genital divergence driven by reinforcement?” Dryad, 2018.","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>"},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.51sd2p5","open_access":"1"}],"article_processing_charge":"No","date_published":"2018-10-17T00:00:00Z","department":[{"_id":"BeVi"}],"oa_version":"Published Version","type":"research_data_reference","date_created":"2021-08-17T08:51:06Z","doi":"10.5061/dryad.51sd2p5","month":"10","title":"Data from: Are assortative mating and genital divergence driven by reinforcement?","oa":1,"publisher":"Dryad","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9929","author":[{"first_name":"Johan","last_name":"Hollander","full_name":"Hollander, Johan"},{"first_name":"Mauricio","last_name":"Montaño-Rendón","full_name":"Montaño-Rendón, Mauricio"},{"last_name":"Bianco","first_name":"Giuseppe","full_name":"Bianco, Giuseppe"},{"last_name":"Yang","first_name":"Xi","full_name":"Yang, Xi"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","orcid":"0000-0003-1050-4969","first_name":"Anja M","full_name":"Westram, Anja M"},{"first_name":"Ludovic","last_name":"Duvaux","full_name":"Duvaux, Ludovic"},{"full_name":"Reid, David G.","first_name":"David G.","last_name":"Reid"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"day":"17","year":"2018","date_updated":"2023-09-19T15:08:53Z","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"}]},{"date_created":"2021-08-17T08:58:47Z","doi":"10.5061/dryad.bp25b65","department":[{"_id":"BeVi"}],"date_published":"2018-07-23T00:00:00Z","type":"research_data_reference","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.5061/dryad.bp25b65","open_access":"1"}],"article_processing_charge":"No","related_material":{"record":[{"id":"9917","relation":"used_in_publication","status":"public"}]},"citation":{"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).","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>","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>.","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>","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>.","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>."},"day":"23","year":"2018","date_updated":"2023-09-19T15:08:24Z","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"}],"_id":"9930","author":[{"first_name":"Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"last_name":"Rafajlović","first_name":"Marina","full_name":"Rafajlović, Marina"},{"last_name":"Chaube","first_name":"Pragya","full_name":"Chaube, Pragya"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"last_name":"Larsson","first_name":"Tomas","full_name":"Larsson, Tomas"},{"last_name":"Panova","first_name":"Marina","full_name":"Panova, Marina"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"},{"first_name":"Anders","last_name":"Blomberg","full_name":"Blomberg, Anders"},{"full_name":"Mehlig, Bernhard","last_name":"Mehlig","first_name":"Bernhard"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger","first_name":"Roger","last_name":"Butlin"}],"title":"Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow","oa":1,"status":"public","publisher":"Dryad","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"07"},{"title":"Sensor synthesis for POMDPs with reachability objectives","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"AAAI Press","alternative_title":["ICAPS"],"day":"01","isi":1,"author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Chemlík","first_name":"Martin","full_name":"Chemlík, Martin"},{"full_name":"Topcu, Ufuk","last_name":"Topcu","first_name":"Ufuk"}],"project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","publist_id":"8021","quality_controlled":"1","volume":2018,"external_id":{"isi":["000492986200006"],"arxiv":["1710.00675"]},"page":"47 - 55","date_created":"2018-12-11T11:44:16Z","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"type":"conference","oa":1,"status":"public","ec_funded":1,"month":"06","year":"2018","abstract":[{"text":"Partially observable Markov decision processes (POMDPs) are widely used in probabilistic planning problems in which an agent interacts with an environment using noisy and imprecise sensors. We study a setting in which the sensors are only partially defined and the goal is to synthesize “weakest” additional sensors, such that in the resulting POMDP, there is a small-memory policy for the agent that almost-surely (with probability 1) satisfies a reachability objective. We show that the problem is NP-complete, and present a symbolic algorithm by encoding the problem into SAT instances. We illustrate trade-offs between the amount of memory of the policy and the number of additional sensors on a simple example. We have implemented our approach and consider three classical POMDP examples from