[{"publication_identifier":{"eissn":["14779129"]},"citation":{"mla":"Zhu, Qiang, et al. “Root Gravity Response Module Guides Differential Growth Determining Both Root Bending and Apical Hook Formation in Arabidopsis.” <i>Development</i>, vol. 146, no. 17, dev175919, The Company of Biologists, 2019, doi:<a href=\"https://doi.org/10.1242/dev.175919\">10.1242/dev.175919</a>.","ista":"Zhu Q, Gallemi M, Pospíšil J, Žádníková P, Strnad M, Benková E. 2019. Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. Development. 146(17), dev175919.","ama":"Zhu Q, Gallemi M, Pospíšil J, Žádníková P, Strnad M, Benková E. Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. <i>Development</i>. 2019;146(17). doi:<a href=\"https://doi.org/10.1242/dev.175919\">10.1242/dev.175919</a>","ieee":"Q. Zhu, M. Gallemi, J. Pospíšil, P. Žádníková, M. Strnad, and E. Benková, “Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis,” <i>Development</i>, vol. 146, no. 17. The Company of Biologists, 2019.","apa":"Zhu, Q., Gallemi, M., Pospíšil, J., Žádníková, P., Strnad, M., &#38; Benková, E. (2019). Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.175919\">https://doi.org/10.1242/dev.175919</a>","chicago":"Zhu, Qiang, Marçal Gallemi, Jiří Pospíšil, Petra Žádníková, Miroslav Strnad, and Eva Benková. “Root Gravity Response Module Guides Differential Growth Determining Both Root Bending and Apical Hook Formation in Arabidopsis.” <i>Development</i>. The Company of Biologists, 2019. <a href=\"https://doi.org/10.1242/dev.175919\">https://doi.org/10.1242/dev.175919</a>.","short":"Q. Zhu, M. Gallemi, J. Pospíšil, P. Žádníková, M. Strnad, E. Benková, Development 146 (2019)."},"article_number":"dev175919","year":"2019","_id":"6897","article_type":"original","volume":146,"project":[{"_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362","name":"Hormonal cross-talk in plant organogenesis","call_identifier":"FP7"}],"ec_funded":1,"day":"12","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"main_file_link":[{"url":"https://doi.org/10.1242/dev.175919","open_access":"1"}],"article_processing_charge":"No","oa_version":"Published Version","month":"09","oa":1,"issue":"17","author":[{"full_name":"Zhu, Qiang","first_name":"Qiang","id":"40A4B9E6-F248-11E8-B48F-1D18A9856A87","last_name":"Zhu"},{"full_name":"Gallemi, Marçal","orcid":"0000-0003-4675-6893","first_name":"Marçal","id":"460C6802-F248-11E8-B48F-1D18A9856A87","last_name":"Gallemi"},{"last_name":"Pospíšil","full_name":"Pospíšil, Jiří","first_name":"Jiří"},{"last_name":"Žádníková","first_name":"Petra","full_name":"Žádníková, Petra"},{"first_name":"Miroslav","full_name":"Strnad, Miroslav","last_name":"Strnad"},{"orcid":"0000-0002-8510-9739","first_name":"Eva","full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"We thank Jiri Friml and Phillip Brewer for inspiring discussion and for help in preparing the manuscript. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility\r\n(BIF), the Life Science Facility (LSF).\r\nThis work was supported by grants from the European Research Council (Starting Independent Research Grant ERC-2007-Stg- 207362-HCPO to E.B.). J.P. and M.S. received funds from European Regional Development Fund-Project ‘Centre for Experimental Plant Biology’ (No. CZ.02.1.01/0.0/0.0/16_019/0000738).","type":"journal_article","status":"public","date_updated":"2025-05-07T11:10:55Z","external_id":{"isi":["000486297400011"],"pmid":["31391194"]},"department":[{"_id":"EvBe"}],"quality_controlled":"1","intvolume":"       146","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"The apical hook is a transiently formed structure that plays a protective role when the germinating seedling penetrates through the soil towards the surface. Crucial for proper bending is the local auxin maxima, which defines the concave (inner) side of the hook curvature. As no sign of asymmetric auxin distribution has been reported in embryonic hypocotyls prior to hook formation, the question of how auxin asymmetry is established in the early phases of seedling germination remains largely unanswered. Here, we analyzed the auxin distribution and expression of PIN auxin efflux carriers from early phases of germination, and show that bending of the root in response to gravity is the crucial initial cue that governs the hypocotyl bending required for apical hook formation. Importantly, polar auxin transport machinery is established gradually after germination starts as a result of tight root-hypocotyl interaction and a proper balance between abscisic acid and gibberellins."}],"pmid":1,"publication":"Development","date_created":"2019-09-22T22:00:36Z","language":[{"iso":"eng"}],"date_published":"2019-09-12T00:00:00Z","isi":1,"publication_status":"published","scopus_import":"1","publisher":"The Company of Biologists","title":"Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis","doi":"10.1242/dev.175919"},{"oa":1,"month":"09","oa_version":"Published Version","issue":"1","ddc":["570"],"author":[{"first_name":"Olga M.","full_name":"Sigalova, Olga M.","last_name":"Sigalova"},{"first_name":"Andrei V.","full_name":"Chaplin, Andrei V.","last_name":"Chaplin"},{"first_name":"Olga","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"last_name":"Shelyakin","full_name":"Shelyakin, Pavel V.","first_name":"Pavel V."},{"first_name":"Vsevolod A.","full_name":"Filaretov, Vsevolod A.","last_name":"Filaretov"},{"full_name":"Akkuratov, Evgeny E.","first_name":"Evgeny E.","last_name":"Akkuratov"},{"last_name":"Burskaia","first_name":"Valentina","full_name":"Burskaia, Valentina"},{"last_name":"Gelfand","full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S."}],"type":"journal_article","date_updated":"2023-08-30T06:20:22Z","status":"public","external_id":{"isi":["000485256100001"]},"related_material":{"record":[{"relation":"research_data","id":"9731","status":"public"},{"status":"public","id":"9783","relation":"research_data"},{"relation":"research_data","id":"9890","status":"public"},{"status":"public","id":"9892","relation":"research_data"},{"status":"public","relation":"research_data","id":"9893"},{"id":"9894","relation":"research_data","status":"public"},{"relation":"research_data","id":"9895","status":"public"},{"id":"9896","relation":"research_data","status":"public"},{"status":"public","id":"9897","relation":"research_data"},{"id":"9898","relation":"research_data","status":"public"},{"status":"public","id":"9899","relation":"research_data"},{"status":"public","id":"9900","relation":"research_data"},{"status":"public","id":"9901","relation":"research_data"}]},"department":[{"_id":"FyKo"}],"citation":{"ieee":"O. M. Sigalova <i>et al.</i>, “Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction,” <i>BMC Genomics</i>, vol. 20, no. 1. BioMed Central, 2019.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. <i>BMC Genomics</i>. 2019;20(1). doi:<a href=\"https://doi.org/10.1186/s12864-019-6059-5\">10.1186/s12864-019-6059-5</a>","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” <i>BMC Genomics</i>. BioMed Central, 2019. <a href=\"https://doi.org/10.1186/s12864-019-6059-5\">https://doi.org/10.1186/s12864-019-6059-5</a>.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, BMC Genomics 20 (2019).","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. <i>BMC Genomics</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s12864-019-6059-5\">https://doi.org/10.1186/s12864-019-6059-5</a>","mla":"Sigalova, Olga M., et al. “Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” <i>BMC Genomics</i>, vol. 20, no. 1, 710, BioMed Central, 2019, doi:<a href=\"https://doi.org/10.1186/s12864-019-6059-5\">10.1186/s12864-019-6059-5</a>.","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics. 20(1), 710."},"article_number":"710","publication_identifier":{"eissn":["14712164"]},"year":"2019","_id":"6898","volume":20,"day":"12","article_processing_charge":"No","date_created":"2019-09-22T22:00:36Z","publication":"BMC Genomics","language":[{"iso":"eng"}],"date_published":"2019-09-12T00:00:00Z","scopus_import":"1","publication_status":"published","isi":1,"has_accepted_license":"1","publisher":"BioMed Central","title":"Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","file_date_updated":"2020-07-14T12:47:44Z","doi":"10.1186/s12864-019-6059-5","quality_controlled":"1","intvolume":"        20","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_name":"2019_BioMed_Sigalova.pdf","file_size":4157175,"file_id":"6924","relation":"main_file","access_level":"open_access","checksum":"b798773c5823012d31c812c9f7975da2","creator":"kschuh","date_updated":"2020-07-14T12:47:44Z","date_created":"2019-10-01T10:33:17Z","content_type":"application/pdf"}],"abstract":[{"text":"Background\r\n\r\nChlamydia are ancient intracellular pathogens with reduced, though strikingly conserved genome. Despite their parasitic lifestyle and isolated intracellular environment, these bacteria managed to avoid accumulation of deleterious mutations leading to subsequent genome degradation characteristic for many parasitic bacteria.\r\nResults\r\n\r\nWe report pan-genomic analysis of sixteen species from genus Chlamydia including identification and functional annotation of orthologous genes, and characterization of gene gains, losses, and rearrangements. We demonstrate the overall genome stability of these bacteria as indicated by a large fraction of common genes with conserved genomic locations. On the other hand, extreme evolvability is confined to several paralogous gene families such as polymorphic membrane proteins and phospholipase D, and likely is caused by the pressure from the host immune system.\r\nConclusions\r\n\r\nThis combination of a large, conserved core genome and a small, evolvable periphery likely reflect the balance between the selective pressure towards genome reduction and the need to adapt to escape from the host immunity.","lang":"eng"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"abstract":[{"text":"Intra-organ communication guides morphogenetic processes that are essential for an organ to carry out complex physiological functions. In the heart, the growth of the myocardium is tightly coupled to that of the endocardium, a specialized endothelial tissue that lines its interior. Several molecular pathways have been implicated in the communication between these tissues including secreted factors, components of the extracellular matrix, or proteins involved in cell-cell communication. Yet, it is unknown how the growth of the endocardium is coordinated with that of the myocardium. Here, we show that an increased expansion of the myocardial atrial chamber volume generates higher junctional forces within endocardial cells. This leads to biomechanical signaling involving VE-cadherin, triggering nuclear localization of the Hippo pathway transcriptional regulator Yap1 and endocardial proliferation. Our work suggests that the growth of the endocardium results from myocardial chamber volume expansion and ends when the tension on the tissue is relaxed.","lang":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:44Z","creator":"kschuh","access_level":"open_access","checksum":"62c2512712e16d27c1797d318d14ba9f","file_name":"2019_Nature_Bornhorst.pdf","file_size":3905793,"relation":"main_file","file_id":"6926","date_created":"2019-10-01T11:18:50Z","content_type":"application/pdf"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pmid":1,"intvolume":"        10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","file_date_updated":"2020-07-14T12:47:44Z","title":"Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions","doi":"10.1038/s41467-019-12068-x","page":"4113","publisher":"Nature Publishing Group","isi":1,"scopus_import":"1","publication_status":"published","has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"Nature communications","date_created":"2019-09-22T22:00:37Z","date_published":"2019-09-11T00:00:00Z","day":"11","article_processing_charge":"No","volume":10,"year":"2019","_id":"6899","publication_identifier":{"eissn":["20411723"]},"citation":{"ama":"Bornhorst D, Xia P, Nakajima H, et al. Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions. <i>Nature communications</i>. 2019;10(1):4113. doi:<a href=\"https://doi.org/10.1038/s41467-019-12068-x\">10.1038/s41467-019-12068-x</a>","ieee":"D. Bornhorst <i>et al.</i>, “Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions,” <i>Nature communications</i>, vol. 10, no. 1. Nature Publishing Group, p. 4113, 2019.","apa":"Bornhorst, D., Xia, P., Nakajima, H., Dingare, C., Herzog, W., Lecaudey, V., … Abdelilah-Seyfried, S. (2019). Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-019-12068-x\">https://doi.org/10.1038/s41467-019-12068-x</a>","short":"D. Bornhorst, P. Xia, H. Nakajima, C. Dingare, W. Herzog, V. Lecaudey, N. Mochizuki, C.-P.J. Heisenberg, D. Yelon, S. Abdelilah-Seyfried, Nature Communications 10 (2019) 4113.","chicago":"Bornhorst, Dorothee, Peng Xia, Hiroyuki Nakajima, Chaitanya Dingare, Wiebke Herzog, Virginie Lecaudey, Naoki Mochizuki, Carl-Philipp J Heisenberg, Deborah Yelon, and Salim Abdelilah-Seyfried. “Biomechanical Signaling within the Developing Zebrafish Heart Attunes Endocardial Growth to Myocardial Chamber Dimensions.” <i>Nature Communications</i>. Nature Publishing Group, 2019. <a href=\"https://doi.org/10.1038/s41467-019-12068-x\">https://doi.org/10.1038/s41467-019-12068-x</a>.","mla":"Bornhorst, Dorothee, et al. “Biomechanical Signaling within the Developing Zebrafish Heart Attunes Endocardial Growth to Myocardial Chamber Dimensions.” <i>Nature Communications</i>, vol. 10, no. 1, Nature Publishing Group, 2019, p. 4113, doi:<a href=\"https://doi.org/10.1038/s41467-019-12068-x\">10.1038/s41467-019-12068-x</a>.","ista":"Bornhorst D, Xia P, Nakajima H, Dingare C, Herzog W, Lecaudey V, Mochizuki N, Heisenberg C-PJ, Yelon D, Abdelilah-Seyfried S. 2019. Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions. Nature communications. 10(1), 4113."},"external_id":{"pmid":["31511517"],"isi":["000485216800009"]},"department":[{"_id":"CaHe"}],"type":"journal_article","status":"public","date_updated":"2023-08-30T06:21:23Z","issue":"1","author":[{"first_name":"Dorothee","full_name":"Bornhorst, Dorothee","last_name":"Bornhorst"},{"last_name":"Xia","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5419-7756","first_name":"Peng","full_name":"Xia, Peng"},{"last_name":"Nakajima","full_name":"Nakajima, Hiroyuki","first_name":"Hiroyuki"},{"first_name":"Chaitanya","full_name":"Dingare, Chaitanya","last_name":"Dingare"},{"last_name":"Herzog","first_name":"Wiebke","full_name":"Herzog, Wiebke"},{"first_name":"Virginie","full_name":"Lecaudey, Virginie","last_name":"Lecaudey"},{"first_name":"Naoki","full_name":"Mochizuki, Naoki","last_name":"Mochizuki"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"},{"full_name":"Yelon, Deborah","first_name":"Deborah","last_name":"Yelon"},{"full_name":"Abdelilah-Seyfried, Salim","first_name":"Salim","last_name":"Abdelilah-Seyfried"}],"ddc":["570"],"oa_version":"Published Version","month":"09","oa":1},{"file":[{"file_name":"2019_PLoS_Cepeda-Humerez.pdf","file_size":3081855,"relation":"main_file","file_id":"6925","access_level":"open_access","checksum":"81bdce1361c9aa8395d6fa635fb6ab47","creator":"kschuh","date_updated":"2020-07-14T12:47:44Z","date_created":"2019-10-01T10:53:45Z","content_type":"application/pdf"}],"abstract":[{"lang":"eng","text":"Across diverse biological systems—ranging from neural networks to intracellular signaling and genetic regulatory networks—the information about changes in the environment is frequently encoded in the full temporal dynamics of the network nodes. A pressing data-analysis challenge has thus been to efficiently estimate the amount of information that these dynamics convey from experimental data. Here we develop and evaluate decoding-based estimation methods to lower bound the mutual information about a finite set of inputs, encoded in single-cell high-dimensional time series data. For biological reaction networks governed by the chemical Master equation, we derive model-based information approximations and analytical upper bounds, against which we benchmark our proposed model-free decoding estimators. In contrast to the frequently-used k-nearest-neighbor estimator, decoding-based estimators robustly extract a large fraction of the available information from high-dimensional trajectories with a realistic number of data samples. We apply these estimators to previously published data on Erk and Ca2+ signaling in mammalian cells and to yeast stress-response, and find that substantial amount of information about environmental state can be encoded by non-trivial response statistics even in stationary signals. We argue that these single-cell, decoding-based information estimates, rather than the commonly-used tests for significant differences between selected population response statistics, provide a proper and unbiased measure for the performance of biological signaling networks."}],"pmid":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"        15","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","title":"Estimating information in time-varying signals","file_date_updated":"2020-07-14T12:47:44Z","page":"e1007290","doi":"10.1371/journal.pcbi.1007290","publisher":"Public Library of Science","scopus_import":"1","publication_status":"published","isi":1,"has_accepted_license":"1","publication":"PLoS computational biology","date_created":"2019-09-22T22:00:37Z","language":[{"iso":"eng"}],"date_published":"2019-09-03T00:00:00Z","day":"03","article_processing_charge":"No","project":[{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"volume":15,"year":"2019","_id":"6900","citation":{"mla":"Cepeda Humerez, Sarah A., et al. “Estimating Information in Time-Varying Signals.” <i>PLoS Computational Biology</i>, vol. 15, no. 9, Public Library of Science, 2019, p. e1007290, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007290\">10.1371/journal.pcbi.1007290</a>.","ista":"Cepeda Humerez SA, Ruess J, Tkačik G. 2019. Estimating information in time-varying signals. PLoS computational biology. 15(9), e1007290.","ama":"Cepeda Humerez SA, Ruess J, Tkačik G. Estimating information in time-varying signals. <i>PLoS computational biology</i>. 2019;15(9):e1007290. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007290\">10.1371/journal.pcbi.1007290</a>","ieee":"S. A. Cepeda Humerez, J. Ruess, and G. Tkačik, “Estimating information in time-varying signals,” <i>PLoS computational biology</i>, vol. 15, no. 9. Public Library of Science, p. e1007290, 2019.","chicago":"Cepeda Humerez, Sarah A, Jakob Ruess, and Gašper Tkačik. “Estimating Information in Time-Varying Signals.” <i>PLoS Computational Biology</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pcbi.1007290\">https://doi.org/10.1371/journal.pcbi.1007290</a>.","short":"S.A. Cepeda Humerez, J. Ruess, G. Tkačik, PLoS Computational Biology 15 (2019) e1007290.","apa":"Cepeda Humerez, S. A., Ruess, J., &#38; Tkačik, G. (2019). Estimating information in time-varying signals. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007290\">https://doi.org/10.1371/journal.pcbi.1007290</a>"},"publication_identifier":{"eissn":["15537358"]},"external_id":{"isi":["000489741800021"],"pmid":["31479447"]},"related_material":{"record":[{"id":"6473","relation":"part_of_dissertation","status":"public"}]},"department":[{"_id":"GaTk"}],"type":"journal_article","date_updated":"2023-09-07T12:55:21Z","status":"public","issue":"9","ddc":["570"],"author":[{"full_name":"Cepeda Humerez, Sarah A","first_name":"Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","last_name":"Cepeda Humerez"},{"full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282","first_name":"Jakob","last_name":"Ruess"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik"}],"month":"09","oa":1,"oa_version":"Published Version"},{"author":[{"first_name":"Andrea C","full_name":"Hofmann, Andrea C","last_name":"Hofmann","id":"340F461A-F248-11E8-B48F-1D18A9856A87"},{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","last_name":"Jirovec","full_name":"Jirovec, Daniel","orcid":"0000-0002-7197-4801","first_name":"Daniel"},{"last_name":"Borovkov","first_name":"Maxim","full_name":"Borovkov, Maxim"},{"last_name":"Prieto Gonzalez","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ivan","orcid":"0000-0002-7370-5357","full_name":"Prieto Gonzalez, Ivan"},{"first_name":"Andrea","full_name":"Ballabio, Andrea","last_name":"Ballabio"},{"full_name":"Frigerio, Jacopo","first_name":"Jacopo","last_name":"Frigerio"},{"last_name":"Chrastina","first_name":"Daniel","full_name":"Chrastina, Daniel"},{"first_name":"Giovanni","full_name":"Isella, Giovanni","last_name":"Isella"},{"last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"acknowledgement":"We thank Matthias Brauns for helpful discussions and careful proofreading of the manuscript. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 844511 and from the FWF project P30207. The research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA machine shop and the nanofabrication\r\nfacility.","month":"10","oa":1,"oa_version":"Preprint","external_id":{"arxiv":["1910.05841"]},"related_material":{"record":[{"id":"10058","relation":"dissertation_contains","status":"public"}]},"department":[{"_id":"GeKa"}],"type":"preprint","date_updated":"2024-03-25T23:30:14Z","status":"public","year":"2019","_id":"10065","citation":{"mla":"Hofmann, Andrea C., et al. “Assessing the Potential of Ge/SiGe Quantum Dots as Hosts for Singlet-Triplet Qubits.” <i>ArXiv</i>, 1910.05841, doi:<a href=\"https://doi.org/10.48550/arXiv.1910.05841\">10.48550/arXiv.1910.05841</a>.","ista":"Hofmann AC, Jirovec D, Borovkov M, Prieto Gonzalez I, Ballabio A, Frigerio J, Chrastina D, Isella G, Katsaros G. Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. arXiv, 1910.05841.","ieee":"A. C. Hofmann <i>et al.</i>, “Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits,” <i>arXiv</i>. .","ama":"Hofmann AC, Jirovec D, Borovkov M, et al. Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.1910.05841\">10.48550/arXiv.1910.05841</a>","short":"A.C. Hofmann, D. Jirovec, M. Borovkov, I. Prieto Gonzalez, A. Ballabio, J. Frigerio, D. Chrastina, G. Isella, G. Katsaros, ArXiv (n.d.).","chicago":"Hofmann, Andrea C, Daniel Jirovec, Maxim Borovkov, Ivan Prieto Gonzalez, Andrea Ballabio, Jacopo Frigerio, Daniel Chrastina, Giovanni Isella, and Georgios Katsaros. “Assessing the Potential of Ge/SiGe Quantum Dots as Hosts for Singlet-Triplet Qubits.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.1910.05841\">https://doi.org/10.48550/arXiv.1910.05841</a>.","apa":"Hofmann, A. C., Jirovec, D., Borovkov, M., Prieto Gonzalez, I., Ballabio, A., Frigerio, J., … Katsaros, G. (n.d.). Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.1910.05841\">https://doi.org/10.48550/arXiv.1910.05841</a>"},"article_number":"1910.05841","ec_funded":1,"day":"13","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"article_processing_charge":"No","main_file_link":[{"url":"https://arxiv.org/abs/1910.05841","open_access":"1"}],"project":[{"name":"Majorana bound states in Ge/SiGe heterostructures","_id":"26A151DA-B435-11E9-9278-68D0E5697425","grant_number":"844511","call_identifier":"H2020"},{"call_identifier":"FWF","grant_number":"P30207","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","name":"Hole spin orbit qubits in Ge quantum wells"}],"publication_status":"submitted","language":[{"iso":"eng"}],"publication":"arXiv","date_created":"2021-10-01T12:14:51Z","date_published":"2019-10-13T00:00:00Z","title":"Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits","arxiv":1,"doi":"10.48550/arXiv.1910.05841","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We study double quantum dots in a Ge/SiGe heterostructure and test their maturity towards singlet-triplet ($S-T_0$) qubits. We demonstrate a large range of tunability, from two single quantum dots to a double quantum dot. We measure Pauli spin blockade and study the anisotropy of the $g$-factor. We use an adjacent quantum dot for sensing charge transitions in the double quantum dot at interest. In conclusion, Ge/SiGe possesses all ingredients necessary for building a singlet-triplet qubit.","lang":"eng"}]},{"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"text":"The verification of concurrent programs remains an open challenge, as thread interaction has to be accounted for, which leads to state-space explosion. Stateless model checking battles this problem by exploring traces rather than states of the program. As there are exponentially many traces, dynamic partial-order reduction (DPOR) techniques are used to partition the trace space into equivalence classes, and explore a few representatives from each class. The standard equivalence that underlies most DPOR techniques is the happens-before equivalence, however recent works have spawned a vivid interest towards coarser equivalences. The efficiency of such approaches is a product of two parameters: (i) the size of the partitioning induced by the equivalence, and (ii) the time spent by the exploration algorithm in each class of the partitioning. In this work, we present a new equivalence, called value-happens-before and show that it has two appealing features. First, value-happens-before is always at least as coarse as the happens-before equivalence, and can be even exponentially coarser. Second, the value-happens-before partitioning is efficiently explorable when the number of threads is bounded. We present an algorithm called value-centric DPOR (VCDPOR), which explores the underlying partitioning using polynomial time per class. Finally, we perform an experimental evaluation of VCDPOR on various benchmarks, and compare it against other state-of-the-art approaches. Our results show that value-happens-before typically induces a significant reduction in the size of the underlying partitioning, which leads to a considerable reduction in the running time for exploring the whole partitioning.","lang":"eng"}],"file":[{"file_name":"2019_ACM_Chatterjee.pdf","file_id":"10278","relation":"main_file","file_size":570829,"checksum":"2149979c46964c4d117af06ccb6c0834","access_level":"open_access","creator":"cchlebak","date_updated":"2021-11-12T11:41:56Z","content_type":"application/pdf","date_created":"2021-11-12T11:41:56Z","success":1}],"quality_controlled":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":"         3","publisher":"ACM","doi":"10.1145/3360550","arxiv":1,"title":"Value-centric dynamic partial order reduction","file_date_updated":"2021-11-12T11:41:56Z","date_published":"2019-10-10T00:00:00Z","language":[{"iso":"eng"}],"publication":"Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications","date_created":"2021-10-27T14:57:06Z","has_accepted_license":"1","publication_status":"published","project":[{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms"}],"conference":{"name":"OOPSLA: Object-oriented Programming, Systems, Languages and Applications","location":"Athens, Greece","end_date":"2019-10-25","start_date":"2019-10-23"},"volume":3,"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://dl.acm.org/doi/10.1145/3360550"}],"day":"10","publication_identifier":{"eissn":["2475-1421"]},"article_number":"124","citation":{"short":"K. Chatterjee, A. Pavlogiannis, V. Toman, in:, Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, ACM, 2019.","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, and Viktor Toman. “Value-Centric Dynamic Partial Order Reduction.” In <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i>, Vol. 3. ACM, 2019. <a href=\"https://doi.org/10.1145/3360550\">https://doi.org/10.1145/3360550</a>.","apa":"Chatterjee, K., Pavlogiannis, A., &#38; Toman, V. (2019). Value-centric dynamic partial order reduction. In <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i> (Vol. 3). Athens, Greece: ACM. <a href=\"https://doi.org/10.1145/3360550\">https://doi.org/10.1145/3360550</a>","ieee":"K. Chatterjee, A. Pavlogiannis, and V. Toman, “Value-centric dynamic partial order reduction,” in <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i>, Athens, Greece, 2019, vol. 3.","ama":"Chatterjee K, Pavlogiannis A, Toman V. Value-centric dynamic partial order reduction. In: <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i>. Vol 3. ACM; 2019. doi:<a href=\"https://doi.org/10.1145/3360550\">10.1145/3360550</a>","ista":"Chatterjee K, Pavlogiannis A, Toman V. 2019. Value-centric dynamic partial order reduction. Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications. OOPSLA: Object-oriented Programming, Systems, Languages and Applications vol. 3, 124.","mla":"Chatterjee, Krishnendu, et al. “Value-Centric Dynamic Partial Order Reduction.” <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i>, vol. 3, 124, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3360550\">10.1145/3360550</a>."},"year":"2019","_id":"10190","status":"public","date_updated":"2025-07-14T09:10:15Z","type":"conference","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10199"}]},"external_id":{"arxiv":["1909.00989"]},"keyword":["safety","risk","reliability and quality","software"],"oa_version":"Published Version","month":"10","oa":1,"acknowledgement":"The authors would also like to thank anonymous referees for their valuable comments and helpful suggestions. This work is supported by the Austrian Science Fund (FWF) NFN grants S11407-N23 (RiSE/SHiNE) and S11402-N23 (RiSE/SHiNE), by the Vienna Science and Technology Fund (WWTF) Project ICT15-003, and by the Austrian Science Fund (FWF) Schrodinger grant J-4220.\r\n","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","full_name":"Pavlogiannis, Andreas"},{"id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","last_name":"Toman","full_name":"Toman, Viktor","first_name":"Viktor","orcid":"0000-0001-9036-063X"}],"ddc":["000"]},{"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pmid":1,"file":[{"date_updated":"2021-11-26T11:37:54Z","creator":"cchlebak","checksum":"31d8bae55a376d30925f53f7e1a02396","access_level":"open_access","file_size":1648926,"relation":"main_file","file_id":"10356","file_name":"2019_BMCBio_Harker_Kirschneck.pdf","success":1,"content_type":"application/pdf","date_created":"2021-11-26T11:37:54Z"}],"abstract":[{"text":"Background\r\nESCRT-III is a membrane remodelling filament with the unique ability to cut membranes from the inside of the membrane neck. It is essential for the final stage of cell division, the formation of vesicles, the release of viruses, and membrane repair. Distinct from other cytoskeletal filaments, ESCRT-III filaments do not consume energy themselves, but work in conjunction with another ATP-consuming complex. Despite rapid progress in describing the cell biology of ESCRT-III, we lack an understanding of the physical mechanisms behind its force production and membrane remodelling.\r\nResults\r\nHere we present a minimal coarse-grained model that captures all the experimentally reported cases of ESCRT-III driven membrane sculpting, including the formation of downward and upward cones and tubules. This model suggests that a change in the geometry of membrane bound ESCRT-III filaments—from a flat spiral to a 3D helix—drives membrane deformation. We then show that such repetitive filament geometry transitions can induce the fission of cargo-containing vesicles.\r\nConclusions\r\nOur model provides a general physical mechanism that explains the full range of ESCRT-III-dependent membrane remodelling and scission events observed in cells. This mechanism for filament force production is distinct from the mechanisms described for other cytoskeletal elements discovered so far. The mechanistic principles revealed here suggest new ways of manipulating ESCRT-III-driven processes in cells and could be used to guide the engineering of synthetic membrane-sculpting systems.","lang":"eng"}],"quality_controlled":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":"        17","publisher":"Springer Nature","doi":"10.1186/s12915-019-0700-2","title":"Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico","file_date_updated":"2021-11-26T11:37:54Z","date_published":"2019-10-22T00:00:00Z","date_created":"2021-11-26T11:25:03Z","publication":"BMC Biology","language":[{"iso":"eng"}],"has_accepted_license":"1","scopus_import":"1","publication_status":"published","volume":17,"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/559898"}],"day":"22","article_number":"82","citation":{"ista":"Harker-Kirschneck L, Baum B, Šarić A. 2019. Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. 17(1), 82.","mla":"Harker-Kirschneck, Lena, et al. “Changes in ESCRT-III Filament Geometry Drive Membrane Remodelling and Fission in Silico.” <i>BMC Biology</i>, vol. 17, no. 1, 82, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1186/s12915-019-0700-2\">10.1186/s12915-019-0700-2</a>.","short":"L. Harker-Kirschneck, B. Baum, A. Šarić, BMC Biology 17 (2019).","chicago":"Harker-Kirschneck, Lena, Buzz Baum, and Anđela Šarić. “Changes in ESCRT-III Filament Geometry Drive Membrane Remodelling and Fission in Silico.” <i>BMC Biology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1186/s12915-019-0700-2\">https://doi.org/10.1186/s12915-019-0700-2</a>.","apa":"Harker-Kirschneck, L., Baum, B., &#38; Šarić, A. (2019). Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. <i>BMC Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s12915-019-0700-2\">https://doi.org/10.1186/s12915-019-0700-2</a>","ama":"Harker-Kirschneck L, Baum B, Šarić A. Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. <i>BMC Biology</i>. 2019;17(1). doi:<a href=\"https://doi.org/10.1186/s12915-019-0700-2\">10.1186/s12915-019-0700-2</a>","ieee":"L. Harker-Kirschneck, B. Baum, and A. Šarić, “Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico,” <i>BMC Biology</i>, vol. 17, no. 1. Springer Nature, 2019."