[{"author":[{"full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","orcid":"0000-0001-8485-1774","first_name":"Radoslav"},{"first_name":"Jan","last_name":"Kynčl","full_name":"Kynčl, Jan"}],"status":"public","alternative_title":["LIPIcs"],"volume":99,"month":"06","page":"40.1 - 40.14","related_material":{"record":[{"id":"11593","relation":"later_version","status":"public"}]},"date_published":"2018-06-11T00:00:00Z","conference":{"location":"Budapest, Hungary","name":"SoCG: Symposium on Computational Geometry","end_date":"2018-06-14","start_date":"2018-06-11"},"abstract":[{"text":"A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The ℤ2-genus of a graph G is the minimum g such that G has an independently even drawing on the orientable surface of genus g. An unpublished result by Robertson and Seymour implies that for every t, every graph of sufficiently large genus contains as a minor a projective t × t grid or one of the following so-called t-Kuratowski graphs: K3, t, or t copies of K5 or K3,3 sharing at most 2 common vertices. We show that the ℤ2-genus of graphs in these families is unbounded in t; in fact, equal to their genus. Together, this implies that the genus of a graph is bounded from above by a function of its ℤ2-genus, solving a problem posed by Schaefer and Štefankovič, and giving an approximate version of the Hanani-Tutte theorem on orientable surfaces.","lang":"eng"}],"citation":{"apa":"Fulek, R., &#38; Kynčl, J. (2018). The ℤ2-Genus of Kuratowski minors (Vol. 99, p. 40.1-40.14). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.40\">https://doi.org/10.4230/LIPIcs.SoCG.2018.40</a>","short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14.","ieee":"R. Fulek and J. Kynčl, “The ℤ2-Genus of Kuratowski minors,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 40.1-40.14.","mla":"Fulek, Radoslav, and Jan Kynčl. <i>The ℤ2-Genus of Kuratowski Minors</i>. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.40\">10.4230/LIPIcs.SoCG.2018.40</a>.","chicago":"Fulek, Radoslav, and Jan Kynčl. “The ℤ2-Genus of Kuratowski Minors,” 99:40.1-40.14. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.40\">https://doi.org/10.4230/LIPIcs.SoCG.2018.40</a>.","ama":"Fulek R, Kynčl J. The ℤ2-Genus of Kuratowski minors. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:40.1-40.14. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.40\">10.4230/LIPIcs.SoCG.2018.40</a>","ista":"Fulek R, Kynčl J. 2018. The ℤ2-Genus of Kuratowski minors. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 40.1-40.14."},"intvolume":"        99","publist_id":"7734","date_updated":"2025-04-14T13:52:37Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2018","publication_status":"published","department":[{"_id":"UlWa"}],"main_file_link":[{"url":"https://arxiv.org/abs/1803.05085","open_access":"1"}],"type":"conference","oa":1,"day":"11","external_id":{"arxiv":["1803.05085"]},"title":"The ℤ2-Genus of Kuratowski minors","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.SoCG.2018.40","scopus_import":"1","oa_version":"Submitted Version","_id":"186","project":[{"grant_number":"M02281","call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs","_id":"261FA626-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","date_created":"2018-12-11T11:45:05Z"},{"intvolume":"        37","pubrep_id":"1038","date_updated":"2025-04-14T07:28:57Z","publist_id":"8043","date_published":"2018-08-04T00:00:00Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/metamolds-molding-a-mold/","relation":"press_release","description":"News on IST Homepage"}]},"citation":{"ista":"Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. 2018. Metamolds: Computational design of silicone molds. ACM Trans. Graph. 37(4), 136.","ama":"Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. Metamolds: Computational design of silicone molds. <i>ACM Trans Graph</i>. 2018;37(4). doi:<a href=\"https://doi.org/10.1145/3197517.3201381\">10.1145/3197517.3201381</a>","chicago":"Alderighi, Thomas, Luigi Malomo, Daniela Giorgi, Nico Pietroni, Bernd Bickel, and Paolo Cignoni. “Metamolds: Computational Design of Silicone Molds.” <i>ACM Trans. Graph.</i> ACM, 2018. <a href=\"https://doi.org/10.1145/3197517.3201381\">https://doi.org/10.1145/3197517.3201381</a>.","short":"T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, P. Cignoni, ACM Trans. Graph. 37 (2018).","ieee":"T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, and P. Cignoni, “Metamolds: Computational design of silicone molds,” <i>ACM Trans. Graph.</i>, vol. 37, no. 4. ACM, 2018.","mla":"Alderighi, Thomas, et al. “Metamolds: Computational Design of Silicone Molds.” <i>ACM Trans. Graph.</i>, vol. 37, no. 4, 136, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3197517.3201381\">10.1145/3197517.3201381</a>.","apa":"Alderighi, T., Malomo, L., Giorgi, D., Pietroni, N., Bickel, B., &#38; Cignoni, P. (2018). Metamolds: Computational design of silicone molds. <i>ACM Trans. Graph.</i> ACM. <a href=\"https://doi.org/10.1145/3197517.3201381\">https://doi.org/10.1145/3197517.3201381</a>"},"abstract":[{"text":"We propose a new method for fabricating digital objects through reusable silicone molds. Molds are generated by casting liquid silicone into custom 3D printed containers called metamolds. Metamolds automatically define the cuts that are needed to extract the cast object from the silicone mold. The shape of metamolds is designed through a novel segmentation technique, which takes into account both geometric and topological constraints involved in the process of mold casting. Our technique is simple, does not require changing the shape or topology of the input objects, and only requires off-the- shelf materials and technologies. We successfully tested our method on a set of challenging examples with complex shapes and rich geometric detail. © 2018 Association for Computing Machinery.","lang":"eng"}],"has_accepted_license":"1","month":"08","volume":37,"ec_funded":1,"ddc":["004"],"article_number":"136","file":[{"content_type":"application/pdf","file_size":91939066,"file_id":"5374","file_name":"IST-2018-1038-v1+1_metamolds_authorversion.pdf","checksum":"61d46273dca4de626accef1d17a0aaad","relation":"main_file","date_created":"2018-12-12T10:18:52Z","access_level":"open_access","date_updated":"2020-07-14T12:44:43Z","creator":"system"}],"status":"public","author":[{"first_name":"Thomas","last_name":"Alderighi","full_name":"Alderighi, Thomas"},{"full_name":"Malomo, Luigi","last_name":"Malomo","first_name":"Luigi"},{"last_name":"Giorgi","first_name":"Daniela","full_name":"Giorgi, Daniela"},{"full_name":"Pietroni, Nico","last_name":"Pietroni","first_name":"Nico"},{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","orcid":"0000-0001-6511-9385","first_name":"Bernd"},{"full_name":"Cignoni, Paolo","last_name":"Cignoni","first_name":"Paolo"}],"issue":"4","publication":"ACM Trans. Graph.","quality_controlled":"1","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","grant_number":"715767"}],"isi":1,"date_created":"2018-12-11T11:44:09Z","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:44:43Z","_id":"13","oa_version":"Submitted Version","scopus_import":"1","doi":"10.1145/3197517.3201381","article_processing_charge":"No","title":"Metamolds: Computational design of silicone molds","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"BeBi"}],"publication_status":"published","year":"2018","publisher":"ACM","day":"04","external_id":{"isi":["000448185000097"]},"oa":1,"type":"journal_article"},{"month":"10","article_processing_charge":"No","title":"Social network plasticity decreases disease transmission in a eusocial insect","ddc":["570"],"license":"https://creativecommons.org/licenses/by/4.0/","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.1480665","open_access":"1"}],"status":"public","department":[{"_id":"SyCr"}],"author":[{"first_name":"Nathalie","last_name":"Stroeymeyt","full_name":"Stroeymeyt, Nathalie"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V","first_name":"Anna V","last_name":"Grasse"},{"first_name":"Alessandro","last_name":"Crespi","full_name":"Crespi, Alessandro"},{"full_name":"Mersch, Danielle","first_name":"Danielle","last_name":"Mersch"},{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868"},{"last_name":"Keller","first_name":"Laurent","full_name":"Keller, Laurent"}],"year":"2018","publisher":"Zenodo","day":"23","oa":1,"type":"research_data_reference","date_updated":"2025-04-15T08:20:52Z","date_created":"2023-05-23T13:24:51Z","date_published":"2018-10-23T00:00:00Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"related_material":{"record":[{"id":"7","status":"public","relation":"used_in_publication"}]},"citation":{"ama":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network plasticity decreases disease transmission in a eusocial insect. 2018. doi:<a href=\"https://doi.org/10.5281/ZENODO.1322669\">10.5281/ZENODO.1322669</a>","chicago":"Stroeymeyt, Nathalie, Anna V Grasse, Alessandro Crespi, Danielle Mersch, Sylvia Cremer, and Laurent Keller. “Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect.” Zenodo, 2018. <a href=\"https://doi.org/10.5281/ZENODO.1322669\">https://doi.org/10.5281/ZENODO.1322669</a>.","short":"N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, (2018).","mla":"Stroeymeyt, Nathalie, et al. <i>Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect</i>. Zenodo, 2018, doi:<a href=\"https://doi.org/10.5281/ZENODO.1322669\">10.5281/ZENODO.1322669</a>.","ieee":"N. Stroeymeyt, A. V. Grasse, A. Crespi, D. Mersch, S. Cremer, and L. Keller, “Social network plasticity decreases disease transmission in a eusocial insect.” Zenodo, 2018.","apa":"Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., &#38; Keller, L. (2018). Social network plasticity decreases disease transmission in a eusocial insect. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.1322669\">https://doi.org/10.5281/ZENODO.1322669</a>","ista":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social network plasticity decreases disease transmission in a eusocial insect, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.1322669\">10.5281/ZENODO.1322669</a>."},"_id":"13055","abstract":[{"text":"Dataset for manuscript 'Social network plasticity decreases disease transmission in a eusocial insect'\r\nCompared to previous versions: - raw image files added\r\n                                                     - correction of URLs within README.txt file\r\n","lang":"eng"}],"oa_version":"Published Version","doi":"10.5281/ZENODO.1322669"},{"author":[{"last_name":"Garriga","first_name":"Edgar","full_name":"Garriga, Edgar"},{"last_name":"di Tommaso","first_name":"Paolo","full_name":"di Tommaso, Paolo"},{"first_name":"Cedrik","last_name":"Magis","full_name":"Magis, Cedrik"},{"full_name":"Erb, Ionas","last_name":"Erb","first_name":"Ionas"},{"last_name":"Mansouri","first_name":"Leila","full_name":"Mansouri, Leila"},{"full_name":"Baltzis, Athanasios","first_name":"Athanasios","last_name":"Baltzis"},{"full_name":"Laayouni, Hafid","first_name":"Hafid","last_name":"Laayouni"},{"first_name":"Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor"},{"full_name":"Floden, Evan","last_name":"Floden","first_name":"Evan"},{"last_name":"Notredame","first_name":"Cedric","full_name":"Notredame, Cedric"}],"status":"public","department":[{"_id":"FyKo"}],"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.3271452","open_access":"1"}],"publisher":"Zenodo","year":"2018","oa":1,"day":"07","type":"research_data_reference","month":"12","title":"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method","ddc":["570"],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2018-12-07T00:00:00Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"related_material":{"record":[{"id":"7181","status":"public","relation":"used_in_publication"}]},"oa_version":"Published Version","citation":{"ista":"Garriga E, di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2018. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.2025846\">10.5281/ZENODO.2025846</a>.","apa":"Garriga, E., di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2018). Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.2025846\">https://doi.org/10.5281/ZENODO.2025846</a>","short":"E. Garriga, P. di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, (2018).","mla":"Garriga, Edgar, et al. <i>Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method</i>. Zenodo, 2018, doi:<a href=\"https://doi.org/10.5281/ZENODO.2025846\">10.5281/ZENODO.2025846</a>.","ieee":"E. Garriga <i>et al.</i>, “Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method.” Zenodo, 2018.","chicago":"Garriga, Edgar, Paolo di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Zenodo, 2018. <a href=\"https://doi.org/10.5281/ZENODO.2025846\">https://doi.org/10.5281/ZENODO.2025846</a>.","ama":"Garriga E, di Tommaso P, Magis C, et al. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. 2018. doi:<a href=\"https://doi.org/10.5281/ZENODO.2025846\">10.5281/ZENODO.2025846</a>"},"_id":"13059","abstract":[{"lang":"eng","text":"This dataset contains a GitHub repository containing all the data, analysis, Nextflow workflows and Jupyter notebooks to replicate the manuscript titled \"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method\".\r\nIt also contains the Multiple Sequence Alignments (MSAs) generated and well as the main figures and tables from the manuscript.\r\nThe repository is also available at GitHub (https://github.com/cbcrg/dpa-analysis) release `v1.2`.\r\nFor details on how to use the regressive alignment algorithm, see the T-Coffee software suite (https://github.com/cbcrg/tcoffee)."}],"doi":"10.5281/ZENODO.2025846","date_updated":"2025-07-10T11:54:19Z","date_created":"2023-05-23T16:08:20Z"},{"file":[{"date_updated":"2020-07-14T12:44:43Z","creator":"dernst","access_level":"open_access","date_created":"2018-12-17T11:55:05Z","relation":"main_file","checksum":"d6331d4385b1fffd6b47b45d5949d841","file_name":"2018_eLife_Picard.pdf","file_id":"5695","file_size":3158125,"content_type":"application/pdf"}],"month":"08","volume":7,"acknowledgement":"We are grateful to Lu Dabing (Soochow University, Suzhou, China) for providing Schistosoma japonicum samples, to Ariana Macon (IST Austria) and Georgette Stovall (JLU Giessen) for technical assistance, to IT support at IST Austria for providing optimal environment to bioinformatic analyses, and to the Vicoso lab for comments on the manuscript.","ddc":["570"],"article_number":"e35684","publication":"eLife","status":"public","author":[{"orcid":"0000-0002-8101-2518","last_name":"Picard","first_name":"Marion A","full_name":"Picard, Marion A","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cosseau, Celine","last_name":"Cosseau","first_name":"Celine"},{"first_name":"Sabrina","last_name":"Ferré","full_name":"Ferré, Sabrina"},{"first_name":"Thomas","last_name":"Quack","full_name":"Quack, Thomas"},{"full_name":"Grevelding, Christoph","first_name":"Christoph","last_name":"Grevelding"},{"last_name":"Couté","first_name":"Yohann","full_name":"Couté, Yohann"},{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2025-04-15T08:18:37Z","publist_id":"7792","intvolume":"         7","citation":{"ista":"Picard MAL, Cosseau C, Ferré S, Quack T, Grevelding C, Couté Y, Vicoso B. 2018. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 7, e35684.","ama":"Picard MAL, Cosseau C, Ferré S, et al. Evolution of gene dosage on the Z-chromosome of schistosome parasites. <i>eLife</i>. 2018;7. doi:<a href=\"https://doi.org/10.7554/eLife.35684\">10.7554/eLife.35684</a>","chicago":"Picard, Marion A L, Celine Cosseau, Sabrina Ferré, Thomas Quack, Christoph Grevelding, Yohann Couté, and Beatriz Vicoso. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” <i>ELife</i>. eLife Sciences Publications, 2018. <a href=\"https://doi.org/10.7554/eLife.35684\">https://doi.org/10.7554/eLife.35684</a>.","mla":"Picard, Marion A. L., et al. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” <i>ELife</i>, vol. 7, e35684, eLife Sciences Publications, 2018, doi:<a href=\"https://doi.org/10.7554/eLife.35684\">10.7554/eLife.35684</a>.","short":"M.A.L. Picard, C. Cosseau, S. Ferré, T. Quack, C. Grevelding, Y. Couté, B. Vicoso, ELife 7 (2018).","ieee":"M. A. L. Picard <i>et al.</i>, “Evolution of gene dosage on the Z-chromosome of schistosome parasites,” <i>eLife</i>, vol. 7. eLife Sciences Publications, 2018.","apa":"Picard, M. A. L., Cosseau, C., Ferré, S., Quack, T., Grevelding, C., Couté, Y., &#38; Vicoso, B. (2018). Evolution of gene dosage on the Z-chromosome of schistosome parasites. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.35684\">https://doi.org/10.7554/eLife.35684</a>"},"abstract":[{"text":"XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno’s classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes. ","lang":"eng"}],"has_accepted_license":"1","date_published":"2018-08-13T00:00:00Z","related_material":{"record":[{"relation":"popular_science","status":"public","id":"5586"}]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","title":"Evolution of gene dosage on the Z-chromosome of schistosome parasites","day":"13","external_id":{"isi":["000441388200001"]},"oa":1,"type":"journal_article","department":[{"_id":"BeVi"}],"publication_status":"published","year":"2018","publisher":"eLife Sciences Publications","isi":1,"date_created":"2018-12-11T11:44:47Z","quality_controlled":"1","project":[{"grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF"}],"_id":"131","oa_version":"Published Version","scopus_import":"1","doi":"10.7554/eLife.35684","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:44:43Z","article_type":"original"},{"volume":46,"acknowledgement":"E.H. is funded by a Junior Research Fellowship from Trinity College, Cam-bridge, a Sir Henry Wellcome Fellowship from the Wellcome Trust, and theBettencourt-Schueller Young Researcher Prize for support.","ddc":["570"],"month":"08","page":"360 - 375","file":[{"file_size":8948384,"content_type":"application/pdf","file_name":"2018_DevelopmentalCell_Sznurkowska.pdf","file_id":"5694","relation":"main_file","checksum":"78d2062b9e3c3b90fe71545aeb6d2f65","date_updated":"2020-07-14T12:44:43Z","creator":"dernst","date_created":"2018-12-17T10:49:49Z","access_level":"open_access"}],"status":"public","author":[{"full_name":"Sznurkowska, Magdalena","last_name":"Sznurkowska","first_name":"Magdalena"},{"orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"full_name":"Azzarelli, Roberta","last_name":"Azzarelli","first_name":"Roberta"},{"full_name":"Rulands, Steffen","last_name":"Rulands","first_name":"Steffen"},{"full_name":"Nestorowa, Sonia","first_name":"Sonia","last_name":"Nestorowa"},{"full_name":"Hindley, Christopher","last_name":"Hindley","first_name":"Christopher"},{"last_name":"Nichols","first_name":"Jennifer","full_name":"Nichols, Jennifer"},{"full_name":"Göttgens, Berthold","first_name":"Berthold","last_name":"Göttgens"},{"first_name":"Meritxell","last_name":"Huch","full_name":"Huch, Meritxell"},{"full_name":"Philpott, Anna","first_name":"Anna","last_name":"Philpott"},{"first_name":"Benjamin","last_name":"Simons","full_name":"Simons, Benjamin"}],"issue":"3","publication":"Developmental Cell","intvolume":"        46","publist_id":"7791","date_updated":"2023-09-11T12:52:41Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2018-08-06T00:00:00Z","has_accepted_license":"1","abstract":[{"text":"Pancreas development involves a coordinated process in which an early phase of cell segregation is followed by a longer phase of lineage restriction, expansion, and tissue remodeling. By combining clonal tracing and whole-mount reconstruction with proliferation kinetics and single-cell transcriptional profiling, we define the functional basis of pancreas morphogenesis. We show that the large-scale organization of mouse pancreas can be traced to the activity of self-renewing precursors positioned at the termini of growing ducts, which act collectively to drive serial rounds of stochastic ductal bifurcation balanced by termination. During this phase of branching morphogenesis, multipotent precursors become progressively fate-restricted, giving rise to self-renewing acinar-committed precursors that are conveyed with growing ducts, as well as ductal progenitors that expand the trailing ducts and give rise to delaminating endocrine cells. These findings define quantitatively how the functional behavior and lineage progression of precursor pools determine the large-scale patterning of pancreatic sub-compartments.","lang":"eng"}],"citation":{"ista":"Sznurkowska M, Hannezo EB, Azzarelli R, Rulands S, Nestorowa S, Hindley C, Nichols J, Göttgens B, Huch M, Philpott A, Simons B. 2018. Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. 46(3), 360–375.","apa":"Sznurkowska, M., Hannezo, E. B., Azzarelli, R., Rulands, S., Nestorowa, S., Hindley, C., … Simons, B. (2018). Defining lineage potential and fate behavior of precursors during pancreas development. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2018.06.028\">https://doi.org/10.1016/j.devcel.2018.06.028</a>","short":"M. Sznurkowska, E.B. Hannezo, R. Azzarelli, S. Rulands, S. Nestorowa, C. Hindley, J. Nichols, B. Göttgens, M. Huch, A. Philpott, B. Simons, Developmental Cell 46 (2018) 360–375.","ieee":"M. Sznurkowska <i>et al.</i>, “Defining lineage potential and fate behavior of precursors during pancreas development,” <i>Developmental Cell</i>, vol. 46, no. 3. Cell Press, pp. 360–375, 2018.","mla":"Sznurkowska, Magdalena, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” <i>Developmental Cell</i>, vol. 46, no. 3, Cell Press, 2018, pp. 360–75, doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.06.028\">10.1016/j.devcel.2018.06.028</a>.","chicago":"Sznurkowska, Magdalena, Edouard B Hannezo, Roberta Azzarelli, Steffen Rulands, Sonia Nestorowa, Christopher Hindley, Jennifer Nichols, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” <i>Developmental Cell</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.devcel.2018.06.028\">https://doi.org/10.1016/j.devcel.2018.06.028</a>.","ama":"Sznurkowska M, Hannezo EB, Azzarelli R, et al. Defining lineage potential and fate behavior of precursors during pancreas development. <i>Developmental Cell</i>. 