the literature, and show that in all the examples the number of sensors can be significantly decreased (as compared to the existing solutions in the literature) without increasing the complexity of the policies.","lang":"eng"}],"arxiv":1,"date_updated":"2023-09-19T14:44:14Z","_id":"34","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.00675"}],"citation":{"short":"K. Chatterjee, M. Chemlík, U. Topcu, in:, AAAI Press, 2018, pp. 47–55.","ama":"Chatterjee K, Chemlík M, Topcu U. Sensor synthesis for POMDPs with reachability objectives. In: Vol 2018. AAAI Press; 2018:47-55.","ieee":"K. Chatterjee, M. Chemlík, and U. Topcu, “Sensor synthesis for POMDPs with reachability objectives,” presented at the ICAPS: International Conference on Automated Planning and Scheduling, Delft, Netherlands, 2018, vol. 2018, pp. 47–55.","apa":"Chatterjee, K., Chemlík, M., &#38; Topcu, U. (2018). Sensor synthesis for POMDPs with reachability objectives (Vol. 2018, pp. 47–55). Presented at the ICAPS: International Conference on Automated Planning and Scheduling, Delft, Netherlands: AAAI Press.","ista":"Chatterjee K, Chemlík M, Topcu U. 2018. Sensor synthesis for POMDPs with reachability objectives. ICAPS: International Conference on Automated Planning and Scheduling, ICAPS, vol. 2018, 47–55.","mla":"Chatterjee, Krishnendu, et al. <i>Sensor Synthesis for POMDPs with Reachability Objectives</i>. Vol. 2018, AAAI Press, 2018, pp. 47–55.","chicago":"Chatterjee, Krishnendu, Martin Chemlík, and Ufuk Topcu. “Sensor Synthesis for POMDPs with Reachability Objectives,” 2018:47–55. AAAI Press, 2018."},"intvolume":"      2018","publication_status":"published","conference":{"name":"ICAPS: International Conference on Automated Planning and Scheduling","start_date":"2018-06-24","location":"Delft, Netherlands","end_date":"2018-06-29"},"date_published":"2018-06-01T00:00:00Z","oa_version":"Preprint"},{"publist_id":"8020","article_processing_charge":"No","external_id":{"isi":["000492986200007"],"arxiv":["1804.07031"]},"quality_controlled":"1","related_material":{"record":[{"id":"9293","status":"public","relation":"later_version"}]},"date_created":"2018-12-11T11:44:17Z","publication":"28th International Conference on Automated Planning and Scheduling ","type":"conference","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"publisher":"AAAI Press","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Algorithms and conditional lower bounds for planning problems","day":"01","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"isi":1,"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"full_name":"Dvorák, Wolfgang","first_name":"Wolfgang","last_name":"Dvorák"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger"},{"last_name":"Svozil","first_name":"Alexander","full_name":"Svozil, Alexander"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.07031"}],"scopus_import":"1","citation":{"short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, A. Svozil, in:, 28th International Conference on Automated Planning and Scheduling , AAAI Press, 2018.","ama":"Chatterjee K, Dvorák W, Henzinger MH, Svozil A. Algorithms and conditional lower bounds for planning problems. In: <i>28th International Conference on Automated Planning and Scheduling </i>. AAAI Press; 2018.","ieee":"K. Chatterjee, W. Dvorák, M. H. Henzinger, and A. Svozil, “Algorithms and conditional lower bounds for planning problems,” in <i>28th International Conference on Automated Planning and Scheduling </i>, Delft, Netherlands, 2018.","mla":"Chatterjee, Krishnendu, et al. “Algorithms and Conditional Lower Bounds for Planning Problems.” <i>28th International Conference on Automated Planning and Scheduling </i>, AAAI Press, 2018.","apa":"Chatterjee, K., Dvorák, W., Henzinger, M. H., &#38; Svozil, A. (2018). Algorithms and conditional lower bounds for planning problems. In <i>28th International Conference on Automated Planning and Scheduling </i>. Delft, Netherlands: AAAI Press.","ista":"Chatterjee K, Dvorák W, Henzinger MH, Svozil A. 2018. Algorithms and conditional lower bounds for planning problems. 28th International Conference on Automated Planning and Scheduling . ICAPS: International Conference on Automated Planning and Scheduling.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Alexander Svozil. “Algorithms and Conditional Lower Bounds for Planning Problems.” In <i>28th International Conference on Automated Planning and Scheduling </i>. AAAI Press, 2018."