[{"date_created":"2021-08-06T12:43:44Z","year":"2018","author":[{"first_name":"Waqas","full_name":"Chaudhry, Waqas","last_name":"Chaudhry"},{"full_name":"Pleska, Maros","first_name":"Maros","orcid":"0000-0001-7460-7479","id":"4569785E-F248-11E8-B48F-1D18A9856A87","last_name":"Pleska"},{"last_name":"Shah","first_name":"Nilang","full_name":"Shah, Nilang"},{"last_name":"Weiss","first_name":"Howard","full_name":"Weiss, Howard"},{"last_name":"Mccall","first_name":"Ingrid","full_name":"Mccall, Ingrid"},{"first_name":"Justin","full_name":"Meyer, Justin","last_name":"Meyer"},{"last_name":"Gupta","full_name":"Gupta, Animesh","first_name":"Animesh"},{"full_name":"Guet, Calin C","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","last_name":"Guet"},{"last_name":"Levin","full_name":"Levin, Bruce","first_name":"Bruce"}],"article_processing_charge":"No","oa_version":"Published Version","month":"08","fulldoi":"https://doi.org/10.1371/journal.pbio.2005971.s008","citation":{"ieee":"W. Chaudhry <i>et al.</i>, “Numerical data used in figures.” Public Library of Science, 2018.","ista":"Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Numerical data used in figures, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2005971.s008\">10.1371/journal.pbio.2005971.s008</a>.","apa":"Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Numerical data used in figures. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2005971.s008\">https://doi.org/10.1371/journal.pbio.2005971.s008</a>","short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, (2018).","chicago":"Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Numerical Data Used in Figures.” Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pbio.2005971.s008\">https://doi.org/10.1371/journal.pbio.2005971.s008</a>.","mla":"Chaudhry, Waqas, et al. <i>Numerical Data Used in Figures</i>. Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005971.s008\">10.1371/journal.pbio.2005971.s008</a>.","ama":"Chaudhry W, Pleska M, Shah N, et al. Numerical data used in figures. 2018. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005971.s008\">10.1371/journal.pbio.2005971.s008</a>"},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9810","date_published":"2018-08-16T00:00:00Z","doi":"10.1371/journal.pbio.2005971.s008","type":"research_data_reference","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"82"}]},"status":"public","date_updated":"2023-09-13T08:45:41Z","title":"Numerical data used in figures","day":"16","department":[{"_id":"CaGu"}],"publisher":"Public Library of Science"},{"abstract":[{"lang":"eng","text":"This document contains additional supporting evidence presented as supplemental tables. (XLSX 50Â kb)"}],"department":[{"_id":"FyKo"}],"day":"31","publisher":"Springer Nature","title":"Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","oa":1,"_id":"9811","doi":"10.6084/m9.figshare.6401390.v1","date_published":"2018-05-31T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"279"}]},"type":"research_data_reference","status":"public","date_updated":"2025-04-15T08:30:30Z","citation":{"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>","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.","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>.","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>.","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>","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>."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.6401390.v1","open_access":"1"}],"article_processing_charge":"No","oa_version":"Preprint","fulldoi":"https://doi.org/10.6084/m9.figshare.6401390.v1","month":"05","year":"2018","author":[{"first_name":"Luis","full_name":"Zapata, Luis","last_name":"Zapata"},{"full_name":"Pich, Oriol","first_name":"Oriol","last_name":"Pich"},{"first_name":"Luis","full_name":"Serrano, Luis","last_name":"Serrano"},{"first_name":"Fyodor","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","orcid":"0000-0001-8243-4694"},{"last_name":"Ossowski","first_name":"Stephan","full_name":"Ossowski, Stephan"},{"last_name":"Schaefer","first_name":"Martin","full_name":"Schaefer, Martin"}],"date_created":"2021-08-06T12:53:49Z"},{"date_created":"2021-08-06T12:58:25Z","author":[{"full_name":"Zapata, Luis","first_name":"Luis","last_name":"Zapata"},{"last_name":"Pich","first_name":"Oriol","full_name":"Pich, Oriol"},{"last_name":"Serrano","full_name":"Serrano, Luis","first_name":"Luis"},{"full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ossowski","full_name":"Ossowski, Stephan","first_name":"Stephan"},{"last_name":"Schaefer","full_name":"Schaefer, Martin","first_name":"Martin"}],"year":"2018","fulldoi":"https://doi.org/10.6084/m9.figshare.6401414.v1","month":"05","oa_version":"Published Version","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.6401414.v1","open_access":"1"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","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>","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.","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>.","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>","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>."},"date_updated":"2025-04-15T08:30:30Z","status":"public","related_material":{"record":[{"id":"279","status":"public","relation":"used_in_publication"}]},"type":"research_data_reference","doi":"10.6084/m9.figshare.6401414.v1","date_published":"2018-05-31T00:00:00Z","_id":"9812","oa":1,"title":"Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","day":"31","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"abstract":[{"text":"This document contains the full list of genes with their respective significance and dN/dS values. (TXT 4499Â kb)","lang":"eng"}]},{"_id":"9813","doi":"10.25386/genetics.6148304.v1","date_published":"2018-04-30T00:00:00Z","status":"public","type":"research_data_reference","related_material":{"record":[{"relation":"used_in_publication","id":"316","status":"public"}]},"date_updated":"2025-04-15T07:17:08Z","abstract":[{"text":"File S1 contains figures that clarify the following features: (i) effect of population size on the average number/frequency of SI classes, (ii) changes in the minimal completeness deficit in time for a single class, and (iii) diversification diagrams for all studied pathways, including the summary figure for k = 8. File S2 contains the code required for a stochastic simulation of the SLF system with an example. This file also includes the output in the form of figures and tables.","lang":"eng"}],"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"Genetics Society of America","day":"30","title":"Supplemental material for Bodova et al., 2018","oa":1,"year":"2018","author":[{"orcid":"0000-0002-7214-0171","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","last_name":"Bod'ová","full_name":"Bod'ová, Katarína","first_name":"Katarína"},{"last_name":"Priklopil","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","first_name":"Tadeas","full_name":"Priklopil, Tadeas"},{"last_name":"Field","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","full_name":"Field, David"},{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Pickup, Melinda","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","orcid":"0000-0001-6118-0541"}],"date_created":"2021-08-06T13:04:32Z","citation":{"short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).","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.","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>.","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>","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>","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>.","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>."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"open_access":"1","url":"https://doi.org/10.25386/genetics.6148304.v1"}],"article_processing_charge":"No","oa_version":"Published Version","month":"04","fulldoi":"https://doi.org/10.25386/genetics.6148304.v1"},{"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>","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>.","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>.","short":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, (2018).","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>","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>.","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."