[{"citation":{"chicago":"Peng, Yakun, Kangkang Ji, Yanbo Mao, Yiqun Wang, Barbara Korbei, Christian Luschnig, Jinbo Shen, Eva Benková, Jiří Friml, and Shutang Tan. “Polarly Localized Bro1 Domain Proteins Regulate PIN-FORMED Abundance and Root Gravitropic Growth in Arabidopsis.” <i>Communications Biology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s42003-024-06747-9\">https://doi.org/10.1038/s42003-024-06747-9</a>.","ista":"Peng Y, Ji K, Mao Y, Wang Y, Korbei B, Luschnig C, Shen J, Benková E, Friml J, Tan S. 2024. Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis. Communications Biology. 7, 1085.","ama":"Peng Y, Ji K, Mao Y, et al. Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis. <i>Communications Biology</i>. 2024;7. doi:<a href=\"https://doi.org/10.1038/s42003-024-06747-9\">10.1038/s42003-024-06747-9</a>","mla":"Peng, Yakun, et al. “Polarly Localized Bro1 Domain Proteins Regulate PIN-FORMED Abundance and Root Gravitropic Growth in Arabidopsis.” <i>Communications Biology</i>, vol. 7, 1085, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s42003-024-06747-9\">10.1038/s42003-024-06747-9</a>.","apa":"Peng, Y., Ji, K., Mao, Y., Wang, Y., Korbei, B., Luschnig, C., … Tan, S. (2024). Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-024-06747-9\">https://doi.org/10.1038/s42003-024-06747-9</a>","ieee":"Y. Peng <i>et al.</i>, “Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis,” <i>Communications Biology</i>, vol. 7. Springer Nature, 2024.","short":"Y. Peng, K. Ji, Y. Mao, Y. Wang, B. Korbei, C. Luschnig, J. Shen, E. Benková, J. Friml, S. Tan, Communications Biology 7 (2024)."},"external_id":{"pmid":["39232040"],"isi":["001306499600002"]},"project":[{"_id":"bd76d395-d553-11ed-ba76-f678c14f9033","name":"Peptide receptors for auxin canalization in Arabidopsis","grant_number":"I06123"},{"name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","grant_number":"P37051","_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6"}],"volume":7,"acknowledgement":"We thank Drs. Erika Isono (University of Constance), Grégory Vert (University of Toulouse), and Liwen Jiang (The Chinese University of Hong Kong) for kindly sharing published Arabidopsis lines; Dr. Yuzhou Zhang (ISTA) for help with molecular cloning, and Drs. Melinda Abas (BOKU), Eugenia Russinova (Ghent University), and Zhaojun Ding (Shandong University) for valuable discussions. This work was supported by grants to S.T. from the National Natural Science Foundation of China (32321001), the USTC Research Funds of the Double First-Class Initiative (YD9100002016), the Research Funds from the Center for Advanced Interdisciplinary Science and Biomedicine of IHM, the Division of Life Sciences and Medicine, the University of Science and Technology of China (QYPY20220012), the Fundamental Research Funds for the Central Universities (WK9100000021), and start-up funding from the University of Science and Technology of China and the Chinese Academy of Sciences (GG9100007007, KY9100000026, KY9100000051, and KJ2070000079). J.S. was supported by the National Natural Science Foundation of China (31970181 and 32170342). J.F. was supported by Austrian Science Fund (FWF; projects I6123 and P37051-B).","publication_status":"published","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"supplementarymaterial":"yes","date_updated":"2026-10-07T22:31:35Z","article_type":"original","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"date_created":"2024-09-17T09:44:29Z","file_size":7718758,"creator":"dernst","access_level":"open_access","date_updated":"2024-09-17T09:44:29Z","file_id":"18084","checksum":"7d66af41c90e73d1b8a375eb652a9561","relation":"main_file","content_type":"application/pdf","file_name":"2024_CommBiology_Peng.pdf","success":1}],"intvolume":"         7","quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-09-15T22:01:38Z","oa_version":"Published Version","researchdata_availability":"yes (supplementary data)","date_published":"2024-09-04T00:00:00Z","dataavailabilitystatement":"The RNA-seq data for this study are available online at the NCBI Sequence Read Archive (accession number: PRJNA1116831). Uncropped images of the DNA gels are provided in the Supplementary Figs. 21 to 22. The source data used to generate the plots are provided in the Supplementary Data 2.","type":"journal_article","has_accepted_license":"1","das_tickbox":"1","isi":1,"article_number":"1085","author":[{"last_name":"Peng","full_name":"Peng, Yakun","first_name":"Yakun"},{"last_name":"Ji","first_name":"Kangkang","full_name":"Ji, Kangkang"},{"last_name":"Mao","full_name":"Mao, Yanbo","first_name":"Yanbo"},{"last_name":"Wang","first_name":"Yiqun","id":"82F537F2-B517-11E9-84D7-6433E6697425","full_name":"Wang, Yiqun"},{"last_name":"Korbei","full_name":"Korbei, Barbara","first_name":"Barbara"},{"first_name":"Christian","full_name":"Luschnig, Christian","last_name":"Luschnig"},{"first_name":"Jinbo","full_name":"Shen, Jinbo","last_name":"Shen"},{"orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","last_name":"Benková"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"first_name":"Shutang","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan"}],"pmid":1,"related_material":{"record":[{"id":"20117","relation":"dissertation_contains","status":"public"}]},"abstract":[{"text":"The developmental plasticity of the root system plays an essential role in the adaptation of plants to the environment. Among many other signals, auxin and its directional, intercellular transport are critical in regulating root growth and development. In particular, the PIN-FORMED2 (PIN2) auxin exporter acts as a key regulator of root gravitropic growth. Multiple regulators have been reported to be involved in PIN2-mediated root growth; however, our information remains incomplete. Here, we identified ROWY Bro1-domain proteins as important regulators of PIN2 sorting control. Genetic analysis revealed that Arabidopsis rowy1 single mutants and higher-order rowy1 rowy2 rowy3 triple mutants presented a wavy root growth phenotype. Cell biological experiments revealed that ROWY1 and PIN2 colocalized to the apical side of the plasma membrane in the root epidermis and that ROWYs are required for correct PM targeting of PIN2. In addition, ROWYs also affected PIN3 protein abundance in the stele, suggesting the potential involvement of additional PIN transporters as well as other proteins. A global transcriptome analysis revealed that ROWY genes are involved in the Fe2+ availability perception pathway. This work establishes ROWYs as important novel regulators of root gravitropic growth by connecting micronutrient availability to the proper subcellular targeting of PIN auxin transporters.","lang":"eng"}],"day":"04","publication_identifier":{"eissn":["2399-3642"]},"doi":"10.1038/s42003-024-06747-9","file_date_updated":"2024-09-17T09:44:29Z","publisher":"Springer Nature","fulldoi":"https://doi.org/10.1038/s42003-024-06747-9","ddc":["570"],"scopus_import":"1","title":"Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis","article_processing_charge":"Yes","oa":1,"_id":"18063","status":"public","month":"09","year":"2024","publication":"Communications Biology"},{"project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692","call_identifier":"H2020"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312","call_identifier":"FWF"},{"grant_number":"P36232","name":"Mechanisms of GABA release in hippocampal circuits","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5"},{"_id":"26B66A3E-B435-11E9-9278-68D0E5697425","name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","grant_number":"25383"}],"supervisor":[{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"ec_funded":1,"citation":{"chicago":"Chen, JingJing. “Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15101\">https://doi.org/10.15479/at:ista:15101</a>.","ista":"Chen J. 2024. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria.","ama":"Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15101\">10.15479/at:ista:15101</a>","mla":"Chen, JingJing. <i>Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15101\">10.15479/at:ista:15101</a>.","apa":"Chen, J. (2024). <i>Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15101\">https://doi.org/10.15479/at:ista:15101</a>","ieee":"J. Chen, “Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse,” Institute of Science and Technology Austria, 2024.","short":"J. Chen, Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse, Institute of Science and Technology Austria, 2024."},"page":"84","oa_version":"Published Version","date_created":"2024-03-11T10:09:54Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"researchdata_availability":"no","date_published":"2024-03-11T00:00:00Z","has_accepted_license":"1","type":"dissertation","department":[{"_id":"GradSch"},{"_id":"PeJo"}],"publication_status":"published","date_updated":"2026-10-02T11:42:02Z","supplementarymaterial":"no","file":[{"relation":"source_file","checksum":"db4947474ffa271e66c254b6fe876a55","file_id":"15104","date_updated":"2024-04-02T22:30:03Z","file_name":"Thesis_Jingjing CHEN.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"jchen","file_size":11271363,"date_created":"2024-03-11T14:10:58Z","access_level":"closed","embargo_to":"open_access"},{"date_created":"2024-03-11T14:11:06Z","creator":"jchen","embargo":"2024-04-01","file_size":16627311,"access_level":"open_access","date_updated":"2024-04-02T22:30:03Z","relation":"main_file","checksum":"a5eeae8b5702cd540f5d03469bc33dde","file_id":"15105","file_name":"Thesis_Jingjing CHEN_merged.pdf","content_type":"application/pdf"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"doi_confirm":"1","author":[{"last_name":"Chen","first_name":"JingJing","full_name":"Chen, JingJing","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"14843"}]},"abstract":[{"text":"The coupling between presynaptic Ca2+ channels and release sensors is a key factor that\r\ndetermines speed and efficacy of synapse transmission. At some excitatory synapses,\r\nchannel–sensor coupling becomes tighter during development, and tightening is often\r\nassociated with a switch in the reliance on different Ca2+ channel subtypes. However, the\r\ncoupling topography at many synapses remains unknown, and it is unclear how it changes\r\nduring development. To address this question, we analyzed the coupling configuration at the\r\ncerebellar basket cell (BC) to Purkinje cell (PC) synapse at different developmental stages,\r\ncombining biophysical analysis, structural analysis, and modeling.\r\nQuantal analysis of BC–PC indicated that release probability decreased, while the\r\nnumber of functional sites increased during development. Although transmitter release\r\npersistently relied on P/Q-type Ca2+ channels in the time period postnatal day 7–23, effects\r\nof the Ca2+ chelator EGTA and BAPTA applied by intracellular pipette perfusion decreased\r\nduring development, indicative of tightening of source-sensor coupling. Furthermore,\r\npresynaptic action potentials became shorter during development, suggesting reduced\r\nefficacy of Ca2+ channel activation.\r\nStructural analysis by freeze-fracture replica labeling (FRL) and transmission electron\r\nmicroscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters\r\nthroughout development, whereas docked vesicles were only clustered at later\r\ndevelopmental stages. The number of functional release sites correlated better with the AZ\r\nnumber early in development, but match better with the Ca2+ channel cluster number at later\r\nstages.\r\nModeling suggested a developmental transformation from a more random to a more\r\nclustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches\r\na point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic\r\ntransmission.","lang":"eng"}],"corr_author":"1","das_tickbox":"0","acknowledged_ssus":[{"_id":"EM-Fac"}],"title":"Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse","oa":1,"article_processing_charge":"No","year":"2024","status":"public","_id":"15101","month":"03","alternative_title":["ISTA Thesis"],"day":"11","publication_identifier":{"issn":["2663-337X"]},"publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:15101","OA_place":"publisher","file_date_updated":"2024-04-02T22:30:03Z","fulldoi":"https://doi.org/10.15479/at:ista:15101","ddc":["570"]},{"project":[{"name":"Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development","grant_number":"26253","_id":"34c9fbcb-11ca-11ed-8bc3-98fa5658610d"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F7805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"}],"acknowledgement":"We thank all Hippenmeyer lab members for support and discussions. This work was supported by the Scientific Service Units (SSU) at ISTA through resources provided by the Imaging & Optics Facility (IOF). O.A.M was a recipient of a DOC Fellowship (26253) of the Austrian Academy of Sciences. This work was supported by ISTA institutional funds, and The Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H.","volume":2831,"external_id":{"pmid":["39134857"]},"page":"283-299","citation":{"chicago":"Miranda, Osvaldo, Giselle T Cheung, and Simon Hippenmeyer. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” In <i>Neuronal Morphogenesis</i>, edited by Kazuhito Toyooka, 1st ed., 2831:283–99. MIMB. New York, NY: Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">https://doi.org/10.1007/978-1-0716-3969-6_19</a>.","apa":"Miranda, O., Cheung, G. T., &#38; Hippenmeyer, S. (2024). Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In K. Toyooka (Ed.), <i>Neuronal Morphogenesis</i> (1st ed., Vol. 2831, pp. 283–299). New York, NY: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">https://doi.org/10.1007/978-1-0716-3969-6_19</a>","mla":"Miranda, Osvaldo, et al. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” <i>Neuronal Morphogenesis</i>, edited by Kazuhito Toyooka, 1st ed., vol. 2831, Springer Nature, 2024, pp. 283–99, doi:<a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">10.1007/978-1-0716-3969-6_19</a>.","ista":"Miranda O, Cheung GT, Hippenmeyer S. 2024.Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Neuronal Morphogenesis. Methods in Molecular Biology, vol. 2831, 283–299.","ama":"Miranda O, Cheung GT, Hippenmeyer S. Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Toyooka K, ed. <i>Neuronal Morphogenesis</i>. Vol 2831. 1st ed. MIMB. New York, NY: Springer Nature; 2024:283-299. doi:<a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">10.1007/978-1-0716-3969-6_19</a>","short":"O. Miranda, G.T. Cheung, S. Hippenmeyer, in:, K. Toyooka (Ed.), Neuronal Morphogenesis, 1st ed., Springer Nature, New York, NY, 2024, pp. 283–299.","ieee":"O. Miranda, G. T. Cheung, and S. Hippenmeyer, “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers,” in <i>Neuronal Morphogenesis</i>, 1st ed., vol. 2831, K. Toyooka, Ed. New York, NY: Springer Nature, 2024, pp. 283–299."