[{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","last_name":"Schur","first_name":"Florian KM"}],"volume":58,"page":"1-9","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Cryo-electron tomography (cryo-ET) provides unprecedented insights into the molecular constituents of biological environments. In combination with an image processing method called subtomogram averaging (STA), detailed 3D structures of biological molecules can be obtained in large, irregular macromolecular assemblies or in situ, without the need for purification. The contextual meta-information these methods also provide, such as a protein’s location within its native environment, can then be combined with functional data. This allows the derivation of a detailed view on the physiological or pathological roles of proteins from the molecular to cellular level. Despite their tremendous potential in in situ structural biology, cryo-ET and STA have been restricted by methodological limitations, such as the low obtainable resolution. Exciting progress now allows one to reach unprecedented resolutions in situ, ranging in optimal cases beyond the nanometer barrier. Here, I review current frontiers and future challenges in routinely determining high-resolution structures in in situ environments using cryo-ET and STA."}],"publication_status":"published","external_id":{"isi":["000494891800004"]},"title":"Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging","year":"2019","date_created":"2019-04-19T11:19:13Z","issue":"10","doi":"10.1016/j.sbi.2019.03.018","publication_identifier":{"issn":["0959-440X"]},"publication":"Current Opinion in Structural Biology","quality_controlled":"1","article_type":"original","intvolume":"        58","oa_version":"None","acknowledgement":"The author acknowledges support from IST Austria and the Austrian Science Fund (FWF).","type":"journal_article","_id":"6343","scopus_import":"1","isi":1,"language":[{"iso":"eng"}],"month":"10","date_published":"2019-10-01T00:00:00Z","publisher":"Elsevier","department":[{"_id":"FlSc"}],"date_updated":"2023-08-25T10:13:31Z","day":"01","status":"public","citation":{"mla":"Schur, Florian KM. “Toward High-Resolution in Situ Structural Biology with Cryo-Electron Tomography and Subtomogram Averaging.” <i>Current Opinion in Structural Biology</i>, vol. 58, no. 10, Elsevier, 2019, pp. 1–9, doi:<a href=\"https://doi.org/10.1016/j.sbi.2019.03.018\">10.1016/j.sbi.2019.03.018</a>.","chicago":"Schur, Florian KM. “Toward High-Resolution in Situ Structural Biology with Cryo-Electron Tomography and Subtomogram Averaging.” <i>Current Opinion in Structural Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.sbi.2019.03.018\">https://doi.org/10.1016/j.sbi.2019.03.018</a>.","apa":"Schur, F. K. (2019). Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. <i>Current Opinion in Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2019.03.018\">https://doi.org/10.1016/j.sbi.2019.03.018</a>","ista":"Schur FK. 2019. Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. Current Opinion in Structural Biology. 58(10), 1–9.","ama":"Schur FK. Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. <i>Current Opinion in Structural Biology</i>. 2019;58(10):1-9. doi:<a href=\"https://doi.org/10.1016/j.sbi.2019.03.018\">10.1016/j.sbi.2019.03.018</a>","ieee":"F. K. Schur, “Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging,” <i>Current Opinion in Structural Biology</i>, vol. 58, no. 10. Elsevier, pp. 1–9, 2019.","short":"F.K. Schur, Current Opinion in Structural Biology 58 (2019) 1–9."}},{"citation":{"ista":"Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. 2019. Resonant electro-optic frequency comb. Nature. 568(7752), 378–381.","ama":"Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. Resonant electro-optic frequency comb. <i>Nature</i>. 2019;568(7752):378-381. doi:<a href=\"https://doi.org/10.1038/s41586-019-1110-x\">10.1038/s41586-019-1110-x</a>","ieee":"A. R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, and H. G. L. Schwefel, “Resonant electro-optic frequency comb,” <i>Nature</i>, vol. 568, no. 7752. Springer Nature, pp. 378–381, 2019.","short":"A.R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, H.G.L. Schwefel, Nature 568 (2019) 378–381.","mla":"Rueda Sanchez, Alfredo R., et al. “Resonant Electro-Optic Frequency Comb.” <i>Nature</i>, vol. 568, no. 7752, Springer Nature, 2019, pp. 378–81, doi:<a href=\"https://doi.org/10.1038/s41586-019-1110-x\">10.1038/s41586-019-1110-x</a>.","chicago":"Rueda Sanchez, Alfredo R, Florian Sedlmeir, Madhuri Kumari, Gerd Leuchs, and Harald G.L. Schwefel. “Resonant Electro-Optic Frequency Comb.” <i>Nature</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41586-019-1110-x\">https://doi.org/10.1038/s41586-019-1110-x</a>.","apa":"Rueda Sanchez, A. R., Sedlmeir, F., Kumari, M., Leuchs, G., &#38; Schwefel, H. G. L. (2019). Resonant electro-optic frequency comb. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-019-1110-x\">https://doi.org/10.1038/s41586-019-1110-x</a>"},"day":"18","status":"public","oa":1,"isi":1,"date_updated":"2025-07-10T11:53:19Z","department":[{"_id":"JoFi"}],"publisher":"Springer Nature","arxiv":1,"date_published":"2019-04-18T00:00:00Z","month":"04","language":[{"iso":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":"       568","scopus_import":"1","_id":"6348","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1808.10608","open_access":"1"}],"date_created":"2019-04-28T21:59:13Z","year":"2019","publication":"Nature","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"doi":"10.1038/s41586-019-1110-x","issue":"7752","publication_status":"published","external_id":{"isi":["000464950700053"],"arxiv":["1808.10608"]},"abstract":[{"text":"High-speed optical telecommunication is enabled by wavelength-division multiplexing, whereby hundreds of individually stabilized lasers encode information within a single-mode optical fibre. Higher bandwidths require higher total optical power, but the power sent into the fibre is limited by optical nonlinearities within the fibre, and energy consumption by the light sources starts to become a substantial cost factor1. Optical frequency combs have been suggested to remedy this problem by generating numerous discrete, equidistant laser lines within a monolithic device; however, at present their stability and coherence allow them to operate only within small parameter ranges2,3,4. Here we show that a broadband frequency comb realized through the electro-optic effect within a high-quality whispering-gallery-mode resonator can operate at low microwave and optical powers. Unlike the usual third-order Kerr nonlinear optical frequency combs, our combs rely on the second-order nonlinear effect, which is much more efficient. Our result uses a fixed microwave signal that is mixed with an optical-pump signal to generate a coherent frequency comb with a precisely determined carrier separation. The resonant enhancement enables us to work with microwave powers that are three orders of magnitude lower than those in commercially available devices. We emphasize the practical relevance of our results to high rates of data communication. To circumvent the limitations imposed by nonlinear effects in optical communication fibres, one has to solve two problems: to provide a compact and fully integrated, yet high-quality and coherent, frequency comb generator; and to calculate nonlinear signal propagation in real time5. We report a solution to the first problem.","lang":"eng"}],"article_processing_charge":"No","page":"378-381","title":"Resonant electro-optic frequency comb","volume":568,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Rueda Sanchez","first_name":"Alfredo R","full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sedlmeir, Florian","last_name":"Sedlmeir","first_name":"Florian"},{"first_name":"Madhuri","last_name":"Kumari","full_name":"Kumari, Madhuri"},{"full_name":"Leuchs, Gerd","first_name":"Gerd","last_name":"Leuchs"},{"last_name":"Schwefel","first_name":"Harald G.L.","full_name":"Schwefel, Harald G.L."}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-019-1220-5"}]}},{"author":[{"first_name":"Andrey Alexandrovich","last_name":"Temnov","full_name":"Temnov, Andrey Alexandrovich"},{"full_name":"Rogov, Konstantin Arkadevich","last_name":"Rogov","first_name":"Konstantin Arkadevich"},{"first_name":"Alla Nikolaevna","last_name":"Sklifas","full_name":"Sklifas, Alla Nikolaevna"},{"full_name":"Klychnikova, Elena Valerievna","last_name":"Klychnikova","first_name":"Elena Valerievna"},{"last_name":"Hartl","first_name":"Markus","full_name":"Hartl, Markus"},{"last_name":"Djinovic-Carugo","first_name":"Kristina","full_name":"Djinovic-Carugo, Kristina"},{"last_name":"Charnagalov","first_name":"Alexej","id":"49F06DBA-F248-11E8-B48F-1D18A9856A87","full_name":"Charnagalov, Alexej"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000470332600049"]},"publication_status":"published","abstract":[{"text":"Chronic overuse of common pharmaceuticals, e.g. acetaminophen (paracetamol), often leads to the development of acute liver failure (ALF). This study aimed to elucidate the effect of cultured mesenchymal stem cells (MSCs) proteome on the onset of liver damage and regeneration dynamics in animals with ALF induced by acetaminophen, to test the liver protective efficacy of MSCs proteome depending on the oxygen tension in cell culture, and to blueprint protein components responsible for the effect. Protein compositions prepared from MSCs cultured in mild hypoxic (5% and 10%  O2) and normal (21%  O2) conditions were used to treat ALF induced in mice by injection of acetaminophen. To test the effect of reduced oxygen tension in cell