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","oa_version":"Published Version","month":"03","fulldoi":"https://doi.org/10.1371/journal.pone.0193049.s001","year":"2018","author":[{"full_name":"Bod’Ová, Katarína","first_name":"Katarína","last_name":"Bod’Ová"},{"first_name":"Gabriel","full_name":"Mitchell, Gabriel","last_name":"Mitchell","id":"315BCD80-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roy","full_name":"Harpaz, Roy","last_name":"Harpaz"},{"last_name":"Schneidman","full_name":"Schneidman, Elad","first_name":"Elad"},{"full_name":"Tkačik, Gašper","first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2021-08-09T07:01:24Z","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"}],"publisher":"Public Library of Science","day":"07","department":[{"_id":"GaTk"}],"title":"Implementation of the inference method in Matlab","_id":"9831","doi":"10.1371/journal.pone.0193049.s001","date_published":"2018-03-07T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"406"}]},"status":"public","type":"research_data_reference","date_updated":"2025-04-15T06:44:30Z"},{"_id":"9837","doi":"10.5061/dryad.72cg113","date_published":"2018-10-09T00:00:00Z","status":"public","related_material":{"record":[{"id":"6095","status":"public","relation":"used_in_publication"}]},"type":"research_data_reference","date_updated":"2023-08-24T14:50:26Z","title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","oa":1,"abstract":[{"text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.","lang":"eng"}],"publisher":"Dryad","day":"09","department":[{"_id":"NiBa"}],"date_created":"2021-08-09T12:46:39Z","year":"2018","author":[{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"full_name":"Chaube, Pragya","first_name":"Pragya","last_name":"Chaube"},{"last_name":"Morales","full_name":"Morales, Hernán E.","first_name":"Hernán E."},{"full_name":"Larsson, Tomas","first_name":"Tomas","last_name":"Larsson"},{"first_name":"Alan R.","full_name":"Lemmon, Alan R.","last_name":"Lemmon"},{"first_name":"Emily M.","full_name":"Lemmon, Emily M.","last_name":"Lemmon"},{"last_name":"Rafajlović","first_name":"Marina","full_name":"Rafajlović, Marina"},{"full_name":"Panova, Marina","first_name":"Marina","last_name":"Panova"},{"full_name":"Ravinet, Mark","first_name":"Mark","last_name":"Ravinet"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","last_name":"Westram","first_name":"Anja M","full_name":"Westram, Anja M"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"}],"article_processing_charge":"No","oa_version":"Published Version","month":"10","fulldoi":"https://doi.org/10.5061/dryad.72cg113","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.72cg113\">https://doi.org/10.5061/dryad.72cg113</a>.","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>.","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>","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>","ieee":"R. Faria <i>et al.</i>, “Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.","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>.","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)."},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.72cg113","open_access":"1"}]},{"doi":"10.5061/dryad.f1s76f2","date_published":"2018-06-14T00:00:00Z","_id":"9838","date_updated":"2025-04-14T13:02:22Z","type":"research_data_reference","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"162"}]},"status":"public","publisher":"Dryad","department":[{"_id":"AnKi"}],"day":"14","abstract":[{"text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts.","lang":"eng"}],"oa":1,"title":"Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","year":"2018","author":[{"first_name":"Marketa","full_name":"Kaucka, Marketa","last_name":"Kaucka"},{"full_name":"Petersen, Julian","first_name":"Julian","last_name":"Petersen"},{"last_name":"Tesarova","full_name":"Tesarova, Marketa","first_name":"Marketa"},{"last_name":"Szarowska","full_name":"Szarowska, Bara","first_name":"Bara"},{"first_name":"Maria Eleni","full_name":"Kastriti, Maria Eleni","last_name":"Kastriti"},{"last_name":"Xie","full_name":"Xie, Meng","first_name":"Meng"},{"orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","full_name":"Kicheva, Anna","first_name":"Anna"},{"first_name":"Karl","full_name":"Annusver, Karl","last_name":"Annusver"},{"last_name":"Kasper","first_name":"Maria","full_name":"Kasper, Maria"},{"first_name":"Orsolya","full_name":"Symmons, Orsolya","last_name":"Symmons"},{"last_name":"Pan","full_name":"Pan, Leslie","first_name":"Leslie"},{"first_name":"Francois","full_name":"Spitz, Francois","last_name":"Spitz"},{"last_name":"Kaiser","full_name":"Kaiser, Jozef","first_name":"Jozef"},{"full_name":"Hovorakova, Maria","first_name":"Maria","last_name":"Hovorakova"},{"full_name":"Zikmund, Tomas","first_name":"Tomas","last_name":"Zikmund"},{"first_name":"Kazunori","full_name":"Sunadome, Kazunori","last_name":"Sunadome"},{"last_name":"Matise","first_name":"Michael P","full_name":"Matise, Michael P"},{"full_name":"Wang, Hui","first_name":"Hui","last_name":"Wang"},{"full_name":"Marklund, Ulrika","first_name":"Ulrika","last_name":"Marklund"},{"last_name":"Abdo","first_name":"Hind","full_name":"Abdo, Hind"},{"full_name":"Ernfors, Patrik","first_name":"Patrik","last_name":"Ernfors"},{"first_name":"Pascal","full_name":"Maire, Pascal","last_name":"Maire"},{"first_name":"Maud","full_name":"Wurmser, Maud","last_name":"Wurmser"},{"full_name":"Chagin, Andrei S","first_name":"Andrei S","last_name":"Chagin"},{"last_name":"Fried","first_name":"Kaj","full_name":"Fried, Kaj"},{"first_name":"Igor","full_name":"Adameyko, Igor","last_name":"Adameyko"}],"date_created":"2021-08-09T12:54:35Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"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>.","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.","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>","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).","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>.","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>","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>."},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.f1s76f2","open_access":"1"}],"oa_version":"Published Version","article_processing_charge":"No","fulldoi":"https://doi.org/10.5061/dryad.f1s76f2","month":"06"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"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>","mla":"Payne, Pavel, et al. <i>Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.42n44\">10.5061/dryad.42n44</a>.","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.42n44\">https://doi.org/10.5061/dryad.42n44</a>.","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).","apa":"Payne, P., Geyrhofer, L., Barton, N. H., &#38; Bollback, J. P. (2018). Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. Dryad. <a href=\"https://doi.org/10.5061/dryad.42n44\">https://doi.org/10.5061/dryad.42n44</a>","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.","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>."},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.42n44","open_access":"1"}],"article_processing_charge":"No","oa_version":"Published Version","month":"03","fulldoi":"https://doi.org/10.5061/dryad.42n44","year":"2018","author":[{"first_name":"Pavel","full_name":"Payne, Pavel","orcid":"0000-0002-2711-9453","last_name":"Payne","id":"35F78294-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Geyrhofer, Lukas","first_name":"Lukas","last_name":"Geyrhofer"},{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"orcid":"0000-0002-4624-4612","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","full_name":"Bollback, Jonathan P"}],"date_created":"2021-08-09T13:10:02Z","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","publisher":"Dryad","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"title":"Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations","oa":1,"_id":"9840","date_published":"2018-03-12T00:00:00Z","doi":"10.5061/dryad.42n44","related_material":{"record":[{"relation":"used_in_publication","id":"423","status":"public"}]},"status":"public","type":"research_data_reference","date_updated":"2025-04-15T08:17:50Z"},{"status":"public","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"448"}]},"type":"research_data_reference","date_updated":"2023-09-11T14:10:56Z","_id":"9841","date_published":"2018-12-12T00:00:00Z","doi":"10.5061/dryad.51d4r","abstract":[{"text":"Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity.","lang":"eng"}],"publisher":"Dryad","day":"12","department":[{"_id":"BeVi"}],"title":"Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality","oa":1,"author":[{"last_name":"Harrison","full_name":"Harrison, Mark C.","first_name":"Mark C."