[{"page":"132","day":"30","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"publisher":"Institute of Science and Technology Austria","date_published":"2019-09-30T00:00:00Z","type":"dissertation","language":[{"iso":"eng"}],"ddc":["000"],"alternative_title":["ISTA Thesis"],"month":"09","status":"public","doi":"10.15479/AT:ISTA:6894","publication_identifier":{"eissn":["2663-337X"]},"title":"Automatic time-unbounded reachability analysis of hybrid systems","publication_status":"published","file_date_updated":"2020-07-14T12:47:43Z","oa_version":"Published Version","article_processing_charge":"No","year":"2019","citation":{"mla":"Giacobbe, Mirco. <i>Automatic Time-Unbounded Reachability Analysis of Hybrid Systems</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6894\">10.15479/AT:ISTA:6894</a>.","short":"M. Giacobbe, Automatic Time-Unbounded Reachability Analysis of Hybrid Systems, Institute of Science and Technology Austria, 2019.","apa":"Giacobbe, M. (2019). <i>Automatic time-unbounded reachability analysis of hybrid systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6894\">https://doi.org/10.15479/AT:ISTA:6894</a>","chicago":"Giacobbe, Mirco. “Automatic Time-Unbounded Reachability Analysis of Hybrid Systems.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6894\">https://doi.org/10.15479/AT:ISTA:6894</a>.","ama":"Giacobbe M. Automatic time-unbounded reachability analysis of hybrid systems. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6894\">10.15479/AT:ISTA:6894</a>","ieee":"M. Giacobbe, “Automatic time-unbounded reachability analysis of hybrid systems,” Institute of Science and Technology Austria, 2019.","ista":"Giacobbe M. 2019. Automatic time-unbounded reachability analysis of hybrid systems. Institute of Science and Technology Austria."},"abstract":[{"text":"Hybrid automata combine finite automata and dynamical systems, and model the interaction of digital with physical systems. Formal analysis that can guarantee the safety of all behaviors or rigorously witness failures, while unsolvable in general, has been tackled algorithmically using, e.g., abstraction, bounded model-checking, assisted theorem proving.\r\nNevertheless, very few methods have addressed the time-unbounded reachability analysis of hybrid automata and, for current sound and automatic tools, scalability remains critical. We develop methods for the polyhedral abstraction of hybrid automata, which construct coarse overapproximations and tightens them incrementally, in a CEGAR fashion. We use template polyhedra, i.e., polyhedra whose facets are normal to a given set of directions.\r\nWhile, previously, directions were given by the user, we introduce (1) the first method\r\nfor computing template directions from spurious counterexamples, so as to generalize and\r\neliminate them. The method applies naturally to convex hybrid automata, i.e., hybrid\r\nautomata with (possibly non-linear) convex constraints on derivatives only, while for linear\r\nODE requires further abstraction. Specifically, we introduce (2) the conic abstractions,\r\nwhich, partitioning the state space into appropriate (possibly non-uniform) cones, divide\r\ncurvy trajectories into relatively straight sections, suitable for polyhedral abstractions.\r\nFinally, we introduce (3) space-time interpolation, which, combining interval arithmetic\r\nand template refinement, computes appropriate (possibly non-uniform) time partitioning\r\nand template directions along spurious trajectories, so as to eliminate them.\r\nWe obtain sound and automatic methods for the reachability analysis over dense\r\nand unbounded time of convex hybrid automata and hybrid automata with linear ODE.\r\nWe build prototype tools and compare—favorably—our methods against the respective\r\nstate-of-the-art tools, on several benchmarks.","lang":"eng"}],"supervisor":[{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"}],"_id":"6894","date_created":"2019-09-22T14:08:44Z","file":[{"checksum":"773beaf4a85dc2acc2c12b578fbe1965","file_id":"6916","creator":"mgiacobbe","content_type":"application/pdf","date_created":"2019-09-27T14:15:05Z","file_size":4100685,"relation":"main_file","date_updated":"2020-07-14T12:47:43Z","file_name":"giacobbe_thesis.pdf","access_level":"open_access"},{"file_id":"6917","creator":"mgiacobbe","content_type":"application/gzip","checksum":"97f1c3da71feefd27e6e625d32b4c75b","access_level":"closed","file_name":"giacobbe_thesis_src.tar.gz","date_updated":"2020-07-14T12:47:43Z","relation":"source_file","file_size":7959732,"date_created":"2019-09-27T14:22:04Z"}],"author":[{"id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8180-0904","full_name":"Giacobbe, Mirco","first_name":"Mirco","last_name":"Giacobbe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"related_material":{"record":[{"id":"631","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"647"},{"id":"140","relation":"part_of_dissertation","status":"public"}]},"degree_awarded":"PhD","department":[{"_id":"ToHe"}],"date_updated":"2023-09-19T09:30:43Z"},{"pmid":1,"publisher":"Elsevier","type":"journal_article","date_published":"2019-12-01T00:00:00Z","external_id":{"pmid":["31521639"],"isi":["000491646600033"]},"language":[{"iso":"eng"}],"status":"public","isi":1,"month":"12","day":"01","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87","full_name":"Oliveira, Bárbara","first_name":"Bárbara","last_name":"Oliveira"},{"first_name":"Aysan