},"publication_status":"published","conference":{"name":"ICAPS: International Conference on Automated Planning and Scheduling","start_date":"2018-06-24","location":"Delft, Netherlands","end_date":"2018-06-29"},"oa_version":"None","date_published":"2018-06-01T00:00:00Z","status":"public","oa":1,"month":"06","ec_funded":1,"date_updated":"2023-09-26T10:41:41Z","arxiv":1,"abstract":[{"lang":"eng","text":"We consider planning problems for graphs, Markov decision processes (MDPs), and games on graphs. While graphs represent the most basic planning model, MDPs represent interaction with nature and games on graphs represent interaction with an adversarial environment. We consider two planning problems where there are k different target sets, and the problems are as follows: (a) the coverage problem asks whether there is a plan for each individual target set; and (b) the sequential target reachability problem asks whether the targets can be reached in sequence. For the coverage problem, we present a linear-time algorithm for graphs, and quadratic conditional lower bound for MDPs and games on graphs. For the sequential target problem, we present a linear-time algorithm for graphs, a sub-quadratic algorithm for MDPs, and a quadratic conditional lower bound for games on graphs. Our results with conditional lower bounds establish (i) model-separation results showing that for the coverage problem MDPs and games on graphs are harder than graphs and for the sequential reachability problem games on graphs are harder than MDPs and graphs; and (ii) objective-separation results showing that for MDPs the coverage problem is harder than the sequential target problem."}],"year":"2018","_id":"35"},{"title":"Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Oxford University Press","file":[{"date_created":"2018-12-18T09:47:51Z","file_name":"2018_JournalExperimBotany_Vu.pdf","date_updated":"2020-07-14T12:46:13Z","access_level":"open_access","creator":"dernst","file_id":"5741","checksum":"34cb0a1611588b75bd6f4913fb4e30f1","file_size":3359316,"content_type":"application/pdf","relation":"main_file"}],"author":[{"full_name":"Vu, Lam","last_name":"Vu","first_name":"Lam"},{"full_name":"Zhu, Tingting","last_name":"Zhu","first_name":"Tingting"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","first_name":"Inge","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge"},{"last_name":"Van De Cotte","first_name":"Brigitte","full_name":"Van De Cotte, Brigitte"},{"last_name":"Gevaert","first_name":"Kris","full_name":"Gevaert, Kris"},{"first_name":"Ive","last_name":"De Smet","full_name":"De Smet, Ive"}],"isi":1,"day":"31","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"TZ is supported by a grant from the Chinese Scholarship Council.","volume":69,"quality_controlled":"1","external_id":{"isi":["000443568700010"]},"article_processing_charge":"No","publist_id":"8019","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"Journal of Experimental Botany","date_created":"2018-12-11T11:44:17Z","page":"4609 - 4624","has_accepted_license":"1","month":"08","oa":1,"status":"public","_id":"36","year":"2018","abstract":[{"text":"Wheat (Triticum ssp.) is one of the most important human food sources. However, this crop is very sensitive to temperature changes. Specifically, processes during wheat leaf, flower, and seed development and photosynthesis, which all contribute to the yield of this crop, are affected by high temperature. While this has to some extent been investigated on physiological, developmental, and molecular levels, very little is known about early signalling events associated with an increase in temperature. Phosphorylation-mediated signalling mechanisms, which are quick and dynamic, are associated with plant growth and development, also under abiotic stress conditions. Therefore, we probed the impact of a short-term and mild increase in temperature on the wheat leaf and spikelet phosphoproteome. In total, 3822 (containing 5178 phosphosites) and 5581 phosphopeptides (containing 7023 phosphosites) were identified in leaf and spikelet samples, respectively. Following statistical analysis, the resulting data set provides the scientific community with a first large-scale plant phosphoproteome under the control of higher ambient temperature. This community resource on the high temperature-mediated wheat phosphoproteome will be valuable for future studies. Our analyses also revealed a core set of common proteins between leaf and spikelet, suggesting some level of conserved regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion of phosphoforms, which probably impacts protein activity.","lang":"eng"}],"issue":"19","date_updated":"2023-09-19T10:00:46Z","citation":{"ieee":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, and I. De Smet, “Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms,” <i>Journal of Experimental Botany</i>, vol. 69, no. 19. Oxford University Press, pp. 4609–4624, 2018.","ama":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. <i>Journal of Experimental Botany</i>. 