culture on resulting MSCs proteome content we applied a combination of high performance liquid chromatography and mass-spectrometry (LC–MS/MS) for the identification of proteins in lysates of MSCs cultured at different  O2 levels. The treatment of acetaminophen-administered animals with proteins released from cultured MSCs resulted in the inhibition of inflammatory reactions in damaged liver; the area of hepatocyte necrosis being reduced in the first 24 h. Compositions obtained from MSCs cultured at lower O2 level were shown to be more potent than a composition prepared from normoxic cells. A comparative characterization of protein pattern and identification of individual components done by a cytokine assay and proteomics analysis of protein compositions revealed that even moderate hypoxia produces discrete changes in the expression of various subsets of proteins responsible for intracellular respiration and cell signaling. The application of proteins prepared from MSCs grown in vitro at reduced oxygen tension significantly accelerates healing process in damaged liver tissue. The proteomics data obtained for different preparations offer new information about the potential candidates in the MSCs protein repertoire sensitive to oxygen tension in culture medium, which can be involved in the generalized mechanisms the cells use to respond to acute liver failure.","lang":"eng"}],"title":"Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure","date_created":"2019-04-28T21:59:14Z","year":"2019","publication_identifier":{"issn":["0301-4851"],"eissn":["1573-4978"]},"doi":"10.1007/s11033-019-04765-z","publication":"Molecular Biology Reports","corr_author":"1","quality_controlled":"1","file":[{"file_name":"2019_MolecularBioReport_Temnov.pdf","content_type":"application/pdf","date_created":"2019-04-30T09:52:36Z","creator":"dernst","file_id":"6362","date_updated":"2020-07-14T12:47:28Z","file_size":1948014,"checksum":"45bf040bbce1cea274f6013fa18ba21b","relation":"main_file","access_level":"open_access"}],"has_accepted_license":"1","ddc":["570"],"oa_version":"Published Version","acknowledgement":"The studies were supported by the Austrian Federal Ministry of Economy, Family and Youth through the initiative “Laura Bassi Centres of Expertise” funding the Center of Optimized Structural Stud-ies, grant No. 253275","type":"journal_article","scopus_import":"1","_id":"6352","isi":1,"file_date_updated":"2020-07-14T12:47:28Z","oa":1,"date_published":"2019-04-12T00:00:00Z","month":"04","language":[{"iso":"eng"}],"date_updated":"2026-04-16T09:49:11Z","department":[{"_id":"LeSa"}],"publisher":"Springer","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"12","status":"public","citation":{"mla":"Temnov, Andrey Alexandrovich, et al. “Protective Properties of the Cultured Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” <i>Molecular Biology Reports</i>, Springer, 2019, doi:<a href=\"https://doi.org/10.1007/s11033-019-04765-z\">10.1007/s11033-019-04765-z</a>.","chicago":"Temnov, Andrey Alexandrovich, Konstantin Arkadevich Rogov, Alla Nikolaevna Sklifas, Elena Valerievna Klychnikova, Markus Hartl, Kristina Djinovic-Carugo, and Alexej Charnagalov. “Protective Properties of the Cultured Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” <i>Molecular Biology Reports</i>. Springer, 2019. <a href=\"https://doi.org/10.1007/s11033-019-04765-z\">https://doi.org/10.1007/s11033-019-04765-z</a>.","apa":"Temnov, A. A., Rogov, K. A., Sklifas, A. N., Klychnikova, E. V., Hartl, M., Djinovic-Carugo, K., &#38; Charnagalov, A. (2019). Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. <i>Molecular Biology Reports</i>. Springer. <a href=\"https://doi.org/10.1007/s11033-019-04765-z\">https://doi.org/10.1007/s11033-019-04765-z</a>","ama":"Temnov AA, Rogov KA, Sklifas AN, et al. Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. <i>Molecular Biology Reports</i>. 2019. doi:<a href=\"https://doi.org/10.1007/s11033-019-04765-z\">10.1007/s11033-019-04765-z</a>","ista":"Temnov AA, Rogov KA, Sklifas AN, Klychnikova EV, Hartl M, Djinovic-Carugo K, Charnagalov A. 2019. Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. Molecular Biology Reports.","short":"A.A. Temnov, K.A. Rogov, A.N. Sklifas, E.V. Klychnikova, M. Hartl, K. Djinovic-Carugo, A. Charnagalov, Molecular Biology Reports (2019).","ieee":"A. A. Temnov <i>et al.</i>, “Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure,” <i>Molecular Biology Reports</i>. Springer, 2019."}},{"citation":{"mla":"Bellstaedt, Julia, et al. “A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” <i>Plant Physiology</i>, vol. 180, no. 2, ASPB, 2019, pp. 757–66, doi:<a href=\"https://doi.org/10.1104/pp.18.01377\">10.1104/pp.18.01377</a>.","apa":"Bellstaedt, J., Trenner, J., Lippmann, R., Poeschl, Y., Zhang, X., Friml, J., … Delker, C. (2019). A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. <i>Plant Physiology</i>. ASPB. <a href=\"https://doi.org/10.1104/pp.18.01377\">https://doi.org/10.1104/pp.18.01377</a>","chicago":"Bellstaedt, Julia, Jana Trenner, Rebecca Lippmann, Yvonne Poeschl, Xixi Zhang, Jiří Friml, Marcel Quint, and Carolin Delker. “A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” <i>Plant Physiology</i>. ASPB, 2019. <a href=\"https://doi.org/10.1104/pp.18.01377\">https://doi.org/10.1104/pp.18.01377</a>.","ama":"Bellstaedt J, Trenner J, Lippmann R, et al. A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. <i>Plant Physiology</i>. 2019;180(2):757-766. doi:<a href=\"https://doi.org/10.1104/pp.18.01377\">10.1104/pp.18.01377</a>","ista":"Bellstaedt J, Trenner J, Lippmann R, Poeschl Y, Zhang X, Friml J, Quint M, Delker C. 2019. A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. Plant Physiology. 180(2), 757–766.","ieee":"J. Bellstaedt <i>et al.</i>, “A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls,” <i>Plant Physiology</i>, vol. 180, no. 2. ASPB, pp. 757–766, 2019.","short":"J. Bellstaedt, J. Trenner, R. Lippmann, Y. Poeschl, X. Zhang, J. Friml, M. Quint, C. Delker, Plant Physiology 180 (2019) 757–766."},"status":"public","day":"01","department":[{"_id":"JiFr"}],"publisher":"ASPB","date_updated":"2026-06-18T19:03:49Z","month":"06","language":[{"iso":"eng"}],"date_published":"2019-06-01T00:00:00Z","oa":1,"isi":1,"_id":"6366","scopus_import":"1","type":"journal_article","article_type":"original","intvolume":"       180","oa_version":"Published Version","ddc":["580"],"main_file_link":[{"open_access":"1","url":"www.doi.org/10.1104/pp.18.01377"}],"quality_controlled":"1","publication":"Plant Physiology","issue":"2","publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"doi":"10.1104/pp.18.01377","year":"2019","date_created":"2019-04-30T15:24:22Z","title":"A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls","abstract":[{"lang":"eng","text":"Plants have a remarkable capacity to adjust their growth and development to elevated ambient temperatures. Increased elongation growth of roots, hypocotyls and petioles in warm temperatures are hallmarks of seedling thermomorphogenesis. In the last decade, significant progress has been made to identify the molecular signaling components regulating these growth responses. Increased ambient temperature utilizes diverse components of the light sensing and signal transduction network to trigger growth adjustments. However, it remains unknown whether temperature sensing and responses are universal processes that occur uniformly in all plant organs. Alternatively, temperature sensing may be confined to specific tissues or organs, which would require a systemic signal that mediates responses in distal parts of the plant. Here we show that Arabidopsis (Arabidopsis thaliana) seedlings show organ-specific transcriptome responses to elevated temperatures, and that thermomorphogenesis involves both autonomous and organ-interdependent temperature sensing and signaling. Seedling roots can sense and respond to temperature in a shoot-independent manner, whereas shoot temperature responses require both local and systemic processes. The induction of cell elongation in hypocotyls requires temperature sensing in cotyledons, followed by generation of a mobile auxin signal. Subsequently, auxin travels to the hypocotyl where it triggers local brassinosteroid-induced cell elongation in seedling stems, which depends upon a distinct, permissive temperature sensor in the hypocotyl."}],"publication_status":"published","external_id":{"isi":["000470086100019"],"pmid":["31000634"]},"page":"757-766","article_processing_charge":"No","pmid":1,"volume":180,"author":[{"full_name":"Bellstaedt, Julia","last_name":"Bellstaedt","first_name":"Julia"},{"full_name":"Trenner, Jana","first_name":"Jana","last_name":"Trenner"},{"full_name":"Lippmann, Rebecca","last_name":"Lippmann","first_name":"Rebecca"},{"first_name":"Yvonne","last_name":"Poeschl","full_name":"Poeschl, Yvonne"},{"full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","first_name":"Xixi","last_name":"Zhang"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří"},{"last_name":"Quint","first_name":"Marcel","full_name":"Quint, Marcel"},{"full_name":"Delker, Carolin","last_name":"Delker","first_name":"Carolin"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"citation":{"apa":"Dejonghe, W., Sharma, I., Denoo, B., De Munck, S., Lu, Q., Mishev, K., … Russinova, E. (2019). Disruption of endocytosis through chemical inhibition of clathrin heavy chain function. <i>Nature Chemical Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41589-019-0262-1\">https://doi.org/10.1038/s41589-019-0262-1</a>","chicago":"Dejonghe, Wim, Isha Sharma, Bram Denoo, Steven De Munck, Qing Lu, Kiril Mishev, Haydar Bulut, et al. “Disruption of Endocytosis through Chemical Inhibition of Clathrin Heavy Chain Function.” <i>Nature Chemical Biology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41589-019-0262-1\">https://doi.org/10.1038/s41589-019-0262-1</a>.","mla":"Dejonghe, Wim, et al. “Disruption of Endocytosis through Chemical Inhibition of Clathrin Heavy Chain Function.” <i>Nature Chemical Biology</i>, vol. 15, no. 6, Springer Nature, 2019, pp. 641–649, doi:<a href=\"https://doi.org/10.1038/s41589-019-0262-1\">10.1038/s41589-019-0262-1</a>.","short":"W. Dejonghe, I. Sharma, B. Denoo, S. De Munck, Q. Lu, K. Mishev, H. Bulut, E. Mylle, R. De Rycke, M.K. Vasileva, D.V. Savatin, W. Nerinckx, A. Staes, A. Drozdzecki, D. Audenaert, K. Yperman, A. Madder, J. Friml, D. Van Damme, K. Gevaert, V. Haucke, S.N. Savvides, J. Winne, E. Russinova, Nature Chemical Biology 15 (2019) 641–649.","ieee":"W. Dejonghe <i>et al.