2018;46(3):360-375. doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.06.028\">10.1016/j.devcel.2018.06.028</a>"},"article_processing_charge":"No","title":"Defining lineage potential and fate behavior of precursors during pancreas development","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","year":"2018","publisher":"Cell Press","department":[{"_id":"EdHa"}],"type":"journal_article","external_id":{"isi":["000441327300012"]},"day":"06","oa":1,"quality_controlled":"1","date_created":"2018-12-11T11:44:48Z","isi":1,"article_type":"original","file_date_updated":"2020-07-14T12:44:43Z","language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2018.06.028","_id":"132","scopus_import":"1","oa_version":"Published Version"},{"title":"Language acquisition with communication between learners","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1742-5662"]},"department":[{"_id":"KrCh"}],"publisher":"The Royal Society","publication_status":"published","year":"2018","oa":1,"external_id":{"isi":["000428576200023"],"pmid":["29593089"]},"day":"01","pmid":1,"type":"journal_article","quality_controlled":"1","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"}],"isi":1,"date_created":"2018-12-11T11:45:09Z","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:22Z","article_type":"original","scopus_import":"1","oa_version":"Submitted Version","_id":"198","doi":"10.1098/rsif.2018.0073","month":"03","article_number":"20180073","ddc":["000"],"ec_funded":1,"volume":15,"file":[{"relation":"main_file","checksum":"444e1a9d98eb0e780671be82b13025f3","creator":"dernst","date_updated":"2020-07-14T12:45:22Z","access_level":"open_access","date_created":"2019-02-12T07:54:37Z","file_size":219837,"content_type":"application/pdf","file_name":"2018_RS_IbsenJensen.pdf","file_id":"5955"}],"author":[{"last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef","first_name":"Josef","last_name":"Tkadlec","orcid":"0000-0002-1097-9684"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"status":"public","issue":"140","publication":"Journal of the Royal Society Interface","intvolume":"        15","date_updated":"2025-04-15T07:26:26Z","publist_id":"7715","date_published":"2018-03-01T00:00:00Z","related_material":{"record":[{"id":"9814","relation":"research_data","status":"public"}],"link":[{"relation":"supplementary_material","url":"https://dx.doi.org/10.6084/m9.figshare.c.4028971"}]},"citation":{"ama":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. Language acquisition with communication between learners. <i>Journal of the Royal Society Interface</i>. 2018;15(140). doi:<a href=\"https://doi.org/10.1098/rsif.2018.0073\">10.1098/rsif.2018.0073</a>","chicago":"Ibsen-Jensen, Rasmus, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Language Acquisition with Communication between Learners.” <i>Journal of the Royal Society Interface</i>. The Royal Society, 2018. <a href=\"https://doi.org/10.1098/rsif.2018.0073\">https://doi.org/10.1098/rsif.2018.0073</a>.","short":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, Journal of the Royal Society Interface 15 (2018).","ieee":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, and M. Nowak, “Language acquisition with communication between learners,” <i>Journal of the Royal Society Interface</i>, vol. 15, no. 140. The Royal Society, 2018.","mla":"Ibsen-Jensen, Rasmus, et al. “Language Acquisition with Communication between Learners.” <i>Journal of the Royal Society Interface</i>, vol. 15, no. 140, 20180073, The Royal Society, 2018, doi:<a href=\"https://doi.org/10.1098/rsif.2018.0073\">10.1098/rsif.2018.0073</a>.","apa":"Ibsen-Jensen, R., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2018). Language acquisition with communication between learners. <i>Journal of the Royal Society Interface</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsif.2018.0073\">https://doi.org/10.1098/rsif.2018.0073</a>","ista":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. 2018. Language acquisition with communication between learners. Journal of the Royal Society Interface. 15(140), 20180073."},"abstract":[{"text":"We consider a class of students learning a language from a teacher. The situation can be interpreted as a group of child learners receiving input from the linguistic environment. The teacher provides sample sentences. The students try to learn the grammar from the teacher. In addition to just listening to the teacher, the students can also communicate with each other. The students hold hypotheses about the grammar and change them if they receive counter evidence. The process stops when all students have converged to the correct grammar. We study how the time to convergence depends on the structure of the classroom by introducing and evaluating various complexity measures. We find that structured communication between students, although potentially introducing confusion, can greatly reduce some of the complexity measures. Our theory can also be interpreted as applying to the scientific process, where nature is the teacher and the scientists are the students.","lang":"eng"}],"has_accepted_license":"1"},{"quality_controlled":"1","date_created":"2018-12-11T11:45:09Z","isi":1,"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:22Z","doi":"10.3390/genes9060294","oa_version":"Published Version","scopus_import":"1","_id":"199","title":"Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"MDPI","year":"2018","publication_status":"published","department":[{"_id":"BeVi"}],"type":"journal_article","oa":1,"day":"12","external_id":{"isi":["000436494200026"]},"intvolume":"         9","publist_id":"7714","date_updated":"2024-12-11T13:13:35Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2018-06-12T00:00:00Z","has_accepted_license":"1","citation":{"ista":"Ma W, Veltsos P, Toups MA, Rodrigues N, Sermier R, Jeffries D, Perrin N. 2018. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 9(6), 294.","mla":"Ma, Wen, et al. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” <i>Genes</i>, vol. 9, no. 6, 294, MDPI, 2018, doi:<a href=\"https://doi.org/10.3390/genes9060294\">10.3390/genes9060294</a>.","short":"W. Ma, P. Veltsos, M.A. Toups, N. Rodrigues, R. Sermier, D. Jeffries, N. Perrin, Genes 9 (2018).","ieee":"W. Ma <i>et al.</i>, “Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes,” <i>Genes</i>, vol. 9, no. 6. MDPI, 2018.","apa":"Ma, W., Veltsos, P., Toups, M. A., Rodrigues, N., Sermier, R., Jeffries, D., &#38; Perrin, N. (2018). Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. <i>Genes</i>. MDPI. <a href=\"https://doi.org/10.3390/genes9060294\">https://doi.org/10.3390/genes9060294</a>","ama":"Ma W, Veltsos P, Toups MA, et al. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. <i>Genes</i>. 2018;9(6). doi:<a href=\"https://doi.org/10.3390/genes9060294\">10.3390/genes9060294</a>","chicago":"Ma, Wen, Paris Veltsos, Melissa A Toups, Nicolas Rodrigues, Roberto Sermier, Daniel Jeffries, and Nicolas Perrin. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” <i>Genes</i>. MDPI, 2018. <a href=\"https://doi.org/10.3390/genes9060294\">https://doi.org/10.3390/genes9060294</a>."},"abstract":[{"text":"Sex-biased genes are central to the study of sexual selection, sexual antagonism, and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome in the common frog Rana temporaria based on five developmental stages and three adult tissues from both sexes, obtained from a population with karyotypically homomorphic but genetically differentiated sex chromosomes. This allows the study of sex-biased gene expression throughout development, and its effect on the rate of gene evolution while accounting for pleiotropic expression, which is known to negatively correlate with the evolutionary rate. Overall, sex-biased genes had little overlap among developmental stages and adult tissues. Late developmental stages and gonad tissues had the highest numbers of stage-or tissue-specific genes. We find that pleiotropic gene expression is a better predictor than sex bias for the evolutionary rate of genes, though it often interacts with sex bias. Although genetically differentiated, the sex chromosomes were not enriched in sex-biased genes, possibly due to a very recent arrest of XY recombination. These results extend our understanding of the developmental dynamics, tissue specificity, and genomic localization of sex-biased genes.","lang":"eng"}],"ddc":["570"],"article_number":"294","volume":9,"month":"06","file":[{"content_type":"application/pdf","file_size":3985796,"file_id":"5905","file_name":"2018_Genes_Ma.pdf","checksum":"423069beb1cd3cdd25bf3f464b38f1d7","relation":"main_file","date_created":"2019-02-01T07:52:28Z","access_level":"open_access","date_updated":"2020-07-14T12:45:22Z","creator":"dernst"}],"author":[{"first_name":"Wen","last_name":"Ma","full_name":"Ma, Wen"},{"full_name":"Veltsos, Paris","first_name":"Paris","last_name":"Veltsos"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A","first_name":"Melissa A","orcid":"0000-0002-9752-7380","last_name":"Toups"},{"full_name":"Rodrigues, Nicolas","first_name":"Nicolas","last_name":"Rodrigues"},{"last_name":"Sermier","first_name":"Roberto","full_name":"Sermier, Roberto"},{"full_name":"Jeffries, Daniel","last_name":"Jeffries","first_name":"Daniel"},{"first_name":"Nicolas","last_name":"Perrin","full_name":"Perrin, Nicolas"}],"status":"public","publication":"Genes","issue":"6"},{"abstract":[{"text":"Background: Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-white) adipocytes. However, acute effects of NE stimulation have not been described at the transcriptional network level. Results: We used RNA-seq to uncover a broad transcriptional response. The inference of protein-protein and protein-DNA interaction networks allowed us to identify a set of immediate-early genes (IEGs) with high betweenness, validating our approach and suggesting a hierarchical control of transcriptional regulation. In addition, we identified a transcriptional regulatory network with IEGs as master regulators, including HSF1 and NFIL3 as novel NE-induced IEG candidates. Moreover, a functional enrichment analysis and gene clustering into functional modules suggest a crosstalk between metabolic, signaling, and immune responses. Conclusions: Altogether, our network biology approach explores for the first time the immediate-early systems level response of human adipocytes to acute sympathetic activation, thereby providing a first network basis of early cell fate programs and crosstalks between metabolic and transcriptional networks required for proper WAT function.","lang":"eng"}],"citation":{"chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” <i>BMC Genomics</i>. BioMed Central, 2018. <a href=\"https://doi.org/10.1186/s12864-018-5173-0\">https://doi.org/10.1186/s12864-018-5173-0</a>.","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. <i>BMC Genomics</i>. 2018;19(1). doi:<a href=\"https://doi.org/10.1186/s12864-018-5173-0\">10.1186/s12864-018-5173-0</a>","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., &#38; Scheideler, M. (2018). Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. <i>BMC Genomics</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s12864-018-5173-0\">https://doi.org/10.1186/s12864-018-5173-0</a>","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, BMC Genomics 19 (2018).","ieee":"J. Higareda Almaraz <i>et al.</i>, “Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes,” <i>BMC Genomics</i>, vol. 19, no. 1. BioMed Central, 2018.","mla":"Higareda Almaraz, Juan, et al. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” <i>BMC Genomics</i>, vol. 19, no. 1, BioMed Central, 2018, doi:<a href=\"https://doi.org/10.1186/s12864-018-5173-0\">10.1186/s12864-018-5173-0</a>.","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 19(1)."},"has_accepted_license":"1","date_published":"2018-11-03T00:00:00Z","related_material":{"record":[{"id":"9807","status":"public","relation":"research_data"},{"id":"9808","relation":"research_data","status":"public"}]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-09-13T09:10:47Z","publist_id":"8035","intvolume":"        19","issue":"1","publication":"BMC Genomics","author":[{"last_name":"Higareda Almaraz","first_name":"Juan","full_name":"Higareda Almaraz, Juan"},{"last_name":"Karbiener","first_name":"Michael","full_name":"Karbiener, Michael"},{"full_name":"Giroud, Maude","first_name":"Maude","last_name":"Giroud"},{"full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Pauler","orcid":"0000-0002-7462-0048"},{"full_name":"Gerhalter, Teresa","last_name":"Gerhalter","first_name":"Teresa"},{"first_name":"Stephan","last_name":"Herzig","full_name":"Herzig, Stephan"},{"last_name":"Scheideler","first_name":"Marcel","full_name":"Scheideler, Marcel"}],"status":"public","file":[{"date_created":"2018-12-17T14:52:57Z","access_level":"open_access","date_updated":"2020-07-14T12:45:23Z","creator":"dernst","checksum":"a56516e734dab589dc7f3e1915973b4d","relation":"main_file","file_id":"5712","file_name":"2018_BMCGenomics_Higareda.pdf","content_type":"application/pdf","file_size":4629784}],"month":"11","ddc":["570"],"volume":19,"acknowledgement":"This work was funded by the German Centre for Diabetes Research (DZD) and the Austrian Science Fund (FWF, P25729-B19).","scopus_import":"1","oa_version":"Published Version","_id":"20","doi":"10.1186/s12864-018-5173-0","file_date_updated":"2020-07-14T12:45:23Z","language":[{"iso":"eng"}],"article_type":"original","isi":1,"date_created":"2018-12-11T11:44:12Z","quality_controlled":"1","oa":1,"day":"03","external_id":{"isi":["000450976700002"]},"type":"journal_article","department":[{"_id":"SiHi"}],"publisher":"BioMed Central","publication_status":"published","year":"2018","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["1471-2164"]},"title":"Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","article_processing_charge":"No"},{"quality_controlled":"1","project":[{"grant_number":"I02979-N35","call_identifier":"FWF","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:45:05Z","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:20Z","oa_version":"Published Version","scopus_import":1,"_id":"188","doi":"10.4230/LIPIcs.SoCG.2018.35","title":"Smallest enclosing spheres and Chernoff points in Bregman geometry","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2018","publication_status":"published","oa":1,"day":"11","type":"conference","intvolume":"        99","date_updated":"2021-01-12T06:53:48Z","publist_id":"7733","date_published":"2018-06-11T00:00:00Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"conference":{"end_date":"2018-06-14","start_date":"2018-06-11","name":"SoCG: Symposium on Computational Geometry","location":"Budapest, Hungary"},"abstract":[{"text":"Smallest enclosing spheres of finite point sets are central to methods in topological data analysis. Focusing on Bregman divergences to measure dissimilarity, we prove bounds on the location of the center of a smallest enclosing sphere. These bounds depend on the range of radii for which Bregman balls are convex.","lang":"eng"}],"citation":{"ieee":"H. Edelsbrunner, Z. Virk, and H. Wagner, “Smallest enclosing spheres and Chernoff points in Bregman geometry,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 35:1-35:13.","short":"H. Edelsbrunner, Z. Virk, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13.","mla":"Edelsbrunner, Herbert, et al. <i>Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry</i>. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.35\">10.4230/LIPIcs.SoCG.2018.35</a>.","apa":"Edelsbrunner, H., Virk, Z., &#38; Wagner, H. (2018). Smallest enclosing spheres and Chernoff points in Bregman geometry (Vol. 99, p. 35:1-35:13). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.35\">https://doi.org/10.4230/LIPIcs.SoCG.2018.35</a>","ama":"Edelsbrunner H, Virk Z, Wagner H. Smallest enclosing spheres and Chernoff points in Bregman geometry. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:35:1-35:13. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.35\">10.4230/LIPIcs.SoCG.2018.35</a>","chicago":"Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry,” 99:35:1-35:13. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.35\">https://doi.org/10.4230/LIPIcs.SoCG.2018.35</a>.","ista":"Edelsbrunner H, Virk Z, Wagner H. 2018. Smallest enclosing spheres and Chernoff points in Bregman geometry. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 35:1-35:13."},"has_accepted_license":"1","month":"06","ddc":["000"],"acknowledgement":"This research is partially supported by the Office of Naval Research, through grant no. N62909-18-1-2038, and the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund","volume":99,"file":[{"date_created":"2018-12-17T16:31:31Z","access_level":"open_access","date_updated":"2020-07-14T12:45:20Z","creator":"dernst","checksum":"7509403803b3ac1aee94bbc2ad293d21","relation":"main_file","file_id":"5724","file_name":"2018_LIPIcs_Edelsbrunner.pdf","content_type":"application/pdf","file_size":489080}],"page":"35:1 - 35:13","author":[{"first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Virk, Ziga","first_name":"Ziga","last_name":"Virk"},{"full_name":"Wagner, Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","first_name":"Hubert","last_name":"Wagner"}],"status":"public","alternative_title":["Leibniz International Proceedings in Information, LIPIcs"]},{"language":[{"iso":"eng"}],"article_type":"original","scopus_import":"1","oa_version":"Submitted Version","_id":"19","doi":"10.1093/molbev/msy163","quality_controlled":"1","isi":1,"date_created":"2018-12-11T11:44:11Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30169679"}],"publisher":"Oxford University Press","publication_status":"published","year":"2018","oa":1,"pmid":1,"external_id":{"isi":["000452567200006"],"pmid":["30169679"]},"day":"28","type":"journal_article","title":"Nonoptimal gene expression creates latent potential for antibiotic resistance","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0737-4038"]},"date_published":"2018-08-28T00:00:00Z","abstract":[{"text":"Bacteria regulate genes to survive antibiotic stress, but regulation can be far from perfect. When regulation is not optimal, mutations that change gene expression can contribute to antibiotic resistance. It is not systematically understood to what extent natural gene regulation is or is not optimal for distinct antibiotics, and how changes in expression of specific genes quantitatively affect antibiotic resistance. Here we discover a simple quantitative relation between fitness, gene expression, and antibiotic potency, which rationalizes our observation that a multitude of genes and even innate antibiotic defense mechanisms have expression that is critically nonoptimal under antibiotic treatment. First, we developed a pooled-strain drug-diffusion assay and screened Escherichia coli overexpression and knockout libraries, finding that resistance to a range of 31 antibiotics could result from changing expression of a large and functionally diverse set of genes, in a primarily but not exclusively drug-specific manner. Second, by synthetically controlling the expression of single-drug and multidrug resistance genes, we observed that their fitness-expression functions changed dramatically under antibiotic treatment in accordance with a log-sensitivity relation. Thus, because many genes are nonoptimally expressed under antibiotic treatment, many regulatory mutations can contribute to resistance by altering expression and by activating latent defenses.","lang":"eng"}],"citation":{"chicago":"Palmer, Adam, Remy P Chait, and Roy Kishony. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/molbev/msy163\">https://doi.org/10.1093/molbev/msy163</a>.","ama":"Palmer A, Chait RP, Kishony R. Nonoptimal gene expression creates latent potential for antibiotic resistance. <i>Molecular Biology and Evolution</i>. 2018;35(11):2669-2684. doi:<a href=\"https://doi.org/10.1093/molbev/msy163\">10.1093/molbev/msy163</a>","apa":"Palmer, A., Chait, R. P., &#38; Kishony, R. (2018). Nonoptimal gene expression creates latent potential for antibiotic resistance. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msy163\">https://doi.org/10.1093/molbev/msy163</a>","short":"A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018) 2669–2684.","ieee":"A. Palmer, R. P. Chait, and R. Kishony, “Nonoptimal gene expression creates latent potential for antibiotic resistance,” <i>Molecular Biology and Evolution</i>, vol. 35, no. 11. Oxford University Press, pp. 2669–2684, 2018.","mla":"Palmer, Adam, et al. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” <i>Molecular Biology and Evolution</i>, vol. 35, no. 11, Oxford University Press, 2018, pp. 2669–84, doi:<a href=\"https://doi.org/10.1093/molbev/msy163\">10.1093/molbev/msy163</a>.","ista":"Palmer A, Chait RP, Kishony R. 2018. Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. 35(11), 2669–2684."},"intvolume":"        35","date_updated":"2023-10-17T11:51:06Z","publist_id":"8036","author":[{"full_name":"Palmer, Adam","last_name":"Palmer","first_name":"Adam"},{"first_name":"Remy P","last_name":"Chait","orcid":"0000-0003-0876-3187","full_name":"Chait, Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kishony","first_name":"Roy","full_name":"Kishony, Roy"}],"status":"public","issue":"11","publication":"Molecular Biology and Evolution","month":"08","volume":35,"page":"2669 - 2684"},{"language":[{"iso":"eng"}],"article_type":"original","oa_version":"Submitted Version","scopus_import":"1","_id":"190","doi":"10.1002/jez.b.22824","quality_controlled":"1","isi":1,"date_created":"2018-12-11T11:45:06Z","main_file_link":[{"url":"https://onlinelibrary.wiley.com/doi/am-pdf/10.1002/jez.b.22824","open_access":"1"}],"department":[{"_id":"BeVi"}],"publisher":"Wiley","publication_status":"published","year":"2018","oa":1,"external_id":{"isi":["000443231000002"],"pmid":["29998472"]},"pmid":1,"day":"11","type":"journal_article","title":"Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-07-11T00:00:00Z","citation":{"apa":"Harrison, M., Arning, N., Kremer, L., Ylla, G., Belles, X., Bornberg Bauer, E., … Schal, C. (2018). Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. Wiley. <a href=\"https://doi.org/10.1002/jez.b.22824\">https://doi.org/10.1002/jez.b.22824</a>","ieee":"M. Harrison <i>et al.</i>, “Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest,” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>, vol. 330. Wiley, pp. 254–264, 2018.","short":"M. Harrison, N. Arning, L. Kremer, G. Ylla, X. Belles, E. Bornberg Bauer, A.K. Huylmans, E. Jongepier, M. Puilachs, S. Richards, C. Schal, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 330 (2018) 254–264.","mla":"Harrison, Mark, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>, vol. 330, Wiley, 2018, pp. 254–64, doi:<a href=\"https://doi.org/10.1002/jez.b.22824\">10.1002/jez.b.22824</a>.","chicago":"Harrison, Mark, Nicolas Arning, Lucas Kremer, Guillem Ylla, Xavier Belles, Erich Bornberg Bauer, Ann K Huylmans, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/jez.b.22824\">https://doi.org/10.1002/jez.b.22824</a>.","ama":"Harrison M, Arning N, Kremer L, et al. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. 2018;330:254-264. doi:<a href=\"https://doi.org/10.1002/jez.b.22824\">10.1002/jez.b.22824</a>","ista":"Harrison M, Arning N, Kremer L, Ylla G, Belles X, Bornberg Bauer E, Huylmans AK, Jongepier E, Puilachs M, Richards S, Schal C. 2018. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 330, 254–264."},"abstract":[{"lang":"eng","text":"The German cockroach, Blattella germanica, is a worldwide pest that infests buildings, including homes, restaurants, and hospitals, often living in unsanitary conditions. As a disease vector and producer of allergens, this species has major health and economic impacts on humans. Factors contributing to the success of the German cockroach include its resistance to a broad range of insecticides, immunity to many pathogens, and its ability, as an extreme generalist omnivore, to survive on most food sources. The recently published genome shows that B. germanica has an exceptionally high number of protein coding genes. In this study, we investigate the functions of the 93 significantly expanded gene families with the aim to better understand the success of B. germanica as a major pest despite such inhospitable conditions. We find major expansions in gene families with functions related to the detoxification of insecticides and allelochemicals, defense against pathogens, digestion, sensory perception, and gene regulation. These expansions might have allowed B. germanica to develop multiple resistance mechanisms to insecticides and pathogens, and enabled a broad, flexible diet, thus explaining its success in unsanitary conditions and under recurrent chemical control. The findings and resources presented here provide insights for better understanding molecular mechanisms that will facilitate more effective cockroach control."}],"intvolume":"       330","date_updated":"2023-09-11T13:59:54Z","publist_id":"7730","author":[{"full_name":"Harrison, Mark","first_name":"Mark","last_name":"Harrison"},{"full_name":"Arning, Nicolas","last_name":"Arning","first_name":"Nicolas"},{"last_name":"Kremer","first_name":"Lucas","full_name":"Kremer, Lucas"},{"first_name":"Guillem","last_name":"Ylla","full_name":"Ylla, Guillem"},{"full_name":"Belles, Xavier","last_name":"Belles","first_name":"Xavier"},{"first_name":"Erich","last_name":"Bornberg Bauer","full_name":"Bornberg Bauer, Erich"},{"full_name":"Huylmans, Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961","last_name":"Huylmans","first_name":"Ann K"},{"last_name":"Jongepier","first_name":"Evelien","full_name":"Jongepier, Evelien"},{"full_name":"Puilachs, Maria","last_name":"Puilachs","first_name":"Maria"},{"last_name":"Richards","first_name":"Stephen","full_name":"Richards, Stephen"},{"full_name":"Schal, Coby","first_name":"Coby","last_name":"Schal"}],"status":"public","publication":"Journal of Experimental Zoology Part B: Molecular and Developmental Evolution","month":"07","volume":330,"page":"254-264"},{"oa_version":"Submitted Version","scopus_import":"1","_id":"192","doi":"10.1038/s41477-018-0190-1","language":[{"iso":"eng"}],"article_type":"original","isi":1,"date_created":"2018-12-11T11:45:07Z","quality_controlled":"1","oa":1,"external_id":{"isi":["000443221200017"],"pmid":["29942048"]},"day":"25","pmid":1,"type":"journal_article","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/29942048","open_access":"1"}],"department":[{"_id":"JiFr"},{"_id":"DaSi"},{"_id":"NanoFab"}],"publisher":"Springer Nature","year":"2018","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Rapid and reversible root growth inhibition by TIR1 auxin signalling","article_processing_charge":"No","abstract":[{"lang":"eng","text":"The phytohormone auxin is the information carrier in a plethora of developmental and physiological processes in plants(1). It has been firmly established that canonical, nuclear auxin signalling acts through regulation of gene transcription(2). Here, we combined microfluidics, live imaging, genetic engineering and computational modelling to reanalyse the classical case of root growth inhibition(3) by auxin. We show that Arabidopsis roots react to addition and removal of auxin by extremely rapid adaptation of growth rate. This process requires intracellular auxin perception but not transcriptional reprogramming. The formation of the canonical TIR1/AFB-Aux/IAA co-receptor complex is required for the growth regulation, hinting to a novel, non-transcriptional branch of this signalling pathway. Our results challenge the current understanding of root growth regulation by auxin and suggest another, presumably non-transcriptional, signalling output of the canonical auxin pathway."}],"citation":{"ama":"Fendrych M, Akhmanova M, Merrin J, et al. Rapid and reversible root growth inhibition by TIR1 auxin signalling. <i>Nature Plants</i>. 2018;4(7):453-459. doi:<a href=\"https://doi.org/10.1038/s41477-018-0190-1\">10.1038/s41477-018-0190-1</a>","chicago":"Fendrych, Matyas, Maria Akhmanova, Jack Merrin, Matous Glanc, Shinya Hagihara, Koji Takahashi, Naoyuki Uchida, Keiko U Torii, and Jiří Friml. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” <i>Nature Plants</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0190-1\">https://doi.org/10.1038/s41477-018-0190-1</a>.","ieee":"M. Fendrych <i>et al.</i>, “Rapid and reversible root growth inhibition by TIR1 auxin signalling,” <i>Nature Plants</i>, vol. 4, no. 7. Springer Nature, pp. 453–459, 2018.","mla":"Fendrych, Matyas, et al. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” <i>Nature Plants</i>, vol. 4, no. 7, Springer Nature, 2018, pp. 453–59, doi:<a href=\"https://doi.org/10.1038/s41477-018-0190-1\">10.1038/s41477-018-0190-1</a>.","short":"M. Fendrych, M. Akhmanova, J. Merrin, M. Glanc, S. Hagihara, K. Takahashi, N. Uchida, K.U. Torii, J. Friml, Nature Plants 4 (2018) 453–459.","apa":"Fendrych, M., Akhmanova, M., Merrin, J., Glanc, M., Hagihara, S., Takahashi, K., … Friml, J. (2018). Rapid and reversible root growth inhibition by TIR1 auxin signalling. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-018-0190-1\">https://doi.org/10.1038/s41477-018-0190-1</a>","ista":"Fendrych M, Akhmanova M, Merrin J, Glanc M, Hagihara S, Takahashi K, Uchida N, Torii KU, Friml J. 2018. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. 4(7), 453–459."},"date_published":"2018-06-25T00:00:00Z","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-mechanism-for-the-plant-hormone-auxin-discovered/"}]},"date_updated":"2023-09-15T12:11:03Z","publist_id":"7728","intvolume":"         4","issue":"7","publication":"Nature Plants","author":[{"first_name":"Matyas","last_name":"Fendrych","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Akhmanova","orcid":"0000-0003-1522-3162","first_name":"Maria","full_name":"Akhmanova, Maria","id":"3425EC26-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Merrin","orcid":"0000-0001-5145-4609","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack"},{"full_name":"Glanc, Matous","first_name":"Matous","last_name":"Glanc"},{"last_name":"Hagihara","first_name":"Shinya","full_name":"Hagihara, Shinya"},{"last_name":"Takahashi","first_name":"Koji","full_name":"Takahashi, Koji"},{"full_name":"Uchida, Naoyuki","last_name":"Uchida","first_name":"Naoyuki"},{"first_name":"Keiko U","last_name":"Torii","full_name":"Torii, Keiko U"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"status":"public","page":"453 - 459","month":"06","volume":4},{"publist_id":"7723","date_updated":"2024-11-04T13:52:29Z","conference":{"name":"ASIACCS: Asia Conference on Computer and Communications Security ","location":"Incheon, Republic of Korea","end_date":"2018-06-08","start_date":"2018-06-04"},"citation":{"ista":"Alwen JF, Gazi P, Kamath Hosdurg C, Klein K, Osang GF, Pietrzak KZ, Reyzin L, Rolinek M, Rybar M. 2018. On the memory hardness of data independent password hashing functions. Proceedings of the 2018 on Asia Conference on Computer and Communication Security. ASIACCS: Asia Conference on Computer and Communications Security , 51–65.","ieee":"J. F. Alwen <i>et al.</i>, “On the memory hardness of data independent password hashing functions,” in <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i>, Incheon, Republic of Korea, 2018, pp. 51–65.","mla":"Alwen, Joel F., et al. “On the Memory Hardness of Data Independent Password Hashing Functions.” <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i>, ACM, 2018, pp. 51–65, doi:<a href=\"https://doi.org/10.1145/3196494.3196534\">10.1145/3196494.3196534</a>.","short":"J.F. Alwen, P. Gazi, C. Kamath Hosdurg, K. Klein, G.F. Osang, K.Z. Pietrzak, L. Reyzin, M. Rolinek, M. Rybar, in:, Proceedings of the 2018 on Asia Conference on Computer and Communication Security, ACM, 2018, pp. 51–65.","apa":"Alwen, J. F., Gazi, P., Kamath Hosdurg, C., Klein, K., Osang, G. F., Pietrzak, K. Z., … Rybar, M. (2018). On the memory hardness of data independent password hashing functions. In <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i> (pp. 51–65). Incheon, Republic of Korea: ACM. <a href=\"https://doi.org/10.1145/3196494.3196534\">https://doi.org/10.1145/3196494.3196534</a>","ama":"Alwen JF, Gazi P, Kamath Hosdurg C, et al. On the memory hardness of data independent password hashing functions. In: <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i>. ACM; 2018:51-65. doi:<a href=\"https://doi.org/10.1145/3196494.3196534\">10.1145/3196494.3196534</a>","chicago":"Alwen, Joel F, Peter Gazi, Chethan Kamath Hosdurg, Karen Klein, Georg F Osang, Krzysztof Z Pietrzak, Lenoid Reyzin, Michal Rolinek, and Michal Rybar. “On the Memory Hardness of Data Independent Password Hashing Functions.” In <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i>, 51–65. ACM, 2018. <a href=\"https://doi.org/10.1145/3196494.3196534\">https://doi.org/10.1145/3196494.3196534</a>."