},"publication_identifier":{"issn":["1741-7007"]},"article_type":"original","year":"2019","_id":"10354","date_updated":"2021-11-26T11:54:29Z","status":"public","type":"journal_article","keyword":["cell biology"],"external_id":{"pmid":["31640700"]},"oa":1,"month":"10","oa_version":"Published Version","ddc":["570"],"acknowledgement":"We thank Jeremy Carlton, Mike Staddon, Geraint Harker, and the Wellcome Trust Consortium “Archaeal Origins of Eukaryotic Cell Organisation” for fruitful conversations. We thank Peter Wirnsberger and Tine Curk for discussions about the membrane model implementation.","author":[{"last_name":"Harker-Kirschneck","first_name":"Lena","full_name":"Harker-Kirschneck, Lena"},{"last_name":"Baum","first_name":"Buzz","full_name":"Baum, Buzz"},{"last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","full_name":"Šarić, Anđela"}],"issue":"1","extern":"1"},{"pmid":1,"abstract":[{"text":"The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, in which a whole macromolecule is represented by a small number of particles, can be of great value in identifying the main driving forces behind self-organisation in cell biology. Such models can incorporate data from both molecular and continuum scales, and their results can be directly compared to experiments. Here we review the state of the art of models for studying the formation and biological function of macromolecular assemblies in living organisms. We outline the key ingredients of each model and their main findings. We illustrate the contribution of this class of simulations to identifying the physical mechanisms behind life and diseases, and discuss their future developments.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":"        58","quality_controlled":"1","page":"43-52","doi":"10.1016/j.sbi.2019.05.018","title":"Minimal coarse-grained models for molecular self-organisation in biology","publisher":"Elsevier","publication_status":"published","scopus_import":"1","date_published":"2019-06-18T00:00:00Z","language":[{"iso":"eng"}],"publication":"Current Opinion in Structural Biology","date_created":"2021-11-26T11:33:21Z","main_file_link":[{"url":"https://arxiv.org/abs/1906.09349","open_access":"1"}],"article_processing_charge":"No","day":"18","volume":58,"article_type":"original","year":"2019","_id":"10355","citation":{"ista":"Hafner AE, Krausser J, Šarić A. 2019. Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. 58, 43–52.","mla":"Hafner, Anne E., et al. “Minimal Coarse-Grained Models for Molecular Self-Organisation in Biology.” <i>Current Opinion in Structural Biology</i>, vol. 58, Elsevier, 2019, pp. 43–52, doi:<a href=\"https://doi.org/10.1016/j.sbi.2019.05.018\">10.1016/j.sbi.2019.05.018</a>.","chicago":"Hafner, Anne E, Johannes Krausser, and Anđela Šarić. “Minimal Coarse-Grained Models for Molecular Self-Organisation in Biology.” <i>Current Opinion in Structural Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.sbi.2019.05.018\">https://doi.org/10.1016/j.sbi.2019.05.018</a>.","short":"A.E. Hafner, J. Krausser, A. Šarić, Current Opinion in Structural Biology 58 (2019) 43–52.","apa":"Hafner, A. E., Krausser, J., &#38; Šarić, A. (2019). Minimal coarse-grained models for molecular self-organisation in biology. <i>Current Opinion in Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2019.05.018\">https://doi.org/10.1016/j.sbi.2019.05.018</a>","ieee":"A. E. Hafner, J. Krausser, and A. Šarić, “Minimal coarse-grained models for molecular self-organisation in biology,” <i>Current Opinion in Structural Biology</i>, vol. 58. Elsevier, pp. 43–52, 2019.","ama":"Hafner AE, Krausser J, Šarić A. Minimal coarse-grained models for molecular self-organisation in biology. <i>Current Opinion in Structural Biology</i>. 2019;58:43-52. doi:<a href=\"https://doi.org/10.1016/j.sbi.2019.05.018\">10.1016/j.sbi.2019.05.018</a>"},"publication_identifier":{"issn":["0959-440X"]},"keyword":["molecular biology","structural biology"],"external_id":{"pmid":["31226513"]},"date_updated":"2021-11-26T11:54:25Z","status":"public","type":"journal_article","author":[{"last_name":"Hafner","first_name":"Anne E","full_name":"Hafner, Anne E"},{"full_name":"Krausser, Johannes","first_name":"Johannes","last_name":"Krausser"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","first_name":"Anđela"}],"acknowledgement":"We acknowledge funding from EPSRC (A.E.H. and A.Š.), the Academy of Medical Sciences (J.K. and A.Š.), the Wellcome Trust (J.K. and A.Š.), and the Royal Society (A.Š.). We thank Shiladitya Banerjee and Nikola Ojkic for critically reading the manuscript, and Claudia Flandoli for helping us with figures and illustrations.","extern":"1","month":"06","oa":1,"oa_version":"Preprint"},{"date_published":"2019-01-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"European Journal of Human Genetics","date_created":"2018-12-11T11:44:39Z","scopus_import":"1","publication_status":"published","isi":1,"publist_id":"7949","publisher":"Springer Nature","doi":"10.1038/s41431-018-0231-2","page":"161-166","title":"CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"        27","pmid":1,"abstract":[{"lang":"eng","text":"Clinical Utility Gene Card. 1. Name of Disease (Synonyms): Pontocerebellar hypoplasia type 9 (PCH9) and spastic paraplegia-63 (SPG63). 2. OMIM# of the Disease: 615809 and 615686. 3. Name of the Analysed Genes or DNA/Chromosome Segments: AMPD2 at 1p13.3. 4. OMIM# of the Gene(s): 102771."}],"month":"01","oa":1,"oa_version":"Published Version","author":[{"full_name":"Marsh, Ashley","first_name":"Ashley","last_name":"Marsh"},{"orcid":"0000-0002-7673-7178","first_name":"Gaia","full_name":"Novarino, Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lockhart","first_name":"Paul","full_name":"Lockhart, Paul"},{"first_name":"Richard","full_name":"Leventer, Richard","last_name":"Leventer"}],"acknowledgement":"This work was supported by EuroGentest2 (Unit 2: “Genetic testing as part of health care”), a Coordination Action under FP7 (Grant Agreement Number 261469) and the European Society of Human Genetics. We acknowledge the participation of the patients and their families in these studies, as well as the generous financial support of the Lefroy and Handbury families. APLM was supported by an Australian Postgraduate Award. PJL is supported by an NHMRC Career Development Fellowship (GNT1032364). RJL is supported by a Melbourne Children’s Clinician Scientist Fellowship.","date_updated":"2023-08-24T14:28:24Z","status":"public","type":"journal_article","department":[{"_id":"GaNo"}],"external_id":{"pmid":["30089829"],"isi":["000454111500019"]},"citation":{"ista":"Marsh A, Novarino G, Lockhart P, Leventer R. 2019. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. 27, 161–166.","mla":"Marsh, Ashley, et al. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” <i>European Journal of Human Genetics</i>, vol. 27, Springer Nature, 2019, pp. 161–66, doi:<a href=\"https://doi.org/10.1038/s41431-018-0231-2\">10.1038/s41431-018-0231-2</a>.","apa":"Marsh, A., Novarino, G., Lockhart, P., &#38; Leventer, R. (2019). CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. <i>European Journal of Human Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41431-018-0231-2\">https://doi.org/10.1038/s41431-018-0231-2</a>","chicago":"Marsh, Ashley, Gaia Novarino, Paul Lockhart, and Richard Leventer. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” <i>European Journal of Human Genetics</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41431-018-0231-2\">https://doi.org/10.1038/s41431-018-0231-2</a>.","short":"A. Marsh, G. Novarino, P. Lockhart, R. Leventer, European Journal of Human Genetics 27 (2019) 161–166.","ama":"Marsh A, Novarino G, Lockhart P, Leventer R. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. <i>European Journal of Human Genetics</i>. 2019;27:161-166. doi:<a href=\"https://doi.org/10.1038/s41431-018-0231-2\">10.1038/s41431-018-0231-2</a>","ieee":"A. Marsh, G. Novarino, P. Lockhart, and R. Leventer, “CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63,” <i>European Journal of Human Genetics</i>, vol. 27. Springer Nature, pp. 161–166, 2019."},"article_type":"original","_id":"105","year":"2019","volume":27,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41431-018-0231-2"}],"article_processing_charge":"No","day":"01"},{"quality_controlled":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":"       367","pmid":1,"abstract":[{"text":"The quantum anomalous Hall (QAH) effect combines topology and magnetism to produce precisely quantized Hall resistance at zero magnetic field. We report the observation of a QAH effect in twisted bilayer graphene aligned to hexagonal boron nitride. The effect is driven by intrinsic strong interactions, which polarize the electrons into a single spin- and valley-resolved moiré miniband with Chern number C = 1. In contrast to magnetically doped systems, the measured transport energy gap is larger than the Curie temperature for magnetic ordering, and quantization to within 0.1% of the von Klitzing constant persists to temperatures of several kelvin at zero magnetic field. Electrical currents as small as 1 nanoampere controllably switch the magnetic order between states of opposite polarization, forming an electrically rewritable magnetic memory.","lang":"eng"}],"date_published":"2019-12-19T00:00:00Z","language":[{"iso":"eng"}],"date_created":"2022-01-13T14:21:32Z","publication":"Science","publication_status":"published","scopus_import":"1","publisher":"American Association for the Advancement of Science","doi":"10.1126/science.aay5533","page":"900-903","arxiv":1,"title":"Intrinsic quantized anomalous Hall effect in a moiré heterostructure","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"citation":{"mla":"Serlin, M., et al. “Intrinsic Quantized Anomalous Hall Effect in a Moiré Heterostructure.” <i>Science</i>, vol. 367, no. 6480, American Association for the Advancement of Science, 2019, pp. 900–03, doi:<a href=\"https://doi.org/10.1126/science.aay5533\">10.1126/science.aay5533</a>.","ista":"Serlin M, Tschirhart CL, Polshyn H, Zhang Y, Zhu J, Watanabe K, Taniguchi T, Balents L, Young AF. 2019. Intrinsic quantized anomalous Hall effect in a moiré heterostructure. Science. 367(6480), 900–903.","ama":"Serlin M, Tschirhart CL, Polshyn H, et al. Intrinsic quantized anomalous Hall effect in a moiré heterostructure. <i>Science</i>. 2019;367(6480):900-903. doi:<a href=\"https://doi.org/10.1126/science.aay5533\">10.1126/science.aay5533</a>","ieee":"M. Serlin <i>et al.</i>, “Intrinsic quantized anomalous Hall effect in a moiré heterostructure,” <i>Science</i>, vol. 367, no. 6480. American Association for the Advancement of Science, pp. 900–903, 2019.","apa":"Serlin, M., Tschirhart, C. L., Polshyn, H., Zhang, Y., Zhu, J., Watanabe, K., … Young, A. F. (2019). Intrinsic quantized anomalous Hall effect in a moiré heterostructure. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aay5533\">https://doi.org/10.1126/science.aay5533</a>","short":"M. Serlin, C.L. Tschirhart, H. Polshyn, Y. Zhang, J. Zhu, K. Watanabe, T. Taniguchi, L. Balents, A.F. Young, Science 367 (2019) 900–903.","chicago":"Serlin, M., C. L. Tschirhart, Hryhoriy Polshyn, Y. Zhang, J. Zhu, K. Watanabe, T. Taniguchi, L. Balents, and A. F. Young. “Intrinsic Quantized Anomalous Hall Effect in a Moiré Heterostructure.” <i>Science</i>. American Association for the Advancement of Science, 2019. <a href=\"https://doi.org/10.1126/science.aay5533\">https://doi.org/10.1126/science.aay5533</a>."},"article_type":"original","year":"2019","_id":"10619","volume":367,"article_processing_charge":"No","main_file_link":[{"url":"https://arxiv.org/abs/1907.00261","open_access":"1"}],"day":"19","oa_version":"Preprint","month":"12","oa":1,"acknowledgement":"The authors acknowledge discussions with A. Macdonald, Y. Saito, and M. Zaletel.","author":[{"full_name":"Serlin, M.","first_name":"M.","last_name":"Serlin"},{"last_name":"Tschirhart","full_name":"Tschirhart, C. L.","first_name":"C. L."},{"orcid":"0000-0001-8223-8896","first_name":"Hryhoriy","full_name":"Polshyn, Hryhoriy","last_name":"Polshyn","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48"},{"full_name":"Zhang, Y.","first_name":"Y.","last_name":"Zhang"},{"last_name":"Zhu","first_name":"J.","full_name":"Zhu, J."