</i>, “Disruption of endocytosis through chemical inhibition of clathrin heavy chain function,” <i>Nature Chemical Biology</i>, vol. 15, no. 6. Springer Nature, pp. 641–649, 2019.","ama":"Dejonghe W, Sharma I, Denoo B, et al. Disruption of endocytosis through chemical inhibition of clathrin heavy chain function. <i>Nature Chemical Biology</i>. 2019;15(6):641–649. doi:<a href=\"https://doi.org/10.1038/s41589-019-0262-1\">10.1038/s41589-019-0262-1</a>","ista":"Dejonghe W, Sharma I, Denoo B, De Munck S, Lu Q, Mishev K, Bulut H, Mylle E, De Rycke R, Vasileva MK, Savatin DV, Nerinckx W, Staes A, Drozdzecki A, Audenaert D, Yperman K, Madder A, Friml J, Van Damme D, Gevaert K, Haucke V, Savvides SN, Winne J, Russinova E. 2019. Disruption of endocytosis through chemical inhibition of clathrin heavy chain function. Nature Chemical Biology. 15(6), 641–649."},"day":"01","status":"public","isi":1,"month":"06","language":[{"iso":"eng"}],"date_published":"2019-06-01T00:00:00Z","publisher":"Springer Nature","department":[{"_id":"JiFr"}],"date_updated":"2026-04-08T13:54:44Z","article_type":"original","intvolume":"        15","oa_version":"None","type":"journal_article","_id":"6377","scopus_import":"1","quality_controlled":"1","year":"2019","date_created":"2019-05-05T21:59:11Z","issue":"6","publication_identifier":{"eissn":["1552-4469"],"issn":["1552-4450"]},"doi":"10.1038/s41589-019-0262-1","publication":"Nature Chemical Biology","page":"641–649","article_processing_charge":"No","abstract":[{"text":"Clathrin-mediated endocytosis (CME) is a highly conserved and essential cellular process in eukaryotic cells, but its dynamic and vital nature makes it challenging to study using classical genetics tools. In contrast, although small molecules can acutely and reversibly perturb CME, the few chemical CME inhibitors that have been applied to plants are either ineffective or show undesirable side effects. Here, we identify the previously described endosidin9 (ES9) as an inhibitor of clathrin heavy chain (CHC) function in both Arabidopsis and human cells through affinity-based target isolation, in vitro binding studies and X-ray crystallography. Moreover, we present a chemically improved ES9 analog, ES9-17, which lacks the undesirable side effects of ES9 while retaining the ability to target CHC. ES9 and ES9-17 have expanded the chemical toolbox used to probe CHC function, and present chemical scaffolds for further design of more specific and potent CHC inhibitors across different systems.","lang":"eng"}],"publication_status":"published","external_id":{"isi":["000468195600018"]},"title":"Disruption of endocytosis through chemical inhibition of clathrin heavy chain function","author":[{"first_name":"Wim","last_name":"Dejonghe","full_name":"Dejonghe, Wim"},{"full_name":"Sharma, Isha","first_name":"Isha","last_name":"Sharma"},{"last_name":"Denoo","first_name":"Bram","full_name":"Denoo, Bram"},{"last_name":"De Munck","first_name":"Steven","full_name":"De Munck, Steven"},{"last_name":"Lu","first_name":"Qing","full_name":"Lu, Qing"},{"last_name":"Mishev","first_name":"Kiril","full_name":"Mishev, Kiril"},{"full_name":"Bulut, Haydar","last_name":"Bulut","first_name":"Haydar"},{"full_name":"Mylle, Evelien","last_name":"Mylle","first_name":"Evelien"},{"full_name":"De Rycke, Riet","first_name":"Riet","last_name":"De Rycke"},{"full_name":"Vasileva, Mina K","id":"3407EB18-F248-11E8-B48F-1D18A9856A87","last_name":"Vasileva","first_name":"Mina K"},{"full_name":"Savatin, Daniel V.","first_name":"Daniel V.","last_name":"Savatin"},{"full_name":"Nerinckx, Wim","first_name":"Wim","last_name":"Nerinckx"},{"full_name":"Staes, An","last_name":"Staes","first_name":"An"},{"full_name":"Drozdzecki, Andrzej","last_name":"Drozdzecki","first_name":"Andrzej"},{"first_name":"Dominique","last_name":"Audenaert","full_name":"Audenaert, Dominique"},{"last_name":"Yperman","first_name":"Klaas","full_name":"Yperman, Klaas"},{"full_name":"Madder, Annemieke","last_name":"Madder","first_name":"Annemieke"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"},{"last_name":"Van Damme","first_name":"Daniël","full_name":"Van Damme, Daniël"},{"full_name":"Gevaert, Kris","first_name":"Kris","last_name":"Gevaert"},{"last_name":"Haucke","first_name":"Volker","full_name":"Haucke, Volker"},{"full_name":"Savvides, Savvas N.","first_name":"Savvas N.","last_name":"Savvides"},{"last_name":"Winne","first_name":"Johan","full_name":"Winne, Johan"},{"full_name":"Russinova, Eugenia","first_name":"Eugenia","last_name":"Russinova"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":15,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"7172"}]}},{"type":"journal_article","oa_version":"Published Version","intvolume":"        10","_id":"6412","scopus_import":"1","oa":1,"file_date_updated":"2020-07-14T12:47:29Z","isi":1,"department":[{"_id":"SaSi"}],"publisher":"Springer Nature","date_updated":"2026-04-03T09:38:23Z","month":"04","language":[{"iso":"eng"}],"date_published":"2019-04-29T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"29","status":"public","citation":{"ista":"Moussa HF, Bsteh D, Yelagandula R, Pribitzer C, Stecher K, Bartalska K, Michetti L, Wang J, Zepeda-Martinez JA, Elling U, Stuckey JI, James LI, Frye SV, Bell O. 2019. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 10(1), 1931.","ama":"Moussa HF, Bsteh D, Yelagandula R, et al. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. <i>Nature Communications</i>. 2019;10(1). doi:<a href=\"https://doi.org/10.1038/s41467-019-09628-6\">10.1038/s41467-019-09628-6</a>","short":"H.F. Moussa, D. Bsteh, R. Yelagandula, C. Pribitzer, K. Stecher, K. Bartalska, L. Michetti, J. Wang, J.A. Zepeda-Martinez, U. Elling, J.I. Stuckey, L.I. James, S.V. Frye, O. Bell, Nature Communications 10 (2019).","ieee":"H. F. Moussa <i>et al.</i>, “Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing,” <i>Nature Communications</i>, vol. 10, no. 1. Springer Nature, 2019.","mla":"Moussa, Hagar F., et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” <i>Nature Communications</i>, vol. 10, no. 1, 1931, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-09628-6\">10.1038/s41467-019-09628-6</a>.","chicago":"Moussa, Hagar F., Daniel Bsteh, Ramesh Yelagandula, Carina Pribitzer, Karin Stecher, Katarina Bartalska, Luca Michetti, et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-09628-6\">https://doi.org/10.1038/s41467-019-09628-6</a>.","apa":"Moussa, H. F., Bsteh, D., Yelagandula, R., Pribitzer, C., Stecher, K., Bartalska, K., … Bell, O. (2019). Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-09628-6\">https://doi.org/10.1038/s41467-019-09628-6</a>"},"volume":10,"author":[{"full_name":"Moussa, Hagar F.","first_name":"Hagar F.","last_name":"Moussa"},{"last_name":"Bsteh","first_name":"Daniel","full_name":"Bsteh, Daniel"},{"full_name":"Yelagandula, Ramesh","first_name":"Ramesh","last_name":"Yelagandula"},{"last_name":"Pribitzer","first_name":"Carina","full_name":"Pribitzer, Carina"},{"full_name":"Stecher, Karin","first_name":"Karin","last_name":"Stecher"},{"last_name":"Bartalska","first_name":"Katarina","full_name":"Bartalska, Katarina","id":"4D883232-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Luca","last_name":"Michetti","full_name":"Michetti, Luca"},{"full_name":"Wang, Jingkui","last_name":"Wang","first_name":"Jingkui"},{"last_name":"Zepeda-Martinez","first_name":"Jorge A.","full_name":"Zepeda-Martinez, Jorge A."},{"full_name":"Elling, Ulrich","first_name":"Ulrich","last_name":"Elling"},{"full_name":"Stuckey, Jacob I.","first_name":"Jacob I.","last_name":"Stuckey"},{"full_name":"James, Lindsey I.","first_name":"Lindsey I.","last_name":"James"},{"full_name":"Frye, Stephen V.","first_name":"Stephen V.","last_name":"Frye"},{"first_name":"Oliver","last_name":"Bell","full_name":"Bell, Oliver"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","abstract":[{"text":"Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct chromatin modifications to enforce gene silencing, but how transcriptional repression is propagated through mitotic cell divisions remains a key unresolved question. Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic stem cells, here we show that PRC1 can trigger transcriptional repression and Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1), but not variant PRC1, maintains gene silencing through cell division upon reversal of tethering. Propagation of gene repression is sustained by cis-acting histone modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic maintenance of gene silencing, potentially enabling dynamic heritable responses to complex stimuli. Our findings reveal how PcG repression is potentially inherited in vertebrates.","lang":"eng"}],"external_id":{"isi":["000466118700002"]},"publication_status":"published","article_processing_charge":"No","title":"Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing","article_number":"1931","year":"2019","date_created":"2019-05-13T07:58:35Z","publication":"Nature Communications","issue":"1","publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-019-09628-6","file":[{"date_updated":"2020-07-14T12:47:29Z","file_size":1223647,"checksum":"6550a328335396c856db4cbdda7d2994","relation":"main_file","access_level":"open_access","file_id":"6448","creator":"dernst","content_type":"application/pdf","file_name":"2019_NatureComm_Moussa.pdf","date_created":"2019-05-14T08:45:51Z"}],"quality_controlled":"1","ddc":["570"],"has_accepted_license":"1"},{"intvolume":"       117","oa_version":"Preprint","article_type":"original","type":"journal_article","scopus_import":"1","_id":"6413","isi":1,"oa":1,"date_published":"2019-08-01T00:00:00Z","month":"08","language":[{"iso":"eng"}],"date_updated":"2026-04-16T09:49:27Z","publisher":"Elsevier","department":[{"_id":"BjHo"}],"arxiv":1,"day":"01","status":"public","citation":{"chicago":"Song, Baofang, Carlos Plana, Jose M Lopez Alonso, and Marc Avila. “Phase-Field Simulation of Core-Annular Pipe Flow.” <i>International Journal of Multiphase Flow</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027\">https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027</a>.","apa":"Song, B., Plana, C., Lopez Alonso, J. M., &#38; Avila, M. (2019). Phase-field simulation of core-annular pipe flow. <i>International Journal of Multiphase Flow</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027\">https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027</a>","mla":"Song, Baofang, et al. “Phase-Field Simulation of Core-Annular Pipe Flow.” <i>International Journal of Multiphase Flow</i>, vol. 117, Elsevier, 2019, pp. 14–24, doi:<a href=\"https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027\">10.1016/j.ijmultiphaseflow.2019.04.027</a>.","short":"B. Song, C. Plana, J.M. Lopez Alonso, M. Avila, International Journal of Multiphase Flow 117 (2019) 14–24.","ieee":"B. Song, C. Plana, J. M. Lopez Alonso, and M. Avila, “Phase-field simulation of core-annular pipe flow,” <i>International Journal of Multiphase Flow</i>, vol. 117. Elsevier, pp. 14–24, 2019.","ista":"Song B, Plana C, Lopez Alonso JM, Avila M. 2019. Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. 117, 14–24.","ama":"Song B, Plana C, Lopez Alonso JM, Avila M. Phase-field simulation of core-annular pipe flow. <i>International Journal of Multiphase Flow</i>. 2019;117:14-24. doi:<a href=\"https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027\">10.1016/j.ijmultiphaseflow.2019.04.027</a>"},"author":[{"last_name":"Song","first_name":"Baofang","full_name":"Song, Baofang"},{"first_name":"Carlos","last_name":"Plana","full_name":"Plana, Carlos"},{"last_name":"Lopez Alonso","first_name":"Jose M","full_name":"Lopez Alonso, Jose M","orcid":"0000-0002-0384-2022","id":"40770848-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marc","last_name":"Avila","full_name":"Avila, Marc"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","volume":117,"article_processing_charge":"No","page":"14-24","publication_status":"published","external_id":{"isi":["000474496000002"],"arxiv":["1902.07351"]},"abstract":[{"text":"Phase-field methods have long been used to model the flow of immiscible fluids. Their ability to naturally capture interface topological changes is widely recognized, but their accuracy in simulating flows of real fluids in practical geometries is not established. We here quantitatively investigate the convergence of the phase-field method to the sharp-interface limit with simulations of two-phase pipe flow. We focus on core-annular flows, in which a highly viscous fluid is lubricated by a less viscous fluid, and validate our simulations with an analytic laminar solution, a formal linear stability analysis and also in the fully nonlinear regime. We demonstrate the ability of the phase-field method to accurately deal with non-rectangular geometry, strong advection, unsteady fluctuations and large viscosity contrast. We argue that phase-field methods are very promising for quantitatively studying moderately turbulent flows, especially at high concentrations of the disperse phase.","lang":"eng"}],"title":"Phase-field simulation of core-annular pipe flow","date_created":"2019-05-13T07:58:35Z","year":"2019","doi":"10.1016/j.ijmultiphaseflow.2019.04.027","publication_identifier":{"issn":["0301-9322"]},"publication":"International Journal of Multiphase Flow","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.07351"}]},{"_id":"6415","scopus_import":"1","type":"journal_article","volume":33,"intvolume":"        33","author":[{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","department":[{"_id":"SyCr"}],"publisher":"Elsevier","date_updated":"2025-07-10T11:53:22Z","language":[{"iso":"eng"}],"month":"06","title":"Pathogens and disease defense of invasive ants","date_published":"2019-06-01T00:00:00Z","abstract":[{"text":"Ant invasions are often harmful to native species communities. Their pathogens and host disease defense mechanisms may be one component of their devastating success. First, they can introduce harmful diseases to their competitors in the introduced range, to which they themselves are tolerant. Second, their supercolonial social structure of huge multi-queen nest networks means that they will harbor a broad pathogen spectrum and high pathogen load while remaining resilient, unlike the smaller, territorial colonies of the native species. Thus, it is likely that invasive ants act as a disease reservoir, promoting their competitive advantage and invasive success.","lang":"eng"}],"publication_status":"published","external_id":{"isi":["000477666000012"]},"page":"63-68","article_processing_charge":"No","isi":1,"day":"01","status":"public","publication":"Current Opinion in Insect Science","doi":"10.1016/j.cois.2019.03.011","publication_identifier":{"issn":["2214-5745"],"eissn":["2214-5753"]},"year":"2019","date_created":"2019-05-13T07:58:36Z","quality_controlled":"1","citation":{"ista":"Cremer S. 2019. Pathogens and disease defense of invasive ants. Current Opinion in Insect Science. 33, 63–68.","ama":"Cremer S. Pathogens and disease defense of invasive ants. <i>Current Opinion in Insect Science</i>. 2019;33:63-68. doi:<a href=\"https://doi.org/10.1016/j.cois.2019.03.011\">10.1016/j.cois.2019.03.011</a>","ieee":"S. Cremer, “Pathogens and disease defense of invasive ants,” <i>Current Opinion in Insect Science</i>, vol. 33. Elsevier, pp. 63–68, 2019.","short":"S. Cremer, Current Opinion in Insect Science 33 (2019) 63–68.","mla":"Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” <i>Current Opinion in Insect Science</i>, vol. 33, Elsevier, 2019, pp. 63–68, doi:<a href=\"https://doi.org/10.1016/j.cois.2019.03.011\">10.1016/j.cois.2019.03.011</a>.","chicago":"Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” <i>Current Opinion in Insect Science</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cois.2019.03.011\">https://doi.org/10.1016/j.cois.2019.03.011</a>.","apa":"Cremer, S. (2019). Pathogens and disease defense of invasive ants. <i>Current Opinion in Insect Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cois.2019.03.011\">https://doi.org/10.1016/j.cois.2019.03.011</a>"}},{"title":"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome","article_processing_charge":"No","page":"1033-1044","publication_status":"published","external_id":{"isi":["000476569800003"]},"abstract":[{"lang":"eng","text":"Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"related_material":{"record":[{"status":"public","id":"6060","relation":"popular_science"}]},"author":[{"last_name":"Huylmans","first_name":"Ann K","full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","last_name":"Toups","first_name":"Melissa A"},{"first_name":"Ariana","last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana"},{"last_name":"Gammerdinger","first_name":"William J","full_name":"Gammerdinger, William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9638-1220"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":11,"has_accepted_license":"1","ddc":["570"],"file":[{"file_id":"6446","file_size":1256303,"date_updated":"2020-07-14T12:47:29Z","access_level":"open_access","relation":"main_file","checksum":"7d0ede297b6741f3dc89cd59017c7642","content_type":"application/pdf","file_name":"2019_GBE_Huylmans.pdf","date_created":"2019-05-14T08:29:38Z","creator":"dernst"}],"quality_controlled":"1","doi":"10.1093/gbe/evz053","publication_identifier":{"eissn":["1759-6653"]},"issue":"4","publication":"Genome biology and evolution","date_created":"2019-05-13T07:58:38Z","year":"2019","date_published":"2019-04-01T00:00:00Z","month":"04","language":[{"iso":"eng"}],"date_updated":"2025-04-14T07:41:21Z","publisher":"Oxford University Press","department":[{"_id":"BeVi"}],"isi":1,"file_date_updated":"2020-07-14T12:47:29Z","oa":1,"scopus_import":"1","_id":"6418","intvolume":"        11","oa_version":"Published Version","type":"journal_article","citation":{"ista":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. 2019. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 11(4), 1033–1044.","ama":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. <i>Genome biology and evolution</i>. 2019;11(4):1033-1044. doi:<a href=\"https://doi.org/10.1093/gbe/evz053\">10.1093/gbe/evz053</a>","ieee":"A. K. Huylmans, M. A. Toups, A. Macon, W. J. Gammerdinger, and B. Vicoso, “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome,” <i>Genome biology and evolution</i>, vol. 11, no. 4. Oxford University Press, pp. 1033–1044, 2019.","short":"A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome Biology and Evolution 11 (2019) 1033–1044.","mla":"Huylmans, Ann K., et al. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” <i>Genome Biology and Evolution</i>, vol. 11, no. 4, Oxford University Press, 2019, pp. 1033–44, doi:<a href=\"https://doi.org/10.1093/gbe/evz053\">10.1093/gbe/evz053</a>.","apa":"Huylmans, A. K., Toups, M. A., Macon, A., Gammerdinger, W. J., &#38; Vicoso, B. (2019). Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evz053\">https://doi.org/10.1093/gbe/evz053</a>","chicago":"Huylmans, Ann K, Melissa A Toups, Ariana Macon, William J Gammerdinger, and Beatriz Vicoso. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/gbe/evz053\">https://doi.org/10.1093/gbe/evz053</a>."},"project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"status":"public","day":"01","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1},{"intvolume":"       122","oa_version":"Preprint","article_type":"original","type":"journal_article","scopus_import":"1","_id":"19818","oa":1,"date_published":"2019-02-22T00:00:00Z","language":[{"iso":"eng"}],"month":"02","date_updated":"2025-06-10T12:34:24Z","publisher":"American Physical Society","arxiv":1,"OA_type":"green","status":"public","day":"22","citation":{"chicago":"Watson, Matthew D., Oliver J. Clark, Federico Mazzola, Igor Marković, Veronika Sunko, Timur K. Kim, Kai Rossnagel, and Philip D. C. King. “Orbital- and 𝑘𝑧-Selective Hybridization of Se 4⁢𝑝 and Ti 3⁢𝑑 States in the Charge Density Wave Phase of TiSe2.” <i>Physical Review Letters</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/physrevlett.122.076404\">https://doi.org/10.1103/physrevlett.122.076404</a>.","apa":"Watson, M. D., Clark, O. J., Mazzola, F., Marković, I., Sunko, V., Kim, T. K., … King, P. D. C. (2019). Orbital- and 𝑘𝑧-selective hybridization of Se 4⁢𝑝 and Ti 3⁢𝑑 states in the charge density wave phase of TiSe2. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.122.076404\">https://doi.org/10.1103/physrevlett.122.076404</a>","mla":"Watson, Matthew D., et al. “Orbital- and 𝑘𝑧-Selective Hybridization of Se 4⁢𝑝 and Ti 3⁢𝑑 States in the Charge Density Wave Phase of TiSe2.” <i>Physical Review Letters</i>, vol. 122, no. 7, 076404, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/physrevlett.122.076404\">10.1103/physrevlett.122.076404</a>.","short":"M.D. Watson, O.J. Clark, F. Mazzola, I. Marković, V. Sunko, T.K. Kim, K. Rossnagel, P.D.C. King, Physical Review Letters 122 (2019).","ieee":"M. D. Watson <i>et al.</i>, “Orbital- and 𝑘𝑧-selective hybridization of Se 4⁢𝑝 and Ti 3⁢𝑑 states in the charge density wave phase of TiSe2,” <i>Physical Review Letters</i>, vol. 122, no. 7. American Physical Society, 2019.","ista":"Watson MD, Clark OJ, Mazzola F, Marković I, Sunko V, Kim TK, Rossnagel K, King PDC. 2019. Orbital- and 𝑘𝑧-selective hybridization of Se 4⁢𝑝 and Ti 3⁢𝑑 states in the charge density wave phase of TiSe2. Physical Review Letters. 122(7), 076404.","ama":"Watson MD, Clark OJ, Mazzola F, et al. Orbital- and 𝑘𝑧-selective hybridization of Se 4⁢𝑝 and Ti 3⁢𝑑 states in the charge density wave phase of TiSe2. <i>Physical Review Letters</i>. 2019;122(7). doi:<a href=\"https://doi.org/10.1103/physrevlett.122.076404\">10.1103/physrevlett.122.076404</a>"},"author":[{"full_name":"Watson, Matthew D.","first_name":"Matthew D.","last_name":"Watson"},{"first_name":"Oliver J.","last_name":"Clark","full_name":"Clark, Oliver J."},{"full_name":"Mazzola, Federico","first_name":"Federico","last_name":"Mazzola"},{"first_name":"Igor","last_name":"Marković","full_name":"Marković, Igor"},{"full_name":"Sunko, Veronika","orcid":"0000-0003-2724-3523","id":"23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3","first_name":"Veronika","last_name":"Sunko"},{"full_name":"Kim, Timur K.","first_name":"Timur K.","last_name":"Kim"},{"first_name":"Kai","last_name":"Rossnagel","full_name":"Rossnagel, Kai"},{"full_name":"King, Philip D. C.","last_name":"King","first_name":"Philip D. C."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","volume":122,"OA_place":"repository","pmid":1,"article_processing_charge":"No","external_id":{"pmid":["30848608"],"arxiv":["1808.07141"]},"publication_status":"published","abstract":[{"lang":"eng","text":"We revisit the enduring problem of the 2×2×2 charge density wave (CDW) order in TiSe2, utilizing photon energy-dependent angle-resolved photoemission spectroscopy to probe the full three-dimensional high- and low-temperature electronic structure. Our measurements demonstrate how a mismatch of dimensionality between the 3D conduction bands and the quasi-2D valence bands in this system leads to a hybridization that is strongly 𝑘𝑧 dependent. While such a momentum-selective coupling can provide the energy gain required to form the CDW, we show how additional “passenger” states remain, which couple only weakly to the CDW and thus dominate the low-energy physics in the ordered phase of TiSe2."}],"title":"Orbital- and 𝑘𝑧-selective hybridization of Se 4⁢𝑝 and Ti 3⁢𝑑 states in the charge density wave phase of TiSe2","date_created":"2025-06-10T09:18:44Z","year":"2019","article_number":"076404","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"doi":"10.1103/physrevlett.122.076404","issue":"7","publication":"Physical Review Letters","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1808.07141"}]},{"citation":{"apa":"Sunko, V., Abarca Morales, E., Marković, I., Barber, M. E., Milosavljević, D., Mazzola, F., … Mackenzie, A. P. (2019). Direct observation of a uniaxial stress-driven Lifshitz transition in Sr2RuO4. <i>Npj Quantum Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41535-019-0185-9\">https://doi.org/10.1038/s41535-019-0185-9</a>","chicago":"Sunko, Veronika, Edgar Abarca Morales, Igor Marković, Mark E. Barber, Dijana Milosavljević, Federico Mazzola, Dmitry A. Sokolov, et al. “Direct Observation of a Uniaxial Stress-Driven Lifshitz Transition in Sr2RuO4.” <i>Npj Quantum Materials</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41535-019-0185-9\">https://doi.org/10.1038/s41535-019-0185-9</a>.","mla":"Sunko, Veronika, et al. “Direct Observation of a Uniaxial Stress-Driven Lifshitz Transition in Sr2RuO4.” <i>Npj Quantum Materials</i>, vol. 4, 46, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41535-019-0185-9\">10.1038/s41535-019-0185-9</a>.","ieee":"V. Sunko <i>et al.</i>, “Direct observation of a uniaxial stress-driven Lifshitz transition in Sr2RuO4,” <i>npj Quantum Materials</i>, vol. 4. Springer Nature, 2019.","short":"V. Sunko, E. Abarca Morales, I. Marković, M.E. Barber, D. Milosavljević, F. Mazzola, D.A. Sokolov, N. Kikugawa, C. Cacho, P. Dudin, H. Rosner, C.W. Hicks, P.D.C. King, A.P. Mackenzie, Npj Quantum Materials 4 (2019).","ista":"Sunko V, Abarca Morales E, Marković I, Barber ME, Milosavljević D, Mazzola F, Sokolov DA, Kikugawa N, Cacho C, Dudin P, Rosner H, Hicks CW, King PDC, Mackenzie AP. 2019. Direct observation of a uniaxial stress-driven Lifshitz transition in Sr2RuO4. npj Quantum Materials. 4, 46.","ama":"Sunko V, Abarca Morales E, Marković I, et al. Direct observation of a uniaxial stress-driven Lifshitz transition in Sr2RuO4. <i>npj Quantum Materials</i>. 2019;4. doi:<a href=\"https://doi.org/10.1038/s41535-019-0185-9\">10.1038/s41535-019-0185-9</a>"},"status":"public","day":"19","OA_type":"gold","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publisher":"Springer Nature","arxiv":1,"date_updated":"2025-06-11T14:14:26Z","month":"08","language":[{"iso":"eng"}],"date_published":"2019-08-19T00:00:00Z","oa":1,"DOAJ_listed":"1","_id":"19824","scopus_import":"1","type":"journal_article","article_type":"original","oa_version":"Published Version","intvolume":"         4","ddc":["530"],"has_accepted_license":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41535-019-0185-9"}],"quality_controlled":"1","publication":"npj Quantum Materials","publication_identifier":{"issn":["2397-4648"]},"doi":"10.1038/s41535-019-0185-9","article_number":"46","year":"2019","date_created":"2025-06-10T09:21:37Z","title":"Direct observation of a uniaxial stress-driven Lifshitz transition in Sr2RuO4","abstract":[{"text":"Pressure represents a clean tuning parameter for traversing the complex phase diagrams of interacting electron systems, and as such has proved of key importance in the study of quantum materials. Application of controlled uniaxial pressure has recently been shown to more than double the transition temperature of the unconventional superconductor Sr2RuO4, leading to a pronounced peak in Tc versus strain whose origin is still under active debate. Here we develop a simple and compact method to passively apply large uniaxial pressures in restricted sample environments, and utilise this to study the evolution of the electronic structure of Sr2RuO4 using angle-resolved photoemission. We directly visualise how uniaxial stress drives a Lifshitz transition of the γ-band Fermi surface, pointing to the key role of strain-tuning its associated van Hove singularity to the Fermi level in mediating the peak in Tc. Our measurements provide stringent constraints for theoretical models of the strain-tuned electronic structure evolution of Sr2RuO4. More generally, our experimental approach opens the door to future studies of strain-tuned phase transitions not only using photoemission but also other experimental techniques where large pressure cells or piezoelectric-based devices may be difficult to implement.","lang":"eng"}],"external_id":{"arxiv":["1903.09581"]},"publication_status":"published","article_processing_charge":"Yes","OA_place":"publisher","volume":4,"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Sunko","first_name":"Veronika","orcid":"0000-0003-2724-3523","id":"23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3","full_name":"Sunko, Veronika"},{"last_name":"Abarca Morales","first_name":"Edgar","full_name":"Abarca Morales, Edgar"},{"last_name":"Marković","first_name":"Igor","full_name":"Marković, Igor"},{"full_name":"Barber, Mark E.","last_name":"Barber","first_name":"Mark E."