},"quality_controlled":"1","intvolume":"      2831","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-08-13T12:16:41Z","oa_version":"None","language":[{"iso":"eng"}],"place":"New York, NY","researchdata_availability":"no","date_published":"2024-08-13T00:00:00Z","type":"book_chapter","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"publication_status":"published","date_updated":"2026-10-07T22:31:34Z","supplementarymaterial":"yes","author":[{"last_name":"Miranda","id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","full_name":"Miranda, Osvaldo","orcid":"0000-0001-6618-6889","first_name":"Osvaldo"},{"full_name":"Cheung, Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572","first_name":"Giselle T","last_name":"Cheung"},{"first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer"}],"editor":[{"last_name":"Toyooka","first_name":"Kazuhito","full_name":"Toyooka, Kazuhito"}],"pmid":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20212"}]},"abstract":[{"lang":"eng","text":"Mosaic Analysis with Double Markers (MADM) is a powerful genetic method typically used for lineage tracing and to disentangle cell autonomous and tissue-wide roles of candidate genes with single cell resolution. Given the relatively sparse labeling, depending on which of the 19 MADM chromosomes one chooses, the MADM approach represents the perfect opportunity for cell morphology analysis. Various MADM studies include reports of morphological anomalies and phenotypes in the central nervous system (CNS). MADM for any candidate gene can easily incorporate morphological analysis within the experimental workflow. Here, we describe the methods of morphological cell analysis which we developed in the course of diverse recent MADM studies. This chapter will specifically focus on methods to quantify aspects of the morphology of neurons and astrocytes within the CNS, but these methods can broadly be applied to any MADM-labeled cells throughout the entire organism. We will cover two analyses—soma volume and dendrite characterization—of physical characteristics of pyramidal neurons in the somatosensory cortex, and two analyses—volume and Sholl analysis—of astrocyte morphology."}],"das_tickbox":"0","corr_author":"1","edition":"1","acknowledged_ssus":[{"_id":"Bio"}],"title":"Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers","scopus_import":"1","article_processing_charge":"No","year":"2024","month":"08","_id":"17425","status":"public","alternative_title":["Methods in Molecular Biology"],"publication":"Neuronal Morphogenesis","day":"13","series_title":"MIMB","publication_identifier":{"eissn":["1940-6029"],"issn":["1064-3745"],"isbn":["9781071639689"],"eisbn":["9781071639696"]},"publisher":"Springer Nature","doi":"10.1007/978-1-0716-3969-6_19","fulldoi":"https://doi.org/10.1007/978-1-0716-3969-6_19"},{"intvolume":"        60","quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2022-06-05T22:01:50Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","date_published":"2023-01-01T00:00:00Z","type":"journal_article","department":[{"_id":"CaMu"}],"publication_status":"published","date_updated":"2024-10-09T20:53:52Z","article_type":"original","acknowledgement":"This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (NRF-2018R1A5A1024958). Model simulation and data transfer were supported by the National Supercomputing Center with supercomputing resources including technical support (KSC-2019-CHA-0005), the National Center for Meteorological Supercomputer of Korea Meteorological Administration, and by the Korea Research Environment Open NETwork (KREONET), respectively. The authors declare no conflicts of interest.","volume":60,"citation":{"ista":"GOSWAMI BB. 2023. Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. Climate Dynamics. 60, 427–442.","ama":"GOSWAMI BB. Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. <i>Climate Dynamics</i>. 2023;60:427-442. doi:<a href=\"https://doi.org/10.1007/s00382-022-06337-7\">10.1007/s00382-022-06337-7</a>","mla":"GOSWAMI, BIDYUT B. “Role of the Eastern Equatorial Indian Ocean Warming in the Indian Summer Monsoon Rainfall Trend.” <i>Climate Dynamics</i>, vol. 60, Springer Nature, 2023, pp. 427–42, doi:<a href=\"https://doi.org/10.1007/s00382-022-06337-7\">10.1007/s00382-022-06337-7</a>.","apa":"GOSWAMI, B. B. (2023). Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. <i>Climate Dynamics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00382-022-06337-7\">https://doi.org/10.1007/s00382-022-06337-7</a>","ieee":"B. B. GOSWAMI, “Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend,” <i>Climate Dynamics</i>, vol. 60. Springer Nature, pp. 427–442, 2023.","short":"B.B. GOSWAMI, Climate Dynamics 60 (2023) 427–442.","chicago":"GOSWAMI, BIDYUT B. “Role of the Eastern Equatorial Indian Ocean Warming in the Indian Summer Monsoon Rainfall Trend.” <i>Climate Dynamics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00382-022-06337-7\">https://doi.org/10.1007/s00382-022-06337-7</a>."},"page":"427-442","external_id":{"isi":["000803119400002"]},"scopus_import":"1","title":"Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend","article_processing_charge":"No","month":"01","_id":"11434","status":"public","year":"2023","publication":"Climate Dynamics","day":"01","publication_identifier":{"issn":["0930-7575"],"eissn":["1432-0894"]},"doi":"10.1007/s00382-022-06337-7","publisher":"Springer Nature","fulldoi":"https://doi.org/10.1007/s00382-022-06337-7","author":[{"last_name":"Goswami","full_name":"Goswami, Bidyut B","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","first_name":"Bidyut B","orcid":"0000-0001-8602-3083"}],"related_material":{"link":[{"relation":"erratum","url":" https://doi.org/10.1007/s00382-022-06401-2"}]},"abstract":[{"text":"The Indian summer monsoon rainfall (ISMR) has been declining since the 1950s. However, since 2002 it is reported to have revived. For these observed changes in the ISMR, several explanations have been reported. Among these explanations, however, the role of the eastern equatorial Indian Ocean (EEIO) is missing despite being one of the warmest regions in the Indian Ocean, and monotonously warming. A recent study reported that EEIO warming impacts the rainfall over northern India. Here we report that warming in the EEIO weakens the low-level Indian summer monsoon circulation and reduces ISMR. A warm EEIO drives easterly winds in the Indo–Pacific sector as a Gill response. The warm EEIO also enhances nocturnal convection offshore the western coast of Sumatra. The latent heating associated with the increased convection augments the Gill response and the resultant circulation opposes the monsoon low-level circulation and weakens the seasonal rainfall.","lang":"eng"}],"isi":1,"corr_author":"1"},{"isi":1,"pmid":1,"author":[{"last_name":"De Jode","first_name":"Aurélien","full_name":"De Jode, Aurélien"},{"first_name":"Alan","full_name":"Le Moan, Alan","last_name":"Le Moan"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski"},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."},{"first_name":"Marina","full_name":"Rafajlović, Marina","last_name":"Rafajlović"},{"orcid":"0000-0001-8441-5075","first_name":"Christelle","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse"}],"abstract":[{"text":"Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results.","lang":"eng"}],"publication_identifier":{"eissn":["1752-4571"]},"day":"01","fulldoi":"https://doi.org/10.1111/eva.13428","ddc":["576"],"publisher":"Wiley","file_date_updated":"2023-02-27T07:10:17Z","doi":"10.1111/eva.13428","oa":1,"article_processing_charge":"No","title":"Ten years of demographic modelling of divergence and speciation in the sea","scopus_import":"1","publication":"Evolutionary Applications","year":"2023","month":"02","_id":"11479","status":"public","issue":"2","external_id":{"pmid":["36793688"],"isi":["000815663700001"]},"page":"542-559","citation":{"ama":"De Jode A, Le Moan A, Johannesson K, et al. Ten years of demographic modelling of divergence and speciation in the sea. <i>Evolutionary Applications</i>. 