2018;69(19):4609-4624. doi:<a href=\"https://doi.org/10.1093/jxb/ery204\">10.1093/jxb/ery204</a>","short":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, I. De Smet, Journal of Experimental Botany 69 (2018) 4609–4624.","apa":"Vu, L., Zhu, T., Verstraeten, I., Van De Cotte, B., Gevaert, K., &#38; De Smet, I. (2018). Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/ery204\">https://doi.org/10.1093/jxb/ery204</a>","ista":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. 2018. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 69(19), 4609–4624.","mla":"Vu, Lam, et al. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” <i>Journal of Experimental Botany</i>, vol. 69, no. 19, Oxford University Press, 2018, pp. 4609–24, doi:<a href=\"https://doi.org/10.1093/jxb/ery204\">10.1093/jxb/ery204</a>.","chicago":"Vu, Lam, Tingting Zhu, Inge Verstraeten, Brigitte Van De Cotte, Kris Gevaert, and Ive De Smet. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/jxb/ery204\">https://doi.org/10.1093/jxb/ery204</a>."},"intvolume":"        69","ddc":["581"],"file_date_updated":"2020-07-14T12:46:13Z","scopus_import":"1","date_published":"2018-08-31T00:00:00Z","oa_version":"Published Version","doi":"10.1093/jxb/ery204","publication_status":"published"},{"department":[{"_id":"AnKi"}],"language":[{"iso":"eng"}],"type":"book_chapter","publication":"Morphogen Gradients ","page":"47 - 63","date_created":"2018-12-11T11:44:17Z","has_accepted_license":"1","volume":1863,"quality_controlled":"1","article_processing_charge":"No","publist_id":"8018","file":[{"checksum":"2a97d0649fdcfcf1bdca7c8ad1dce71b","file_id":"8656","creator":"dernst","access_level":"open_access","file_name":"2018_MIMB_Zagorski.pdf","date_updated":"2020-10-13T14:20:37Z","date_created":"2020-10-13T14:20:37Z","content_type":"application/pdf","relation":"main_file","file_size":4906815,"success":1}],"author":[{"orcid":"0000-0001-7896-7762","first_name":"Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","last_name":"Zagórski","full_name":"Zagórski, Marcin P"},{"full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","orcid":"0000-0003-4509-4998","first_name":"Anna"}],"project":[{"_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037","call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord"}],"day":"16","series_title":"MIMB","alternative_title":["Methods in Molecular Biology"],"title":"Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","date_published":"2018-10-16T00:00:00Z","oa_version":"Submitted Version","doi":"10.1007/978-1-4939-8772-6_4","publication_status":"published","citation":{"mla":"Zagórski, Marcin P., and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” <i>Morphogen Gradients </i>, vol. 1863, Springer Nature, 2018, pp. 47–63, doi:<a href=\"https://doi.org/10.1007/978-1-4939-8772-6_4\">10.1007/978-1-4939-8772-6_4</a>.","apa":"Zagórski, M. P., &#38; Kicheva, A. (2018). Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In <i>Morphogen Gradients </i> (Vol. 1863, pp. 47–63). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-4939-8772-6_4\">https://doi.org/10.1007/978-1-4939-8772-6_4</a>","ista":"Zagórski MP, Kicheva A. 2018.Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: Morphogen Gradients . Methods in Molecular Biology, vol. 1863, 47–63.","chicago":"Zagórski, Marcin P, and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” In <i>Morphogen Gradients </i>, 1863:47–63. MIMB. Springer Nature, 2018. <a href=\"https://doi.org/10.1007/978-1-4939-8772-6_4\">https://doi.org/10.1007/978-1-4939-8772-6_4</a>.","ama":"Zagórski MP, Kicheva A. Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: <i>Morphogen Gradients </i>. Vol 1863. MIMB. Springer Nature; 2018:47-63. doi:<a href=\"https://doi.org/10.1007/978-1-4939-8772-6_4\">10.1007/978-1-4939-8772-6_4</a>","ieee":"M. P. Zagórski and A. Kicheva, “Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube,” in <i>Morphogen Gradients </i>, vol. 1863, Springer Nature, 2018, pp. 47–63.","short":"M.P. Zagórski, A. Kicheva, in:, Morphogen Gradients , Springer Nature, 2018, pp. 47–63."},"intvolume":"      1863","ddc":["570"],"file_date_updated":"2020-10-13T14:20:37Z","scopus_import":"1","_id":"37","year":"2018","abstract":[{"lang":"eng","text":"Developmental processes are inherently dynamic and understanding them requires quantitative measurements of gene and protein expression levels in space and time. While live imaging is a powerful approach for obtaining such data, it is still a challenge to apply it over long periods of time to large tissues, such as the embryonic spinal cord in mouse and chick. Nevertheless, dynamics of gene expression and signaling activity patterns in this organ can be studied by collecting tissue sections at different developmental stages. In combination with immunohistochemistry, this