},{"first_name":"K.","full_name":"Watanabe, K.","last_name":"Watanabe"},{"last_name":"Taniguchi","first_name":"T.","full_name":"Taniguchi, T."},{"last_name":"Balents","first_name":"L.","full_name":"Balents, L."},{"first_name":"A. F.","full_name":"Young, A. F.","last_name":"Young"}],"extern":"1","issue":"6480","status":"public","date_updated":"2023-02-21T16:00:09Z","type":"journal_article","related_material":{"record":[{"status":"public","id":"10697","relation":"other"},{"relation":"other","id":"10698","status":"public"},{"id":"10699","relation":"other","status":"public"}]},"external_id":{"pmid":["31857492"],"arxiv":["1907.00261"]},"keyword":["multidisciplinary"]},{"intvolume":"        15","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","quality_controlled":"1","abstract":[{"text":"Twisted bilayer graphene has recently emerged as a platform for hosting correlated phenomena. For twist angles near θ ≈ 1.1°, the low-energy electronic structure of twisted bilayer graphene features isolated bands with a flat dispersion1,2. Recent experiments have observed a variety of low-temperature phases that appear to be driven by electron interactions, including insulating states, superconductivity and magnetism3,4,5,6. Here we report electrical transport measurements up to room temperature for twist angles varying between 0.75° and 2°. We find that the resistivity, ρ, scales linearly with temperature, T, over a wide range of T before falling again owing to interband activation. The T-linear response is much larger than observed in monolayer graphene for all measured devices, and in particular increases by more than three orders of magnitude in the range where the flat band exists. Our results point to the dominant role of electron–phonon scattering in twisted bilayer graphene, with possible implications for the origin of the observed superconductivity.","lang":"eng"}],"scopus_import":"1","publication_status":"published","language":[{"iso":"eng"}],"publication":"Nature Physics","date_created":"2022-01-13T15:00:58Z","date_published":"2019-08-05T00:00:00Z","title":"Large linear-in-temperature resistivity in twisted bilayer graphene","arxiv":1,"doi":"10.1038/s41567-019-0596-3","page":"1011-1016","publisher":"Springer Nature","_id":"10621","year":"2019","article_type":"original","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"citation":{"mla":"Polshyn, Hryhoriy, et al. “Large Linear-in-Temperature Resistivity in Twisted Bilayer Graphene.” <i>Nature Physics</i>, vol. 15, no. 10, Springer Nature, 2019, pp. 1011–16, doi:<a href=\"https://doi.org/10.1038/s41567-019-0596-3\">10.1038/s41567-019-0596-3</a>.","ista":"Polshyn H, Yankowitz M, Chen S, Zhang Y, Watanabe K, Taniguchi T, Dean CR, Young AF. 2019. Large linear-in-temperature resistivity in twisted bilayer graphene. Nature Physics. 15(10), 1011–1016.","ama":"Polshyn H, Yankowitz M, Chen S, et al. Large linear-in-temperature resistivity in twisted bilayer graphene. <i>Nature Physics</i>. 2019;15(10):1011-1016. doi:<a href=\"https://doi.org/10.1038/s41567-019-0596-3\">10.1038/s41567-019-0596-3</a>","ieee":"H. Polshyn <i>et al.</i>, “Large linear-in-temperature resistivity in twisted bilayer graphene,” <i>Nature Physics</i>, vol. 15, no. 10. Springer Nature, pp. 1011–1016, 2019.","apa":"Polshyn, H., Yankowitz, M., Chen, S., Zhang, Y., Watanabe, K., Taniguchi, T., … Young, A. F. (2019). Large linear-in-temperature resistivity in twisted bilayer graphene. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-019-0596-3\">https://doi.org/10.1038/s41567-019-0596-3</a>","short":"H. Polshyn, M. Yankowitz, S. Chen, Y. Zhang, K. Watanabe, T. Taniguchi, C.R. Dean, A.F. Young, Nature Physics 15 (2019) 1011–1016.","chicago":"Polshyn, Hryhoriy, Matthew Yankowitz, Shaowen Chen, Yuxuan Zhang, K. Watanabe, T. Taniguchi, Cory R. Dean, and Andrea F. Young. “Large Linear-in-Temperature Resistivity in Twisted Bilayer Graphene.” <i>Nature Physics</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41567-019-0596-3\">https://doi.org/10.1038/s41567-019-0596-3</a>."},"day":"05","article_processing_charge":"No","main_file_link":[{"url":"https://arxiv.org/abs/1902.00763","open_access":"1"}],"volume":15,"extern":"1","issue":"10","acknowledgement":"The authors thank S. Das Sarma and F. Wu for sharing their unpublished theoretical results, and acknowledge further discussions with L. Balents and T. Senthil. Work at both Columbia and UCSB was funded by the Army Research Office under award W911NF-17-1-0323. Sample device design and fabrication was partially supported by DoE Pro-QM EFRC (DE-SC0019443). A.F.Y. and C.R.D. separately acknowledge the support of the David and Lucile Packard Foundation. K.W. and T.T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan and the CREST (JPMJCR15F3), JST. A portion of this work was carried out at the KITP, Santa Barbara, supported by the National Science Foundation under grant number NSF PHY-1748958.","author":[{"id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","last_name":"Polshyn","full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","first_name":"Hryhoriy"},{"last_name":"Yankowitz","full_name":"Yankowitz, Matthew","first_name":"Matthew"},{"last_name":"Chen","full_name":"Chen, Shaowen","first_name":"Shaowen"},{"last_name":"Zhang","first_name":"Yuxuan","full_name":"Zhang, Yuxuan"},{"first_name":"K.","full_name":"Watanabe, K.","last_name":"Watanabe"},{"first_name":"T.","full_name":"Taniguchi, T.","last_name":"Taniguchi"},{"first_name":"Cory R.","full_name":"Dean, Cory R.","last_name":"Dean"},{"full_name":"Young, Andrea F.","first_name":"Andrea F.","last_name":"Young"}],"oa_version":"Preprint","oa":1,"month":"08","external_id":{"arxiv":["1902.00763"]},"keyword":["general physics and astronomy"],"type":"journal_article","status":"public","date_updated":"2022-01-20T09:33:38Z"},{"pmid":1,"abstract":[{"text":"We demonstrate a method for manipulating small ensembles of vortices in multiply connected superconducting structures. A micron-size magnetic particle attached to the tip of a silicon cantilever is used to locally apply magnetic flux through the superconducting structure. By scanning the tip over the surface of the device and by utilizing the dynamical coupling between the vortices and the cantilever, a high-resolution spatial map of the different vortex configurations is obtained. Moving the tip to a particular location in the map stabilizes a distinct multivortex configuration. Thus, the scanning of the tip over a particular trajectory in space permits nontrivial operations to be performed, such as braiding of individual vortices within a larger vortex ensemble—a key capability required by many proposals for topological quantum computing.","lang":"eng"}],"user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","intvolume":"        19","quality_controlled":"1","arxiv":1,"doi":"10.1021/acs.nanolett.9b01983","page":"5476-5482","title":"Manipulating multivortex states in superconducting structures","publisher":"American Chemical Society","publication_status":"published","scopus_import":"1","date_published":"2019-06-27T00:00:00Z","publication":"Nano Letters","date_created":"2022-01-13T15:11:14Z","language":[{"iso":"eng"}],"article_processing_charge":"No","main_file_link":[{"url":"https://arxiv.org/abs/1905.06303","open_access":"1"}],"day":"27","volume":19,"article_type":"original","year":"2019","_id":"10622","citation":{"ieee":"H. Polshyn, T. Naibert, and R. Budakian, “Manipulating multivortex states in superconducting structures,” <i>Nano Letters</i>, vol. 19, no. 8. American Chemical Society, pp. 5476–5482, 2019.","ama":"Polshyn H, Naibert T, Budakian R. Manipulating multivortex states in superconducting structures. <i>Nano Letters</i>. 2019;19(8):5476-5482. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.9b01983\">10.1021/acs.nanolett.9b01983</a>","apa":"Polshyn, H., Naibert, T., &#38; Budakian, R. (2019). Manipulating multivortex states in superconducting structures. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.9b01983\">https://doi.org/10.1021/acs.nanolett.9b01983</a>","chicago":"Polshyn, Hryhoriy, Tyler Naibert, and Raffi Budakian. “Manipulating Multivortex States in Superconducting Structures.” <i>Nano Letters</i>. American Chemical Society, 2019. <a href=\"https://doi.org/10.1021/acs.nanolett.9b01983\">https://doi.org/10.1021/acs.nanolett.9b01983</a>.","short":"H. Polshyn, T. Naibert, R. Budakian, Nano Letters 19 (2019) 5476–5482.","mla":"Polshyn, Hryhoriy, et al. “Manipulating Multivortex States in Superconducting Structures.” <i>Nano Letters</i>, vol. 19, no. 8, American Chemical Society, 2019, pp. 5476–82, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.9b01983\">10.1021/acs.nanolett.9b01983</a>.","ista":"Polshyn H, Naibert T, Budakian R. 2019. Manipulating multivortex states in superconducting structures. Nano Letters. 19(8), 5476–5482."},"publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"keyword":["mechanical engineering","condensed matter physics","general materials science","general chemistry","bioengineering"],"external_id":{"pmid":["31246034"],"arxiv":["1905.06303"]},"date_updated":"2022-01-13T15:41:24Z","status":"public","type":"journal_article","acknowledgement":"We are grateful to Nadya Mason, Taylor Hughes, and Alexey Bezryadin for useful discussions. This work was supported by the DOE Basic Energy Sciences under DE-SC0012649 and the Department of Physics and the Frederick Seitz Materials Research Laboratory Central Facilities at the University of Illinois.","author":[{"full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","first_name":"Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","last_name":"Polshyn"},{"last_name":"Naibert","full_name":"Naibert, Tyler","first_name":"Tyler"},{"last_name":"Budakian","first_name":"Raffi","full_name":"Budakian, Raffi"}],"issue":"8","extern":"1","month":"06","oa":1,"oa_version":"Preprint"},{"intvolume":"       363","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","quality_controlled":"1","abstract":[{"lang":"eng","text":"The discovery of superconductivity and exotic insulating phases in twisted bilayer graphene has established this material as a model system of strongly correlated electrons. To achieve superconductivity, the two layers of graphene need to be at a very precise angle with respect to each other. Yankowitz et al. now show that another experimental knob, hydrostatic pressure, can be used to tune the phase diagram of twisted bilayer graphene (see the Perspective by Feldman). Applying pressure increased the coupling between the layers, which shifted the superconducting transition to higher angles and somewhat higher temperatures."}],"pmid":1,"scopus_import":"1","publication_status":"published","language":[{"iso":"eng"}],"publication":"Science","date_created":"2022-01-14T12:14:58Z","date_published":"2019-01-24T00:00:00Z","title":"Tuning superconductivity in twisted bilayer graphene","arxiv":1,"doi":"10.1126/science.aav1910","page":"1059-1064","publisher":"American Association for the Advancement of Science (AAAS)","_id":"10625","year":"2019","article_type":"original","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"citation":{"ista":"Yankowitz M, Chen S, Polshyn H, Zhang Y, Watanabe K, Taniguchi T, Graf D, Young AF, Dean CR. 2019. Tuning superconductivity in twisted bilayer graphene. Science. 