},{"full_name":"Milosavljević, Dijana","first_name":"Dijana","last_name":"Milosavljević"},{"last_name":"Mazzola","first_name":"Federico","full_name":"Mazzola, Federico"},{"full_name":"Sokolov, Dmitry A.","last_name":"Sokolov","first_name":"Dmitry A."},{"full_name":"Kikugawa, Naoki","first_name":"Naoki","last_name":"Kikugawa"},{"full_name":"Cacho, Cephise","first_name":"Cephise","last_name":"Cacho"},{"first_name":"Pavel","last_name":"Dudin","full_name":"Dudin, Pavel"},{"first_name":"Helge","last_name":"Rosner","full_name":"Rosner, Helge"},{"last_name":"Hicks","first_name":"Clifford W.","full_name":"Hicks, Clifford W."},{"full_name":"King, Philip D. C.","last_name":"King","first_name":"Philip D. C."},{"last_name":"Mackenzie","first_name":"Andrew P.","full_name":"Mackenzie, Andrew P."}]},{"extern":"1","author":[{"last_name":"Usui","first_name":"Hidetomo","full_name":"Usui, Hidetomo"},{"full_name":"Ochi, Masayuki","first_name":"Masayuki","last_name":"Ochi"},{"full_name":"Kitamura, Sota","last_name":"Kitamura","first_name":"Sota"},{"full_name":"Oka, Takashi","last_name":"Oka","first_name":"Takashi"},{"full_name":"Ogura, Daisuke","last_name":"Ogura","first_name":"Daisuke"},{"last_name":"Rosner","first_name":"Helge","full_name":"Rosner, Helge"},{"full_name":"Haverkort, Maurits W.","first_name":"Maurits W.","last_name":"Haverkort"},{"full_name":"Sunko, Veronika","id":"23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3","orcid":"0000-0003-2724-3523","last_name":"Sunko","first_name":"Veronika"},{"full_name":"King, Philip D. C.","last_name":"King","first_name":"Philip D. C."},{"last_name":"Mackenzie","first_name":"Andrew P.","full_name":"Mackenzie, Andrew P."},{"first_name":"Kazuhiko","last_name":"Kuroki","full_name":"Kuroki, Kazuhiko"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"repository","volume":3,"title":"Hidden kagome-lattice picture and origin of high conductivity in delafossite PtCoO2","article_processing_charge":"No","abstract":[{"lang":"eng","text":"We study the electronic structure of delafossite PtCoO2 to elucidate its extremely small resistivity and high mobility. The band exhibits steep dispersion near the Fermi level despite the fact that it is formed mainly by Pt 𝑑 orbitals that are typically localized. We propose a picture based on two hidden kagome-lattice-like electronic structures: one originating from Pt 𝑠+𝑝𝑥/𝑝𝑦 orbitals, and the other from Pt 𝑑3⁢𝑧2−𝑟2+𝑑𝑥⁢𝑦/𝑑𝑥2−𝑦2 orbitals, each placed on the bonds of the triangular lattice. In particular, we find that the underlying Pt 𝑠+𝑝𝑥/𝑝𝑦 bands actually determine the steepness of the original dispersion, so that the large Fermi velocity can be attributed to the large width of the Pt 𝑠+𝑝𝑥/𝑝𝑦 band. In addition, the kagome-like electronic structure gives rise to “orbital-momentum locking” on the Fermi surface, which reduces the electron scattering by impurities. We conclude that the combination of the large Fermi velocity and the orbital-momentum locking is likely to be the origin of the extremely small resistivity in PtCoO2."}],"external_id":{"arxiv":["1812.07213"]},"publication_status":"published","issue":"4","doi":"10.1103/physrevmaterials.3.045002","publication_identifier":{"issn":["2475-9953"]},"publication":"Physical Review Materials","year":"2019","date_created":"2025-06-10T09:22:04Z","article_number":"045002","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1812.07213"}],"quality_controlled":"1","_id":"19825","scopus_import":"1","article_type":"original","oa_version":"Preprint","intvolume":"         3","type":"journal_article","language":[{"iso":"eng"}],"month":"04","date_published":"2019-04-12T00:00:00Z","arxiv":1,"publisher":"American Physical Society","date_updated":"2025-06-11T06:05:56Z","oa":1,"day":"12","status":"public","OA_type":"green","citation":{"chicago":"Usui, Hidetomo, Masayuki Ochi, Sota Kitamura, Takashi Oka, Daisuke Ogura, Helge Rosner, Maurits W. Haverkort, et al. “Hidden Kagome-Lattice Picture and Origin of High Conductivity in Delafossite PtCoO2.” <i>Physical Review Materials</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/physrevmaterials.3.045002\">https://doi.org/10.1103/physrevmaterials.3.045002</a>.","apa":"Usui, H., Ochi, M., Kitamura, S., Oka, T., Ogura, D., Rosner, H., … Kuroki, K. (2019). Hidden kagome-lattice picture and origin of high conductivity in delafossite PtCoO2. <i>Physical Review Materials</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevmaterials.3.045002\">https://doi.org/10.1103/physrevmaterials.3.045002</a>","mla":"Usui, Hidetomo, et al. “Hidden Kagome-Lattice Picture and Origin of High Conductivity in Delafossite PtCoO2.” <i>Physical Review Materials</i>, vol. 3, no. 4, 045002, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/physrevmaterials.3.045002\">10.1103/physrevmaterials.3.045002</a>.","ieee":"H. Usui <i>et al.</i>, “Hidden kagome-lattice picture and origin of high conductivity in delafossite PtCoO2,” <i>Physical Review Materials</i>, vol. 3, no. 4. American Physical Society, 2019.","short":"H. Usui, M. Ochi, S. Kitamura, T. Oka, D. Ogura, H. Rosner, M.W. Haverkort, V. Sunko, P.D.C. King, A.P. Mackenzie, K. Kuroki, Physical Review Materials 3 (2019).","ama":"Usui H, Ochi M, Kitamura S, et al. Hidden kagome-lattice picture and origin of high conductivity in delafossite PtCoO2. <i>Physical Review Materials</i>. 2019;3(4). doi:<a href=\"https://doi.org/10.1103/physrevmaterials.3.045002\">10.1103/physrevmaterials.3.045002</a>","ista":"Usui H, Ochi M, Kitamura S, Oka T, Ogura D, Rosner H, Haverkort MW, Sunko V, King PDC, Mackenzie AP, Kuroki K. 2019. Hidden kagome-lattice picture and origin of high conductivity in delafossite PtCoO2. Physical Review Materials. 3(4), 045002."}},{"oa":1,"publisher":"American Physical Society","arxiv":1,"date_updated":"2025-06-11T06:08:51Z","month":"01","language":[{"iso":"eng"}],"date_published":"2019-01-25T00:00:00Z","type":"journal_article","article_type":"original","intvolume":"        99","oa_version":"Preprint","_id":"19826","scopus_import":"1","citation":{"apa":"Clark, O. J., Mazzola, F., Feng, J., Sunko, V., Marković, I., Bawden, L., … Bahramy, M. S. (2019). Dual quantum confinement and anisotropic spin splitting in the multivalley semimetal PtSe2. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.99.045438\">https://doi.org/10.1103/physrevb.99.045438</a>","chicago":"Clark, O. J., F. Mazzola, J. Feng, Veronika Sunko, I. Marković, L. Bawden, T. K. Kim, P. D. C. King, and M. S. Bahramy. “Dual Quantum Confinement and Anisotropic Spin Splitting in the Multivalley Semimetal PtSe2.” <i>Physical Review B</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/physrevb.99.045438\">https://doi.org/10.1103/physrevb.99.045438</a>.","mla":"Clark, O. J., et al. “Dual Quantum Confinement and Anisotropic Spin Splitting in the Multivalley Semimetal PtSe2.” <i>Physical Review B</i>, vol. 99, no. 4, 045438, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/physrevb.99.045438\">10.1103/physrevb.99.045438</a>.","ieee":"O. J. Clark <i>et al.</i>, “Dual quantum confinement and anisotropic spin splitting in the multivalley semimetal PtSe2,” <i>Physical Review B</i>, vol. 99, no. 4. American Physical Society, 2019.","short":"O.J. Clark, F. Mazzola, J. Feng, V. Sunko, I. Marković, L. Bawden, T.K. Kim, P.D.C. King, M.S. Bahramy, Physical Review B 99 (2019).","ista":"Clark OJ, Mazzola F, Feng J, Sunko V, Marković I, Bawden L, Kim TK, King PDC, Bahramy MS. 2019. Dual quantum confinement and anisotropic spin splitting in the multivalley semimetal PtSe2. Physical Review B. 99(4), 045438.","ama":"Clark OJ, Mazzola F, Feng J, et al. Dual quantum confinement and anisotropic spin splitting in the multivalley semimetal PtSe2. <i>Physical Review B</i>. 2019;99(4). doi:<a href=\"https://doi.org/10.1103/physrevb.99.045438\">10.1103/physrevb.99.045438</a>"},"OA_type":"green","status":"public","day":"25","abstract":[{"lang":"eng","text":"We investigate the electronic structure of a two-dimensional electron gas created at the surface of the multivalley semimetal 1⁢T −PtSe2. Using angle-resolved photoemission and first-principles-based surface space-charge calculations, we show how the induced quantum well sub-band states form multiple Fermi surfaces, which exhibit highly anisotropic Rashba-like spin splittings. We further show how the presence of both electronlike and holelike bulk carriers causes the near-surface band bending potential to develop an unusual nonmonotonic form, with spatially segregated electron accumulation and hole accumulation regions, which in turn amplifies the induced spin splitting. Our results thus demonstrate the novel environment that semimetals provide for tailoring electrostatically induced potential profiles and their corresponding quantum sub-band states."}],"publication_status":"published","external_id":{"arxiv":["1812.04485"]},"article_processing_charge":"No","title":"Dual quantum confinement and anisotropic spin splitting in the multivalley semimetal PtSe2","volume":99,"OA_place":"repository","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Clark, O. J.","last_name":"Clark","first_name":"O. J."},{"full_name":"Mazzola, F.","last_name":"Mazzola","first_name":"F."},{"full_name":"Feng, J.","first_name":"J.","last_name":"Feng"},{"orcid":"0000-0003-2724-3523","id":"23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3","full_name":"Sunko, Veronika","last_name":"Sunko","first_name":"Veronika"},{"full_name":"Marković, I.","last_name":"Marković","first_name":"I."