},{"full_name":"Jongepier, Evelien","first_name":"Evelien","last_name":"Jongepier"},{"full_name":"Robertson, Hugh M.","first_name":"Hugh M.","last_name":"Robertson"},{"first_name":"Nicolas","full_name":"Arning, Nicolas","last_name":"Arning"},{"first_name":"Tristan","full_name":"Bitard-Feildel, Tristan","last_name":"Bitard-Feildel"},{"last_name":"Chao","first_name":"Hsu","full_name":"Chao, Hsu"},{"full_name":"Childers, Christopher P.","first_name":"Christopher P.","last_name":"Childers"},{"full_name":"Dinh, Huyen","first_name":"Huyen","last_name":"Dinh"},{"full_name":"Doddapaneni, Harshavardhan","first_name":"Harshavardhan","last_name":"Doddapaneni"},{"last_name":"Dugan","first_name":"Shannon","full_name":"Dugan, Shannon"},{"last_name":"Gowin","full_name":"Gowin, Johannes","first_name":"Johannes"},{"last_name":"Greiner","full_name":"Greiner, Carolin","first_name":"Carolin"},{"first_name":"Yi","full_name":"Han, Yi","last_name":"Han"},{"last_name":"Hu","full_name":"Hu, Haofu","first_name":"Haofu"},{"first_name":"Daniel S. T.","full_name":"Hughes, Daniel S. T.","last_name":"Hughes"},{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans","orcid":"0000-0001-8871-4961","first_name":"Ann K","full_name":"Huylmans, Ann K"},{"last_name":"Kemena","first_name":"Carsten","full_name":"Kemena, Carsten"},{"full_name":"Kremer, Lukas P. M.","first_name":"Lukas P. M.","last_name":"Kremer"},{"full_name":"Lee, Sandra L.","first_name":"Sandra L.","last_name":"Lee"},{"last_name":"Lopez-Ezquerra","first_name":"Alberto","full_name":"Lopez-Ezquerra, Alberto"},{"last_name":"Mallet","full_name":"Mallet, Ludovic","first_name":"Ludovic"},{"last_name":"Monroy-Kuhn","first_name":"Jose M.","full_name":"Monroy-Kuhn, Jose M."},{"last_name":"Moser","full_name":"Moser, Annabell","first_name":"Annabell"},{"full_name":"Murali, Shwetha C.","first_name":"Shwetha C.","last_name":"Murali"},{"last_name":"Muzny","full_name":"Muzny, Donna M.","first_name":"Donna M."},{"last_name":"Otani","full_name":"Otani, Saria","first_name":"Saria"},{"last_name":"Piulachs","full_name":"Piulachs, Maria-Dolors","first_name":"Maria-Dolors"},{"last_name":"Poelchau","full_name":"Poelchau, Monica","first_name":"Monica"},{"last_name":"Qu","full_name":"Qu, Jiaxin","first_name":"Jiaxin"},{"full_name":"Schaub, Florentine","first_name":"Florentine","last_name":"Schaub"},{"full_name":"Wada-Katsumata, Ayako","first_name":"Ayako","last_name":"Wada-Katsumata"},{"last_name":"Worley","first_name":"Kim C.","full_name":"Worley, Kim C."},{"full_name":"Xie, Qiaolin","first_name":"Qiaolin","last_name":"Xie"},{"last_name":"Ylla","first_name":"Guillem","full_name":"Ylla, Guillem"},{"full_name":"Poulsen, Michael","first_name":"Michael","last_name":"Poulsen"},{"last_name":"Gibbs","full_name":"Gibbs, Richard A.","first_name":"Richard A."},{"last_name":"Schal","first_name":"Coby","full_name":"Schal, Coby"},{"last_name":"Richards","full_name":"Richards, Stephen","first_name":"Stephen"},{"last_name":"Belles","full_name":"Belles, Xavier","first_name":"Xavier"},{"last_name":"Korb","first_name":"Judith","full_name":"Korb, Judith"},{"last_name":"Bornberg-Bauer","full_name":"Bornberg-Bauer, Erich","first_name":"Erich"}],"year":"2018","date_created":"2021-08-09T13:13:48Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.51d4r"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"short":"M.C. Harrison, E. Jongepier, H.M. Robertson, N. Arning, T. Bitard-Feildel, H. Chao, C.P. Childers, H. Dinh, H. Doddapaneni, S. Dugan, J. Gowin, C. Greiner, Y. Han, H. Hu, D.S.T. Hughes, A.K. Huylmans, C. Kemena, L.P.M. Kremer, S.L. Lee, A. Lopez-Ezquerra, L. Mallet, J.M. Monroy-Kuhn, A. Moser, S.C. Murali, D.M. Muzny, S. Otani, M.-D. Piulachs, M. Poelchau, J. Qu, F. Schaub, A. Wada-Katsumata, K.C. Worley, Q. Xie, G. Ylla, M. Poulsen, R.A. Gibbs, C. Schal, S. Richards, X. Belles, J. Korb, E. Bornberg-Bauer, (2018).","ieee":"M. C. Harrison <i>et al.</i>, “Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality.” Dryad, 2018.","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>.","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>","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>","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>."},"month":"12","fulldoi":"https://doi.org/10.5061/dryad.51d4r","article_processing_charge":"No","oa_version":"Published Version"},{"author":[{"first_name":"Barbara","full_name":"Petritsch, Barbara","orcid":"0000-0003-2724-4614","last_name":"Petritsch","id":"406048EC-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","year":"2018","date_created":"2019-05-16T07:27:14Z","citation":{"ieee":"B. Petritsch, <i>Open Access at IST Austria 2009-2017</i>. IST Austria, 2018.","ista":"Petritsch B. 2018. Open Access at IST Austria 2009-2017, IST Austria,p.","apa":"Petritsch, B. (2018). <i>Open Access at IST Austria 2009-2017</i>. Presented at the OAT: Open Access Tage, Graz, Austria: IST Austria. <a href=\"https://doi.org/10.5281/zenodo.1410279\">https://doi.org/10.5281/zenodo.1410279</a>","short":"B. Petritsch, Open Access at IST Austria 2009-2017, IST Austria, 2018.","chicago":"Petritsch, Barbara. <i>Open Access at IST Austria 2009-2017</i>. IST Austria, 2018. <a href=\"https://doi.org/10.5281/zenodo.1410279\">https://doi.org/10.5281/zenodo.1410279</a>.","mla":"Petritsch, Barbara. <i>Open Access at IST Austria 2009-2017</i>. IST Austria, 2018, doi:<a href=\"https://doi.org/10.5281/zenodo.1410279\">10.5281/zenodo.1410279</a>.","ama":"Petritsch B. <i>Open Access at IST Austria 2009-2017</i>. IST Austria; 2018. doi:<a href=\"https://doi.org/10.5281/zenodo.1410279\">10.5281/zenodo.1410279</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.5281/zenodo.1410279","month":"09","oa_version":"Published Version","file":[{"access_level":"open_access","date_created":"2019-05-16T07:26:25Z","date_updated":"2020-07-14T12:47:30Z","file_name":"Poster_Beitrag_125_Petritsch.pdf","file_id":"6460","checksum":"9063ab4d10ea93353c3a03bbf53fbcf1","creator":"dernst","file_size":1967778,"relation":"main_file","content_type":"application/pdf"}],"keyword":["Open Access","Publication Analysis"],"article_processing_charge":"No","date_updated":"2026-03-31T12:35:03Z","type":"conference_poster","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_status":"published","date_published":"2018-09-24T00:00:00Z","doi":"10.5281/zenodo.1410279","_id":"6459","ddc":["020"],"language":[{"iso":"eng"}],"day":"24","department":[{"_id":"E-Lib"}],"publisher":"IST Austria","conference":{"end_date":"2018-09-26","start_date":"2018-09-24","location":"Graz, Austria","name":"OAT: Open Access Tage"},"oa":1,"file_date_updated":"2020-07-14T12:47:30Z","title":"Open Access at IST Austria 2009-2017"},{"page":"1869–1890","date_created":"2019-05-28T12:36:47Z","has_accepted_license":"1","author":[{"last_name":"Moalli","first_name":"Federica","full_name":"Moalli, Federica"},{"last_name":"Ficht","full_name":"Ficht, Xenia","first_name":"Xenia"},{"last_name":"Germann","first_name":"Philipp","full_name":"Germann, Philipp"},{"last_name":"Vladymyrov","full_name":"Vladymyrov, Mykhailo","first_name":"Mykhailo"},{"last_name":"Stolp","first_name":"Bettina","full_name":"Stolp, Bettina"},{"id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","last_name":"de Vries","first_name":"Ingrid","full_name":"de Vries, Ingrid"},{"full_name":"Lyck, Ruth","first_name":"Ruth","last_name":"Lyck"},{"last_name":"Balmer","first_name":"Jasmin","full_name":"Balmer, Jasmin"},{"last_name":"Fiocchi","first_name":"Amleto","full_name":"Fiocchi, Amleto"},{"last_name":"Kreutzfeldt","first_name":"Mario","full_name":"Kreutzfeldt, Mario"},{"first_name":"Doron","full_name":"Merkler, Doron","last_name":"Merkler"},{"last_name":"Iannacone","full_name":"Iannacone, Matteo","first_name":"Matteo"},{"first_name":"Akitaka","full_name":"Ariga, Akitaka","last_name":"Ariga"},{"full_name":"Stoffel, Michael H.","first_name":"Michael H.","last_name":"Stoffel"},{"first_name":"James","full_name":"Sharpe, James","last_name":"Sharpe"},{"last_name":"Bähler","full_name":"Bähler, Martin","first_name":"Martin"},{"first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"},{"first_name":"Alba","full_name":"Diz-Muñoz, Alba","last_name":"Diz-Muñoz"},{"full_name":"Stein, Jens V.","first_name":"Jens V.","last_name":"Stein"}],"article_processing_charge":"No","oa_version":"Published Version","month":"06","fulldoi":"https://doi.org/10.1084/jem.20170896","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"ddc":["570"],"publication_status":"published","publication":"The Journal of Experimental Medicine","isi":1,"scopus_import":"1","publisher":"Rockefeller University Press","day":"06","department":[{"_id":"MiSi"}],"year":"2018","file":[{"content_type":"application/pdf","relation":"main_file","file_size":3841660,"creator":"kschuh","checksum":"86ae5331f9bfced9a6358a790a04bef4","file_id":"6498","file_name":"2018_rupress_Moalli.pdf","date_updated":"2020-07-14T12:47:32Z","access_level":"open_access","date_created":"2019-05-28T12:40:05Z"}],"intvolume":"      2015","citation":{"apa":"Moalli, F., Ficht, X., Germann, P., Vladymyrov, M., Stolp, B., de Vries, I., … Stein, J. V. (2018). The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. <i>The Journal of Experimental Medicine</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1084/jem.20170896\">https://doi.org/10.1084/jem.20170896</a>","ista":"Moalli F, Ficht X, Germann P, Vladymyrov M, Stolp B, de Vries I, Lyck R, Balmer J, Fiocchi A, Kreutzfeldt M, Merkler D, Iannacone M, Ariga A, Stoffel MH, Sharpe J, Bähler M, Sixt MK, Diz-Muñoz A, Stein JV. 2018. The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. The Journal of Experimental Medicine. 