363(6431), 1059–1064.","mla":"Yankowitz, Matthew, et al. “Tuning Superconductivity in Twisted Bilayer Graphene.” <i>Science</i>, vol. 363, no. 6431, American Association for the Advancement of Science (AAAS), 2019, pp. 1059–64, doi:<a href=\"https://doi.org/10.1126/science.aav1910\">10.1126/science.aav1910</a>.","chicago":"Yankowitz, Matthew, Shaowen Chen, Hryhoriy Polshyn, Yuxuan Zhang, K. Watanabe, T. Taniguchi, David Graf, Andrea F. Young, and Cory R. Dean. “Tuning Superconductivity in Twisted Bilayer Graphene.” <i>Science</i>. American Association for the Advancement of Science (AAAS), 2019. <a href=\"https://doi.org/10.1126/science.aav1910\">https://doi.org/10.1126/science.aav1910</a>.","short":"M. Yankowitz, S. Chen, H. Polshyn, Y. Zhang, K. Watanabe, T. Taniguchi, D. Graf, A.F. Young, C.R. Dean, Science 363 (2019) 1059–1064.","apa":"Yankowitz, M., Chen, S., Polshyn, H., Zhang, Y., Watanabe, K., Taniguchi, T., … Dean, C. R. (2019). Tuning superconductivity in twisted bilayer graphene. <i>Science</i>. American Association for the Advancement of Science (AAAS). <a href=\"https://doi.org/10.1126/science.aav1910\">https://doi.org/10.1126/science.aav1910</a>","ieee":"M. Yankowitz <i>et al.</i>, “Tuning superconductivity in twisted bilayer graphene,” <i>Science</i>, vol. 363, no. 6431. American Association for the Advancement of Science (AAAS), pp. 1059–1064, 2019.","ama":"Yankowitz M, Chen S, Polshyn H, et al. Tuning superconductivity in twisted bilayer graphene. <i>Science</i>. 2019;363(6431):1059-1064. doi:<a href=\"https://doi.org/10.1126/science.aav1910\">10.1126/science.aav1910</a>"},"day":"24","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.07865"}],"volume":363,"extern":"1","issue":"6431","author":[{"last_name":"Yankowitz","first_name":"Matthew","full_name":"Yankowitz, Matthew"},{"last_name":"Chen","first_name":"Shaowen","full_name":"Chen, Shaowen"},{"full_name":"Polshyn, Hryhoriy","first_name":"Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","last_name":"Polshyn"},{"first_name":"Yuxuan","full_name":"Zhang, Yuxuan","last_name":"Zhang"},{"last_name":"Watanabe","first_name":"K.","full_name":"Watanabe, K."},{"first_name":"T.","full_name":"Taniguchi, T.","last_name":"Taniguchi"},{"last_name":"Graf","full_name":"Graf, David","first_name":"David"},{"last_name":"Young","first_name":"Andrea F.","full_name":"Young, Andrea F."},{"last_name":"Dean","full_name":"Dean, Cory R.","first_name":"Cory R."}],"acknowledgement":"We thank J. Zhu and H. Zhou for experimental assistance and D. Shahar, A. Millis, O. Vafek, M. Zaletel, L. Balents, C. Xu, A. Bernevig, L. Fu, M. Koshino, and P. Moon for helpful discussions.","oa_version":"Preprint","oa":1,"month":"01","external_id":{"arxiv":["1808.07865"],"pmid":["30679385 "]},"keyword":["multidisciplinary"],"type":"journal_article","status":"public","date_updated":"2022-01-14T13:48:32Z"},{"volume":"03","abstract":[{"text":"Since the discovery of correlated insulators and superconductivity in magic-angle twisted bilayer graphene (tBLG) ([1, 2], JCCM April 2018), theorists have been excitedly pursuing the alluring mix of band topology, symmetry breaking, Mott insulators and superconductivity at play, as well as the potential relation (if any) to high-Tc physics. Now a new stream\r\nof experimental work is arriving which further enriches the story. To briefly recap Episodes 1 and 2 (JCCM April and November 2018), when two graphene layers are stacked with a small rotational mismatch θ, the resulting long-wavelength moire pattern leads to a superlattice potential which reconstructs the low energy band structure. When θ approaches the “magic-angle” θM ∼ 1 ◦, the band structure features eight nearly-flat bands which fill when the electron number per moire unit cell, n/n0, lies between −4 < n/n0 < 4. The bands can be counted as 8 = 2 × 2 × 2: for each spin (2×) and valley (2×) characteristic of monolayergraphene, tBLG has has 2× flat bands which cross at mini-Dirac points.","lang":"eng"}],"day":"28","main_file_link":[{"url":"https://www.condmatjclub.org/?p=3541","open_access":"1"}],"article_processing_charge":"No","citation":{"mla":"Yankowitz, Mathew, et al. “New Correlated Phenomena in Magic-Angle Twisted Bilayer Graphene/S.” <i>Journal Club for Condensed Matter Physics</i>, vol. 03, Simons Foundation ; University of California, Riverside, 2019, doi:<a href=\"https://doi.org/10.36471/jccm_february_2019_03\">10.36471/jccm_february_2019_03</a>.","ista":"Yankowitz M, Chen S, Polshyn H, Watanabe K, Taniguchi T, Graf D, Young AF, Dean CR, Sharpe AL, Fox EJ, Barnard AW, Finney J. 2019. New correlated phenomena in magic-angle twisted bilayer graphene/s. Journal Club for Condensed Matter Physics. 03.","ama":"Yankowitz M, Chen S, Polshyn H, et al. New correlated phenomena in magic-angle twisted bilayer graphene/s. <i>Journal Club for Condensed Matter Physics</i>. 2019;03. doi:<a href=\"https://doi.org/10.36471/jccm_february_2019_03\">10.36471/jccm_february_2019_03</a>","ieee":"M. Yankowitz <i>et al.</i>, “New correlated phenomena in magic-angle twisted bilayer graphene/s,” <i>Journal Club for Condensed Matter Physics</i>, vol. 03. Simons Foundation ; University of California, Riverside, 2019.","apa":"Yankowitz, M., Chen, S., Polshyn, H., Watanabe, K., Taniguchi, T., Graf, D., … Finney, J. (2019). New correlated phenomena in magic-angle twisted bilayer graphene/s. <i>Journal Club for Condensed Matter Physics</i>. Simons Foundation ; University of California, Riverside. <a href=\"https://doi.org/10.36471/jccm_february_2019_03\">https://doi.org/10.36471/jccm_february_2019_03</a>","chicago":"Yankowitz, Mathew, Shaowen Chen, Hryhoriy Polshyn, K. Watanabe, T. Taniguchi, David Graf, Andrea F. Young, et al. “New Correlated Phenomena in Magic-Angle Twisted Bilayer Graphene/S.” <i>Journal Club for Condensed Matter Physics</i>. Simons Foundation ; University of California, Riverside, 2019. <a href=\"https://doi.org/10.36471/jccm_february_2019_03\">https://doi.org/10.36471/jccm_february_2019_03</a>.","short":"M. Yankowitz, S. Chen, H. Polshyn, K. Watanabe, T. Taniguchi, D. Graf, A.F. Young, C.R. Dean, A.L. Sharpe, E.J. Fox, A.W. Barnard, J. Finney, Journal Club for Condensed Matter Physics 03 (2019)."},"quality_controlled":"1","intvolume":"         3","_id":"10664","year":"2019","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_type":"original","type":"journal_article","publisher":"Simons Foundation ; University of California, Riverside","date_updated":"2022-01-25T15:56:39Z","status":"public","title":"New correlated phenomena in magic-angle twisted bilayer graphene/s","doi":"10.36471/jccm_february_2019_03","date_created":"2022-01-25T15:09:58Z","oa":1,"language":[{"iso":"eng"}],"publication":"Journal Club for Condensed Matter Physics","month":"02","oa_version":"Published Version","date_published":"2019-02-28T00:00:00Z","publication_status":"published","author":[{"last_name":"Yankowitz","first_name":"Mathew","full_name":"Yankowitz, Mathew"},{"last_name":"Chen","full_name":"Chen, Shaowen","first_name":"Shaowen"},{"full_name":"Polshyn, Hryhoriy","first_name":"Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","last_name":"Polshyn"},{"last_name":"Watanabe","first_name":"K.","full_name":"Watanabe, K."},{"full_name":"Taniguchi, T.","first_name":"T.","last_name":"Taniguchi"},{"full_name":"Graf, David","first_name":"David","last_name":"Graf"},{"last_name":"Young","full_name":"Young, Andrea F.","first_name":"Andrea F."},{"full_name":"Dean, Cory R.","first_name":"Cory R.","last_name":"Dean"},{"last_name":"Sharpe","first_name":"Aaron L.","full_name":"Sharpe, Aaron L."},{"first_name":"E.J.","full_name":"Fox, E.J.","last_name":"Fox"},{"full_name":"Barnard, A.W.","first_name":"A.W.","last_name":"Barnard"},{"last_name":"Finney","full_name":"Finney, Joe","first_name":"Joe"}]},{"oa_version":"Published Version","month":"03","oa":1,"extern":"1","issue":"2","author":[{"last_name":"Serlin","first_name":"Marec","full_name":"Serlin, Marec"},{"last_name":"Tschirhart","first_name":"Charles","full_name":"Tschirhart, Charles"},{"full_name":"Polshyn, Hryhoriy","first_name":"Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","last_name":"Polshyn"},{"full_name":"Zhu, Jiacheng","first_name":"Jiacheng","last_name":"Zhu"},{"last_name":"Huber","full_name":"Huber, Martin E.","first_name":"Martin E."},{"last_name":"Young","full_name":"Young, Andrea","first_name":"Andrea"}],"type":"conference","status":"public","date_updated":"2022-02-08T10:25:30Z","publication_identifier":{"issn":["0003-0503"]},"citation":{"mla":"Serlin, Marec, et al. “Direct Imaging of Magnetic Structure in Twisted Bilayer Graphene with Scanning NanoSQUID-On-Tip Microscopy.” <i>APS March Meeting 2019</i>, vol. 64, no. 2, L14.00006, American Physical Society, 2019.","ista":"Serlin M, Tschirhart C, Polshyn H, Zhu J, Huber ME, Young A. 2019. Direct Imaging of magnetic structure in twisted bilayer graphene with scanning nanoSQUID-On-Tip microscopy. APS March Meeting 2019. APS: American Physical Society, Bulletin of the American Physical Society, vol. 64, L14.00006.","ieee":"M. Serlin, C. Tschirhart, H. Polshyn, J. Zhu, M. E. Huber, and A. Young, “Direct Imaging of magnetic structure in twisted bilayer graphene with scanning nanoSQUID-On-Tip microscopy,” in <i>APS March Meeting 2019</i>, Boston, MA, United States, 2019, vol. 64, no. 2.","ama":"Serlin M, Tschirhart C, Polshyn H, Zhu J, Huber ME, Young A. Direct Imaging of magnetic structure in twisted bilayer graphene with scanning nanoSQUID-On-Tip microscopy. In: <i>APS March Meeting 2019</i>. Vol 64. American Physical Society; 2019.","apa":"Serlin, M., Tschirhart, C., Polshyn, H., Zhu, J., Huber, M. E., &#38; Young, A. (2019). Direct Imaging of magnetic structure in twisted bilayer graphene with scanning nanoSQUID-On-Tip microscopy. In <i>APS March Meeting 2019</i> (Vol. 64). Boston, MA, United States: American Physical Society.","short":"M. Serlin, C. Tschirhart, H. Polshyn, J. Zhu, M.E. Huber, A. Young, in:, APS March Meeting 2019, American Physical Society, 2019.","chicago":"Serlin, Marec, Charles Tschirhart, Hryhoriy Polshyn, Jiacheng Zhu, Martin E. Huber, and Andrea Young. “Direct Imaging of Magnetic Structure in Twisted Bilayer Graphene with Scanning NanoSQUID-On-Tip Microscopy.” In <i>APS March Meeting 2019</i>, Vol. 64. American Physical Society, 2019."},"article_number":"L14.00006","year":"2019","_id":"10722","volume":64,"conference":{"name":"APS: American Physical Society","start_date":"2019-03-04","end_date":"2019-03-08","location":"Boston, MA, United States"},"alternative_title":["Bulletin of the American Physical Society"],"day":"01","main_file_link":[{"url":"https://meetings.aps.org/Meeting/MAR19/Session/L14.6","open_access":"1"}],"article_processing_charge":"No","publication":"APS March Meeting 2019","date_created":"2022-02-04T11:54:21Z","language":[{"iso":"eng"}],"date_published":"2019-03-01T00:00:00Z","publication_status":"published","publisher":"American Physical Society","title":"Direct Imaging of magnetic structure in twisted bilayer graphene with scanning nanoSQUID-On-Tip microscopy","quality_controlled":"1","intvolume":"        64","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"Bilayer graphene, rotationally faulted to ~1.1 degree misalignment, has recently been shown to host superconducting and resistive states associated with the formation of a flat electronic band. While numerous theories exist for the origins of both states, direct validation of these theories remains an outstanding experimental problem. Here, we focus on the resistive states occurring at commensurate filling (1/2, 1/4, and 3/4) of the two lowest superlattice bands. We test theoretical proposals that these states arise due to broken spin—and/or valley—symmetry by performing direct magnetic imaging with nanoscale SQUID-on-tip microscopy. This technique provides single-spin resolved magnetometry on sub-100nm length scales. I will present imaging data from our 4.2K nSOT microscope on graphite-gated twisted bilayers near the flat band condition and discuss the implications for the physics of the commensurate resistive states."