Çerağ","last_name":"Yahya","id":"365A65F8-F248-11E8-B48F-1D18A9856A87","full_name":"Yahya, Aysan Çerağ"},{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino"}],"volume":1724,"intvolume":"      1724","date_updated":"2023-08-30T06:19:49Z","publication":"Brain Research","department":[{"_id":"GaNo"}],"publication_identifier":{"eissn":["18726240"],"issn":["00068993"]},"article_type":"original","scopus_import":"1","doi":"10.1016/j.brainres.2019.146458","oa_version":"None","article_processing_charge":"No","title":"Modeling cell-cell interactions in the brain using cerebral organoids","publication_status":"published","abstract":[{"text":"Until recently, a great amount of brain studies have been conducted in human post mortem tissues, cell lines and model organisms. These researches provided useful insights regarding cell-cell interactions occurring in the brain. However, such approaches suffer from technical limitations and inaccurate modeling of the tissue 3D cytoarchitecture. Importantly, they might lack a human genetic background essential for disease modeling. With the development of protocols to generate human cerebral organoids, we are now closer to reproducing the early stages of human brain development in vitro. As a result, more relevant cell-cell interaction studies can be conducted.\r\n\r\nIn this review, we discuss the advantages of 3D cultures over 2D in modulating brain cell-cell interactions during physiological and pathological development, as well as the progress made in developing organoids in which neurons, macroglia, microglia and vascularization are present. Finally, we debate the limitations of those models and possible future directions.","lang":"eng"}],"citation":{"ama":"Oliveira B, Yahya AÇ, Novarino G. Modeling cell-cell interactions in the brain using cerebral organoids. <i>Brain Research</i>. 2019;1724. doi:<a href=\"https://doi.org/10.1016/j.brainres.2019.146458\">10.1016/j.brainres.2019.146458</a>","ista":"Oliveira B, Yahya AÇ, Novarino G. 2019. Modeling cell-cell interactions in the brain using cerebral organoids. Brain Research. 1724, 146458.","ieee":"B. Oliveira, A. Ç. Yahya, and G. Novarino, “Modeling cell-cell interactions in the brain using cerebral organoids,” <i>Brain Research</i>, vol. 1724. Elsevier, 2019.","mla":"Oliveira, Bárbara, et al. “Modeling Cell-Cell Interactions in the Brain Using Cerebral Organoids.” <i>Brain Research</i>, vol. 1724, 146458, Elsevier, 2019, doi:<a href=\"https://doi.org/10.1016/j.brainres.2019.146458\">10.1016/j.brainres.2019.146458</a>.","apa":"Oliveira, B., Yahya, A. Ç., &#38; Novarino, G. (2019). Modeling cell-cell interactions in the brain using cerebral organoids. <i>Brain Research</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.brainres.2019.146458\">https://doi.org/10.1016/j.brainres.2019.146458</a>","chicago":"Oliveira, Bárbara, Aysan Çerağ Yahya, and Gaia Novarino. “Modeling Cell-Cell Interactions in the Brain Using Cerebral Organoids.” <i>Brain Research</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.brainres.2019.146458\">https://doi.org/10.1016/j.brainres.2019.146458</a>.","short":"B. Oliveira, A.Ç. Yahya, G. Novarino, Brain Research 1724 (2019)."},"article_number":"146458","year":"2019","date_created":"2019-09-22T22:00:35Z","_id":"6896"},{"quality_controlled":"1","day":"12","project":[{"_id":"253FCA6A-B435-11E9-9278-68D0E5697425","name":"Hormonal cross-talk in plant organogenesis","grant_number":"207362","call_identifier":"FP7"}],"issue":"17","type":"journal_article","date_published":"2019-09-12T00:00:00Z","external_id":{"isi":["000486297400011"],"pmid":["31391194"]},"pmid":1,"publisher":"The Company of Biologists","status":"public","isi":1,"month":"09","language":[{"iso":"eng"}],"article_processing_charge":"No","oa_version":"Published Version","title":"Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis","publication_status":"published","publication_identifier":{"eissn":["14779129"]},"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).","article_type":"original","scopus_import":"1","doi":"10.1242/dev.175919","main_file_link":[{"url":"https://doi.org/10.1242/dev.175919","open_access":"1"}],"date_created":"2019-09-22T22:00:36Z","_id":"6897","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."}],"citation":{"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.","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>","short":"Q. Zhu, M. Gallemi, J. Pospíšil, P. Žádníková, M. Strnad, E. Benková, Development 146 (2019).","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>.","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>","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>."