2015(7), 1869–1890.","ieee":"F. Moalli <i>et al.</i>, “The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells,” <i>The Journal of Experimental Medicine</i>, vol. 2015, no. 7. Rockefeller University Press, pp. 1869–1890, 2018.","short":"F. Moalli, X. Ficht, P. Germann, M. Vladymyrov, B. Stolp, I. de Vries, R. Lyck, J. Balmer, A. Fiocchi, M. Kreutzfeldt, D. Merkler, M. Iannacone, A. Ariga, M.H. Stoffel, J. Sharpe, M. Bähler, M.K. Sixt, A. Diz-Muñoz, J.V. Stein, The Journal of Experimental Medicine 2015 (2018) 1869–1890.","chicago":"Moalli, Federica, Xenia Ficht, Philipp Germann, Mykhailo Vladymyrov, Bettina Stolp, Ingrid de Vries, Ruth Lyck, et al. “The Rho Regulator Myosin IXb Enables Nonlymphoid Tissue Seeding of Protective CD8+T Cells.” <i>The Journal of Experimental Medicine</i>. Rockefeller University Press, 2018. <a href=\"https://doi.org/10.1084/jem.20170896\">https://doi.org/10.1084/jem.20170896</a>.","ama":"Moalli F, Ficht X, Germann P, et al. The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. <i>The Journal of Experimental Medicine</i>. 2018;2015(7):1869–1890. doi:<a href=\"https://doi.org/10.1084/jem.20170896\">10.1084/jem.20170896</a>","mla":"Moalli, Federica, et al. “The Rho Regulator Myosin IXb Enables Nonlymphoid Tissue Seeding of Protective CD8+T Cells.” <i>The Journal of Experimental Medicine</i>, vol. 2015, no. 7, Rockefeller University Press, 2018, pp. 1869–1890, doi:<a href=\"https://doi.org/10.1084/jem.20170896\">10.1084/jem.20170896</a>."},"_id":"6497","date_published":"2018-06-06T00:00:00Z","tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"doi":"10.1084/jem.20170896","status":"public","type":"journal_article","date_updated":"2023-09-19T14:52:08Z","volume":2015,"issue":"7","title":"The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells","publication_identifier":{"issn":["0022-1007"],"eissn":["1540-9538"]},"file_date_updated":"2020-07-14T12:47:32Z","oa":1,"abstract":[{"lang":"eng","text":"T cells are actively scanning pMHC-presenting cells in lymphoid organs and nonlymphoid tissues (NLTs) with divergent topologies and confinement. How the T cell actomyosin cytoskeleton facilitates this task in distinct environments is incompletely understood. Here, we show that lack of Myosin IXb (Myo9b), a negative regulator of the small GTPase Rho, led to increased Rho-GTP levels and cell surface stiffness in primary T cells. Nonetheless, intravital imaging revealed robust motility of Myo9b−/− CD8+ T cells in lymphoid tissue and similar expansion and differentiation during immune responses. In contrast, accumulation of Myo9b−/− CD8+ T cells in NLTs was strongly impaired. Specifically, Myo9b was required for T cell crossing of basement membranes, such as those which are present between dermis and epidermis. As consequence, Myo9b−/− CD8+ T cells showed impaired control of skin infections. In sum, we show that Myo9b is critical for the CD8+ T cell adaptation from lymphoid to NLT surveillance and the establishment of protective tissue–resident T cell populations."}],"external_id":{"isi":["000440822900011"]}},{"publication":"EMBO reports","ddc":["580"],"language":[{"iso":"eng"}],"publication_status":"published","department":[{"_id":"JoDa"}],"publisher":"Embo Press","day":"01","scopus_import":"1","isi":1,"has_accepted_license":"1","author":[{"last_name":"Truckenbrodt","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","first_name":"Sven M","full_name":"Truckenbrodt, Sven M"},{"full_name":"Maidorn, Manuel","first_name":"Manuel","last_name":"Maidorn"},{"last_name":"Crzan","first_name":"Dagmar","full_name":"Crzan, Dagmar"},{"last_name":"Wildhagen","full_name":"Wildhagen, Hanna","first_name":"Hanna"},{"last_name":"Kabatas","first_name":"Selda","full_name":"Kabatas, Selda"},{"full_name":"Rizzoli, Silvio O","first_name":"Silvio O","last_name":"Rizzoli"}],"date_created":"2019-05-28T13:16:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","fulldoi":"https://doi.org/10.15252/embr.201845836","quality_controlled":"1","article_processing_charge":"No","oa_version":"Published Version","article_number":"e45836","issue":"9","volume":19,"status":"public","type":"journal_article","date_updated":"2024-12-11T11:48:40Z","_id":"6499","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_published":"2018-09-01T00:00:00Z","doi":"10.15252/embr.201845836","abstract":[{"lang":"eng","text":"Expansion microscopy is a recently introduced imaging technique that achieves super‐resolution through physically expanding the specimen by ~4×, after embedding into a swellable gel. The resolution attained is, correspondingly, approximately fourfold better than the diffraction limit, or ~70 nm. This is a major improvement over conventional microscopy, but still lags behind modern STED or STORM setups, whose resolution can reach 20–30 nm. We addressed this issue here by introducing an improved gel recipe that enables an expansion factor of ~10× in each dimension, which corresponds to an expansion of the sample volume by more than 1,000‐fold. Our protocol, which we termed X10 microscopy, achieves a resolution of 25–30 nm on conventional epifluorescence microscopes. X10 provides multi‐color images similar or even superior to those produced with more challenging methods, such as STED, STORM, and iterative expansion microscopy (iExM). X10 is therefore the cheapest and easiest option for high‐quality super‐resolution imaging currently available. X10 should be usable in any laboratory, irrespective of the machinery owned or of the technical knowledge."}],"external_id":{"isi":["000443682200009"]},"file_date_updated":"2020-07-14T12:47:32Z","publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"title":"X10 expansion microscopy enables 25‐nm resolution on conventional microscopes","oa":1,"year":"2018","citation":{"apa":"Truckenbrodt, S. M., Maidorn, M., Crzan, D., Wildhagen, H., Kabatas, S., &#38; Rizzoli, S. O. (2018). X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. <i>EMBO Reports</i>. Embo Press. <a href=\"https://doi.org/10.15252/embr.201845836\">https://doi.org/10.15252/embr.201845836</a>","ieee":"S. M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, and S. O. Rizzoli, “X10 expansion microscopy enables 25‐nm resolution on conventional microscopes,” <i>EMBO reports</i>, vol. 19, no. 9. Embo Press, 2018.","ista":"Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. 2018. X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. EMBO reports. 19(9), e45836.","short":"S.M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, S.O. Rizzoli, EMBO Reports 19 (2018).","chicago":"Truckenbrodt, Sven M, Manuel Maidorn, Dagmar Crzan, Hanna Wildhagen, Selda Kabatas, and Silvio O Rizzoli. “X10 Expansion Microscopy Enables 25‐nm Resolution on Conventional Microscopes.” <i>EMBO Reports</i>. Embo Press, 2018. <a href=\"https://doi.org/10.15252/embr.201845836\">https://doi.org/10.15252/embr.201845836</a>.","ama":"Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. <i>EMBO reports</i>. 2018;19(9). doi:<a href=\"https://doi.org/10.15252/embr.201845836\">10.15252/embr.201845836</a>","mla":"Truckenbrodt, Sven M., et al. “X10 Expansion Microscopy Enables 25‐nm Resolution on Conventional Microscopes.” <i>EMBO Reports</i>, vol. 19, no. 9, e45836, Embo Press, 2018, doi:<a href=\"https://doi.org/10.15252/embr.201845836\">10.15252/embr.201845836</a>."