}]},{"conference":{"end_date":"2019-03-08","location":"Boston, MA, United States","start_date":"2019-03-04","name":"APS: American Physical Society"},"volume":64,"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR19/Session/P01.4"}],"day":"01","abstract":[{"text":"In monolayer graphene, the interplay of electronic correlations with the internal spin- and valley- degrees of freedom leads to a complex phase diagram of isospin symmetry breaking at high magnetic fields. Recently, Wei et al. (Science (2018)) demonstrated that spin waves can be electrically generated and detected in graphene heterojunctions, allowing direct experiment access to the spin degree of freedom. Here, we apply this technique to high quality graphite-gated graphene devices showing robust fractional quantum Hall phases and isospin phase transitions. We use an edgeless Corbino geometry to eliminate the contributions of edge states to the spin-wave mediated nonlocal voltage, allowing unambiguous identification of spin wave transport signatures. Our data reveal two phases within the ν = 1 plateau. For exactly ν=1, charge is localized but spin waves propagate freely while small carrier doping completely quenches the low-energy spin-wave transport, even as those charges remain localized. We identify this new phase as a spin textured electron solid. We also find that spin-wave transport is modulated by phase transitions in the valley order that preserve spin polarization, suggesting that this technique is sensitive to both spin and valley order.","lang":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["0003-0503"]},"citation":{"mla":"Zhou, Haoxin, et al. “Spin Wave Transport through Electron Solids and Fractional Quantum Hall Liquids in Graphene.” <i>APS March Meeting 2019</i>, vol. 64, no. 2, P01.00004, American Physical Society, 2019.","ista":"Zhou H, Polshyn H, Tanaguchi T, Watanabe K, Young A. 2019. Spin wave transport through electron solids and fractional quantum Hall liquids in graphene. APS March Meeting 2019. APS: American Physical Society vol. 64, P01.00004.","ama":"Zhou H, Polshyn H, Tanaguchi T, Watanabe K, Young A. Spin wave transport through electron solids and fractional quantum Hall liquids in graphene. In: <i>APS March Meeting 2019</i>. Vol 64. American Physical Society; 2019.","ieee":"H. Zhou, H. Polshyn, T. Tanaguchi, K. Watanabe, and A. Young, “Spin wave transport through electron solids and fractional quantum Hall liquids in graphene,” in <i>APS March Meeting 2019</i>, Boston, MA, United States, 2019, vol. 64, no. 2.","chicago":"Zhou, Haoxin, Hryhoriy Polshyn, Takashi Tanaguchi, Kenji Watanabe, and Andrea Young. “Spin Wave Transport through Electron Solids and Fractional Quantum Hall Liquids in Graphene.” In <i>APS March Meeting 2019</i>, Vol. 64. American Physical Society, 2019.","short":"H. Zhou, H. Polshyn, T. Tanaguchi, K. Watanabe, A. Young, in:, APS March Meeting 2019, American Physical Society, 2019.","apa":"Zhou, H., Polshyn, H., Tanaguchi, T., Watanabe, K., &#38; Young, A. (2019). Spin wave transport through electron solids and fractional quantum Hall liquids in graphene. In <i>APS March Meeting 2019</i> (Vol. 64). Boston, MA, United States: American Physical Society."},"article_number":"P01.00004","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10723","year":"2019","intvolume":"        64","status":"public","date_updated":"2022-02-04T13:59:47Z","publisher":"American Physical Society","type":"conference","title":"Spin wave transport through electron solids and fractional quantum Hall liquids in graphene","date_published":"2019-03-01T00:00:00Z","oa_version":"Published Version","date_created":"2022-02-04T12:14:02Z","publication":"APS March Meeting 2019","month":"03","oa":1,"language":[{"iso":"eng"}],"author":[{"last_name":"Zhou","full_name":"Zhou, Haoxin","first_name":"Haoxin"},{"full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","first_name":"Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","last_name":"Polshyn"},{"last_name":"Tanaguchi","full_name":"Tanaguchi, Takashi","first_name":"Takashi"},{"first_name":"Kenji","full_name":"Watanabe, Kenji","last_name":"Watanabe"},{"last_name":"Young","full_name":"Young, Andrea","first_name":"Andrea"}],"extern":"1","issue":"2","publication_status":"published"},{"title":"Normal state transport in superconducting twisted bilayer graphene","publisher":"American Physical Society","publication_status":"published","date_published":"2019-03-01T00:00:00Z","date_created":"2022-02-04T12:25:04Z","publication":"APS March Meeting 2019","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Twisted bilayer graphene (tBLG) near the flat band condition is a versatile new platform for the study of correlated physics in 2D. Resistive states have been observed at several commensurate fillings of the flat miniband, along with superconducting states near half filling. To better understand the electronic structure of this system, we study electronic transport of graphite gated superconducting tBLG devices in the normal regime. At high magnetic fields, we observe full lifting of the spin and valley degeneracy. The transitions in the splitting of this four-fold degeneracy as a function of carrier density indicate Landau level (LL) crossings, which tilted field measurements show occur between LLs with different valley polarization. Similar LL structure measured in two devices, one with twist angle θ=1.08° at ambient pressure and one at θ=1.27° and 1.33GPa, suggests that the dimensionless combination of twist angle and interlayer coupling controls the relevant details of the band structure. In addition, we find that the temperature dependence of the resistance at B=0 shows linear growth at several hundred Ohm/K in a broad range of temperatures. We discuss the implications for modeling the scattering processes in this system."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":"        64","quality_controlled":"1","date_updated":"2022-02-08T10:23:13Z","status":"public","type":"conference","author":[{"full_name":"Polshyn, Hryhoriy","first_name":"Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","last_name":"Polshyn"},{"last_name":"Zhang","first_name":"Yuxuan","full_name":"Zhang, Yuxuan"},{"full_name":"Yankowitz, Matthew","first_name":"Matthew","last_name":"Yankowitz"},{"last_name":"Chen","first_name":"Shaowen","full_name":"Chen, Shaowen"},{"full_name":"Taniguchi, Takashi","first_name":"Takashi","last_name":"Taniguchi"},{"full_name":"Watanabe, Kenji","first_name":"Kenji","last_name":"Watanabe"},{"last_name":"Graf","first_name":"David E.","full_name":"Graf, David E."},{"first_name":"Cory R.","full_name":"Dean, Cory R.","last_name":"Dean"},{"last_name":"Young","first_name":"Andrea","full_name":"Young, Andrea"}],"issue":"2","extern":"1","oa":1,"month":"03","oa_version":"Published Version","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR19/Session/V14.8"}],"day":"01","volume":64,"alternative_title":["Bulletin of the American Physical Society"],"conference":{"location":"Boston, MA, United States","end_date":"2019-03-08","start_date":"2019-03-04","name":"APS: American Physical Society"},"_id":"10724","year":"2019","citation":{"mla":"Polshyn, Hryhoriy, et al. “Normal State Transport in Superconducting Twisted Bilayer Graphene.” <i>APS March Meeting 2019</i>, vol. 64, no. 2, V14.00008, American Physical Society, 2019.","ista":"Polshyn H, Zhang Y, Yankowitz M, Chen S, Taniguchi T, Watanabe K, Graf DE, Dean CR, Young A. 2019. Normal state transport in superconducting twisted bilayer graphene. APS March Meeting 2019. APS: American Physical Society, Bulletin of the American Physical Society, vol. 64, V14.00008.","ieee":"H. Polshyn <i>et al.</i>, “Normal state transport in superconducting twisted bilayer graphene,” in <i>APS March Meeting 2019</i>, Boston, MA, United States, 2019, vol. 64, no. 2.","ama":"Polshyn H, Zhang Y, Yankowitz M, et al. Normal state transport in superconducting twisted bilayer graphene. In: <i>APS March Meeting 2019</i>. Vol 64. American Physical Society; 2019.","apa":"Polshyn, H., Zhang, Y., Yankowitz, M., Chen, S., Taniguchi, T., Watanabe, K., … Young, A. (2019). Normal state transport in superconducting twisted bilayer graphene. In <i>APS March Meeting 2019</i> (Vol. 64). Boston, MA, United States: American Physical Society.","chicago":"Polshyn, Hryhoriy, Yuxuan Zhang, Matthew Yankowitz, Shaowen Chen, Takashi Taniguchi, Kenji Watanabe, David E. Graf, Cory R. Dean, and Andrea Young. “Normal State Transport in Superconducting Twisted Bilayer Graphene.” In <i>APS March Meeting 2019</i>, Vol. 64. American Physical Society, 2019.","short":"H. Polshyn, Y. Zhang, M. Yankowitz, S. Chen, T. Taniguchi, K. Watanabe, D.E. Graf, C.R. Dean, A. Young, in:, APS March Meeting 2019, American Physical Society, 2019."},"article_number":"V14.00008","publication_identifier":{"issn":["0003-0503"]}},{"month":"03","oa":1,"oa_version":"Published Version","issue":"2","extern":"1","author":[{"full_name":"Chen, Shaowen","first_name":"Shaowen","last_name":"Chen"},{"full_name":"Yankowitz, Matthew","first_name":"Matthew","last_name":"Yankowitz"},{"id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","last_name":"Polshyn","full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","first_name":"Hryhoriy"},{"last_name":"Watanabe","first_name":"Kenji","full_name":"Watanabe, Kenji"},{"last_name":"Taniguchi","first_name":"Takashi","full_name":"Taniguchi, Takashi"},{"full_name":"Graf, David E.","first_name":"David E.","last_name":"Graf"},{"last_name":"Young","first_name":"Andrea","full_name":"Young, Andrea"},{"full_name":"Dean, Cory R.","first_name":"Cory R.","last_name":"Dean"}],"type":"conference","date_updated":"2022-02-08T10:24:13Z","status":"public","related_material":{"link":[{"url":"https://arxiv.org/abs/1808.07865","relation":"used_in_publication"}]},"article_number":"R14.00004","citation":{"ama":"Chen S, Yankowitz M, Polshyn H, et al. Correlated insulating and superconducting phases in twisted bilayer graphene. In: <i>APS March Meeting 2019</i>. Vol 64. American Physical Society; 2019.","ieee":"S. Chen <i>et al.</i>, “Correlated insulating and superconducting phases in twisted bilayer graphene,” in <i>APS March Meeting 2019</i>, Boston, MA, United States, 2019, vol. 64, no. 2.","short":"S. Chen, M. Yankowitz, H. Polshyn, K. Watanabe, T. Taniguchi, D.E. Graf, A. Young, C.R. Dean, in:, APS March Meeting 2019, American Physical Society, 2019.","chicago":"Chen, Shaowen, Matthew Yankowitz, Hryhoriy Polshyn, Kenji Watanabe, Takashi Taniguchi, David E. Graf, Andrea Young, and Cory R. Dean. “Correlated Insulating and Superconducting Phases in Twisted Bilayer Graphene.” In <i>APS March Meeting 2019</i>, Vol. 64. American Physical Society, 2019.","apa":"Chen, S., Yankowitz, M., Polshyn, H., Watanabe, K., Taniguchi, T., Graf, D. E., … Dean, C. R. (2019). Correlated insulating and superconducting phases in twisted bilayer graphene. In <i>APS March Meeting 2019</i> (Vol. 64). Boston, MA, United States: American Physical Society.","mla":"Chen, Shaowen, et al. “Correlated Insulating and Superconducting Phases in Twisted Bilayer Graphene.” <i>APS March Meeting 2019</i>, vol. 64, no. 2, R14.00004, American Physical Society, 2019.","ista":"Chen S, Yankowitz M, Polshyn H, Watanabe K, Taniguchi T, Graf DE, Young A, Dean CR. 2019. Correlated insulating and superconducting phases in twisted bilayer graphene. APS March Meeting 2019. APS: American Physical Society, Bulletin of the American Physical Society, vol. 64, R14.00004."