allows for measuring the levels of multiple developmental regulators in a quantitative manner with high spatiotemporal resolution. The mean protein expression levels over time, as well as embryo-to-embryo variability can be analyzed. A key aspect of the approach is the ability to compare protein levels across different samples. This requires a number of considerations in sample preparation, imaging and data analysis. Here we present a protocol for obtaining time course data of dorsoventral expression patterns from mouse and chick neural tube in the first 3 days of neural tube development. The described workflow starts from embryo dissection and ends with a processed dataset. Software scripts for data analysis are included. The protocol is adaptable and instructions that allow the user to modify different steps are provided. Thus, the procedure can be altered for analysis of time-lapse images and applied to systems other than the neural tube."}],"date_updated":"2021-01-12T07:49:03Z","ec_funded":1,"month":"10","publication_identifier":{"issn":["1064-3745"],"isbn":["978-1-4939-8771-9"]},"oa":1,"status":"public"},{"month":"10","oa":1,"publication_identifier":{"issn":["00278424"]},"status":"public","_id":"38","year":"2018","date_updated":"2023-09-18T08:36:49Z","issue":"43","abstract":[{"text":"Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightlylinked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence, while heterogeneous gene flow flattens the surrounding \"sea,\" making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation.","lang":"eng"}],"intvolume":"       115","citation":{"ieee":"H. Tavares <i>et al.</i>, “Selection and gene flow shape genomic islands that control floral guides,” <i>PNAS</i>, vol. 115, no. 43. National Academy of Sciences, pp. 11006–11011, 2018.","ama":"Tavares H, Whitley A, Field D, et al. Selection and gene flow shape genomic islands that control floral guides. <i>PNAS</i>. 2018;115(43):11006-11011. doi:<a href=\"https://doi.org/10.1073/pnas.1801832115\">10.1073/pnas.1801832115</a>","short":"H. Tavares, A. Whitley, D. Field, D. Bradley, M. Couchman, L. Copsey, J. Elleouet, M. Burrus, C. Andalo, M. Li, Q. Li, Y. Xue, A.B. Rebocho, N.H. Barton, E. Coen, PNAS 115 (2018) 11006–11011.","chicago":"Tavares, Hugo, Annabel Whitley, David Field, Desmond Bradley, Matthew Couchman, Lucy Copsey, Joane Elleouet, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1801832115\">https://doi.org/10.1073/pnas.1801832115</a>.","mla":"Tavares, Hugo, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” <i>PNAS</i>, vol. 115, no. 43, National Academy of Sciences, 2018, pp. 11006–11, doi:<a href=\"https://doi.org/10.1073/pnas.1801832115\">10.1073/pnas.1801832115</a>.","apa":"Tavares, H., Whitley, A., Field, D., Bradley, D., Couchman, M., Copsey, L., … Coen, E. (2018). Selection and gene flow shape genomic islands that control floral guides. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1801832115\">https://doi.org/10.1073/pnas.1801832115</a>","ista":"Tavares H, Whitley A, Field D, Bradley D, Couchman M, Copsey L, Elleouet J, Burrus M, Andalo C, Li M, Li Q, Xue Y, Rebocho AB, Barton NH, Coen E. 2018. Selection and gene flow shape genomic islands that control floral guides. PNAS. 115(43), 11006–11011."},"ddc":["570"],"scopus_import":"1","file_date_updated":"2020-07-14T12:46:16Z","date_published":"2018-10-23T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1073/pnas.1801832115","title":"Selection and gene flow shape genomic islands that control floral guides","publisher":"National Academy of Sciences","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_id":"5683","creator":"dernst","checksum":"d2305d0cc81dbbe4c1c677d64ad6f6d1","access_level":"open_access","file_name":"11006.full.pdf","date_updated":"2020-07-14T12:46:16Z","date_created":"2018-12-17T08:44:03Z","relation":"main_file","content_type":"application/pdf","file_size":1911302}],"isi":1,"author":[{"first_name":"Hugo","last_name":"Tavares","full_name":"Tavares, Hugo"},{"first_name":"Annabel","last_name":"Whitley","full_name":"Whitley, Annabel"},{"full_name":"Field, David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","orcid":"0000-0002-4014-8478"},{"last_name":"Bradley","first_name":"Desmond","full_name":"Bradley, Desmond"},{"first_name":"Matthew","last_name":"Couchman","full_name":"Couchman, Matthew"},{"last_name":"Copsey","first_name":"Lucy","full_name":"Copsey, Lucy"},{"full_name":"Elleouet, Joane","first_name":"Joane","last_name":"Elleouet"},{"last_name":"Burrus","first_name":"Monique","full_name":"Burrus, Monique"},{"last_name":"Andalo","first_name":"Christophe","full_name":"Andalo, Christophe"},{"last_name":"Li","first_name":"Miaomiao","full_name":"Li, Miaomiao"},{"full_name":"Li, Qun","first_name":"Qun","last_name":"Li"},{"last_name":"Xue","first_name":"Yongbiao","full_name":"Xue, Yongbiao"},{"first_name":"Alexandra