},{"first_name":"L.","last_name":"Bawden","full_name":"Bawden, L."},{"last_name":"Kim","first_name":"T. K.","full_name":"Kim, T. K."},{"full_name":"King, P. D. C.","last_name":"King","first_name":"P. D. C."},{"full_name":"Bahramy, M. S.","first_name":"M. S.","last_name":"Bahramy"}],"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1812.04485","open_access":"1"}],"article_number":"045438","year":"2019","date_created":"2025-06-10T09:22:38Z","publication":"Physical Review B","issue":"4","doi":"10.1103/physrevb.99.045438","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]}},{"oa_version":"Preprint","intvolume":"         2","acknowledgement":"Y.Y. would like to thank the organizers of the MATRIX program Geometric R-Matrices: from Geometry to Probability for their kind invitation, and many participants of the program for useful discussions, including Vassily Gorbounov, Andrei Okounkov, Allen Knutson, Hitoshi Konno, Paul Zinn-Justin. Proposition 1 and Sect. 3.3 are new, for which we thank Hitoshi Konno for interesting discussions and communications. These notes were written when both authors were visiting the Perimeter Institute for Theoretical Physics (PI). We are grateful to PI for the hospitality.","type":"book_chapter","_id":"19987","oa":1,"date_published":"2019-03-25T00:00:00Z","language":[{"iso":"eng"}],"month":"03","date_updated":"2025-09-23T11:59:52Z","department":[{"_id":"TaHa"}],"publisher":"Springer International Publishing","arxiv":1,"OA_type":"green","place":"Cham","alternative_title":["MATRIX Book Series"],"series_title":"MXBS","day":"25","status":"public","citation":{"short":"Y. Yang, G. Zhao, in:, 2017 MATRIX Annals, Springer International Publishing, Cham, 2019, pp. 675–691.","ieee":"Y. Yang and G. Zhao, “How to Sheafify an Elliptic Quantum Group,” in <i>2017 MATRIX Annals</i>, vol. 2, Cham: Springer International Publishing, 2019, pp. 675–691.","ista":"Yang Y, Zhao G. 2019.How to Sheafify an Elliptic Quantum Group. In: 2017 MATRIX Annals. MATRIX Book Series, vol. 2, 675–691.","ama":"Yang Y, Zhao G. How to Sheafify an Elliptic Quantum Group. In: <i>2017 MATRIX Annals</i>. Vol 2. MXBS. Cham: Springer International Publishing; 2019:675-691. doi:<a href=\"https://doi.org/10.1007/978-3-030-04161-8_54\">10.1007/978-3-030-04161-8_54</a>","chicago":"Yang, Yaping, and Gufang Zhao. “How to Sheafify an Elliptic Quantum Group.” In <i>2017 MATRIX Annals</i>, 2:675–91. MXBS. Cham: Springer International Publishing, 2019. <a href=\"https://doi.org/10.1007/978-3-030-04161-8_54\">https://doi.org/10.1007/978-3-030-04161-8_54</a>.","apa":"Yang, Y., &#38; Zhao, G. (2019). How to Sheafify an Elliptic Quantum Group. In <i>2017 MATRIX Annals</i> (Vol. 2, pp. 675–691). Cham: Springer International Publishing. <a href=\"https://doi.org/10.1007/978-3-030-04161-8_54\">https://doi.org/10.1007/978-3-030-04161-8_54</a>","mla":"Yang, Yaping, and Gufang Zhao. “How to Sheafify an Elliptic Quantum Group.” <i>2017 MATRIX Annals</i>, vol. 2, Springer International Publishing, 2019, pp. 675–91, doi:<a href=\"https://doi.org/10.1007/978-3-030-04161-8_54\">10.1007/978-3-030-04161-8_54</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"360D8648-F248-11E8-B48F-1D18A9856A87","full_name":"Yang, Yaping","last_name":"Yang","first_name":"Yaping"},{"last_name":"Zhao","first_name":"Gufang","id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87","full_name":"Zhao, Gufang"}],"OA_place":"repository","volume":2,"article_processing_charge":"No","page":"675-691","publication_status":"published","external_id":{"arxiv":["1803.06627"]},"abstract":[{"text":"These lecture notes are based on Yang’s talk at the MATRIX program Geometric R-Matrices: from Geometry to Probability, at the University of Melbourne, Dec. 18–22, 2017, and Zhao’s talk at Perimeter Institute for Theoretical Physics in January 2018. We give an introductory survey of the results in Yang and Zhao (Quiver varieties and elliptic quantum groups, 2017. arxiv1708.01418). We discuss a sheafified elliptic quantum group associated to any symmetric Kac-Moody Lie algebra. The sheafification is obtained by applying the equivariant elliptic cohomological theory to the moduli space of representations of a preprojective algebra. By construction, the elliptic quantum group naturally acts on the equivariant elliptic cohomology of Nakajima quiver varieties. As an application, we obtain a relation between the sheafified elliptic quantum group and the global affine Grassmannian over an elliptic curve.","lang":"eng"}],"title":"How to Sheafify an Elliptic Quantum Group","date_created":"2025-07-10T13:31:38Z","year":"2019","publication_identifier":{"eissn":["2523-305X"],"isbn":["9783030041601"],"issn":["2523-3041"],"eisbn":["9783030041618"]},"doi":"10.1007/978-3-030-04161-8_54","publication":"2017 MATRIX Annals","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1803.06627","open_access":"1"}]},{"type":"book_chapter","oa_version":"Preprint","_id":"19988","oa":1,"arxiv":1,"department":[{"_id":"GaTk"}],"publisher":"World Scientific Publishing","date_updated":"2025-09-23T11:53:34Z","language":[{"iso":"eng"}],"month":"09","date_published":"2019-09-01T00:00:00Z","OA_type":"green","day":"01","status":"public","citation":{"ama":"De Martino A, De Martino D, Marinari E. The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges. In: <i>Chemical Kinetics</i>. World Scientific Publishing; 2019:455-471. doi:<a href=\"https://doi.org/10.1142/9781786347015_0018\">10.1142/9781786347015_0018</a>","ista":"De Martino A, De Martino D, Marinari E. 2019.The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges. In: Chemical Kinetics. , 455–471.","short":"A. De Martino, D. De Martino, E. Marinari, in:, Chemical Kinetics, World Scientific Publishing, 2019, pp. 455–471.","ieee":"A. De Martino, D. De Martino, and E. Marinari, “The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges,” in <i>Chemical Kinetics</i>, World Scientific Publishing, 2019, pp. 455–471.","mla":"De Martino, A., et al. “The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges.” <i>Chemical Kinetics</i>, World Scientific Publishing, 2019, pp. 455–71, doi:<a href=\"https://doi.org/10.1142/9781786347015_0018\">10.1142/9781786347015_0018</a>.","chicago":"De Martino, A, Daniele De Martino, and E Marinari. “The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges.” In <i>Chemical Kinetics</i>, 455–71. World Scientific Publishing, 2019. <a href=\"https://doi.org/10.1142/9781786347015_0018\">https://doi.org/10.1142/9781786347015_0018</a>.","apa":"De Martino, A., De Martino, D., &#38; Marinari, E. (2019). The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges. In <i>Chemical Kinetics</i> (pp. 455–471). World Scientific Publishing. <a href=\"https://doi.org/10.1142/9781786347015_0018\">https://doi.org/10.1142/9781786347015_0018</a>"},"OA_place":"repository","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"De Martino","first_name":"A","full_name":"De Martino, A"},{"first_name":"Daniele","last_name":"De Martino","orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele"},{"first_name":"E","last_name":"Marinari","full_name":"Marinari, E"}],"abstract":[{"lang":"eng","text":"Quantitative studies of cell metabolism are often based on large chemical reaction network models. A steady-state approach is suited to analyze phenomena on the timescale of cell growth and circumvents the problem of incomplete experimental knowledge on kinetic laws and parameters, but it should be supported by a correct implementation of thermodynamic constraints. In this chapter, we review the latter aspect, highlighting its computational challenges and physical insights. The simple introduction of Gibbs inequalities avoids the presence of unfeasible loops allowing for correct timescale analysis, but leads to possibly non-convex feasible flux spaces whose exploration needs efficient algorithms. We briefly review the implementation of thermodynamics through variational principles in constraint-based models of metabolic networks."}],"publication_status":"published","external_id":{"arxiv":["1902.07129"]},"page":"455-471","article_processing_charge":"No","title":"The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges","year":"2019","date_created":"2025-07-10T13:34:01Z","publication":"Chemical Kinetics","doi":"10.1142/9781786347015_0018","publication_identifier":{"isbn":["9781786347008"],"eisbn":["9781786347022"]},"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1902.07129"}]},{"edition":"32","article_processing_charge":"No","page":"72-82","publication_status":"published","abstract":[{"lang":"ger","text":"Neurone empfangen Eingangssignale, konvertieren diese in Aktionspotenziale und generieren schließlich Ausgangssignale auf ihren Zielzellen. Dabei sind die zu überwindenden räumlichen Distanzen oft groß. Daher ist entscheidend, dass elektrische Signale in Nervenzellen schnell von einem zum anderen Ort geleitet werden können. Diese wichtige Aufgabe erfüllt das Axon, der „Ausgangsfortsatz“ der Nervenzelle. Für die schnelle Leitung des Aktionspotenzials sind sowohl die passiven Eigenschaften des axonalen Kabels als auch die aktiven Eigenschaften der Zellmembran von entscheidender Bedeutung. Die Evolution bedient sich zweier Tricks, um die Leitungsgeschwindigkeit des Aktionspotenzials zu maximieren. Der eine Trick ist die Zunahme des Axondurchmessers. Der andere Trick ist die Ausbildung von Markscheiden. Dies führt bei nahezu gleichem Platzbedarf zu einer Zunahme der Leistungsgeschwindigkeit um fast zwei Größenordnungen. Die Aktionspotenzialleitung an myelinisierten Axonen erfolgt „saltatorisch“."