2023;16(2):542-559. doi:<a href=\"https://doi.org/10.1111/eva.13428\">10.1111/eva.13428</a>","ista":"De Jode A, Le Moan A, Johannesson K, Faria R, Stankowski S, Westram AM, Butlin RK, Rafajlović M, Fraisse C. 2023. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 16(2), 542–559.","apa":"De Jode, A., Le Moan, A., Johannesson, K., Faria, R., Stankowski, S., Westram, A. M., … Fraisse, C. (2023). Ten years of demographic modelling of divergence and speciation in the sea. <i>Evolutionary Applications</i>. Wiley. <a href=\"https://doi.org/10.1111/eva.13428\">https://doi.org/10.1111/eva.13428</a>","mla":"De Jode, Aurélien, et al. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” <i>Evolutionary Applications</i>, vol. 16, no. 2, Wiley, 2023, pp. 542–59, doi:<a href=\"https://doi.org/10.1111/eva.13428\">10.1111/eva.13428</a>.","ieee":"A. De Jode <i>et al.</i>, “Ten years of demographic modelling of divergence and speciation in the sea,” <i>Evolutionary Applications</i>, vol. 16, no. 2. Wiley, pp. 542–559, 2023.","short":"A. De Jode, A. Le Moan, K. Johannesson, R. Faria, S. Stankowski, A.M. Westram, R.K. Butlin, M. Rafajlović, C. Fraisse, Evolutionary Applications 16 (2023) 542–559.","chicago":"De Jode, Aurélien, Alan Le Moan, Kerstin Johannesson, Rui Faria, Sean Stankowski, Anja M Westram, Roger K. Butlin, Marina Rafajlović, and Christelle Fraisse. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” <i>Evolutionary Applications</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/eva.13428\">https://doi.org/10.1111/eva.13428</a>."},"volume":16,"acknowledgement":"We greatly thank all the corresponding authors of the studies that were included in our synthesis for the sharing of additional data: Thomas Broquet, Dmitry Filatov, Quentin Rougemont, Paolo Momigliano, Pierre-Alexandre Gagnaire, Carlos Prada, Ahmed Souissi, Michael Møller Hansen, Sylvie Lapègue, Joseph Di Battista, Michael Hellberg and Carlos Prada. RKB and ADJ were supported by the European Research Council. MR was supported by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243; to MR) and Formas (grant number 2019-00882; to KJ and MR), and by additional grants from the European Research Council (to RKB) and Vetenskapsrådet (to KJ) through the Centre for Marine Evolutionary Biology (https://www.gu.se/en/cemeb-marine-evolutionary-biology).","date_updated":"2025-04-23T08:49:14Z","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"publication_status":"published","file":[{"access_level":"open_access","file_size":2269822,"creator":"dernst","date_created":"2023-02-27T07:10:17Z","success":1,"content_type":"application/pdf","file_name":"2023_EvolutionaryApplications_DeJode.pdf","file_id":"12685","checksum":"d4d6fa9ddf36643af994a6a757919afb","relation":"main_file","date_updated":"2023-02-27T07:10:17Z"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-07-03T22:01:33Z","language":[{"iso":"eng"}],"intvolume":"        16","quality_controlled":"1","has_accepted_license":"1","type":"journal_article","date_published":"2023-02-01T00:00:00Z"},{"_id":"11706","status":"public","month":"07","year":"2023","publication":"Random Structures and Algorithms","scopus_import":"1","title":"Asymmetric Ramsey properties of random graphs involving cliques and cycles","article_processing_charge":"Yes (in subscription journal)","oa":1,"doi":"10.1002/rsa.21106","file_date_updated":"2023-10-04T09:37:26Z","publisher":"Wiley","ddc":["510"],"fulldoi":"https://doi.org/10.1002/rsa.21106","day":"01","license":"https://creativecommons.org/licenses/by-nc/4.0/","publication_identifier":{"eissn":["1098-2418"],"issn":["1042-9832"]},"abstract":[{"lang":"eng","text":"We say that (Formula presented.) if, in every edge coloring (Formula presented.), we can find either a 1-colored copy of (Formula presented.) or a 2-colored copy of (Formula presented.). The well-known states that the threshold for the property (Formula presented.) is equal to (Formula presented.), where (Formula presented.) is given by (Formula presented.) for any pair of graphs (Formula presented.) and (Formula presented.) with (Formula presented.). In this article, we show the 0-statement of the Kohayakawa–Kreuter conjecture for every pair of cycles and cliques. "}],"author":[{"first_name":"Anita","full_name":"Liebenau, Anita","last_name":"Liebenau"},{"last_name":"Mattos","first_name":"Letícia","full_name":"Mattos, Letícia"},{"id":"12c6bd4d-2cd0-11ec-a0da-e28f42f65ebd","full_name":"Mendonca Dos Santos, Walner","first_name":"Walner","last_name":"Mendonca Dos Santos"},{"first_name":"Jozef","full_name":"Skokan, Jozef","last_name":"Skokan"}],"isi":1,"date_published":"2023-07-01T00:00:00Z","type":"journal_article","has_accepted_license":"1","intvolume":"        62","quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-07-31T22:01:49Z","oa_version":"Published Version","article_type":"original","tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"file":[{"access_level":"open_access","file_size":1362334,"creator":"dernst","date_created":"2023-10-04T09:37:26Z","success":1,"content_type":"application/pdf","file_name":"2023_RandomStructureAlgorithms_Liebenau.pdf","file_id":"14389","relation":"main_file","checksum":"3a5969d0c512aef01c30f3dc81c6d59b","date_updated":"2023-10-04T09:37:26Z"}],"publication_status":"published","department":[{"_id":"MaKw"}],"date_updated":"2023-10-04T09:38:45Z","volume":62,"acknowledgement":"This work was started at the thematic program GRAPHS@IMPA (January–March 2018), in Rio de Janeiro. We thank IMPA and the organisers for the hospitality and for providing a pleasant research environment. We thank Rob Morris for helpful discussions, and the anonymous referees for their careful reading and many helpful suggestions. Open Access funding enabled and organized by Projekt DEAL.\r\nA. Liebenau was supported by an ARC DECRA Fellowship Grant DE170100789. L. Mattos was supported by CAPES and by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy – The Berlin Mathematics Research Center MATH+ (EXC-2046/1, project ID: 390685689). W. Mendonça was supported by CAPES project 88882.332408/2010-01.","page":"1035-1055","citation":{"ama":"Liebenau A, Mattos L, Mendonca dos Santos W, Skokan J. Asymmetric Ramsey properties of random graphs involving cliques and cycles. <i>Random Structures and Algorithms</i>. 2023;62(4):1035-1055. doi:<a href=\"https://doi.org/10.1002/rsa.21106\">10.1002/rsa.21106</a>","ista":"Liebenau A, Mattos L, Mendonca dos Santos W, Skokan J. 2023. Asymmetric Ramsey properties of random graphs involving cliques and cycles. Random Structures and Algorithms. 62(4), 1035–1055.","apa":"Liebenau, A., Mattos, L., Mendonca dos Santos, W., &#38; Skokan, J. (2023). Asymmetric Ramsey properties of random graphs involving cliques and cycles. <i>Random Structures and Algorithms</i>. Wiley. <a href=\"https://doi.org/10.1002/rsa.21106\">https://doi.org/10.1002/rsa.21106</a>","mla":"Liebenau, Anita, et al. “Asymmetric Ramsey Properties of Random Graphs Involving Cliques and Cycles.” <i>Random Structures and Algorithms</i>, vol. 62, no. 4, Wiley, 2023, pp. 1035–55, doi:<a href=\"https://doi.org/10.1002/rsa.21106\">10.1002/rsa.21106</a>.","ieee":"A. Liebenau, L. Mattos, W. Mendonca dos Santos, and J. Skokan, “Asymmetric Ramsey properties of random graphs involving cliques and cycles,” <i>Random Structures and Algorithms</i>, vol. 62, no. 4. Wiley, pp. 1035–1055, 2023.","short":"A. Liebenau, L. Mattos, W. Mendonca dos Santos, J. Skokan, Random Structures and Algorithms 62 (2023) 1035–1055.","chicago":"Liebenau, Anita, Letícia Mattos, Walner Mendonca dos Santos, and Jozef Skokan. “Asymmetric Ramsey Properties of Random Graphs Involving Cliques and Cycles.” <i>Random Structures and Algorithms</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/rsa.21106\">https://doi.org/10.1002/rsa.21106</a>."