B","last_name":"Rebocho","full_name":"Rebocho, Alexandra B"},{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"full_name":"Coen, Enrico","last_name":"Coen","first_name":"Enrico"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"day":"23","pmid":1,"acknowledgement":" ERC Grant 201252 (to N.H.B.)","external_id":{"isi":["000448040500065"],"pmid":["30297406"]},"quality_controlled":"1","volume":115,"publist_id":"8017","article_processing_charge":"No","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"type":"journal_article","page":"11006 - 11011","date_created":"2018-12-11T11:44:18Z","publication":"PNAS","has_accepted_license":"1"},{"_id":"384","issue":"3","abstract":[{"lang":"eng","text":"Can orthologous proteins differ in terms of their ability to be secreted? To answer this question, we investigated the distribution of signal peptides within the orthologous groups of Enterobacterales. Parsimony analysis and sequence comparisons revealed a large number of signal peptide gain and loss events, in which signal peptides emerge or disappear in the course of evolution. Signal peptide losses prevail over gains, an effect which is especially pronounced in the transition from the free-living or commensal to the endosymbiotic lifestyle. The disproportionate decline in the number of signal peptide-containing proteins in endosymbionts cannot be explained by the overall reduction of their genomes. Signal peptides can be gained and lost either by acquisition/elimination of the corresponding N-terminal regions or by gradual accumulation of mutations. The evolutionary dynamics of signal peptides in bacterial proteins represents a powerful mechanism of functional diversification."}],"date_updated":"2023-09-11T13:56:52Z","year":"2018","month":"03","status":"public","oa":1,"oa_version":"Published Version","date_published":"2018-03-01T00:00:00Z","doi":"10.1093/gbe/evy049","publication_status":"published","citation":{"short":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, D. Frishman, Genome Biology and Evolution 10 (2018) 928–938.","ieee":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, and D. Frishman, “Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss,” <i>Genome Biology and Evolution</i>, vol. 10, no. 3. Oxford University Press, pp. 928–938, 2018.","ama":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. <i>Genome Biology and Evolution</i>. 2018;10(3):928-938. doi:<a href=\"https://doi.org/10.1093/gbe/evy049\">10.1093/gbe/evy049</a>","apa":"Hönigschmid, P., Bykova, N., Schneider, R., Ivankov, D., &#38; Frishman, D. (2018). Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evy049\">https://doi.org/10.1093/gbe/evy049</a>","ista":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. 2018. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. 10(3), 928–938.","mla":"Hönigschmid, Peter, et al. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” <i>Genome Biology and Evolution</i>, vol. 10, no. 3, Oxford University Press, 2018, pp. 928–38, doi:<a href=\"https://doi.org/10.1093/gbe/evy049\">10.1093/gbe/evy049</a>.","chicago":"Hönigschmid, Peter, Nadya Bykova, René Schneider, Dmitry Ivankov, and Dmitrij Frishman. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/gbe/evy049\">https://doi.org/10.1093/gbe/evy049</a>."},"intvolume":"        10","scopus_import":"1","file_date_updated":"2020-07-14T12:46:16Z","ddc":["576"],"isi":1,"author":[{"first_name":"Peter","last_name":"Hönigschmid","full_name":"Hönigschmid, Peter"},{"full_name":"Bykova, Nadya","last_name":"Bykova","first_name":"Nadya"},{"full_name":"Schneider, René","last_name":"Schneider","first_name":"René"},{"full_name":"Ivankov, Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","last_name":"Ivankov","first_name":"Dmitry"},{"first_name":"Dmitrij","last_name":"Frishman","full_name":"Frishman, Dmitrij"}],"file":[{"file_size":691602,"content_type":"application/pdf","relation":"main_file","date_created":"2018-12-12T10:08:07Z","date_updated":"2020-07-14T12:46:16Z","file_name":"IST-2018-999-v1+1_2018_Ivankov_Evolutionary_interplay.pdf","access_level":"open_access","file_id":"4667","creator":"system","checksum":"458a7c2c2e79528567edfeb0f326cbe0"}],"acknowledgement":"his work was supported by the Deutsche Forschungsgemeinschaft  (grant  number  FR  1411/9-1).  