},"year":"2019","article_number":"dev175919","volume":146,"oa":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Qiang","last_name":"Zhu","id":"40A4B9E6-F248-11E8-B48F-1D18A9856A87","full_name":"Zhu, Qiang"},{"last_name":"Gallemi","first_name":"Marçal","full_name":"Gallemi, Marçal","orcid":"0000-0003-4675-6893","id":"460C6802-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pospíšil, Jiří","first_name":"Jiří","last_name":"Pospíšil"},{"full_name":"Žádníková, Petra","first_name":"Petra","last_name":"Žádníková"},{"full_name":"Strnad, Miroslav","first_name":"Miroslav","last_name":"Strnad"},{"last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2025-05-07T11:10:55Z","ec_funded":1,"publication":"Development","department":[{"_id":"EvBe"}],"intvolume":"       146"},{"day":"12","quality_controlled":"1","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"issue":"1","publisher":"BioMed Central","type":"journal_article","date_published":"2019-09-12T00:00:00Z","external_id":{"isi":["000485256100001"]},"ddc":["570"],"language":[{"iso":"eng"}],"status":"public","isi":1,"month":"09","publication_identifier":{"eissn":["14712164"]},"scopus_import":"1","doi":"10.1186/s12864-019-6059-5","article_processing_charge":"No","oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:44Z","title":"Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","publication_status":"published","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"}],"citation":{"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.","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>","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>","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>.","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>."},"article_number":"710","year":"2019","file":[{"file_id":"6924","creator":"kschuh","content_type":"application/pdf","checksum":"b798773c5823012d31c812c9f7975da2","file_name":"2019_BioMed_Sigalova.pdf","access_level":"open_access","relation":"main_file","date_created":"2019-10-01T10:33:17Z","file_size":4157175,"date_updated":"2020-07-14T12:47:44Z"}],"date_created":"2019-09-22T22:00:36Z","_id":"6898","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Sigalova","first_name":"Olga M.","full_name":"Sigalova, Olga M."},{"first_name":"Andrei V.","last_name":"Chaplin","full_name":"Chaplin, Andrei V."},{"last_name":"Bochkareva","first_name":"Olga","full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"last_name":"Shelyakin","first_name":"Pavel V.","full_name":"Shelyakin, Pavel V."},{"first_name":"Vsevolod A.","last_name":"Filaretov","full_name":"Filaretov, Vsevolod A."},{"full_name":"Akkuratov, Evgeny E.","last_name":"Akkuratov","first_name":"Evgeny E."},{"first_name":"Valentina","last_name":"Burskaia","full_name":"Burskaia, Valentina"},{"last_name":"Gelfand","first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S."}],"volume":20,"related_material":{"record":[{"id":"9731","status":"public","relation":"research_data"},{"relation":"research_data","status":"public","id":"9783"},{"status":"public","relation":"research_data","id":"9890"},{"id":"9892","status":"public","relation":"research_data"},{"status":"public","relation":"research_data","id":"9893"},{"relation":"research_data","status":"public","id":"9894"},{"relation":"research_data","status":"public","id":"9895"},{"id":"9896","status":"public","relation":"research_data"},{"id":"9897","status":"public","relation":"research_data"},{"id":"9898","relation":"research_data","status":"public"},{"relation":"research_data","status":"public","id":"9899"},{"status":"public","relation":"research_data","id":"9900"},{"id":"9901","status":"public","relation":"research_data"}]},"oa":1,"intvolume":"        20","date_updated":"2023-08-30T06:20:22Z","publication":"BMC Genomics","department":[{"_id":"FyKo"}]},{"pmid":1,"publisher":"Nature Publishing Group","type":"journal_article","date_published":"2019-09-11T00:00:00Z","external_id":{"isi":["000485216800009"],"pmid":["31511517"]},"ddc":["570"],"language":[{"iso":"eng"}],"status":"public","isi":1,"month":"09","day":"11","page":"4113","quality_controlled":"1","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"issue":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Bornhorst, Dorothee","first_name":"Dorothee","last_name":"Bornhorst"},{"first_name":"Peng","last_name":"Xia","orcid":"0000-0002-5419-7756","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","full_name":"Xia, Peng"},{"full_name":"Nakajima, Hiroyuki","first_name":"Hiroyuki","last_name":"Nakajima"},{"first_name":"Chaitanya","last_name":"Dingare","full_name":"Dingare, Chaitanya"},{"full_name":"Herzog, Wiebke","last_name":"Herzog","first_name":"Wiebke"},{"full_name":"Lecaudey, Virginie","last_name":"Lecaudey","first_name":"Virginie"},{"full_name":"Mochizuki, Naoki","first_name":"Naoki","last_name":"Mochizuki"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"},{"last_name":"Yelon","first_name":"Deborah","full_name":"Yelon, Deborah"},{"last_name":"Abdelilah-Seyfried","first_name":"Salim","full_name":"Abdelilah-Seyfried, Salim"}],"volume":10,"oa":1,"intvolume":"        