},"abstract":[{"text":"We show attacks on five data-independent memory-hard functions (iMHF) that were submitted to the password hashing competition (PHC). Informally, an MHF is a function which cannot be evaluated on dedicated hardware, like ASICs, at significantly lower hardware and/or energy cost than evaluating a single instance on a standard single-core architecture. Data-independent means the memory access pattern of the function is independent of the input; this makes iMHFs harder to construct than data-dependent ones, but the latter can be attacked by various side-channel attacks. Following [Alwen-Blocki'16], we capture the evaluation of an iMHF as a directed acyclic graph (DAG). The cumulative parallel pebbling complexity of this DAG is a measure for the hardware cost of evaluating the iMHF on an ASIC. Ideally, one would like the complexity of a DAG underlying an iMHF to be as close to quadratic in the number of nodes of the graph as possible. Instead, we show that (the DAGs underlying) the following iMHFs are far from this bound: Rig.v2, TwoCats and Gambit each having an exponent no more than 1.75. Moreover, we show that the complexity of the iMHF modes of the PHC finalists Pomelo and Lyra2 have exponents at most 1.83 and 1.67 respectively. To show this we investigate a combinatorial property of each underlying DAG (called its depth-robustness. By establishing upper bounds on this property we are then able to apply the general technique of [Alwen-Block'16] for analyzing the hardware costs of an iMHF.","lang":"eng"}],"date_published":"2018-06-01T00:00:00Z","page":"51 - 65","acknowledgement":"Leonid Reyzin was supported in part by IST Austria and by US NSF grants 1012910, 1012798, and 1422965; this research was performed while he was visiting IST Austria.","ec_funded":1,"month":"06","publication":"Proceedings of the 2018 on Asia Conference on Computer and Communication Security","author":[{"first_name":"Joel F","last_name":"Alwen","full_name":"Alwen, Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gazi, Peter","first_name":"Peter","last_name":"Gazi"},{"last_name":"Kamath Hosdurg","first_name":"Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","full_name":"Kamath Hosdurg, Chethan"},{"full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","last_name":"Klein","first_name":"Karen"},{"id":"464B40D6-F248-11E8-B48F-1D18A9856A87","full_name":"Osang, Georg F","last_name":"Osang","orcid":"0000-0002-8882-5116","first_name":"Georg F"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"},{"last_name":"Reyzin","first_name":"Lenoid","full_name":"Reyzin, Lenoid"},{"last_name":"Rolinek","first_name":"Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal"},{"last_name":"Rybar","first_name":"Michal","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","full_name":"Rybar, Michal"}],"status":"public","date_created":"2018-12-11T11:45:07Z","isi":1,"project":[{"call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160"},{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815"}],"quality_controlled":"1","doi":"10.1145/3196494.3196534","oa_version":"Submitted Version","scopus_import":"1","_id":"193","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"On the memory hardness of data independent password hashing functions","article_processing_charge":"No","type":"conference","oa":1,"day":"01","external_id":{"isi":["000516620100005"]},"publisher":"ACM","publication_status":"published","year":"2018","department":[{"_id":"KrPi"},{"_id":"HeEd"},{"_id":"VlKo"}],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/783"}]},{"issue":"4","publication":"Physical Review B - Condensed Matter and Materials Physics","status":"public","author":[{"last_name":"Yakaboylu","orcid":"0000-0001-5973-0874","first_name":"Enderalp","full_name":"Yakaboylu, Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"month":"07","volume":98,"ec_funded":1,"article_number":"045402","citation":{"ista":"Yakaboylu E, Lemeshko M. 2018. Anyonic statistics of quantum impurities in two dimensions. Physical Review B - Condensed Matter and Materials Physics. 98(4), 045402.","ieee":"E. Yakaboylu and M. Lemeshko, “Anyonic statistics of quantum impurities in two dimensions,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 98, no. 4. American Physical Society, 2018.","mla":"Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum Impurities in Two Dimensions.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 98, no. 4, 045402, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevB.98.045402\">10.1103/PhysRevB.98.045402</a>.","short":"E. Yakaboylu, M. Lemeshko, Physical Review B - Condensed Matter and Materials Physics 98 (2018).","apa":"Yakaboylu, E., &#38; Lemeshko, M. (2018). Anyonic statistics of quantum impurities in two dimensions. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.98.045402\">https://doi.org/10.1103/PhysRevB.98.045402</a>","ama":"Yakaboylu E, Lemeshko M. Anyonic statistics of quantum impurities in two dimensions. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2018;98(4). doi:<a href=\"https://doi.org/10.1103/PhysRevB.98.045402\">10.1103/PhysRevB.98.045402</a>","chicago":"Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum Impurities in Two Dimensions.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevB.98.045402\">https://doi.org/10.1103/PhysRevB.98.045402</a>."},"abstract":[{"text":"We demonstrate that identical impurities immersed in a two-dimensional many-particle bath can be viewed as flux-tube-charged-particle composites described by fractional statistics. In particular, we find that the bath manifests itself as an external magnetic flux tube with respect to the impurities, and hence the time-reversal symmetry is broken for the effective Hamiltonian describing the impurities. The emerging flux tube acts as a statistical gauge field after a certain critical coupling. This critical coupling corresponds to the intersection point between the quasiparticle state and the phonon wing, where the angular momentum is transferred from the impurity to the bath. This amounts to a novel configuration with emerging anyons. The proposed setup paves the way to realizing anyons using electrons interacting with superfluid helium or lattice phonons, as well as using atomic impurities in ultracold gases.","lang":"eng"}],"corr_author":"1","date_published":"2018-07-15T00:00:00Z","date_updated":"2025-04-15T06:50:28Z","intvolume":"        98","day":"15","external_id":{"arxiv":["1712.00308"],"isi":["000436939100007"]},"oa":1,"type":"journal_article","department":[{"_id":"MiLe"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.00308"}],"publication_status":"published","year":"2018","publisher":"American Physical Society","arxiv":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","title":"Anyonic statistics of quantum impurities in two dimensions","_id":"195","scopus_import":"1","oa_version":"Submitted Version","doi":"10.1103/PhysRevB.98.045402","language":[{"iso":"eng"}],"isi":1,"date_created":"2018-12-11T11:45:08Z","quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"},{"call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902"}]},{"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2018-11-13T00:00:00Z","has_accepted_license":"1","citation":{"ama":"Bulatov E, Sayarova R, Mingaleeva R, et al. Isatin-Schiff base-copper (II) complex induces cell death in p53-positive tumors. <i>Cell Death Discovery</i>. 2018;4. doi:<a href=\"https://doi.org/10.1038/s41420-018-0120-z\">10.1038/s41420-018-0120-z</a>","chicago":"Bulatov, Emil, Regina Sayarova, Rimma Mingaleeva, Regina Miftakhova, Marina Gomzikova, Iurii Ignatev, Alexey Petukhov, Pavel Davidovich, Albert Rizvanov, and Nickolai A. Barlev. “Isatin-Schiff Base-Copper (II) Complex Induces Cell Death in P53-Positive Tumors.” <i>Cell Death Discovery</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41420-018-0120-z\">https://doi.org/10.1038/s41420-018-0120-z</a>.","ieee":"E. Bulatov <i>et al.</i>, “Isatin-Schiff base-copper (II) complex induces cell death in p53-positive tumors,” <i>Cell Death Discovery</i>, vol. 4. Springer Nature, 2018.","short":"E. Bulatov, R. Sayarova, R. Mingaleeva, R. Miftakhova, M. Gomzikova, I. Ignatev, A. Petukhov, P. Davidovich, A. Rizvanov, N.A. Barlev, Cell Death Discovery 4 (2018).","mla":"Bulatov, Emil, et al. “Isatin-Schiff Base-Copper (II) Complex Induces Cell Death in P53-Positive Tumors.” <i>Cell Death Discovery</i>, vol. 4, 103, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41420-018-0120-z\">10.1038/s41420-018-0120-z</a>.","apa":"Bulatov, E., Sayarova, R., Mingaleeva, R., Miftakhova, R., Gomzikova, M., Ignatev, I., … Barlev, N. A. (2018). Isatin-Schiff base-copper (II) complex induces cell death in p53-positive tumors. <i>Cell Death Discovery</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41420-018-0120-z\">https://doi.org/10.1038/s41420-018-0120-z</a>","ista":"Bulatov E, Sayarova R, Mingaleeva R, Miftakhova R, Gomzikova M, Ignatev I, Petukhov A, Davidovich P, Rizvanov A, Barlev NA. 2018. Isatin-Schiff base-copper (II) complex induces cell death in p53-positive tumors. Cell Death Discovery. 4, 103."},"abstract":[{"text":"Medicinal bioinorganic chemistry is a thriving field of drug research for cancer treatment. Transition metal complexes coordinated to essential biological scaffolds represent a highly promising class of compounds for design of novel target-specific therapeutics. We report here the biological evaluation of a novel Isatin-Schiff base derivative and its Cu(II) complex in several tumor cell lines by assessing their effects on cellular metabolism, real-time cell proliferation and induction of apoptosis. Further, the impact of compounds on the p53 protein and expression of its target genes, including MDM2, p21/CDKN1A, and PUMA was evaluated. Results obtained in this study provide further evidence in support of our prior data suggesting the p53-mediated mechanism of action for Isatin-Schiff base derivatives and their complexes and also shed light on potential use of these compounds for stimulation of apoptosis in breast cancer cells via activation of the pro-apoptotic PUMA gene.","lang":"eng"}],"intvolume":"         4","date_updated":"2025-07-10T11:51:52Z","extern":"1","status":"public","author":[{"last_name":"Bulatov","first_name":"Emil","full_name":"Bulatov, Emil"},{"last_name":"Sayarova","first_name":"Regina","full_name":"Sayarova, Regina"},{"full_name":"Mingaleeva, Rimma","first_name":"Rimma","last_name":"Mingaleeva"},{"first_name":"Regina","last_name":"Miftakhova","full_name":"Miftakhova, Regina"},{"last_name":"Gomzikova","first_name":"Marina","full_name":"Gomzikova, Marina"},{"last_name":"Ignatev","first_name":"Iurii","full_name":"Ignatev, Iurii","id":"2ac71786-dc7d-11ea-9b2f-c5ad4b9faff6"},{"first_name":"Alexey","last_name":"Petukhov","full_name":"Petukhov, Alexey"},{"last_name":"Davidovich","first_name":"Pavel","full_name":"Davidovich, Pavel"},{"last_name":"Rizvanov","first_name":"Albert","full_name":"Rizvanov, Albert"},{"full_name":"Barlev, Nickolai A.","last_name":"Barlev","first_name":"Nickolai A."}],"publication":"Cell Death Discovery","volume":4,"article_number":"103","ddc":["570"],"month":"11","DOAJ_listed":"1","article_type":"original","OA_place":"publisher","language":[{"iso":"eng"}],"doi":"10.1038/s41420-018-0120-z","_id":"19544","oa_version":"Published Version","quality_controlled":"1","date_created":"2025-04-11T01:31:42Z","year":"2018","OA_type":"gold","publication_status":"published","publisher":"Springer Nature","main_file_link":[{"url":"https://doi.org/10.1038/s41420-018-0120-z","open_access":"1"}],"department":[{"_id":"GradSch"},{"_id":"LoSw"}],"type":"journal_article","pmid":1,"day":"13","external_id":{"pmid":["30455989 "]},"oa":1,"article_processing_charge":"Yes","title":"Isatin-Schiff base-copper (II) complex induces cell death in p53-positive tumors","publication_identifier":{"issn":["2058-7716"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_published":"2018-12-01T00:00:00Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"lang":"eng","text":"The importance of astrocytic l-lactate (LL) for normal functioning of neural circuits such as those regulating learning/memory, sleep/wake state, autonomic homeostasis, or emotional behaviour is being increasingly recognised. l-Lactate can act on neurones as a metabolic or redox substrate, but transmembrane receptor targets are also emerging. A comparative review of the hydroxy-carboxylic acid receptor (HCA1, formerly known as GPR81), Olfactory Receptor Family 51 Subfamily E Member 2 (OR51E2), and orphan receptor GPR4 highlights differences in their LL sensitivity, pharmacology, intracellular coupling, and localisation in the brain. In addition, a putative Gs-coupled receptor on noradrenergic neurones, LLRx, which we previously postulated, remains to be identified. Next-generation sequencing revealed several orphan receptors expressed in locus coeruleus neurones. Screening of a selection of these suggests additional LL-sensitive receptors: GPR180 which inhibits and GPR137 which activates intracellular cyclic AMP signalling in response to LL in a heterologous expression system. To further characterise binding of LL at LLRx, we carried out a structure–activity relationship study which demonstrates that carboxyl and 2-hydroxyl moieties of LL are essential for triggering d-lactate-sensitive noradrenaline release in locus coeruleus, and that the size of the LL binding pocket is limited towards the methyl group position. The evidence accumulating to date suggests that LL acts via multiple receptor targets to modulate distinct brain functions."