},"publication_identifier":{"issn":["0003-0503"]},"year":"2019","_id":"10725","conference":{"name":"APS: American Physical Society","start_date":"2019-03-04","end_date":"2019-03-08","location":"Boston, MA, United States"},"volume":64,"alternative_title":["Bulletin of the American Physical Society"],"day":"01","main_file_link":[{"url":"https://meetings.aps.org/Meeting/MAR19/Session/R14.4","open_access":"1"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"date_created":"2022-02-04T13:48:04Z","publication":"APS March Meeting 2019","date_published":"2019-03-01T00:00:00Z","publication_status":"published","publisher":"American Physical Society","title":"Correlated insulating and superconducting phases in twisted bilayer graphene","quality_controlled":"1","intvolume":"        64","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"Bilayer graphene with ~ 1.1 degrees twist mismatch between the layers hosts a low energy flat band in which the Coulomb interaction is large relative to the bandwidth, promoting correlated insulating states at half band filling, and superconducting (SC) phases with dome-like structure neighboring correlated insulating states. Here we show measurements of a dual-graphite-gated twisted bilayer graphene device, which minimizes charge inhomogeneity. We observe new correlated phases, including for the first time a SC pocket near half-filling of the electron-doped band and resistive states at quarter-filling of both bands that emerge in a magnetic field. Changing the layer polarization with vertical electric field reveals an unexpected competition between SC and correlated insulator phases, which we interpret to result from differences in disorder of each graphene layer and underscores the spatial inhomogeneity like twist angle as a significant source of disorder in these devices [1]."}]},{"publisher":"National Academy of Sciences","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","doi":"10.1073/pnas.1821435116","page":"9652-9657","title":"DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm","file_date_updated":"2021-06-04T12:50:47Z","date_published":"2019-05-07T00:00:00Z","date_created":"2021-06-04T12:38:20Z","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences","has_accepted_license":"1","publication_status":"published","scopus_import":"1","pmid":1,"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"abstract":[{"lang":"eng","text":"Epigenetic reprogramming is required for proper regulation of gene expression in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for seed viability, pollen function, and successful reproduction. The DEMETER (DME) DNA glycosylase initiates localized DNA demethylation in vegetative and central cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively. In rice, the central cell genome displays local DNA hypomethylation, suggesting that active DNA demethylation also occurs in rice; however, the enzyme responsible for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING 1a (ROS1a) gene, which is related to DME and is essential for rice seed viability and pollen function. Here, we report genome-wide analyses of DNA methylation in wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative cell genome is locally hypomethylated compared with sperm by a process that requires ROS1a activity. We show that many ROS1a target sequences in the vegetative cell are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation is indirectly promoted by DNA demethylation in the vegetative cell. These results reveal that DNA glycosylase-mediated DNA demethylation processes are conserved in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally, although global non-CG methylation levels of sperm and egg differ, the maternal and paternal embryo genomes show similar non-CG methylation levels, suggesting that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell fusion."}],"file":[{"checksum":"5b0ae3779b8b21b5223bd2d3cceede3a","access_level":"open_access","file_size":1142540,"file_id":"9461","relation":"main_file","file_name":"2019_PNAS_Kim.pdf","date_updated":"2021-06-04T12:50:47Z","creator":"asandaue","success":1,"content_type":"application/pdf","date_created":"2021-06-04T12:50:47Z"}],"quality_controlled":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":"       116","status":"public","date_updated":"2021-12-14T07:52:30Z","type":"journal_article","department":[{"_id":"DaZi"}],"external_id":{"pmid":["31000601"]},"keyword":["Multidisciplinary"],"oa_version":"Published Version","oa":1,"month":"05","author":[{"last_name":"Kim","first_name":"M. Yvonne","full_name":"Kim, M. Yvonne"},{"full_name":"Ono, Akemi","first_name":"Akemi","last_name":"Ono"},{"last_name":"Scholten","full_name":"Scholten, Stefan","first_name":"Stefan"},{"last_name":"Kinoshita","first_name":"Tetsu","full_name":"Kinoshita, Tetsu"},{"orcid":"0000-0002-0123-8649","first_name":"Daniel","full_name":"Zilberman, Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"first_name":"Takashi","full_name":"Okamoto, Takashi","last_name":"Okamoto"},{"last_name":"Fischer","first_name":"Robert L.","full_name":"Fischer, Robert L."}],"ddc":["580"],"extern":"1","issue":"19","volume":116,"article_processing_charge":"No","day":"07","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"citation":{"ama":"Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. <i>Proceedings of the National Academy of Sciences</i>. 2019;116(19):9652-9657. doi:<a href=\"https://doi.org/10.1073/pnas.1821435116\">10.1073/pnas.1821435116</a>","ieee":"M. Y. Kim <i>et al.</i>, “DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 116, no. 19. National Academy of Sciences, pp. 9652–9657, 2019.","apa":"Kim, M. Y., Ono, A., Scholten, S., Kinoshita, T., Zilberman, D., Okamoto, T., &#38; Fischer, R. L. (2019). DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1821435116\">https://doi.org/10.1073/pnas.1821435116</a>","short":"M.Y. Kim, A. Ono, S. Scholten, T. Kinoshita, D. Zilberman, T. Okamoto, R.L. Fischer, Proceedings of the National Academy of Sciences 116 (2019) 9652–9657.","chicago":"Kim, M. Yvonne, Akemi Ono, Stefan Scholten, Tetsu Kinoshita, Daniel Zilberman, Takashi Okamoto, and Robert L. Fischer. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2019. <a href=\"https://doi.org/10.1073/pnas.1821435116\">https://doi.org/10.1073/pnas.1821435116</a>.","mla":"Kim, M. Yvonne, et al. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 116, no. 19, National Academy of Sciences, 2019, pp. 9652–57, doi:<a href=\"https://doi.org/10.1073/pnas.1821435116\">10.1073/pnas.1821435116</a>.","ista":"Kim MY, Ono A, Scholten S, Kinoshita T, Zilberman D, Okamoto T, Fischer RL. 2019. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 116(19), 9652–9657."},"article_type":"original","_id":"9460","year":"2019"},{"doi":"10.1186/s13072-019-0307-4","title":"DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development","file_date_updated":"2021-06-08T09:29:19Z","publisher":"Springer Nature","has_accepted_license":"1","scopus_import":"1","publication_status":"published","date_published":"2019-10-10T00:00:00Z","language":[{"iso":"eng"}],"publication":"Epigenetics and Chromatin","date_created":"2021-06-08T09:21:51Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pmid":1,"file":[{"content_type":"application/pdf","date_created":"2021-06-08T09:29:19Z","success":1,"creator":"asandaue","date_updated":"2021-06-08T09:29:19Z","file_name":"2019_EpigeneticsAndChromatin_Harris.pdf","relation":"main_file","file_size":3221067,"file_id":"9531","access_level":"open_access","checksum":"86ff50a7517891511af2733c76c81b67"}],"abstract":[{"text":"Background\r\nDNA methylation of active genes, also known as gene body methylation, is found in many animal and plant genomes. Despite this, the transcriptional and developmental role of such methylation remains poorly understood. Here, we explore the dynamic range of DNA methylation in honey bee, a model organism for gene body methylation.\r\n\r\nResults\r\nOur data show that CG methylation in gene bodies globally fluctuates during honey bee development. However, these changes cause no gene expression alterations. Intriguingly, despite the global alterations, tissue-specific CG methylation patterns of complete genes or exons are rare, implying robust maintenance of genic methylation during development. Additionally, we show that CG methylation maintenance fluctuates in somatic cells, while reaching maximum fidelity in sperm cells. Finally, unlike universally present CG methylation, we discovered non-CG methylation specifically in bee heads that resembles such methylation in mammalian brain tissue.\r\n\r\nConclusions\r\nBased on these results, we propose that gene body CG methylation can oscillate during development if it is kept to a level adequate to preserve function. Additionally, our data suggest that heightened non-CG methylation is a conserved regulator of animal nervous systems.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":"        12","quality_controlled":"1","department":[{"_id":"DaZi"}],"external_id":{"pmid":["31601251"]},"date_updated":"2021-12-14T07:53:00Z","status":"public","type":"journal_article","ddc":["570"],"author":[{"full_name":"Harris, Keith D.","first_name":"Keith D.","last_name":"Harris"},{"last_name":"Lloyd","first_name":"James P. B.","full_name":"Lloyd, James P. B."},{"last_name":"Domb","first_name":"Katherine","full_name":"Domb, Katherine"},{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman"},{"first_name":"Assaf","full_name":"Zemach, Assaf","last_name":"Zemach"}],"extern":"1","month":"10","oa":1,"oa_version":"Published Version","article_processing_charge":"No","day":"10","volume":12,"article_type":"original","year":"2019","_id":"9530","article_number":"62","citation":{"ista":"Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. 2019. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. 12, 62.","mla":"Harris, Keith D., et al. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” <i>Epigenetics and Chromatin</i>, vol. 12, 62, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1186/s13072-019-0307-4\">10.1186/s13072-019-0307-4</a>.","short":"K.D. Harris, J.P.B. Lloyd, K. Domb, D. Zilberman, A. Zemach, Epigenetics and Chromatin 12 (2019).","chicago":"Harris, Keith D., James P. B. Lloyd, Katherine Domb, Daniel Zilberman, and Assaf Zemach. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” <i>Epigenetics and Chromatin</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1186/s13072-019-0307-4\">https://doi.org/10.1186/s13072-019-0307-4</a>.","apa":"Harris, K. D., Lloyd, J. P. B., Domb, K., Zilberman, D., &#38; Zemach, A. (2019). DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. <i>Epigenetics and Chromatin</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13072-019-0307-4\">https://doi.org/10.1186/s13072-019-0307-4</a>","ieee":"K. D. Harris, J. P. B. Lloyd, K. Domb, D. Zilberman, and A. Zemach, “DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development,” <i>Epigenetics and Chromatin</i>, vol. 12. Springer Nature, 2019.","ama":"Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. <i>Epigenetics and Chromatin</i>. 2019;12. doi:<a href=\"https://doi.org/10.1186/s13072-019-0307-4\">10.1186/s13072-019-0307-4</a>"},"publication_identifier":{"eissn":["1756-8935"]}}]