10","date_updated":"2023-08-30T06:21:23Z","publication":"Nature communications","department":[{"_id":"CaHe"}],"publication_identifier":{"eissn":["20411723"]},"scopus_import":"1","doi":"10.1038/s41467-019-12068-x","oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:44Z","publication_status":"published","title":"Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions","abstract":[{"lang":"eng","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."}],"citation":{"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.","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>","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>.","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>","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.","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."},"year":"2019","date_created":"2019-09-22T22:00:37Z","file":[{"access_level":"open_access","file_name":"2019_Nature_Bornhorst.pdf","date_updated":"2020-07-14T12:47:44Z","date_created":"2019-10-01T11:18:50Z","file_size":3905793,"relation":"main_file","content_type":"application/pdf","creator":"kschuh","file_id":"6926","checksum":"62c2512712e16d27c1797d318d14ba9f"}],"_id":"6899"},{"publication_identifier":{"eissn":["15537358"]},"doi":"10.1371/journal.pcbi.1007290","scopus_import":"1","file_date_updated":"2020-07-14T12:47:44Z","article_processing_charge":"No","oa_version":"Published Version","publication_status":"published","title":"Estimating information in time-varying signals","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."}],"year":"2019","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>.","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>","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>.","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>","ista":"Cepeda Humerez SA, Ruess J, Tkačik G. 2019. Estimating information in time-varying signals. PLoS computational biology. 15(9), e1007290.","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."},"_id":"6900","date_created":"2019-09-22T22:00:37Z","file":[{"file_id":"6925","creator":"kschuh","content_type":"application/pdf","checksum":"81bdce1361c9aa8395d6fa635fb6ab47","file_name":"2019_PLoS_Cepeda-Humerez.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:44Z","file_size":3081855,"relation":"main_file","date_created":"2019-10-01T10:53:45Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","full_name":"Cepeda Humerez, Sarah A","first_name":"Sarah A","last_name":"Cepeda Humerez"},{"orcid":"0000-0003-1615-3282","full_name":"Ruess, Jakob","first_name":"Jakob","last_name":"Ruess"},{"last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"related_material":{"record":[{"id":"6473","status":"public","relation":"part_of_dissertation"}]},"oa":1,"volume":15,"intvolume":"        15","publication":"PLoS computational biology","date_updated":"2023-09-07T12:55:21Z","department":[{"_id":"GaTk"}],"day":"03","page":"e1007290","quality_controlled":"1","project":[{"grant_number":"P28844-B27","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","issue":"9","publisher":"Public Library of Science","pmid":1,"external_id":{"isi":["000489741800021"],"pmid":["31479447"]},"date_published":"2019-09-03T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"ddc":["570"],"status":"public","month":"09","isi":1},{"project":[{"call_identifier":"H2020","grant_number":"844511","name":"Majorana bound states in Ge/SiGe heterostructures","_id":"26A151DA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"P30207","name":"Hole spin orbit qubits in Ge quantum wells","_id":"2641CE5E-B435-11E9-9278-68D0E5697425"}],"day":"13","language":[{"iso":"eng"}],"status":"public","month":"10","external_id":{"arxiv":["1910.05841"]},"date_published":"2019-10-13T00:00:00Z","type":"preprint","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"}],"year":"2019","article_number":"1910.05841","citation":{"short":"A.C. Hofmann, D. Jirovec, M. Borovkov, I. Prieto Gonzalez, A. Ballabio, J. Frigerio, D. Chrastina, G. Isella, G. Katsaros, ArXiv (n.d.).","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>","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>.","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>.","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>","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>. ."