},"intvolume":"        19","file":[{"file_size":2005572,"content_type":"application/pdf","relation":"main_file","creator":"kschuh","date_updated":"2020-07-14T12:47:32Z","access_level":"open_access","date_created":"2019-05-28T13:17:19Z","checksum":"6ec90abc637f09cca3a7b6424d7e7a26","file_id":"6500","file_name":"2018_embo_Truckenbrodt.pdf"}]},{"citation":{"ista":"Hausel T, Mellit A, Pei D. 2018.Mirror symmetry with branes by equivariant verlinde formulas. In: Geometry and Physics: Volume I. , 189–218.","ieee":"T. Hausel, A. Mellit, and D. Pei, “Mirror symmetry with branes by equivariant verlinde formulas,” in <i>Geometry and Physics: Volume I</i>, Oxford University Press, 2018, pp. 189–218.","apa":"Hausel, T., Mellit, A., &#38; Pei, D. (2018). Mirror symmetry with branes by equivariant verlinde formulas. In <i>Geometry and Physics: Volume I</i> (pp. 189–218). Oxford University Press. <a href=\"https://doi.org/10.1093/oso/9780198802013.003.0009\">https://doi.org/10.1093/oso/9780198802013.003.0009</a>","short":"T. Hausel, A. Mellit, D. Pei, in:, Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218.","chicago":"Hausel, Tamás, Anton Mellit, and Du Pei. “Mirror Symmetry with Branes by Equivariant Verlinde Formulas.” In <i>Geometry and Physics: Volume I</i>, 189–218. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/oso/9780198802013.003.0009\">https://doi.org/10.1093/oso/9780198802013.003.0009</a>.","ama":"Hausel T, Mellit A, Pei D. Mirror symmetry with branes by equivariant verlinde formulas. In: <i>Geometry and Physics: Volume I</i>. Oxford University Press; 2018:189-218. doi:<a href=\"https://doi.org/10.1093/oso/9780198802013.003.0009\">10.1093/oso/9780198802013.003.0009</a>","mla":"Hausel, Tamás, et al. “Mirror Symmetry with Branes by Equivariant Verlinde Formulas.” <i>Geometry and Physics: Volume I</i>, Oxford University Press, 2018, pp. 189–218, doi:<a href=\"https://doi.org/10.1093/oso/9780198802013.003.0009\">10.1093/oso/9780198802013.003.0009</a>."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","quality_controlled":"1","fulldoi":"https://doi.org/10.1093/oso/9780198802013.003.0009","month":"01","article_processing_charge":"No","oa_version":"None","author":[{"first_name":"Tamás","full_name":"Hausel, Tamás","orcid":"0000-0002-9582-2634","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel"},{"first_name":"Anton","full_name":"Mellit, Anton","id":"388D3134-F248-11E8-B48F-1D18A9856A87","last_name":"Mellit"},{"full_name":"Pei, Du","first_name":"Du","last_name":"Pei"}],"year":"2018","date_created":"2019-06-06T12:42:01Z","page":"189-218","abstract":[{"text":"This chapter finds an agreement of equivariant indices of semi-classical homomorphisms between pairwise mirror branes in the GL2 Higgs moduli space on a Riemann surface. On one side of the agreement, components of the Lagrangian brane of U(1,1) Higgs bundles, whose mirror was proposed by Hitchin to be certain even exterior powers of the hyperholomorphic Dirac bundle on the SL2 Higgs moduli space, are present. The agreement arises from a mysterious functional equation. This gives strong computational evidence for Hitchin’s proposal.","lang":"eng"}],"department":[{"_id":"TaHa"}],"day":"01","publisher":"Oxford University Press","title":"Mirror symmetry with branes by equivariant verlinde formulas","scopus_import":"1","publication_identifier":{"isbn":["9780198802013"],"eisbn":["9780191840500"]},"publication":"Geometry and Physics: Volume I","status":"public","type":"book_chapter","date_updated":"2026-04-16T10:30:22Z","language":[{"iso":"eng"}],"_id":"6525","date_published":"2018-01-01T00:00:00Z","doi":"10.1093/oso/9780198802013.003.0009","publication_status":"published"},{"conference":{"name":"NeurIPS: Conference on Neural Information Processing Systems","start_date":"2018-12-02","location":"Montreal, Canada","end_date":"2018-12-08"},"day":"01","department":[{"_id":"DaAl"}],"publisher":"Neural Information Processing Systems Foundation","isi":1,"scopus_import":"1","publication":"Advances in Neural Information Processing Systems","language":[{"iso":"eng"}],"ddc":["000"],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","oa_version":"Published Version","quality_controlled":"1","month":"12","author":[{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","last_name":"Alistarh"},{"first_name":"Zeyuan","full_name":"Allen-Zhu, Zeyuan","last_name":"Allen-Zhu"},{"last_name":"Li","first_name":"Jerry","full_name":"Li, Jerry"}],"date_created":"2019-06-13T08:22:37Z","page":"4613-4623","abstract":[{"lang":"eng","text":"This paper studies the problem of distributed stochastic optimization in an adversarial setting where, out of m machines which allegedly compute stochastic gradients every iteration, an α-fraction are Byzantine, and may behave adversarially. Our main result is a variant of stochastic gradient descent (SGD) which finds ε-approximate minimizers of convex functions in T=O~(1/ε²m+α²/ε²) iterations. In contrast, traditional mini-batch SGD needs T=O(1/ε²m) iterations, but cannot tolerate Byzantine failures. Further, we provide a lower bound showing that, up to logarithmic factors, our algorithm is information-theoretically optimal both in terms of sample complexity and time complexity."}],"external_id":{"isi":["000461823304061"],"arxiv":["1803.08917"]},"title":"Byzantine stochastic gradient descent","oa":1,"volume":2018,"_id":"6558","date_published":"2018-12-01T00:00:00Z","type":"conference","status":"public","date_updated":"2026-06-18T19:08:25Z","citation":{"chicago":"Alistarh, Dan-Adrian, Zeyuan Allen-Zhu, and Jerry Li. “Byzantine Stochastic Gradient Descent.” In <i>Advances in Neural Information Processing Systems</i>, 2018:4613–23. Neural Information Processing Systems Foundation, 2018.","ama":"Alistarh D-A, Allen-Zhu Z, Li J. Byzantine stochastic gradient descent. In: <i>Advances in Neural Information Processing Systems</i>. Vol 2018. Neural Information Processing Systems Foundation; 2018:4613-4623.","mla":"Alistarh, Dan-Adrian, et al. “Byzantine Stochastic Gradient Descent.” <i>Advances in Neural Information Processing Systems</i>, vol. 2018, Neural Information Processing Systems Foundation, 2018, pp. 4613–23.","ista":"Alistarh D-A, Allen-Zhu Z, Li J. 2018. Byzantine stochastic gradient descent. Advances in Neural Information Processing Systems. NeurIPS: Conference on Neural Information Processing Systems vol. 2018, 4613–4623.","ieee":"D.-A. Alistarh, Z. Allen-Zhu, and J. Li, “Byzantine stochastic gradient descent,” in <i>Advances in Neural Information Processing Systems</i>, Montreal, Canada, 2018, vol. 2018, pp. 4613–4623.","apa":"Alistarh, D.-A., Allen-Zhu, Z., &#38; Li, J. (2018). Byzantine stochastic gradient descent. In <i>Advances in Neural Information Processing Systems</i> (Vol. 2018, pp. 4613–4623). Montreal, Canada: Neural Information Processing Systems Foundation.","short":"D.-A. Alistarh, Z. Allen-Zhu, J. Li, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2018, pp. 4613–4623."},"main_file_link":[{"url":"https://arxiv.org/abs/1803.08917","open_access":"1"}],"arxiv":1,"intvolume":"      2018","year":"2018"},{"extern":"1","oa_version":"Preprint","month":"12","fulldoi":"https://doi.org/10.1109/istc.2018.8625281","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Hashemi, Seyyed Ali, et al. “Decoding Reed-Muller and Polar Codes by Successive Factor Graph Permutations.” <i>2018 IEEE 10th International Symposium on Turbo Codes &#38; Iterative Information Processing</i>, IEEE, 2018, pp. 1–5, doi:<a href=\"https://doi.org/10.1109/istc.2018.8625281\">10.1109/istc.2018.8625281</a>.","ama":"Hashemi SA, Doan N, Mondelli M, Gross W. Decoding Reed-Muller and polar codes by successive factor graph permutations. In: <i>2018 IEEE 10th International Symposium on Turbo Codes &#38; Iterative Information Processing</i>. IEEE; 2018:1-5. doi:<a href=\"https://doi.org/10.1109/istc.2018.8625281\">10.1109/istc.2018.8625281</a>","chicago":"Hashemi, Seyyed Ali, Nghia Doan, Marco Mondelli, and Warren  Gross. “Decoding Reed-Muller and Polar Codes by Successive Factor Graph Permutations.” In <i>2018 IEEE 10th International Symposium on Turbo Codes &#38; Iterative Information Processing</i>, 1–5. IEEE, 2018. <a href=\"https://doi.org/10.1109/istc.2018.8625281\">https://doi.org/10.1109/istc.2018.8625281</a>.","short":"S.A. Hashemi, N. Doan, M. Mondelli, W. Gross, in:, 2018 IEEE 10th International Symposium on Turbo Codes &#38; Iterative Information Processing, IEEE, 2018, pp. 1–5.","ieee":"S. A. Hashemi, N. Doan, M. Mondelli, and W. Gross, “Decoding Reed-Muller and polar codes by successive factor graph permutations,” in <i>2018 IEEE 10th International Symposium on Turbo Codes &#38; Iterative Information Processing</i>, Hong Kong, China, 2018, pp. 1–5.","ista":"Hashemi SA, Doan N, Mondelli M, Gross W. 2018. Decoding Reed-Muller and polar codes by successive factor graph permutations. 