}],"citation":{"ista":"Mosienko V, Rasooli-Nejad S, Kishi K, De Both M, Jane D, Huentelman MJ, Kasparov S, Teschemacher AG. 2018. Putative receptors underpinning L-Lactate signalling in locus coeruleus. Neuroglia. 1(2), 365–380.","chicago":"Mosienko, Valentina, Seyed Rasooli-Nejad, Kasumi Kishi, Matt De Both, David Jane, Matt J. Huentelman, Sergey Kasparov, and Anja G. Teschemacher. “Putative Receptors Underpinning L-Lactate Signalling in Locus Coeruleus.” <i>Neuroglia</i>. MDPI, 2018. <a href=\"https://doi.org/10.3390/neuroglia1020025\">https://doi.org/10.3390/neuroglia1020025</a>.","ama":"Mosienko V, Rasooli-Nejad S, Kishi K, et al. Putative receptors underpinning L-Lactate signalling in locus coeruleus. <i>Neuroglia</i>. 2018;1(2):365-380. doi:<a href=\"https://doi.org/10.3390/neuroglia1020025\">10.3390/neuroglia1020025</a>","apa":"Mosienko, V., Rasooli-Nejad, S., Kishi, K., De Both, M., Jane, D., Huentelman, M. J., … Teschemacher, A. G. (2018). Putative receptors underpinning L-Lactate signalling in locus coeruleus. <i>Neuroglia</i>. MDPI. <a href=\"https://doi.org/10.3390/neuroglia1020025\">https://doi.org/10.3390/neuroglia1020025</a>","mla":"Mosienko, Valentina, et al. “Putative Receptors Underpinning L-Lactate Signalling in Locus Coeruleus.” <i>Neuroglia</i>, vol. 1, no. 2, MDPI, 2018, pp. 365–80, doi:<a href=\"https://doi.org/10.3390/neuroglia1020025\">10.3390/neuroglia1020025</a>.","ieee":"V. Mosienko <i>et al.</i>, “Putative receptors underpinning L-Lactate signalling in locus coeruleus,” <i>Neuroglia</i>, vol. 1, no. 2. MDPI, pp. 365–380, 2018.","short":"V. Mosienko, S. Rasooli-Nejad, K. Kishi, M. De Both, D. Jane, M.J. Huentelman, S. Kasparov, A.G. Teschemacher, Neuroglia 1 (2018) 365–380."},"has_accepted_license":"1","intvolume":"         1","date_updated":"2025-05-19T08:28:40Z","author":[{"full_name":"Mosienko, Valentina","first_name":"Valentina","last_name":"Mosienko"},{"first_name":"Seyed","last_name":"Rasooli-Nejad","full_name":"Rasooli-Nejad, Seyed"},{"first_name":"Kasumi","last_name":"Kishi","full_name":"Kishi, Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"De Both, Matt","first_name":"Matt","last_name":"De Both"},{"first_name":"David","last_name":"Jane","full_name":"Jane, David"},{"last_name":"Huentelman","first_name":"Matt J.","full_name":"Huentelman, Matt J."},{"last_name":"Kasparov","first_name":"Sergey","full_name":"Kasparov, Sergey"},{"full_name":"Teschemacher, Anja G.","last_name":"Teschemacher","first_name":"Anja G."}],"status":"public","issue":"2","publication":"Neuroglia","month":"12","ddc":["570"],"volume":1,"acknowledgement":"This work was supported by grants from BBSRC BB/L019396/1, and MRC MR/L020661/1. David Kleinfeld for his gift of CNiFER cells, Lesley Arberry for expert technical support, Andrew Herman for support with FACS sorting.","file":[{"file_id":"19711","success":1,"file_name":"2018_Neuroglia_Mosienko.pdf","content_type":"application/pdf","file_size":1909402,"date_created":"2025-05-19T08:20:19Z","access_level":"open_access","creator":"dernst","date_updated":"2025-05-19T08:20:19Z","checksum":"cadb56618f72edf4703b6a9855e84baa","relation":"main_file"}],"page":"365-380","OA_place":"publisher","file_date_updated":"2025-05-19T08:20:19Z","language":[{"iso":"eng"}],"article_type":"original","DOAJ_listed":"1","oa_version":"Published Version","scopus_import":"1","_id":"19706","doi":"10.3390/neuroglia1020025","quality_controlled":"1","date_created":"2025-05-18T22:02:51Z","department":[{"_id":"AnKi"}],"publisher":"MDPI","publication_status":"published","year":"2018","OA_type":"gold","oa":1,"day":"01","type":"journal_article","title":"Putative receptors underpinning L-Lactate signalling in locus coeruleus","article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2571-6980"]}},{"page":"448 - 464.e24","ec_funded":1,"acknowledgement":"In-Data-Review","volume":174,"month":"07","issue":"2","publication":"Cell","status":"public","author":[{"full_name":"Nishiyama, Tomoaki","last_name":"Nishiyama","first_name":"Tomoaki"},{"first_name":"Hidetoshi","last_name":"Sakayama","full_name":"Sakayama, Hidetoshi"},{"last_name":"De Vries","first_name":"Jan","full_name":"De Vries, Jan"},{"full_name":"Buschmann, Henrik","last_name":"Buschmann","first_name":"Henrik"},{"full_name":"Saint Marcoux, Denis","last_name":"Saint Marcoux","first_name":"Denis"},{"last_name":"Ullrich","first_name":"Kristian","full_name":"Ullrich, Kristian"},{"last_name":"Haas","first_name":"Fabian","full_name":"Haas, Fabian"},{"full_name":"Vanderstraeten, Lisa","last_name":"Vanderstraeten","first_name":"Lisa"},{"first_name":"Dirk","last_name":"Becker","full_name":"Becker, Dirk"},{"first_name":"Daniel","last_name":"Lang","full_name":"Lang, Daniel"},{"full_name":"Vosolsobě, Stanislav","first_name":"Stanislav","last_name":"Vosolsobě"},{"full_name":"Rombauts, Stephane","first_name":"Stephane","last_name":"Rombauts"},{"first_name":"Per","last_name":"Wilhelmsson","full_name":"Wilhelmsson, Per"},{"first_name":"Philipp","last_name":"Janitza","full_name":"Janitza, Philipp"},{"full_name":"Kern, Ramona","last_name":"Kern","first_name":"Ramona"},{"last_name":"Heyl","first_name":"Alexander","full_name":"Heyl, Alexander"},{"first_name":"Florian","last_name":"Rümpler","full_name":"Rümpler, Florian"},{"full_name":"Calderón Villalobos, Luz","first_name":"Luz","last_name":"Calderón Villalobos"},{"first_name":"John","last_name":"Clay","full_name":"Clay, John"},{"last_name":"Skokan","first_name":"Roman","full_name":"Skokan, Roman"},{"full_name":"Toyoda, Atsushi","first_name":"Atsushi","last_name":"Toyoda"},{"last_name":"Suzuki","first_name":"Yutaka","full_name":"Suzuki, Yutaka"},{"full_name":"Kagoshima, Hiroshi","last_name":"Kagoshima","first_name":"Hiroshi"},{"first_name":"Elio","last_name":"Schijlen","full_name":"Schijlen, Elio"},{"first_name":"Navindra","last_name":"Tajeshwar","full_name":"Tajeshwar, Navindra"},{"last_name":"Catarino","first_name":"Bruno","full_name":"Catarino, Bruno"},{"last_name":"Hetherington","first_name":"Alexander","full_name":"Hetherington, Alexander"},{"full_name":"Saltykova, Assia","last_name":"Saltykova","first_name":"Assia"},{"first_name":"Clemence","last_name":"Bonnot","full_name":"Bonnot, Clemence"},{"full_name":"Breuninger, Holger","last_name":"Breuninger","first_name":"Holger"},{"full_name":"Symeonidi, Aikaterini","last_name":"Symeonidi","first_name":"Aikaterini"},{"last_name":"Radhakrishnan","first_name":"Guru","full_name":"Radhakrishnan, Guru"},{"first_name":"Filip","last_name":"Van Nieuwerburgh","full_name":"Van Nieuwerburgh, Filip"},{"full_name":"Deforce, Dieter","last_name":"Deforce","first_name":"Dieter"},{"full_name":"Chang, Caren","first_name":"Caren","last_name":"Chang"},{"full_name":"Karol, Kenneth","first_name":"Kenneth","last_name":"Karol"},{"last_name":"Hedrich","first_name":"Rainer","full_name":"Hedrich, Rainer"},{"first_name":"Peter","last_name":"Ulvskov","full_name":"Ulvskov, Peter"},{"full_name":"Glöckner, Gernot","first_name":"Gernot","last_name":"Glöckner"},{"first_name":"Charles","last_name":"Delwiche","full_name":"Delwiche, Charles"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"first_name":"Yves","last_name":"Van De Peer","full_name":"Van De Peer, Yves"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Beilby, Mary","first_name":"Mary","last_name":"Beilby"},{"first_name":"Liam","last_name":"Dolan","full_name":"Dolan, Liam"},{"full_name":"Kohara, Yuji","first_name":"Yuji","last_name":"Kohara"},{"first_name":"Sumio","last_name":"Sugano","full_name":"Sugano, Sumio"},{"full_name":"Fujiyama, Asao","first_name":"Asao","last_name":"Fujiyama"},{"full_name":"Delaux, Pierre Marc","last_name":"Delaux","first_name":"Pierre Marc"},{"last_name":"Quint","first_name":"Marcel","full_name":"Quint, Marcel"},{"last_name":"Theissen","first_name":"Gunter","full_name":"Theissen, Gunter"},{"last_name":"Hagemann","first_name":"Martin","full_name":"Hagemann, Martin"},{"last_name":"Harholt","first_name":"Jesper","full_name":"Harholt, Jesper"},{"full_name":"Dunand, Christophe","first_name":"Christophe","last_name":"Dunand"},{"last_name":"Zachgo","first_name":"Sabine","full_name":"Zachgo, Sabine"},{"last_name":"Langdale","first_name":"Jane","full_name":"Langdale, Jane"},{"first_name":"Florian","last_name":"Maumus","full_name":"Maumus, Florian"},{"last_name":"Van Der Straeten","first_name":"Dominique","full_name":"Van Der Straeten, Dominique"},{"first_name":"Sven B","last_name":"Gould","full_name":"Gould, Sven B"},{"first_name":"Stefan","last_name":"Rensing","full_name":"Rensing, Stefan"}],"publist_id":"7774","date_updated":"2025-04-14T07:45:02Z","intvolume":"       174","citation":{"ama":"Nishiyama T, Sakayama H, De Vries J, et al. The Chara genome: Secondary complexity and implications for plant terrestrialization. <i>Cell</i>. 2018;174(2):448-464.e24. doi:<a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">10.1016/j.cell.2018.06.033</a>","chicago":"Nishiyama, Tomoaki, Hidetoshi Sakayama, Jan De Vries, Henrik Buschmann, Denis Saint Marcoux, Kristian Ullrich, Fabian Haas, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” <i>Cell</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">https://doi.org/10.1016/j.cell.2018.06.033</a>.","short":"T. Nishiyama, H. Sakayama, J. De Vries, H. Buschmann, D. Saint Marcoux, K. Ullrich, F. Haas, L. Vanderstraeten, D. Becker, D. Lang, S. Vosolsobě, S. Rombauts, P. Wilhelmsson, P. Janitza, R. Kern, A. Heyl, F. Rümpler, L. Calderón Villalobos, J. Clay, R. Skokan, A. Toyoda, Y. Suzuki, H. Kagoshima, E. Schijlen, N. Tajeshwar, B. Catarino, A. Hetherington, A. Saltykova, C. Bonnot, H. Breuninger, A. Symeonidi, G. Radhakrishnan, F. Van Nieuwerburgh, D. Deforce, C. Chang, K. Karol, R. Hedrich, P. Ulvskov, G. Glöckner, C. Delwiche, J. Petrášek, Y. Van De Peer, J. Friml, M. Beilby, L. Dolan, Y. Kohara, S. Sugano, A. Fujiyama, P.M. Delaux, M. Quint, G. Theissen, M. Hagemann, J. Harholt, C. Dunand, S. Zachgo, J. Langdale, F. Maumus, D. Van Der Straeten, S.B. Gould, S. Rensing, Cell 174 (2018) 448–464.e24.","ieee":"T. Nishiyama <i>et al.