},"_id":"10065","date_created":"2021-10-01T12:14:51Z","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.","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1910.05841"}],"doi":"10.48550/arXiv.1910.05841","oa_version":"Preprint","article_processing_charge":"No","title":"Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits","publication_status":"submitted","arxiv":1,"publication":"arXiv","ec_funded":1,"date_updated":"2024-03-25T23:30:14Z","department":[{"_id":"GeKa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Hofmann","first_name":"Andrea C","full_name":"Hofmann, Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7197-4801","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","full_name":"Jirovec, Daniel","first_name":"Daniel","last_name":"Jirovec"},{"first_name":"Maxim","last_name":"Borovkov","full_name":"Borovkov, Maxim"},{"first_name":"Ivan","last_name":"Prieto Gonzalez","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5357","full_name":"Prieto Gonzalez, Ivan"},{"last_name":"Ballabio","first_name":"Andrea","full_name":"Ballabio, Andrea"},{"full_name":"Frigerio, Jacopo","last_name":"Frigerio","first_name":"Jacopo"},{"last_name":"Chrastina","first_name":"Daniel","full_name":"Chrastina, Daniel"},{"last_name":"Isella","first_name":"Giovanni","full_name":"Isella, Giovanni"},{"last_name":"Katsaros","first_name":"Georgios","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"10058","status":"public","relation":"dissertation_contains"}]},"oa":1,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}]},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas"},{"first_name":"Viktor","last_name":"Toman","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9036-063X","full_name":"Toman, Viktor"}],"volume":3,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10199"}]},"oa":1,"intvolume":"         3","arxiv":1,"date_updated":"2025-07-14T09:10:15Z","publication":"Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"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","publication_identifier":{"eissn":["2475-1421"]},"doi":"10.1145/3360550","main_file_link":[{"open_access":"1","url":"https://dl.acm.org/doi/10.1145/3360550"}],"article_processing_charge":"No","oa_version":"Published Version","file_date_updated":"2021-11-12T11:41:56Z","title":"Value-centric dynamic partial order reduction","publication_status":"published","abstract":[{"lang":"eng","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."}],"citation":{"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>","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.","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>.","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.","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>","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>."},"article_number":"124","year":"2019","file":[{"checksum":"2149979c46964c4d117af06ccb6c0834","file_id":"10278","creator":"cchlebak","content_type":"application/pdf","date_created":"2021-11-12T11:41:56Z","file_size":570829,"date_updated":"2021-11-12T11:41:56Z","relation":"main_file","access_level":"open_access","success":1,"file_name":"2019_ACM_Chatterjee.pdf"}],"date_created":"2021-10-27T14:57:06Z","_id":"10190","conference":{"location":"Athens, Greece","name":"OOPSLA: Object-oriented Programming, Systems, Languages and Applications","end_date":"2019-10-25","start_date":"2019-10-23"},"publisher":"ACM","type":"conference","date_published":"2019-10-10T00:00:00Z","external_id":{"arxiv":["1909.00989"]},"keyword":["safety","risk","reliability and quality","software"],"ddc":["000"],"language":[{"iso":"eng"}],"status":"public","month":"10","day":"10","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","project":[{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF","grant_number":"S11407"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"},{"name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","call_identifier":"FWF"}]},{"page":"161-166","day":"01","quality_controlled":"1","publisher":"Springer Nature","pmid":1,"external_id":{"pmid":["30089829"],"isi":["000454111500019"]},"date_published":"2019-01-01T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"month":"01","isi":1,"status":"public","publist_id":"7949","main_file_link":[{"url":"https://doi.org/10.1038/s41431-018-0231-2","open_access":"1"}],"doi":"10.1038/s41431-018-0231-2","scopus_import":"1","article_type":"original","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.","publication_status":"published","title":"CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63","oa_version":"Published Version","article_processing_charge":"No","year":"2019","citation":{"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>.","short":"A. Marsh, G. Novarino, P. Lockhart, R. Leventer, European Journal of Human Genetics 27 (2019) 161–166.","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>.","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.","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.","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>"},"abstract":[{"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.","lang":"eng"}],"_id":"105","date_created":"2018-12-11T11:44:39Z","author":[{"full_name":"Marsh, Ashley","first_name":"Ashley","last_name":"Marsh"},{"last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lockhart","first_name":"Paul","full_name":"Lockhart, Paul"},{"first_name":"Richard","last_name":"Leventer","full_name":"Leventer, Richard"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"volume":27,"intvolume":"        