2018 IEEE 10th International Symposium on Turbo Codes &#38; Iterative Information Processing. ISTC: Symposium on Turbo Codes &#38; Iterative Information Processing, 1–5.","apa":"Hashemi, S. A., Doan, N., Mondelli, M., &#38; Gross, W. (2018). Decoding Reed-Muller and polar codes by successive factor graph permutations. In <i>2018 IEEE 10th International Symposium on Turbo Codes &#38; Iterative Information Processing</i> (pp. 1–5). Hong Kong, China: IEEE. <a href=\"https://doi.org/10.1109/istc.2018.8625281\">https://doi.org/10.1109/istc.2018.8625281</a>"},"arxiv":1,"main_file_link":[{"url":"https://arxiv.org/abs/1807.03912","open_access":"1"}],"page":"1-5","date_created":"2019-07-23T09:12:43Z","year":"2018","author":[{"last_name":"Hashemi","first_name":"Seyyed Ali","full_name":"Hashemi, Seyyed Ali"},{"last_name":"Doan","full_name":"Doan, Nghia","first_name":"Nghia"},{"first_name":"Marco","full_name":"Mondelli, Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"last_name":"Gross","full_name":"Gross, Warren ","first_name":"Warren "}],"title":"Decoding Reed-Muller and polar codes by successive factor graph permutations","oa":1,"abstract":[{"lang":"eng","text":"Reed-Muller (RM) and polar codes are a class of capacity-achieving channel coding schemes with the same factor graph representation. Low-complexity decoding algorithms fall short in providing a good error-correction performance for RM and polar codes. Using the symmetric group of RM and polar codes, the specific decoding algorithm can be carried out on multiple permutations of the factor graph to boost the error-correction performance. However, this approach results in high decoding complexity. In this paper, we first derive the total number of factor graph permutations on which the decoding can be performed. We further propose a successive permutation (SP) scheme which finds the permutations on the fly, thus the decoding always progresses on a single factor graph permutation. We show that SP can be used to improve the error-correction performance of RM and polar codes under successive-cancellation (SC) and SC list (SCL) decoding, while keeping the memory requirements of the decoders unaltered. Our results for RM and polar codes of length 128 and rate 0.5 show that when SP is used and at a target frame error rate of 10 -4 , up to 0.5 dB and 0.1 dB improvement can be achieved for RM and polar codes respectively."}],"day":"01","publisher":"IEEE","external_id":{"arxiv":["1807.03912"]},"conference":{"name":"ISTC: Symposium on Turbo Codes & Iterative Information Processing","end_date":"2018-12-07","location":"Hong Kong, China","start_date":"2018-12-03"},"_id":"6664","language":[{"iso":"eng"}],"publication_status":"published","date_published":"2018-12-01T00:00:00Z","doi":"10.1109/istc.2018.8625281","type":"conference","status":"public","date_updated":"2021-01-12T08:08:29Z","publication":"2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing"},{"oa_version":"Preprint","extern":"1","fulldoi":"https://doi.org/10.1109/itw.2018.8613428","month":"11","quality_controlled":"1","citation":{"apa":"Fazeli, A., Hassani, H., Mondelli, M., &#38; Vardy, A. (2018). Binary linear codes with optimal scaling: Polar codes with large kernels. In <i>2018 IEEE Information Theory Workshop</i> (pp. 1–5). Guangzhou, China: IEEE. <a href=\"https://doi.org/10.1109/itw.2018.8613428\">https://doi.org/10.1109/itw.2018.8613428</a>","ieee":"A. Fazeli, H. Hassani, M. Mondelli, and A. Vardy, “Binary linear codes with optimal scaling: Polar codes with large kernels,” in <i>2018 IEEE Information Theory Workshop</i>, Guangzhou, China, 2018, pp. 1–5.","ista":"Fazeli A, Hassani H, Mondelli M, Vardy A. 2018. Binary linear codes with optimal scaling: Polar codes with large kernels. 2018 IEEE Information Theory Workshop. ITW: Information Theory Workshop, 1–5.","short":"A. Fazeli, H. Hassani, M. Mondelli, A. Vardy, in:, 2018 IEEE Information Theory Workshop, IEEE, 2018, pp. 1–5.","chicago":"Fazeli, Arman, Hamed Hassani, Marco Mondelli, and Alexander Vardy. “Binary Linear Codes with Optimal Scaling: Polar Codes with Large Kernels.” In <i>2018 IEEE Information Theory Workshop</i>, 1–5. IEEE, 2018. <a href=\"https://doi.org/10.1109/itw.2018.8613428\">https://doi.org/10.1109/itw.2018.8613428</a>.","mla":"Fazeli, Arman, et al. “Binary Linear Codes with Optimal Scaling: Polar Codes with Large Kernels.” <i>2018 IEEE Information Theory Workshop</i>, IEEE, 2018, pp. 1–5, doi:<a href=\"https://doi.org/10.1109/itw.2018.8613428\">10.1109/itw.2018.8613428</a>.","ama":"Fazeli A, Hassani H, Mondelli M, Vardy A. Binary linear codes with optimal scaling: Polar codes with large kernels. In: <i>2018 IEEE Information Theory Workshop</i>. IEEE; 2018:1-5. doi:<a href=\"https://doi.org/10.1109/itw.2018.8613428\">10.1109/itw.2018.8613428</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.01339"}],"arxiv":1,"date_created":"2019-07-23T11:01:42Z","page":"1-5","year":"2018","author":[{"full_name":"Fazeli, Arman","first_name":"Arman","last_name":"Fazeli"},{"first_name":"Hamed","full_name":"Hassani, Hamed","last_name":"Hassani"},{"full_name":"Mondelli, Marco","first_name":"Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"first_name":"Alexander","full_name":"Vardy, Alexander","last_name":"Vardy"}],"oa":1,"title":"Binary linear codes with optimal scaling: Polar codes with large kernels","conference":{"name":"ITW: Information Theory Workshop","location":"Guangzhou, China","start_date":"2018-11-25","end_date":"2018-11-29"},"external_id":{"arxiv":["1711.01339"]},"publisher":"IEEE","day":"01","abstract":[{"lang":"eng","text":"We prove that, at least for the binary erasure channel, the polar-coding paradigm gives rise to codes that not only approach the Shannon limit but, in fact, do so under the best possible scaling of their block length as a function of the gap to capacity. This result exhibits the first known family of binary codes that attain both optimal scaling and quasi-linear complexity of encoding and decoding. Specifically, for any fixed δ > 0, we exhibit binary linear codes that ensure reliable communication at rates within ε > 0 of capacity with block length n = O(1/ε 2+δ ), construction complexity Θ(n), and encoding/decoding complexity Θ(n log n)."}],"publication_status":"published","date_published":"2018-11-01T00:00:00Z","doi":"10.1109/itw.2018.8613428","_id":"6665","language":[{"iso":"eng"}],"date_updated":"2025-09-10T09:59:12Z","type":"conference","status":"public","related_material":{"record":[{"relation":"later_version","status":"public","id":"9002"}]},"publication":"2018 IEEE Information Theory Workshop"},{"type":"journal_article","status":"public","date_updated":"2021-01-12T08:08:31Z","language":[{"iso":"eng"}],"_id":"6674","date_published":"2018-09-01T00:00:00Z","doi":"10.1109/tcomm.2018.2832207","publication_status":"published","issue":"9","volume":66,"publication":"IEEE Transactions on Communications","title":"Decoder partitioning: Towards practical list decoding of polar codes","publication_identifier":{"eissn":["1558-0857"]},"abstract":[{"lang":"eng","text":"Polar codes represent one of the major recent breakthroughs in coding theory and, because of their attractive features, they have been selected for the incoming 5G standard. As such, a lot of attention has been devoted to the development of decoding algorithms with good error performance and efficient hardware implementation. One of the leading candidates in this regard is represented by successive-cancellation list (SCL) decoding. However, its hardware implementation requires a large amount of memory. Recently, a partitioned SCL (PSCL) decoder has been proposed to significantly reduce the memory consumption. In this paper, we consider the paradigm of PSCL decoding from a practical standpoint, and we provide several improvements. First, by changing the target signal-to-noise ratio and consequently modifying the construction of the code, we are able to improve the performance at no additional computational, latency, or memory cost. Second, we bridge the performance gap between SCL and PSCL decoding by introducing a generalized PSCL decoder and a layered PSCL decoder. In this way, we obtain almost the same performance of the SCL decoder with a significantly lower memory requirement, as testified by hardware implementation results. Third, we present an optimal scheme to allocate cyclic redundancy checks. Finally, we provide a lower bound on the list size that guarantees optimal maximum a posteriori performance for the binary erasure channel."