This work  was  supported  by  the  German  Research  Foundation (DFG) and the Technical University of Munich within the fund- ing programme Open Access Publish\r\nWe thank Goar Frishman for help with the annotation of the\r\nsymbiont status of the organisms and Michael Galperin for\r\nuseful comments. T","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Oxford University Press","title":"Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss","type":"journal_article","department":[{"_id":"FyKo"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Genome Biology and Evolution","page":"928 - 938","date_created":"2018-12-11T11:46:10Z","quality_controlled":"1","volume":10,"external_id":{"isi":["000429483700022"]},"pubrep_id":"999","article_processing_charge":"No","publist_id":"7445"},{"department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"Genetics","date_created":"2018-12-11T11:44:18Z","page":"1411-1427","quality_controlled":"1","volume":210,"external_id":{"isi":["000452315900021"]},"article_processing_charge":"No","article_type":"original","isi":1,"author":[{"last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","full_name":"Sachdeva, Himani"},{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"day":"04","title":"Replicability of introgression under linked, polygenic selection","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Genetics Society of America","date_published":"2018-12-04T00:00:00Z","oa_version":"Preprint","doi":"10.1534/genetics.118.301429","publication_status":"published","intvolume":"       210","citation":{"chicago":"Sachdeva, Himani, and Nicholas H Barton. “Replicability of Introgression under Linked, Polygenic Selection.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.118.301429\">https://doi.org/10.1534/genetics.118.301429</a>.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Replicability of Introgression under Linked, Polygenic Selection.” <i>Genetics</i>, vol. 210, no. 4, Genetics Society of America, 2018, pp. 1411–27, doi:<a href=\"https://doi.org/10.1534/genetics.118.301429\">10.1534/genetics.118.301429</a>.","ista":"Sachdeva H, Barton NH. 2018. Replicability of introgression under linked, polygenic selection. Genetics. 210(4), 1411–1427.","apa":"Sachdeva, H., &#38; Barton, N. H. (2018). Replicability of introgression under linked, polygenic selection. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.118.301429\">https://doi.org/10.1534/genetics.118.301429</a>","ieee":"H. Sachdeva and N. H. Barton, “Replicability of introgression under linked, polygenic selection,” <i>Genetics</i>, vol. 210, no. 4. Genetics Society of America, pp. 1411–1427, 2018.","ama":"Sachdeva H, Barton NH. Replicability of introgression under linked, polygenic selection. <i>Genetics</i>. 2018;210(4):1411-1427. doi:<a href=\"https://doi.org/10.1534/genetics.118.301429\">10.1534/genetics.118.301429</a>","short":"H. Sachdeva, N.H. Barton, Genetics 210 (2018) 1411–1427."},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/379578v1"}],"scopus_import":"1","_id":"39","year":"2018","abstract":[{"lang":"eng","text":"We study how a block of genome with a large number of weakly selected loci introgresses under directional selection into a genetically homogeneous population. We derive exact expressions for the expected rate of growth of any fragment of the introduced block during the initial phase of introgression, and show that the growth rate of a single-locus variant is largely insensitive to its own additive effect, but depends instead on the combined effect of all loci within a characteristic linkage scale. The expected growth rate of a fragment is highly correlated with its long-term introgression probability in populations of moderate size, and can hence identify variants that are likely to introgress across replicate populations. We clarify how the introgression probability of an individual variant is determined by the interplay between hitchhiking with relatively large fragments during the early phase of introgression and selection on fine-scale variation within these, which at longer times results in differential introgression probabilities for beneficial and deleterious loci within successful fragments. By simulating individuals, we also investigate how introgression probabilities at individual loci depend on the variance of fitness effects, the net fitness of the introduced block, and the size of the recipient population, and how this shapes the net advance under selection. Our work suggests that even highly replicable substitutions may be associated with a range of selective effects, which makes it challenging to fine map the causal loci that underlie polygenic adaptation."