}],"date_published":"2019-04-02T00:00:00Z","language":[{"iso":"ger"}],"month":"04","title":"Aktionspotenzial: Fortleitung im Axon","date_updated":"2025-09-23T11:44:57Z","department":[{"_id":"PeJo"}],"publisher":"Springer Nature","oa_version":"None","author":[{"first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"book_chapter","_id":"19989","citation":{"ama":"Jonas PM. Aktionspotenzial: Fortleitung im Axon. In: <i>Physiologie des Menschen</i>. 32nd ed. Springer-Lehrbuch. Berlin, Heidelberg: Springer Nature; 2019:72-82. doi:<a href=\"https://doi.org/10.1007/978-3-662-56468-4_7\">10.1007/978-3-662-56468-4_7</a>","ista":"Jonas PM. 2019.Aktionspotenzial: Fortleitung im Axon. In: Physiologie des Menschen. , 72–82.","ieee":"P. M. Jonas, “Aktionspotenzial: Fortleitung im Axon,” in <i>Physiologie des Menschen</i>, 32nd ed., Berlin, Heidelberg: Springer Nature, 2019, pp. 72–82.","short":"P.M. Jonas, in:, Physiologie des Menschen, 32nd ed., Springer Nature, Berlin, Heidelberg, 2019, pp. 72–82.","mla":"Jonas, Peter M. “Aktionspotenzial: Fortleitung im Axon.” <i>Physiologie des Menschen</i>, 32nd ed., Springer Nature, 2019, pp. 72–82, doi:<a href=\"https://doi.org/10.1007/978-3-662-56468-4_7\">10.1007/978-3-662-56468-4_7</a>.","apa":"Jonas, P. M. (2019). Aktionspotenzial: Fortleitung im Axon. In <i>Physiologie des Menschen</i> (32nd ed., pp. 72–82). Berlin, Heidelberg: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-662-56468-4_7\">https://doi.org/10.1007/978-3-662-56468-4_7</a>","chicago":"Jonas, Peter M. “Aktionspotenzial: Fortleitung im Axon.” In <i>Physiologie des Menschen</i>, 32nd ed., 72–82. Springer-Lehrbuch. Berlin, Heidelberg: Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-662-56468-4_7\">https://doi.org/10.1007/978-3-662-56468-4_7</a>."},"corr_author":"1","quality_controlled":"1","date_created":"2025-07-10T13:36:36Z","year":"2019","OA_type":"closed access","doi":"10.1007/978-3-662-56468-4_7","publication_identifier":{"isbn":["9783662564677"],"eisbn":["9783662564684"],"issn":["0937-7433"],"eissn":["2512-5214"]},"place":"Berlin, Heidelberg","series_title":"Springer-Lehrbuch","status":"public","day":"02","publication":"Physiologie des Menschen"},{"file_date_updated":"2021-11-12T11:41:56Z","oa":1,"date_updated":"2026-04-08T07:00:31Z","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"arxiv":1,"publisher":"ACM","date_published":"2019-10-10T00:00:00Z","language":[{"iso":"eng"}],"month":"10","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","type":"conference","intvolume":"         3","oa_version":"Published Version","scopus_import":"1","_id":"10190","project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"}],"citation":{"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>.","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>.","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.","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.","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."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"hybrid","day":"10","status":"public","publication_status":"published","external_id":{"arxiv":["1909.00989"]},"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."}],"article_processing_charge":"No","keyword":["safety","risk","reliability and quality","software"],"title":"Value-centric dynamic partial order reduction","OA_place":"publisher","volume":3,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","first_name":"Andreas"},{"last_name":"Toman","first_name":"Viktor","full_name":"Toman, Viktor","orcid":"0000-0001-9036-063X","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"10199","status":"public"}]},"quality_controlled":"1","file":[{"access_level":"open_access","checksum":"2149979c46964c4d117af06ccb6c0834","relation":"main_file","file_size":570829,"date_updated":"2021-11-12T11:41:56Z","file_id":"10278","success":1,"creator":"cchlebak","date_created":"2021-11-12T11:41:56Z","file_name":"2019_ACM_Chatterjee.pdf","content_type":"application/pdf"}],"corr_author":"1","conference":{"name":"OOPSLA: Object-oriented Programming, Systems, Languages and Applications","start_date":"2019-10-23","location":"Athens, Greece","end_date":"2019-10-25"},"ddc":["000"],"has_accepted_license":"1","article_number":"124","date_created":"2021-10-27T14:57:06Z","year":"2019","publication":"Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications","publication_identifier":{"eissn":["2475-1421"]},"doi":"10.1145/3360550"},{"ddc":["570"],"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/559898","open_access":"1"}],"has_accepted_license":"1","quality_controlled":"1","file":[{"access_level":"open_access","checksum":"31d8bae55a376d30925f53f7e1a02396","relation":"main_file","file_size":1648926,"date_updated":"2021-11-26T11:37:54Z","file_id":"10356","success":1,"creator":"cchlebak","date_created":"2021-11-26T11:37:54Z","content_type":"application/pdf","file_name":"2019_BMCBio_Harker_Kirschneck.pdf"}],"publication":"BMC Biology","doi":"10.1186/s12915-019-0700-2","publication_identifier":{"issn":["1741-7007"]},"issue":"1","article_number":"82","date_created":"2021-11-26T11:25:03Z","year":"2019","keyword":["cell biology"],"title":"Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico","external_id":{"pmid":["31640700"]},"publication_status":"published","abstract":[{"lang":"eng","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."}],"article_processing_charge":"No","pmid":1,"volume":17,"author":[{"first_name":"Lena","last_name":"Harker-Kirschneck","full_name":"Harker-Kirschneck, Lena"},{"first_name":"Buzz","last_name":"Baum","full_name":"Baum, Buzz"},{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","citation":{"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>.","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>","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.","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.","short":"L. Harker-Kirschneck, B. Baum, A. Šarić, BMC Biology 17 (2019)."},"status":"public","day":"22","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_updated":"2021-11-26T11:54:29Z","publisher":"Springer Nature","date_published":"2019-10-22T00:00:00Z","month":"10","language":[{"iso":"eng"}],"file_date_updated":"2021-11-26T11:37:54Z","oa":1,"scopus_import":"1","_id":"10354","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.","type":"journal_article","intvolume":"        17","oa_version":"Published Version","article_type":"original"},{"day":"18","status":"public","citation":{"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>.","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>","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>.","short":"A.E. Hafner, J. Krausser, A. Šarić, Current Opinion in Structural Biology 58 (2019) 43–52.","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>","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."},"scopus_import":"1","_id":"10355","oa_version":"Preprint","intvolume":"        58","article_type":"original","type":"journal_article","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.","date_published":"2019-06-18T00:00:00Z","language":[{"iso":"eng"}],"month":"06","date_updated":"2021-11-26T11:54:25Z","publisher":"Elsevier","oa":1,"publication_identifier":{"issn":["0959-440X"]},"doi":"10.1016/j.sbi.2019.05.018","publication":"Current Opinion in Structural Biology","date_created":"2021-11-26T11:33:21Z","year":"2019","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.09349"}],"quality_controlled":"1","pmid":1,"author":[{"full_name":"Hafner, Anne E","last_name":"Hafner","first_name":"Anne E"},{"last_name":"Krausser","first_name":"Johannes","full_name":"Krausser, Johannes"},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","volume":58,"keyword":["molecular biology","structural biology"],"title":"Minimal coarse-grained models for molecular self-organisation in biology","article_processing_charge":"No","page":"43-52","external_id":{"pmid":["31226513"]},"publication_status":"published","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"}]},{"date_published":"2019-01-01T00:00:00Z","month":"01","language":[{"iso":"eng"}],"date_updated":"2026-06-18T08:42:55Z","publisher":"Springer Nature","department":[{"_id":"GaNo"}],"isi":1,"oa":1,"publist_id":"7949","scopus_import":"1","_id":"105","intvolume":"        27","oa_version":"Published Version","article_type":"original","type":"journal_article","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.","citation":{"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.","short":"A. Marsh, G. Novarino, P. Lockhart, R. Leventer, European Journal of Human Genetics 27 (2019) 161–166.","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>","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>.","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>."},"day":"01","status":"public","title":"CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63","article_processing_charge":"No","page":"161-166","publication_status":"published","external_id":{"isi":["000454111500019"],"pmid":["30089829"]},"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."}],"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Marsh, Ashley","last_name":"Marsh","first_name":"Ashley"},{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino"},{"first_name":"Paul","last_name":"Lockhart","full_name":"Lockhart, Paul"},{"first_name":"Richard","last_name":"Leventer","full_name":"Leventer, Richard"}],"volume":27,"main_file_link":[{"url":"https://doi.org/10.1038/s41431-018-0231-2","open_access":"1"}],"ddc":["570"],"quality_controlled":"1","doi":"10.1038/s41431-018-0231-2","publication":"European Journal of Human Genetics","date_created":"2018-12-11T11:44:39Z","year":"2019"}]