}],"publisher":"IEEE","day":"01","page":"3749-3759","date_created":"2019-07-24T08:59:41Z","author":[{"last_name":"Hashemi","first_name":"Seyyed Ali","full_name":"Hashemi, Seyyed Ali"},{"full_name":"Mondelli, Marco","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","last_name":"Mondelli"},{"first_name":"S. Hamed","full_name":"Hassani, S. Hamed","last_name":"Hassani"},{"first_name":"Carlo","full_name":"Condo, Carlo","last_name":"Condo"},{"first_name":"Rudiger L.","full_name":"Urbanke, Rudiger L.","last_name":"Urbanke"},{"last_name":"Gross","full_name":"Gross, Warren J.","first_name":"Warren J."}],"year":"2018","fulldoi":"https://doi.org/10.1109/tcomm.2018.2832207","month":"09","intvolume":"        66","quality_controlled":"1","extern":"1","oa_version":"None","citation":{"mla":"Hashemi, Seyyed Ali, et al. “Decoder Partitioning: Towards Practical List Decoding of Polar Codes.” <i>IEEE Transactions on Communications</i>, vol. 66, no. 9, IEEE, 2018, pp. 3749–59, doi:<a href=\"https://doi.org/10.1109/tcomm.2018.2832207\">10.1109/tcomm.2018.2832207</a>.","ama":"Hashemi SA, Mondelli M, Hassani SH, Condo C, Urbanke RL, Gross WJ. Decoder partitioning: Towards practical list decoding of polar codes. <i>IEEE Transactions on Communications</i>. 2018;66(9):3749-3759. doi:<a href=\"https://doi.org/10.1109/tcomm.2018.2832207\">10.1109/tcomm.2018.2832207</a>","chicago":"Hashemi, Seyyed Ali, Marco Mondelli, S. Hamed Hassani, Carlo Condo, Rudiger L. Urbanke, and Warren J. Gross. “Decoder Partitioning: Towards Practical List Decoding of Polar Codes.” <i>IEEE Transactions on Communications</i>. IEEE, 2018. <a href=\"https://doi.org/10.1109/tcomm.2018.2832207\">https://doi.org/10.1109/tcomm.2018.2832207</a>.","short":"S.A. Hashemi, M. Mondelli, S.H. Hassani, C. Condo, R.L. Urbanke, W.J. Gross, IEEE Transactions on Communications 66 (2018) 3749–3759.","ista":"Hashemi SA, Mondelli M, Hassani SH, Condo C, Urbanke RL, Gross WJ. 2018. Decoder partitioning: Towards practical list decoding of polar codes. IEEE Transactions on Communications. 66(9), 3749–3759.","ieee":"S. A. Hashemi, M. Mondelli, S. H. Hassani, C. Condo, R. L. Urbanke, and W. J. Gross, “Decoder partitioning: Towards practical list decoding of polar codes,” <i>IEEE Transactions on Communications</i>, vol. 66, no. 9. IEEE, pp. 3749–3759, 2018.","apa":"Hashemi, S. A., Mondelli, M., Hassani, S. H., Condo, C., Urbanke, R. L., &#38; Gross, W. J. (2018). Decoder partitioning: Towards practical list decoding of polar codes. <i>IEEE Transactions on Communications</i>. IEEE. <a href=\"https://doi.org/10.1109/tcomm.2018.2832207\">https://doi.org/10.1109/tcomm.2018.2832207</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"citation":{"short":"M. Mondelli, H. Hassani, R. Urbanke, in:, 2018 IEEE International Symposium on Information Theory, IEEE, 2018, pp. 351–355.","apa":"Mondelli, M., Hassani, H., &#38; Urbanke, R. (2018). A new coding paradigm for the primitive relay channel. In <i>2018 IEEE International Symposium on Information Theory</i> (pp. 351–355). Vail, CO, United States: IEEE. <a href=\"https://doi.org/10.1109/isit.2018.8437479\">https://doi.org/10.1109/isit.2018.8437479</a>","ieee":"M. Mondelli, H. Hassani, and R. Urbanke, “A new coding paradigm for the primitive relay channel,” in <i>2018 IEEE International Symposium on Information Theory</i>, Vail, CO, United States, 2018, pp. 351–355.","ista":"Mondelli M, Hassani H, Urbanke R. 2018. A new coding paradigm for the primitive relay channel. 2018 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory , 351–355.","ama":"Mondelli M, Hassani H, Urbanke R. A new coding paradigm for the primitive relay channel. In: <i>2018 IEEE International Symposium on Information Theory</i>. IEEE; 2018:351-355. doi:<a href=\"https://doi.org/10.1109/isit.2018.8437479\">10.1109/isit.2018.8437479</a>","mla":"Mondelli, Marco, et al. “A New Coding Paradigm for the Primitive Relay Channel.” <i>2018 IEEE International Symposium on Information Theory</i>, IEEE, 2018, pp. 351–55, doi:<a href=\"https://doi.org/10.1109/isit.2018.8437479\">10.1109/isit.2018.8437479</a>.","chicago":"Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “A New Coding Paradigm for the Primitive Relay Channel.” In <i>2018 IEEE International Symposium on Information Theory</i>, 351–55. IEEE, 2018. <a href=\"https://doi.org/10.1109/isit.2018.8437479\">https://doi.org/10.1109/isit.2018.8437479</a>."},"arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1801.03153"}],"extern":"1","year":"2018","abstract":[{"lang":"eng","text":"We present a coding paradigm that provides a new achievable rate for the primitive relay channel by combining compress-and-forward and decode-and-forward with a chaining construction. In the primitive relay channel model, the source broadcasts a message to the relay and to the destination; and the relay facilitates this communication by sending an additional message to the destination through a separate channel. Two well-known coding approaches for this setting are decode-and-forward and compress-and-forward: in the former, the relay decodes the message and sends some of the information to the destination; in the latter, the relay does not attempt to decode, but it sends a compressed description of the received sequence to the destination via Wyner-Ziv coding. In our scheme, we transmit over pairs of blocks and we use compress-and-forward for the first block and decode-and-forward for the second. In particular, in the first block, the relay does not attempt to decode and it sends only a part of the compressed description of the received sequence; in the second block, the relay decodes the message and sends this information plus the remaining part of the compressed sequence relative to the first block. As a result, we strictly outperform both compress-and- forward and decode-and-forward. Furthermore, this paradigm can be implemented with a low-complexity polar coding scheme that has the typical attractive features of polar codes, i.e., quasi-linear encoding/decoding complexity and super-polynomial decay of the error probability. Throughout the paper we consider as a running example the special case of the erasure relay channel and we compare the rates achievable by our proposed scheme with the existing upper and lower bounds."}],"external_id":{"arxiv":["1801.03153"]},"title":"A new coding paradigm for the primitive relay channel","publication_identifier":{"eissn":["2157-8117"]},"oa":1,"_id":"6675","doi":"10.1109/isit.2018.8437479","date_published":"2018-06-16T00:00:00Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"7007"}]},"type":"conference","status":"public","date_updated":"2024-10-09T20:59:04Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","fulldoi":"https://doi.org/10.1109/isit.2018.8437479","quality_controlled":"1","month":"06","author":[{"first_name":"Marco","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"first_name":"Hamed","full_name":"Hassani, Hamed","last_name":"Hassani"},{"last_name":"Urbanke","first_name":"Rudiger","full_name":"Urbanke, Rudiger"}],"date_created":"2019-07-24T09:10:38Z","page":"351-355","day":"16","conference":{"name":"ISIT: International Symposium on Information Theory ","start_date":"2018-06-17","location":"Vail, CO, United States","end_date":"2018-06-22"},"publisher":"IEEE","publication":"2018 IEEE International Symposium on Information Theory","language":[{"iso":"eng"}],"publication_status":"published"},{"month":"05","fulldoi":"https://doi.org/10.1109/tit.2018.2789885","quality_controlled":"1","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2019-07-24T12:38:49Z","page":"3371-3393","author":[{"full_name":"Mondelli, Marco","first_name":"Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"full_name":"Hassani, Hamed","first_name":"Hamed","last_name":"Hassani"},{"first_name":"Rudiger ","full_name":"Urbanke, Rudiger ","last_name":"Urbanke"}],"day":"01","publisher":"IEEE","language":[{"iso":"eng"}],"article_type":"original","publication_status":"published","publication":"IEEE Transactions on Information Theory","intvolume":"        64","extern":"1","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1406.7373"}],"citation":{"chicago":"Mondelli, Marco, Hamed Hassani, and Rudiger  Urbanke. “How to Achieve the Capacity of Asymmetric Channels.