27","department":[{"_id":"GaNo"}],"publication":"European Journal of Human Genetics","date_updated":"2023-08-24T14:28:24Z"},{"type":"journal_article","date_published":"2019-05-07T00:00:00Z","external_id":{"pmid":["31000601"]},"pmid":1,"publisher":"National Academy of Sciences","month":"05","status":"public","ddc":["580"],"language":[{"iso":"eng"}],"extern":"1","keyword":["Multidisciplinary"],"quality_controlled":"1","page":"9652-9657","day":"07","issue":"19","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","volume":116,"oa":1,"author":[{"full_name":"Kim, M. Yvonne","first_name":"M. Yvonne","last_name":"Kim"},{"full_name":"Ono, Akemi","first_name":"Akemi","last_name":"Ono"},{"full_name":"Scholten, Stefan","last_name":"Scholten","first_name":"Stefan"},{"last_name":"Kinoshita","first_name":"Tetsu","full_name":"Kinoshita, Tetsu"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman"},{"full_name":"Okamoto, Takashi","first_name":"Takashi","last_name":"Okamoto"},{"full_name":"Fischer, Robert L.","last_name":"Fischer","first_name":"Robert L."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"date_updated":"2021-12-14T07:52:30Z","publication":"Proceedings of the National Academy of Sciences","intvolume":"       116","title":"DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm","publication_status":"published","oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2021-06-04T12:50:47Z","scopus_import":"1","doi":"10.1073/pnas.1821435116","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"article_type":"original","file":[{"file_name":"2019_PNAS_Kim.pdf","success":1,"access_level":"open_access","file_size":1142540,"date_created":"2021-06-04T12:50:47Z","date_updated":"2021-06-04T12:50:47Z","relation":"main_file","file_id":"9461","creator":"asandaue","content_type":"application/pdf","checksum":"5b0ae3779b8b21b5223bd2d3cceede3a"}],"date_created":"2021-06-04T12:38:20Z","_id":"9460","citation":{"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>.","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>.","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.","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>","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.","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.","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>"},"year":"2019","abstract":[{"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.","lang":"eng"}]},{"_id":"9530","date_created":"2021-06-08T09:21:51Z","file":[{"date_updated":"2021-06-08T09:29:19Z","relation":"main_file","file_size":3221067,"date_created":"2021-06-08T09:29:19Z","success":1,"access_level":"open_access","file_name":"2019_EpigeneticsAndChromatin_Harris.pdf","checksum":"86ff50a7517891511af2733c76c81b67","content_type":"application/pdf","creator":"asandaue","file_id":"9531"}],"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"}],"year":"2019","article_number":"62","citation":{"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>","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.","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.","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>.","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>","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>."},"file_date_updated":"2021-06-08T09:29:19Z","article_processing_charge":"No","oa_version":"Published Version","title":"DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development","publication_status":"published","article_type":"original","publication_identifier":{"eissn":["1756-8935"]},"doi":"10.1186/s13072-019-0307-4","scopus_import":"1","publication":"Epigenetics and Chromatin","date_updated":"2021-12-14T07:53:00Z","department":[{"_id":"DaZi"}],"intvolume":"        12","oa":1,"volume":12,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"first_name":"Keith D.","last_name":"Harris","full_name":"Harris, Keith D."},{"full_name":"Lloyd, James P. B.","last_name":"Lloyd","first_name":"James P. B."},{"full_name":"Domb, Katherine","first_name":"Katherine","last_name":"Domb"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman"},{"first_name":"Assaf","last_name":"Zemach","full_name":"Zemach, Assaf"}],"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"quality_controlled":"1","day":"10","status":"public","month":"10","extern":"1","language":[{"iso":"eng"}],"ddc":["570"],"date_published":"2019-10-10T00:00:00Z","external_id":{"pmid":["31601251"]},"type":"journal_article","publisher":"Springer Nature","pmid":1},{"year":"2019","citation":{"mla":"Ucar, Mehmet C., and Reinhard Lipowsky. <i>Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding</i>. American Chemical Society , 2019, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s001\">10.1021/acs.nanolett.9b04445.s001</a>.","chicago":"Ucar, Mehmet C, and Reinhard Lipowsky. “Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.” American Chemical Society , 2019. <a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s001\">https://doi.org/10.1021/acs.nanolett.9b04445.s001</a>.","short":"M.C. Ucar, R. Lipowsky, (2019).","apa":"Ucar, M. C., &#38; Lipowsky, R. (2019). Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. American Chemical Society . <a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s001\">https://doi.org/10.1021/acs.nanolett.9b04445.s001</a>","ista":"Ucar MC, Lipowsky R. 2019. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding, American Chemical Society , <a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s001\">10.1021/acs.nanolett.9b04445.s001</a>.","ieee":"M. C. Ucar and R. Lipowsky, “Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding.” American Chemical Society , 2019.","ama":"Ucar MC, Lipowsky R. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. 2019. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s001\">10.1021/acs.nanolett.9b04445.s001</a>"},"abstract":[{"lang":"eng","text":"A detailed description of the two stochastic models, table of parameters, supplementary data for Figures 4 and 5, parameter dependence of the results, and an analysis on motors with different force–velocity functions (PDF)"}],"_id":"9726","date_created":"2021-07-27T09:51:46Z","doi":"10.1021/acs.nanolett.9b04445.s001","day":"19","title":"Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding","article_processing_charge":"No","oa_version":"Published Version","month":"12","department":[{"_id":"EdHa"}],"status":"public","date_updated":"2023-08-17T14:07:52Z","publisher":"American Chemical Society ","author":[{"full_name":"Ucar, Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217","last_name":"Ucar","first_name":"Mehmet C"},{"full_name":"Lipowsky, Reinhard","last_name":"Lipowsky","first_name":"Reinhard"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_published":"2019-12-19T00:00:00Z","type":"research_data_reference","related_material":{"record":[{"id":"7166","status":"public","relation":"used_in_publication"}]}},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"full_name":"Sigalova, Olga","first_name":"Olga","last_name":"Sigalova"},{"first_name":"Andrei","last_name":"Chaplin","full_name":"Chaplin, Andrei"},{"first_name":"Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga"},{"last_name":"Shelyakin","first_name":"Pavel","full_name":"Shelyakin, Pavel"},{"full_name":"Filaretov, Vsevolod","last_name":"Filaretov","first_name":"Vsevolod"},{"last_name":"Akkuratov","first_name":"Evgeny","full_name":"Akkuratov, Evgeny"},{"first_name":"Valentina","last_name":"Burskaia","full_name":"Burskaia, Valentina"},{"last_name":"Gelfand","first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S."}],"publisher":"Springer Nature","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6898"}]},"oa":1,"type":"research_data_reference","date_published":"2019-09-12T00:00:00Z","date_updated":"2023-08-30T06:20:21Z","status":"public","department":[{"_id":"FyKo"}],"month":"09","day":"12","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808772.v1","open_access":"1"}],"doi":"10.6084/m9.figshare.9808772.v1","article_processing_charge":"No","oa_version":"Published Version","title":"Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","abstract":[{"text":"OGs with putative pseudogenes by the number of affected genomes in different chlamydial species. Frameshift and nonsense mutations located less than 60 bp upstreamof the gene end or present in a single genome from the corresponding OG were excluded. (CSV 31 kb)","lang":"eng"}],"citation":{"ieee":"O. Sigalova <i>et al.</i>, “Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","ista":"Sigalova O, Chaplin A, Bochkareva O, Shelyakin P, Filaretov V, Akkuratov E, Burskaia V, Gelfand MS. 2019. Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.9808772.v1\">10.6084/m9.figshare.9808772.v1</a>.","ama":"Sigalova O, Chaplin A, Bochkareva O, et al. Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808772.v1\">10.6084/m9.figshare.9808772.v1</a>","mla":"Sigalova, Olga, et al. <i>Additional File 11 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>. Springer Nature, 2019, doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808772.v1\">10.6084/m9.figshare.9808772.v1</a>.","apa":"Sigalova, O., Chaplin, A., Bochkareva, O., Shelyakin, P., Filaretov, V., Akkuratov, E., … Gelfand, M. S. (2019). Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.9808772.v1\">https://doi.org/10.6084/m9.figshare.9808772.v1</a>","chicago":"Sigalova, Olga, Andrei Chaplin, Olga Bochkareva, Pavel Shelyakin, Vsevolod Filaretov, Evgeny Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 11 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. <a href=\"https://doi.org/10.6084/m9.figshare.9808772.v1\">https://doi.org/10.6084/m9.figshare.9808772.v1</a>.","short":"O. Sigalova, A. Chaplin, O. Bochkareva, P. Shelyakin, V. Filaretov, E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019)."