},"external_id":{"isi":["000828530400001"]},"issue":"4"},{"corr_author":"1","isi":1,"abstract":[{"lang":"eng","text":"Following E. Wigner’s original vision, we prove that sampling the eigenvalue gaps within the bulk spectrum of a fixed (deformed) Wigner matrix H yields the celebrated Wigner-Dyson-Mehta universal statistics with high probability. Similarly, we prove universality for a monoparametric family of deformed Wigner matrices H+xA with a deterministic Hermitian matrix A and a fixed Wigner matrix H, just using the randomness of a single scalar real random variable x. Both results constitute quenched versions of bulk universality that has so far only been proven in annealed sense with respect to the probability space of the matrix ensemble."}],"author":[{"orcid":"0000-0002-4901-7992","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","full_name":"Cipolloni, Giorgio","last_name":"Cipolloni"},{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","orcid":"0000-0001-5366-9603","last_name":"Erdös"},{"last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87","full_name":"Schröder, Dominik J","first_name":"Dominik J","orcid":"0000-0002-2904-1856"}],"file_date_updated":"2023-08-14T12:47:32Z","doi":"10.1007/s00440-022-01156-7","publisher":"Springer Nature","fulldoi":"https://doi.org/10.1007/s00440-022-01156-7","ddc":["510"],"day":"01","publication_identifier":{"eissn":["1432-2064"],"issn":["0178-8051"]},"status":"public","_id":"11741","month":"04","year":"2023","publication":"Probability Theory and Related Fields","scopus_import":"1","title":"Quenched universality for deformed Wigner matrices","article_processing_charge":"Yes (via OA deal)","oa":1,"page":"1183–1218","citation":{"chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Quenched Universality for Deformed Wigner Matrices.” <i>Probability Theory and Related Fields</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00440-022-01156-7\">https://doi.org/10.1007/s00440-022-01156-7</a>.","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2023). Quenched universality for deformed Wigner matrices. <i>Probability Theory and Related Fields</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00440-022-01156-7\">https://doi.org/10.1007/s00440-022-01156-7</a>","mla":"Cipolloni, Giorgio, et al. “Quenched Universality for Deformed Wigner Matrices.” <i>Probability Theory and Related Fields</i>, vol. 185, Springer Nature, 2023, pp. 1183–1218, doi:<a href=\"https://doi.org/10.1007/s00440-022-01156-7\">10.1007/s00440-022-01156-7</a>.","ama":"Cipolloni G, Erdös L, Schröder DJ. Quenched universality for deformed Wigner matrices. <i>Probability Theory and Related Fields</i>. 2023;185:1183–1218. doi:<a href=\"https://doi.org/10.1007/s00440-022-01156-7\">10.1007/s00440-022-01156-7</a>","ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. 185, 1183–1218.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields 185 (2023) 1183–1218.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Quenched universality for deformed Wigner matrices,” <i>Probability Theory and Related Fields</i>, vol. 185. Springer Nature, pp. 1183–1218, 2023."},"external_id":{"arxiv":["2106.10200"],"isi":["000830344500001"]},"acknowledgement":"The authors are indebted to Sourav Chatterjee for forwarding the very inspiring question that Stephen Shenker originally addressed to him which initiated the current paper. They are also grateful that the authors of [23] kindly shared their preliminary numerical results in June 2021.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","volume":185,"article_type":"original","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"success":1,"content_type":"application/pdf","file_name":"2023_ProbabilityTheory_Cipolloni.pdf","file_id":"14054","relation":"main_file","checksum":"b9247827dae5544d1d19c37abe547abc","date_updated":"2023-08-14T12:47:32Z","access_level":"open_access","file_size":782278,"creator":"dernst","date_created":"2023-08-14T12:47:32Z"}],"publication_status":"published","department":[{"_id":"LaEr"}],"date_updated":"2024-10-09T21:03:02Z","date_published":"2023-04-01T00:00:00Z","type":"journal_article","has_accepted_license":"1","quality_controlled":"1","arxiv":1,"intvolume":"       185","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-08-07T22:02:00Z","oa_version":"Published Version"},{"fulldoi":"https://doi.org/10.1007/s00454-022-00394-9","ddc":["510"],"publisher":"Springer Nature","doi":"10.1007/s00454-022-00394-9","file_date_updated":"2022-08-29T11:23:15Z","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"day":"01","publication":"Discrete and Computational Geometry","year":"2023","_id":"11999","status":"public","month":"04","oa":1,"article_processing_charge":"Yes (in subscription journal)","title":"Inserting one edge into a simple drawing is hard","scopus_import":"1","isi":1,"abstract":[{"text":"A simple drawing D(G) of a graph G is one where each pair of edges share at most one point: either a common endpoint or a proper crossing. An edge e in the complement of G can be inserted into D(G) if there exists a simple drawing of G+e extending D(G). As a result of Levi’s Enlargement Lemma, if a drawing is rectilinear (pseudolinear), that is, the edges can be extended into an arrangement of lines (pseudolines), then any edge in the complement of G can be inserted. In contrast, we show that it is NP-complete to decide whether one edge can be inserted into a simple drawing. This remains true even if we assume that the drawing is pseudocircular, that is, the edges can be extended to an arrangement of pseudocircles. On the positive side, we show that, given an arrangement of pseudocircles A and a pseudosegment σ, it can be decided in polynomial time whether there exists a pseudocircle Φσ extending σ for which A∪{Φσ} is again an arrangement of pseudocircles.","lang":"eng"}],"author":[{"first_name":"Alan M","orcid":"0000-0003-2401-8670","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","full_name":"Arroyo Guevara, Alan M","last_name":"Arroyo Guevara"},{"last_name":"Klute","first_name":"Fabian","full_name":"Klute, Fabian"},{"last_name":"Parada","first_name":"Irene","full_name":"Parada, Irene"},{"first_name":"Birgit","full_name":"Vogtenhuber, Birgit","last_name":"Vogtenhuber"},{"last_name":"Seidel","first_name":"Raimund","full_name":"Seidel, Raimund"},{"last_name":"Wiedera","first_name":"Tilo","full_name":"Wiedera, Tilo"}],"file":[{"checksum":"def7ae3b28d9fd6aec16450e40090302","relation":"main_file","file_id":"12006","date_updated":"2022-08-29T11:23:15Z","success":1,"file_name":"2022_DiscreteandComputionalGeometry_Arroyo.pdf","content_type":"application/pdf","creator":"alisjak","file_size":1002218,"date_created":"2022-08-29T11:23:15Z","access_level":"open_access"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","date_updated":"2025-04-14T07:43:59Z","publication_status":"published","department":[{"_id":"UlWa"}],"has_accepted_license":"1","type":"journal_article","date_published":"2023-04-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-08-28T22:02:01Z","oa_version":"Published Version","language":[{"iso":"eng"}],"arxiv":1,"quality_controlled":"1","intvolume":"        69","external_id":{"arxiv":["1909.07347"],"isi":["000840292800001"]},"citation":{"chicago":"Arroyo Guevara, Alan M, Fabian Klute, Irene Parada, Birgit Vogtenhuber, Raimund Seidel, and Tilo Wiedera. “Inserting One Edge into a Simple Drawing Is Hard.