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2018. <a href=\"https://doi.org/10.1109/tit.2018.2789885\">https://doi.org/10.1109/tit.2018.2789885</a>.","mla":"Mondelli, Marco, et al. “How to Achieve the Capacity of Asymmetric Channels.” <i>IEEE Transactions on Information Theory</i>, vol. 64, no. 5, IEEE, 2018, pp. 3371–93, doi:<a href=\"https://doi.org/10.1109/tit.2018.2789885\">10.1109/tit.2018.2789885</a>.","ama":"Mondelli M, Hassani H, Urbanke R. How to achieve the capacity of asymmetric channels. <i>IEEE Transactions on Information Theory</i>. 2018;64(5):3371-3393. doi:<a href=\"https://doi.org/10.1109/tit.2018.2789885\">10.1109/tit.2018.2789885</a>","ista":"Mondelli M, Hassani H, Urbanke R. 2018. How to achieve the capacity of asymmetric channels. IEEE Transactions on Information Theory. 64(5), 3371–3393.","ieee":"M. Mondelli, H. Hassani, and R. Urbanke, “How to achieve the capacity of asymmetric channels,” <i>IEEE Transactions on Information Theory</i>, vol. 64, no. 5. IEEE, pp. 3371–3393, 2018.","apa":"Mondelli, M., Hassani, H., &#38; Urbanke, R. (2018). How to achieve the capacity of asymmetric channels. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/tit.2018.2789885\">https://doi.org/10.1109/tit.2018.2789885</a>","short":"M. Mondelli, H. Hassani, R. Urbanke, IEEE Transactions on Information Theory 64 (2018) 3371–3393."},"year":"2018","title":"How to achieve the capacity of asymmetric channels","publication_identifier":{"issn":["0018-9448","1557-9654"]},"oa":1,"abstract":[{"lang":"eng","text":"We survey coding techniques that enable reliable transmission at rates that approach the capacity of an arbitrary discrete memoryless channel. In particular, we take the point of view of modern coding theory and discuss how recent advances in coding for symmetric channels help provide more efficient solutions for the asymmetric case. We consider, in more detail, three basic coding paradigms. The first one is Gallager's scheme that consists of concatenating a linear code with a non-linear mapping so that the input distribution can be appropriately shaped. We explicitly show that both polar codes and spatially coupled codes can be employed in this scenario. Furthermore, we derive a scaling law between the gap to capacity, the cardinality of the input and output alphabets, and the required size of the mapper. The second one is an integrated scheme in which the code is used both for source coding, in order to create codewords distributed according to the capacity-achieving input distribution, and for channel coding, in order to provide error protection. Such a technique has been recently introduced by Honda and Yamamoto in the context of polar codes, and we show how to apply it also to the design of sparse graph codes. The third paradigm is based on an idea of Böcherer and Mathar, and separates the two tasks of source coding and channel coding by a chaining construction that binds together several codewords. We present conditions for the source code and the channel code, and we describe how to combine any source code with any channel code that fulfill those conditions, in order to provide capacity-achieving schemes for asymmetric channels. In particular, we show that polar codes, spatially coupled codes, and homophonic codes are suitable as basic building blocks of the proposed coding strategy. Rather than focusing on the exact details of the schemes, the purpose of this tutorial is to present different coding techniques that can then be implemented with many variants. There is no absolute winner and, in order to understand the most suitable technique for a specific application scenario, we provide a detailed comparison that takes into account several performance metrics."}],"external_id":{"arxiv":["1406.7373"]},"related_material":{"record":[{"id":"6740","status":"public","relation":"earlier_version"}]},"status":"public","type":"journal_article","date_updated":"2023-02-23T12:50:46Z","_id":"6678","date_published":"2018-05-01T00:00:00Z","doi":"10.1109/tit.2018.2789885","issue":"5","volume":64},{"fulldoi":"https://doi.org/10.1109/glocom.2018.8647308","month":"12","quality_controlled":"1","oa_version":"Preprint","extern":"1","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.11195"}],"citation":{"short":"N. Doan, S.A. Hashemi, M. Mondelli, W.J. Gross, in:, 2018 IEEE Global Communications Conference , IEEE, 2018.","ieee":"N. Doan, S. A. Hashemi, M. Mondelli, and W. J. Gross, “On the decoding of polar codes on permuted factor graphs,” in <i>2018 IEEE Global Communications Conference </i>, Abu Dhabi, United Arab Emirates, 2018.","ista":"Doan N, Hashemi SA, Mondelli M, Gross WJ. 2018. On the decoding of polar codes on permuted factor graphs. 2018 IEEE Global Communications Conference . GLOBECOM: Global Communications Conference.","apa":"Doan, N., Hashemi, S. A., Mondelli, M., &#38; Gross, W. J. (2018). On the decoding of polar codes on permuted factor graphs. In <i>2018 IEEE Global Communications Conference </i>. Abu Dhabi, United Arab Emirates: IEEE. <a href=\"https://doi.org/10.1109/glocom.2018.8647308\">https://doi.org/10.1109/glocom.2018.8647308</a>","mla":"Doan, Nghia, et al. “On the Decoding of Polar Codes on Permuted Factor Graphs.” <i>2018 IEEE Global Communications Conference </i>, IEEE, 2018, doi:<a href=\"https://doi.org/10.1109/glocom.2018.8647308\">10.1109/glocom.2018.8647308</a>.","ama":"Doan N, Hashemi SA, Mondelli M, Gross WJ. On the decoding of polar codes on permuted factor graphs. In: <i>2018 IEEE Global Communications Conference </i>. IEEE; 2018. doi:<a href=\"https://doi.org/10.1109/glocom.2018.8647308\">10.1109/glocom.2018.8647308</a>","chicago":"Doan, Nghia, Seyyed Ali Hashemi, Marco Mondelli, and Warren J. Gross. “On the Decoding of Polar Codes on Permuted Factor Graphs.” In <i>2018 IEEE Global Communications Conference </i>. IEEE, 2018. <a href=\"https://doi.org/10.1109/glocom.2018.8647308\">https://doi.org/10.1109/glocom.2018.8647308</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2019-07-30T06:43:15Z","author":[{"full_name":"Doan, Nghia","first_name":"Nghia","last_name":"Doan"},{"first_name":"Seyyed Ali","full_name":"Hashemi, Seyyed Ali","last_name":"Hashemi"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","orcid":"0000-0002-3242-7020","first_name":"Marco","full_name":"Mondelli, Marco"},{"first_name":"Warren J.","full_name":"Gross, Warren J.","last_name":"Gross"}],"year":"2018","oa":1,"title":"On the decoding of polar codes on permuted factor graphs","publication_identifier":{"isbn":["9781538647271"]},"day":"01","external_id":{"arxiv":["1806.11195"]},"publisher":"IEEE","conference":{"name":"GLOBECOM: Global Communications Conference","location":"Abu Dhabi, United Arab Emirates","start_date":"2018-12-09","end_date":"2018-12-13"},"abstract":[{"lang":"eng","text":"Polar codes are a channel coding scheme for the next generation of wireless communications standard (5G). The belief propagation (BP) decoder allows for parallel decoding of polar codes, making it suitable for high throughput applications. However, the error-correction performance of polar codes under BP decoding is far from the requirements of 5G. It has been shown that the error-correction performance of BP can be improved if the decoding is performed on multiple permuted factor graphs of polar codes. However, a different BP decoding scheduling is required for each factor graph permutation which results in the design of a different decoder for each permutation. Moreover, the selection of the different factor graph permutations is at random, which prevents the decoder to achieve a desirable error correction performance with a small number of permutations. In this paper, we first show that the permutations on the factor graph can be mapped into suitable permutations on the codeword positions. As a result, we can make use of a single decoder for all the permutations. In addition, we introduce a method to construct a set of predetermined permutations which can provide the correct codeword if the decoding fails on the original permutation. We show that for the 5G polar code of length 1024, the error-correction performance of the proposed decoder is more than 0.25 dB better than that of the BP decoder with the same number of random permutations at the frame error rate of 10 -4 ."}],"date_updated":"2021-01-12T08:08:42Z","status":"public","type":"conference","date_published":"2018-12-01T00:00:00Z","publication_status":"published","doi":"10.1109/glocom.2018.8647308","_id":"6728","language":[{"iso":"eng"}],"publication":"2018 IEEE Global Communications Conference "}]