},"year":"2019","date_created":"2021-07-27T14:09:11Z","_id":"9731"},{"title":"Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","oa_version":"Published Version","article_processing_charge":"No","doi":"10.6084/m9.figshare.9808760.v1","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808760.v1","open_access":"1"}],"day":"12","_id":"9783","date_created":"2021-08-06T07:59:56Z","year":"2019","citation":{"mla":"Sigalova, Olga M., et al. <i>Additional File 10 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>. Springer Nature, 2019, doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808760.v1\">10.6084/m9.figshare.9808760.v1</a>.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.9808760.v1\">https://doi.org/10.6084/m9.figshare.9808760.v1</a>","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 10 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. <a href=\"https://doi.org/10.6084/m9.figshare.9808760.v1\">https://doi.org/10.6084/m9.figshare.9808760.v1</a>.","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.9808760.v1\">10.6084/m9.figshare.9808760.v1</a>.","ieee":"O. M. Sigalova <i>et al.</i>, “Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808760.v1\">10.6084/m9.figshare.9808760.v1</a>"},"abstract":[{"text":"Predicted frameshift and nonsense mutations in Chlamydial pan-genome. For the analysis of putative pseudogenes, events located less than 60 bp. away from gene end or present in a single genome from the corresponding OG were excluded. (CSV 600 kb)","lang":"eng"}],"date_published":"2019-09-12T00:00:00Z","type":"research_data_reference","oa":1,"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6898"}]},"publisher":"Springer Nature","author":[{"full_name":"Sigalova, Olga M.","last_name":"Sigalova","first_name":"Olga M."},{"full_name":"Chaplin, Andrei V.","first_name":"Andrei V.","last_name":"Chaplin"},{"last_name":"Bochkareva","first_name":"Olga","full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"first_name":"Pavel V.","last_name":"Shelyakin","full_name":"Shelyakin, Pavel V."},{"full_name":"Filaretov, Vsevolod A.","first_name":"Vsevolod A.","last_name":"Filaretov"},{"last_name":"Akkuratov","first_name":"Evgeny E.","full_name":"Akkuratov, Evgeny E."},{"full_name":"Burskaia, Valentina","first_name":"Valentina","last_name":"Burskaia"},{"full_name":"Gelfand, Mikhail S.","last_name":"Gelfand","first_name":"Mikhail S."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"09","department":[{"_id":"FyKo"}],"status":"public","date_updated":"2023-08-30T06:20:21Z"},{"author":[{"full_name":"Antoniou, Michael N.","first_name":"Michael N.","last_name":"Antoniou"},{"id":"2A103192-F248-11E8-B48F-1D18A9856A87","full_name":"Nicolas, Armel","first_name":"Armel","last_name":"Nicolas"},{"full_name":"Mesnage, Robin","first_name":"Robin","last_name":"Mesnage"},{"full_name":"Biserni, Martina","first_name":"Martina","last_name":"Biserni"},{"last_name":"Rao","first_name":"Francesco V.","full_name":"Rao, Francesco V."},{"full_name":"Martin, Cristina Vazquez","first_name":"Cristina Vazquez","last_name":"Martin"}],"publisher":"Springer Nature","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","date_published":"2019-08-09T00:00:00Z","oa":1,"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6819"}]},"department":[{"_id":"LifeSc"}],"month":"08","date_updated":"2023-02-23T12:52:29Z","status":"public","doi":"10.6084/m9.figshare.9411761.v1","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9411761.v1","open_access":"1"}],"day":"09","title":"MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells","article_processing_charge":"No","oa_version":"Published Version","citation":{"ama":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 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Kinetics of MDA-MB-231 cell growth in either the presence or absence of 100Â mg/L glyphosate. Cell counts are given at day-1 of seeding flasks and following 6-days of continuous culture. Note: no differences in cell numbers were observed between negative control and glyphosate treated cultures."}],"date_created":"2021-08-06T08:14:05Z","_id":"9784"},{"_id":"9786","date_created":"2021-08-06T08:23:43Z","year":"2019","citation":{"apa":"Ruess, J., Pleska, M., Guet, C. C., &#38; Tkačik, G. (2019). Supporting text and results. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007168.s001\">https://doi.org/10.1371/journal.pcbi.1007168.s001</a>","short":"J. Ruess, M. Pleska, C.C. Guet, G. 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Owen"},{"full_name":"Jiggins, Chris D.","last_name":"Jiggins","first_name":"Chris D."}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6022"}]},"date_published":"2019-02-07T00:00:00Z","type":"research_data_reference","status":"public","date_updated":"2023-08-24T14:46:23Z","month":"02","department":[{"_id":"NiBa"}]}]