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00454-022-00394-9\">https://doi.org/10.1007/s00454-022-00394-9</a>.","ista":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. 2023. Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. 69, 745–770.","ama":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. Inserting one edge into a simple drawing is hard. <i>Discrete and Computational Geometry</i>. 2023;69:745–770. doi:<a href=\"https://doi.org/10.1007/s00454-022-00394-9\">10.1007/s00454-022-00394-9</a>","apa":"Arroyo Guevara, A. M., Klute, F., Parada, I., Vogtenhuber, B., Seidel, R., &#38; Wiedera, T. (2023). Inserting one edge into a simple drawing is hard. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-022-00394-9\">https://doi.org/10.1007/s00454-022-00394-9</a>","mla":"Arroyo Guevara, Alan M., et al. “Inserting One Edge into a Simple Drawing Is Hard.” <i>Discrete and Computational Geometry</i>, vol. 69, Springer Nature, 2023, pp. 745–770, doi:<a href=\"https://doi.org/10.1007/s00454-022-00394-9\">10.1007/s00454-022-00394-9</a>.","ieee":"A. M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, and T. Wiedera, “Inserting one edge into a simple drawing is hard,” <i>Discrete and Computational Geometry</i>, vol. 69. Springer Nature, pp. 745–770, 2023.","short":"A.M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, T. Wiedera, Discrete and Computational Geometry 69 (2023) 745–770."},"page":"745–770","ec_funded":1,"acknowledgement":"This work was started during the 6th Austrian–Japanese–Mexican–Spanish Workshop on Discrete Geometry in June 2019 in Austria. We thank all the participants for the good atmosphere as well as discussions on the topic. Also, we thank Jan Kynčl for sending us remarks on a preliminary version of this work and an anonymous referee for further helpful comments.Alan Arroyo was funded by the Marie Skłodowska-Curie grant agreement No 754411. Fabian Klute was partially supported by the Netherlands Organisation for Scientific Research (NWO) under project no. 612.001.651 and by the Austrian Science Fund (FWF): J-4510. Irene Parada and Birgit Vogtenhuber were partially supported by the Austrian Science Fund (FWF): W1230 and within the collaborative DACH project Arrangements and Drawings as FWF project I 3340-N35. Irene Parada was also partially supported by the Independent Research Fund Denmark grant 2020-2023 (9131-00044B) Dynamic Network Analysis and by the Margarita Salas Fellowship funded by the Ministry of Universities of Spain and the European Union (NextGenerationEU). Tilo Wiedera was supported by the German Research Foundation (DFG) grant CH 897/2-2.","volume":69,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"}]},{"citation":{"ieee":"H. Edelsbrunner and G. F. Osang, “A simple algorithm for higher-order Delaunay mosaics and alpha shapes,” <i>Algorithmica</i>, vol. 85. Springer Nature, pp. 277–295, 2023.","short":"H. Edelsbrunner, G.F. Osang, Algorithmica 85 (2023) 277–295.","ista":"Edelsbrunner H, Osang GF. 2023. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 85, 277–295.","ama":"Edelsbrunner H, Osang GF. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. <i>Algorithmica</i>. 2023;85:277-295. doi:<a href=\"https://doi.org/10.1007/s00453-022-01027-6\">10.1007/s00453-022-01027-6</a>","mla":"Edelsbrunner, Herbert, and Georg F. Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” <i>Algorithmica</i>, vol. 85, Springer Nature, 2023, pp. 277–95, doi:<a href=\"https://doi.org/10.1007/s00453-022-01027-6\">10.1007/s00453-022-01027-6</a>.","apa":"Edelsbrunner, H., &#38; Osang, G. F. (2023). A simple algorithm for higher-order Delaunay mosaics and alpha shapes. <i>Algorithmica</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00453-022-01027-6\">https://doi.org/10.1007/s00453-022-01027-6</a>","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” <i>Algorithmica</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00453-022-01027-6\">https://doi.org/10.1007/s00453-022-01027-6</a>."},"page":"277-295","external_id":{"isi":["000846967100001"],"pmid":["36687803"]},"ec_funded":1,"project":[{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","name":"Mathematics, Computer Science","call_identifier":"FWF"},{"grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"acknowledgement":"Open access funding provided by Austrian Science Fund (FWF). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.","volume":85,"article_type":"original","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"date_created":"2023-01-20T10:02:48Z","file_size":911017,"creator":"dernst","access_level":"open_access","date_updated":"2023-01-20T10:02:48Z","file_id":"12322","checksum":"71685ca5121f4c837f40c3f8eb50c915","relation":"main_file","content_type":"application/pdf","file_name":"2023_Algorithmica_Edelsbrunner.pdf","success":1}],"publication_status":"published","department":[{"_id":"HeEd"}],"date_updated":"2025-04-23T08:46:48Z","date_published":"2023-01-01T00:00:00Z","type":"journal_article","has_accepted_license":"1","intvolume":"        85","quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","date_created":"2022-09-11T22:01:57Z","isi":1,"corr_author":"1","abstract":[{"text":"We present a simple algorithm for computing higher-order Delaunay mosaics that works in Euclidean spaces of any finite dimensions. The algorithm selects the vertices of the order-k mosaic from incrementally constructed lower-order mosaics and uses an algorithm for weighted first-order Delaunay mosaics as a black-box to construct the order-k mosaic from its vertices. Beyond this black-box, the algorithm uses only combinatorial operations, thus facilitating easy implementation. We extend this algorithm to compute higher-order α-shapes and provide open-source implementations. We present experimental results for properties of higher-order Delaunay mosaics of random point sets.","lang":"eng"}],"author":[{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"orcid":"0000-0002-8882-5116","first_name":"Georg F","full_name":"Osang, Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang"}],"pmid":1,"doi":"10.1007/s00453-022-01027-6","file_date_updated":"2023-01-20T10:02:48Z","publisher":"Springer Nature","ddc":["510"],"fulldoi":"https://doi.org/10.1007/s00453-022-01027-6","day":"01","publication_identifier":{"issn":["0178-4617"],"eissn":["1432-0541"]},"_id":"12086","month":"01","status":"public","year":"2023","publication":"Algorithmica","scopus_import":"1","title":"A simple algorithm for higher-order Delaunay mosaics and alpha shapes","article_processing_charge":"Yes (via OA deal)","oa":1},{"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"eb958bca-77a9-11ec-83b8-c565cb50d8d6","name":"Curvature-dimension in noncommutative analysis","grant_number":"M03337"},{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"},{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"volume":24,"acknowledgement":"H.Z. is supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 and the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337. M.W. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 716117) and from the Austrian Science Fund (FWF) through grant number F65. Both authors would like to thank Jan Maas for fruitful discussions and helpful comments. Open access funding provided by Austrian Science Fund (FWF).","page":"717-750","citation":{"ieee":"M. Wirth and H. Zhang, “Curvature-dimension conditions for symmetric quantum Markov semigroups,” <i>Annales Henri Poincare</i>, vol. 24. Springer Nature, pp. 717–750, 2023.","short":"M. Wirth, H. Zhang, Annales Henri Poincare 24 (2023) 717–750.","ista":"Wirth M, Zhang H. 2023. Curvature-dimension conditions for symmetric quantum Markov semigroups. Annales Henri Poincare. 24, 717–750.","ama":"Wirth M, Zhang H. Curvature-dimension conditions for symmetric quantum Markov semigroups. <i>Annales Henri Poincare</i>. 2023;24:717-750. doi:<a href=\"https://doi.org/10.1007/s00023-022-01220-x\">10.1007/s00023-022-01220-x</a>","mla":"Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for Symmetric Quantum Markov Semigroups.” <i>Annales Henri Poincare</i>, vol. 24, Springer Nature, 2023, pp. 717–50, doi:<a href=\"https://doi.org/10.1007/s00023-022-01220-x\">10.1007/s00023-022-01220-x</a>.","apa":"Wirth, M., &#38; Zhang, H. (2023). Curvature-dimension conditions for symmetric quantum Markov semigroups. <i>Annales Henri Poincare</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-022-01220-x\">https://doi.org/10.1007/s00023-022-01220-x</a>","chicago":"Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for Symmetric Quantum Markov Semigroups.” <i>Annales Henri Poincare</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00023-022-01220-x\">https://doi.org/10.1007/s00023-022-01220-x</a>."},"external_id":{"arxiv":["2105.08303"],"pmid":["36950223"],"isi":["000837499800002"]},"ec_funded":1,"date_published":"2023-03-01T00:00:00Z","type":"journal_article","has_accepted_license":"1","quality_controlled":"1","intvolume":"        24","arxiv":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-09-11T22:01:57Z","article_type":"original","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"access_level":"open_access","creator":"dernst","file_size":554871,"date_created":"2023-08-14T11:38:28Z","success":1,"file_name":"2023_AnnalesHenriPoincare_Wirth.pdf","content_type":"application/pdf","relation":"main_file","checksum":"8c7b185eba5ccd92ef55c120f654222c","file_id":"14051","date_updated":"2023-08-14T11:38:28Z"}],"publication_status":"published","department":[{"_id":"JaMa"}],"date_updated":"2025-04-23T08:53:05Z","abstract":[{"lang":"eng","text":"Following up on the recent work on lower Ricci curvature bounds for quantum systems, we introduce two noncommutative versions of curvature-dimension bounds for symmetric quantum Markov semigroups over matrix algebras. Under suitable such curvature-dimension conditions, we prove a family of dimension-dependent functional inequalities, a version of the Bonnet–Myers theorem and concavity of entropy power in the noncommutative setting. We also provide examples satisfying certain curvature-dimension conditions, including Schur multipliers over matrix algebras, Herz–Schur multipliers over group algebras and generalized depolarizing semigroups."}],"author":[{"full_name":"Wirth, Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","orcid":"0000-0002-0519-4241","first_name":"Melchior","last_name":"Wirth"},{"last_name":"Zhang","first_name":"Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425","full_name":"Zhang, Haonan"}],"pmid":1,"corr_author":"1","isi":1,"_id":"12087","status":"public","month":"03","year":"2023","publication":"Annales Henri Poincare","scopus_import":"1","title":"Curvature-dimension conditions for symmetric quantum Markov semigroups","article_processing_charge":"Yes (via OA deal)","oa":1,"file_date_updated":"2023-08-14T11:38:28Z","doi":"10.1007/s00023-022-01220-x","publisher":"Springer Nature","fulldoi":"https://doi.org/10.1007/s00023-022-01220-x","ddc":["510"],"day":"01","publication_identifier":{"issn":["1424-0637"]}},{"project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"},{"call_identifier":"H2020","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"grant_number":"E208","name":"Configuration Spaces over Non-Smooth Spaces","_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c"},{"grant_number":"ESP156_N","name":"Gradient flow techniques for quantum Markov semigroups","_id":"34c6ea2d-11ca-11ed-8bc3-c04f3c502833"}],"acknowledgement":"Research supported by the Austrian Science Fund (FWF) grant F65 at the Institute of Science and Technology Austria and by the European Research Council (ERC) (Grant agreement No. 716117 awarded to Prof. Dr. Jan Maas). L.D.S. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 208). M.W. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 156).","volume":23,"external_id":{"isi":["000906214600004"],"pmid":["36597554"]},"citation":{"short":"L. Dello Schiavo, M. Wirth, Journal of Evolution Equations 23 (2023).","ieee":"L. Dello Schiavo and M. Wirth, “Ergodic decompositions of Dirichlet forms under order isomorphisms,” <i>Journal of Evolution Equations</i>, vol. 23, no. 1. Springer Nature, 2023.","mla":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” <i>Journal of Evolution Equations</i>, vol. 23, no. 1, 9, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s00028-022-00859-7\">10.1007/s00028-022-00859-7</a>.","apa":"Dello Schiavo, L., &#38; Wirth, M. (2023). Ergodic decompositions of Dirichlet forms under order isomorphisms. <i>Journal of Evolution Equations</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00028-022-00859-7\">https://doi.org/10.1007/s00028-022-00859-7</a>","ista":"Dello Schiavo L, Wirth M. 2023. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 23(1), 9.","ama":"Dello Schiavo L, Wirth M. Ergodic decompositions of Dirichlet forms under order isomorphisms. <i>Journal of Evolution Equations</i>. 2023;23(1). doi:<a href=\"https://doi.org/10.1007/s00028-022-00859-7\">10.1007/s00028-022-00859-7</a>","chicago":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” <i>Journal of Evolution Equations</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00028-022-00859-7\">https://doi.org/10.1007/s00028-022-00859-7</a>."},"ec_funded":1,"issue":"1","date_published":"2023-01-01T00:00:00Z","has_accepted_license":"1","type":"journal_article","quality_controlled":"1","intvolume":"        23","oa_version":"Published Version","date_created":"2023-01-08T23:00:53Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"article_type":"original","file":[{"access_level":"open_access","date_created":"2023-01-20T10:45:06Z","file_size":422612,"creator":"dernst","content_type":"application/pdf","file_name":"2023_JourEvolutionEquations_DelloSchiavo.pdf","success":1,"date_updated":"2023-01-20T10:45:06Z","file_id":"12325","checksum":"1f34f3e2cb521033de6154f274ea3a4e","relation":"main_file"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_status":"published","department":[{"_id":"JaMa"}],"date_updated":"2025-04-23T08:45:56Z","abstract":[{"lang":"eng","text":"We study ergodic decompositions of Dirichlet spaces under intertwining via unitary order isomorphisms. We show that the ergodic decomposition of a quasi-regular Dirichlet space is unique up to a unique isomorphism of the indexing space. Furthermore, every unitary order isomorphism intertwining two quasi-regular Dirichlet spaces is decomposable over their ergodic decompositions up to conjugation via an isomorphism of the corresponding indexing spaces."