</i>, “The Chara genome: Secondary complexity and implications for plant terrestrialization,” <i>Cell</i>, vol. 174, no. 2. Cell Press, p. 448–464.e24, 2018.","mla":"Nishiyama, Tomoaki, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” <i>Cell</i>, vol. 174, no. 2, Cell Press, 2018, p. 448–464.e24, doi:<a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">10.1016/j.cell.2018.06.033</a>.","apa":"Nishiyama, T., Sakayama, H., De Vries, J., Buschmann, H., Saint Marcoux, D., Ullrich, K., … Rensing, S. (2018). The Chara genome: Secondary complexity and implications for plant terrestrialization. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">https://doi.org/10.1016/j.cell.2018.06.033</a>","ista":"Nishiyama T, Sakayama H, De Vries J, Buschmann H, Saint Marcoux D, Ullrich K, Haas F, Vanderstraeten L, Becker D, Lang D, Vosolsobě S, Rombauts S, Wilhelmsson P, Janitza P, Kern R, Heyl A, Rümpler F, Calderón Villalobos L, Clay J, Skokan R, Toyoda A, Suzuki Y, Kagoshima H, Schijlen E, Tajeshwar N, Catarino B, Hetherington A, Saltykova A, Bonnot C, Breuninger H, Symeonidi A, Radhakrishnan G, Van Nieuwerburgh F, Deforce D, Chang C, Karol K, Hedrich R, Ulvskov P, Glöckner G, Delwiche C, Petrášek J, Van De Peer Y, Friml J, Beilby M, Dolan L, Kohara Y, Sugano S, Fujiyama A, Delaux PM, Quint M, Theissen G, Hagemann M, Harholt J, Dunand C, Zachgo S, Langdale J, Maumus F, Van Der Straeten D, Gould SB, Rensing S. 2018. The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. 174(2), 448–464.e24."},"abstract":[{"lang":"eng","text":"Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote."}],"date_published":"2018-07-12T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","title":"The Chara genome: Secondary complexity and implications for plant terrestrialization","type":"journal_article","external_id":{"isi":["000438482800019"],"pmid":["30007417"]},"day":"12","pmid":1,"oa":1,"publication_status":"published","year":"2018","publisher":"Cell Press","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30007417","open_access":"1"}],"department":[{"_id":"JiFr"}],"date_created":"2018-12-11T11:44:53Z","isi":1,"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985"}],"quality_controlled":"1","doi":"10.1016/j.cell.2018.06.033","_id":"148","scopus_import":"1","oa_version":"Published Version","language":[{"iso":"eng"}]},{"date_published":"2018-08-29T00:00:00Z","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-018-0505-4"}]},"citation":{"chicago":"Dick, Robert, Kaneil K Zadrozny, Chaoyi Xu, Florian KM Schur, Terri D Lyddon, Clifton L Ricana, Jonathan M Wagner, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” <i>Nature</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41586-018-0396-4\">https://doi.org/10.1038/s41586-018-0396-4</a>.","ama":"Dick R, Zadrozny KK, Xu C, et al. Inositol phosphates are assembly co-factors for HIV-1. <i>Nature</i>. 2018;560(7719):509–512. doi:<a href=\"https://doi.org/10.1038/s41586-018-0396-4\">10.1038/s41586-018-0396-4</a>","apa":"Dick, R., Zadrozny, K. K., Xu, C., Schur, F. K., Lyddon, T. D., Ricana, C. L., … Vogt, V. (2018). Inositol phosphates are assembly co-factors for HIV-1. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41586-018-0396-4\">https://doi.org/10.1038/s41586-018-0396-4</a>","ieee":"R. Dick <i>et al.</i>, “Inositol phosphates are assembly co-factors for HIV-1,” <i>Nature</i>, vol. 560, no. 7719. Nature Publishing Group, pp. 509–512, 2018.","short":"R. Dick, K.K. Zadrozny, C. Xu, F.K. Schur, T.D. Lyddon, C.L. Ricana, J.M. Wagner, J.R. Perilla, P.B.K. Ganser, M.C. Johnson, O. Pornillos, V. Vogt, Nature 560 (2018) 509–512.","mla":"Dick, Robert, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” <i>Nature</i>, vol. 560, no. 7719, Nature Publishing Group, 2018, pp. 509–512, doi:<a href=\"https://doi.org/10.1038/s41586-018-0396-4\">10.1038/s41586-018-0396-4</a>.","ista":"Dick R, Zadrozny KK, Xu C, Schur FK, Lyddon TD, Ricana CL, Wagner JM, Perilla JR, Ganser PBK, Johnson MC, Pornillos O, Vogt V. 2018. Inositol phosphates are assembly co-factors for HIV-1. Nature. 560(7719), 509–512."},"abstract":[{"lang":"eng","text":"A short, 14-amino-acid segment called SP1, located in the Gag structural protein1, has a critical role during the formation of the HIV-1 virus particle. During virus assembly, the SP1 peptide and seven preceding residues fold into a six-helix bundle, which holds together the Gag hexamer and facilitates the formation of a curved immature hexagonal lattice underneath the viral membrane2,3. Upon completion of assembly and budding, proteolytic cleavage of Gag leads to virus maturation, in which the immature lattice is broken down; the liberated CA domain of Gag then re-assembles into the mature conical capsid that encloses the viral genome and associated enzymes. Folding and proteolysis of the six-helix bundle are crucial rate-limiting steps of both Gag assembly and disassembly, and the six-helix bundle is an established target of HIV-1 inhibitors4,5. Here, using a combination of structural and functional analyses, we show that inositol hexakisphosphate (InsP6, also known as IP6) facilitates the formation of the six-helix bundle and assembly of the immature HIV-1 Gag lattice. IP6 makes ionic contacts with two rings of lysine residues at the centre of the Gag hexamer. Proteolytic cleavage then unmasks an alternative binding site, where IP6 interaction promotes the assembly of the mature capsid lattice. These studies identify IP6 as a naturally occurring small molecule that promotes both assembly and maturation of HIV-1."}],"intvolume":"       560","date_updated":"2023-09-12T07:44:37Z","status":"public","author":[{"last_name":"Dick","first_name":"Robert","full_name":"Dick, Robert"},{"full_name":"Zadrozny, Kaneil K","last_name":"Zadrozny","first_name":"Kaneil K"},{"last_name":"Xu","first_name":"Chaoyi","full_name":"Xu, Chaoyi"},{"full_name":"Schur, Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Schur","orcid":"0000-0003-4790-8078"},{"full_name":"Lyddon, Terri D","first_name":"Terri D","last_name":"Lyddon"},{"first_name":"Clifton L","last_name":"Ricana","full_name":"Ricana, Clifton L"},{"last_name":"Wagner","first_name":"Jonathan M","full_name":"Wagner, Jonathan M"},{"first_name":"Juan R","last_name":"Perilla","full_name":"Perilla, Juan R"},{"full_name":"Ganser, Pornillos Barbie K","first_name":"Pornillos Barbie K","last_name":"Ganser"},{"last_name":"Johnson","first_name":"Marc C","full_name":"Johnson, Marc C"},{"full_name":"Pornillos, Owen","last_name":"Pornillos","first_name":"Owen"},{"full_name":"Vogt, Volker","last_name":"Vogt","first_name":"Volker"}],"publication":"Nature","issue":"7719","month":"08","volume":560,"page":"509–512","language":[{"iso":"eng"}],"article_type":"original","_id":"150","scopus_import":"1","oa_version":"Submitted Version","doi":"10.1038/s41586-018-0396-4","quality_controlled":"1","isi":1,"date_created":"2018-12-11T11:44:53Z","department":[{"_id":"FlSc"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/","open_access":"1"}],"publication_status":"published","year":"2018","publisher":"Nature Publishing Group","pmid":1,"external_id":{"pmid":["30158708"],"isi":["000442483400046"]},"day":"29","oa":1,"type":"journal_article","article_processing_charge":"No","title":"Inositol phosphates are assembly co-factors for HIV-1","publication_identifier":{"eissn":["1476-4687"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"status":"public","author":[{"full_name":"Fiedorczuk, Karol","id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","first_name":"Karol","last_name":"Fiedorczuk"},{"last_name":"Sazanov","orcid":"0000-0002-0977-7989","first_name":"Leonid A","full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"issue":"10","publication":"Trends in Cell Biology","volume":28,"ddc":["572"],"month":"07","page":"835 - 867","file":[{"file_size":2185385,"content_type":"application/pdf","file_name":"SasanovFinalMS+EdComments_LS_allacc_withFigs.pdf","file_id":"6994","relation":"main_file","checksum":"ef6d2b4e1fd63948539639242610bfa6","creator":"lsazanov","date_updated":"2020-07-14T12:45:00Z","access_level":"open_access","date_created":"2019-11-07T12:55:20Z"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"date_published":"2018-07-26T00:00:00Z","has_accepted_license":"1","citation":{"short":"K. Fiedorczuk, L.A. Sazanov, Trends in Cell Biology 28 (2018) 835–867.","ieee":"K. Fiedorczuk and L. A. Sazanov, “Mammalian mitochondrial complex I structure and disease causing mutations,” <i>Trends in Cell Biology</i>, vol. 28, no. 10. Elsevier, pp. 835–867, 2018.","mla":"Fiedorczuk, Karol, and Leonid A. Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” <i>Trends in Cell Biology</i>, vol. 28, no. 10, Elsevier, 2018, pp. 835–67, doi:<a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">10.1016/j.tcb.2018.06.006</a>.","apa":"Fiedorczuk, K., &#38; Sazanov, L. A. (2018). Mammalian mitochondrial complex I structure and disease causing mutations. <i>Trends in Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">https://doi.org/10.1016/j.tcb.2018.06.006</a>","ama":"Fiedorczuk K, Sazanov LA. Mammalian mitochondrial complex I structure and disease causing mutations. <i>Trends in Cell Biology</i>. 2018;28(10):835-867. doi:<a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">10.1016/j.tcb.2018.06.006</a>","chicago":"Fiedorczuk, Karol, and Leonid A Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” <i>Trends in Cell Biology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">https://doi.org/10.1016/j.tcb.2018.06.006</a>.","ista":"Fiedorczuk K, Sazanov LA. 2018. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 28(10), 835–867."},"abstract":[{"lang":"eng","text":"Complex I has an essential role in ATP production by coupling electron transfer from NADH to quinone with translocation of protons across the inner mitochondrial membrane. Isolated complex I deficiency is a frequent cause of mitochondrial inherited diseases. Complex I has also been implicated in cancer, ageing, and neurodegenerative conditions. Until recently, the understanding of complex I deficiency on the molecular level was limited due to the lack of high-resolution structures of the enzyme. However, due to developments in single particle cryo-electron microscopy (cryo-EM), recent studies have reported nearly atomic resolution maps and models of mitochondrial complex I. These structures significantly add to our understanding of complex I mechanism and assembly. The disease-causing mutations are discussed here in their structural context."}],"intvolume":"        28","publist_id":"7769","date_updated":"2023-09-13T08:51:56Z","year":"2018","publication_status":"published","publisher":"Elsevier","department":[{"_id":"LeSa"}],"type":"journal_article","day":"26","external_id":{"isi":["000445118200007"]},"oa":1,"article_processing_charge":"No","title":"Mammalian mitochondrial complex I structure and disease causing mutations","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","article_type":"original","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:00Z","doi":"10.1016/j.tcb.2018.06.006","_id":"152","scopus_import":"1","oa_version":"Submitted Version","quality_controlled":"1","date_created":"2018-12-11T11:44:54Z","isi":1}]