}],"issue":"4","date_updated":"2023-09-18T08:10:29Z","month":"12","publication_identifier":{"issn":["00166731"]},"oa":1,"status":"public"},{"degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"supervisor":[{"full_name":"Novarino, Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","orcid":"0000-0002-7673-7178"}],"publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"The branched chain amino acids in autism spectrum disorders ","project":[{"call_identifier":"FWF","name":"Transmembrane Transporters in Health and Disease","_id":"25473368-B435-11E9-9278-68D0E5697425","grant_number":"F03523"}],"author":[{"last_name":"Tarlungeanu","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","first_name":"Dora-Clara","full_name":"Tarlungeanu, Dora-Clara"}],"file":[{"file_size":43684035,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","embargo_to":"open_access","date_created":"2019-04-05T09:19:17Z","date_updated":"2021-02-11T23:30:15Z","file_name":"2018_Thesis_Tarlungeanu_source.docx","access_level":"closed","checksum":"9f5231c96e0ad945040841a8630232da","creator":"dernst","file_id":"6217"},{"relation":"main_file","content_type":"application/pdf","file_size":30511532,"embargo":"2018-03-15","file_name":"2018_Thesis_Tarlungeanu.pdf","date_updated":"2021-02-11T11:17:16Z","date_created":"2019-04-05T09:19:17Z","creator":"dernst","file_id":"6218","checksum":"0c33c370aa2010df5c552db57a6d01e9","access_level":"open_access"}],"day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1183"}]},"publist_id":"7434","pubrep_id":"992","article_processing_charge":"No","type":"dissertation","language":[{"iso":"eng"}],"department":[{"_id":"GaNo"}],"has_accepted_license":"1","page":"88","date_created":"2018-12-11T11:46:14Z","month":"03","status":"public","oa":1,"publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"}],"_id":"395","date_updated":"2023-09-07T12:38:59Z","abstract":[{"lang":"eng","text":"Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. Despite the remarkable number of scientific breakthroughs of the last 100 years, the treatment of neurodevelopmental disorders (e.g. autism spectrum disorder, intellectual disability, epilepsy) remains a great challenge. Recent advancements in geno mics, like whole-exome or whole-genome sequencing, have enabled scientists to identify numerous mutations underlying neurodevelopmental disorders. Given the few hundred risk genes that were discovered, the etiological variability and the heterogeneous phenotypic outcomes, the need for genotype -along with phenotype- based diagnosis of individual patients becomes a requisite. Driven by this rationale, in a previous study our group described mutations, identified via whole - exome sequencing, in the gene BCKDK – encoding for a key regulator of branched chain amin o acid (BCAA) catabolism - as a cause of ASD. Following up on the role of BCAAs, in the study described here we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized mainly at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation and severe neurolo gical abnormalities. Additionally, deletion of Slc7a5 from the neural progenitor cell population leads to microcephaly. Interestingly, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Furthermore, whole - exome sequencing of patients diagnosed with neurological dis o r ders helped us identify several patients with autistic traits, microcephaly and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. In conclusion, our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for t he BCAA s in human bra in function. Together with r ecent studies (described in chapter two) that have successfully made the transition into clinical practice, our findings on the role of B CAAs might have a crucial impact on the development of novel individualized therapeutic strategies for ASD. "}],"year":"2018","citation":{"ista":"Tarlungeanu D-C. 2018. The branched chain amino acids in autism spectrum disorders . Institute of Science and Technology Austria.","apa":"Tarlungeanu, D.-C. (2018). <i>The branched chain amino acids in autism spectrum disorders </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_992\">https://doi.org/10.15479/AT:ISTA:th_992</a>","mla":"Tarlungeanu, Dora-Clara. <i>The Branched Chain Amino Acids in Autism Spectrum Disorders </i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_992\">10.15479/AT:ISTA:th_992</a>.","chicago":"Tarlungeanu, Dora-Clara. “The Branched Chain Amino Acids in Autism Spectrum Disorders .” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_992\">https://doi.org/10.15479/AT:ISTA:th_992</a>.","short":"D.-C. Tarlungeanu, The Branched Chain Amino Acids in Autism Spectrum Disorders , Institute of Science and Technology Austria, 2018.","ieee":"D.-C. Tarlungeanu, “The branched chain amino acids in autism spectrum disorders ,” Institute of Science and Technology Austria, 2018.","ama":"Tarlungeanu D-C. The branched chain amino acids in autism spectrum disorders . 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_992\">10.15479/AT:ISTA:th_992</a>"},"file_date_updated":"2021-02-11T23:30:15Z","ddc":["570","616"],"oa_version":"Published Version","date_published":"2018-03-01T00:00:00Z","publication_status":"published","doi":"10.15479/AT:ISTA:th_992"}]