}],"author":[{"orcid":"0000-0002-9881-6870","first_name":"Lorenzo","full_name":"Dello Schiavo, Lorenzo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","last_name":"Dello Schiavo"},{"last_name":"Wirth","first_name":"Melchior","orcid":"0000-0002-0519-4241","full_name":"Wirth, Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E"}],"pmid":1,"article_number":"9","isi":1,"corr_author":"1","year":"2023","month":"01","_id":"12104","status":"public","publication":"Journal of Evolution Equations","title":"Ergodic decompositions of Dirichlet forms under order isomorphisms","scopus_import":"1","oa":1,"article_processing_charge":"Yes (via OA deal)","publisher":"Springer Nature","file_date_updated":"2023-01-20T10:45:06Z","doi":"10.1007/s00028-022-00859-7","ddc":["510"],"fulldoi":"https://doi.org/10.1007/s00028-022-00859-7","day":"01","publication_identifier":{"eissn":["1424-3202"],"issn":["1424-3199"]}},{"page":"813–823","citation":{"chicago":"Yeung, Jake, Maria Florescu, Peter Zeller, Buys Anton De Barbanson, Max D. Wellenstein, and Alexander Van Oudenaarden. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” <i>Nature Biotechnology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41587-022-01560-3\">https://doi.org/10.1038/s41587-022-01560-3</a>.","apa":"Yeung, J., Florescu, M., Zeller, P., De Barbanson, B. A., Wellenstein, M. D., &#38; Van Oudenaarden, A. (2023). scChIX-seq infers dynamic relationships between histone modifications in single cells. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-022-01560-3\">https://doi.org/10.1038/s41587-022-01560-3</a>","mla":"Yeung, Jake, et al. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” <i>Nature Biotechnology</i>, vol. 41, Springer Nature, 2023, pp. 813–823, doi:<a href=\"https://doi.org/10.1038/s41587-022-01560-3\">10.1038/s41587-022-01560-3</a>.","ama":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. scChIX-seq infers dynamic relationships between histone modifications in single cells. <i>Nature Biotechnology</i>. 2023;41:813–823. doi:<a href=\"https://doi.org/10.1038/s41587-022-01560-3\">10.1038/s41587-022-01560-3</a>","ista":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. 2023. scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. 41, 813–823.","short":"J. Yeung, M. Florescu, P. Zeller, B.A. De Barbanson, M.D. Wellenstein, A. Van Oudenaarden, Nature Biotechnology 41 (2023) 813–823.","ieee":"J. Yeung, M. Florescu, P. Zeller, B. A. De Barbanson, M. D. Wellenstein, and A. Van Oudenaarden, “scChIX-seq infers dynamic relationships between histone modifications in single cells,” <i>Nature Biotechnology</i>, vol. 41. Springer Nature, pp. 813–823, 2023."},"external_id":{"isi":["000909067600003"],"pmid":["36593403"]},"acknowledgement":"We thank M. van Loenhout for experimental advice on purifying cell types from the bone marrow, R. van der Linden for expertise with FACS and M. Blotenburg for help with cell typing the mouse organogenesis dataset. We thank M. Saraswat and O. Stegle for discussions on multinomial distributions. This work was supported by a European Research Council Advanced grant (ERC-AdG 742225-IntScOmics); Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP grant (NWO CW 714.016.001) and NWO grant (OCENW.GROOT.2019.017); the Swiss National Science Foundation Early Postdoc Mobility (P2ELP3-184488 to P.Z. and P2BSP3-174991 to J.Y.); Marie Sklodowska-Curie Actions Postdoc (798573 to P.Z.) and the Human Frontier for Science Program Long-Term Fellowships (LT000209-2018-L to P.Z. and LT000097-2019-L to J.Y.). This work is part of the Oncode Institute which is financed partly by the Dutch Cancer Society.","volume":41,"date_updated":"2025-04-23T08:45:24Z","department":[{"_id":"ScienComp"}],"publication_status":"published","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_size":12040976,"creator":"dernst","date_created":"2023-08-16T11:30:45Z","access_level":"open_access","file_id":"14066","checksum":"668447a1c8d360b68f8aaf9e08ed644f","relation":"main_file","date_updated":"2023-08-16T11:30:45Z","success":1,"content_type":"application/pdf","file_name":"2023_NatureBioTech_Yeung.pdf"}],"article_type":"original","language":[{"iso":"eng"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-01-08T23:00:53Z","quality_controlled":"1","intvolume":"        41","type":"journal_article","has_accepted_license":"1","date_published":"2023-06-01T00:00:00Z","isi":1,"corr_author":"1","pmid":1,"author":[{"last_name":"Yeung","first_name":"Jake","orcid":"0000-0003-1732-1559","full_name":"Yeung, Jake","id":"123012b2-db30-11eb-b4d8-a35840c0551b"},{"last_name":"Florescu","first_name":"Maria","full_name":"Florescu, Maria"},{"full_name":"Zeller, Peter","first_name":"Peter","last_name":"Zeller"},{"first_name":"Buys Anton","full_name":"De Barbanson, Buys Anton","last_name":"De Barbanson"},{"full_name":"Wellenstein, Max D.","first_name":"Max D.","last_name":"Wellenstein"},{"last_name":"Van Oudenaarden","full_name":"Van Oudenaarden, Alexander","first_name":"Alexander"}],"abstract":[{"text":"Regulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here, we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing sequencing), to map several histone marks in single cells. scChIX-seq multiplexes two histone marks together in single cells, then computationally deconvolves the signal using training data from respective histone mark profiles. This framework learns the cell-type-specific correlation structure between histone marks, and therefore does not require a priori assumptions of their genomic distributions. Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single cells across a range of mark combinations. Modeling dynamics of in vitro macrophage differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq unlocks systematic interrogation of the interplay between histone modifications in single cells.","lang":"eng"}],"publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"day":"01","fulldoi":"https://doi.org/10.1038/s41587-022-01560-3","ddc":["570"],"doi":"10.1038/s41587-022-01560-3","file_date_updated":"2023-08-16T11:30:45Z","publisher":"Springer Nature","article_processing_charge":"No","oa":1,"scopus_import":"1","title":"scChIX-seq infers dynamic relationships between histone modifications in single cells","publication":"Nature Biotechnology","status":"public","_id":"12106","month":"06","year":"2023"},{"isi":1,"article_number":"156101","keyword":["Surfaces","Coatings and Films","Condensed Matter Physics","Surfaces and Interfaces","General Physics and Astronomy","General Chemistry"],"OA_type":"closed access","abstract":[{"text":"The power factor of poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) film can be significantly improved by optimizing the oxidation level of the film in oxidation and reduction processes. However, precise control over the oxidation and reduction effects in PEDOT:PSS remains a challenge, which greatly sacrifices both S and σ. Here, we propose a two-step post-treatment using a mixture of ethylene glycol (EG) and Arginine (Arg) and sulfuric acid (H2SO4) in sequence to engineer high-performance PEDOT:PSS thermoelectric films. The high-polarity EG dopant removes the excess non-ionized PSS and induces benzenoid-to-quinoid conformational change in the PEDOT:PSS films. In particular, basic amino acid Arg tunes the oxidation level of PEDOT:PSS and prevents the films from over-oxidation during H2SO4 post-treatment, leading to increased S. The following H2SO4 post-treatment further induces highly orientated lamellar stacking microstructures to increase σ, yielding a maximum power factor of 170.6 μW m−1 K−2 at 460 K. Moreover, a novel trigonal-shape thermoelectric device is designed and assembled by the as-prepared PEDOT:PSS films in order to harvest heat via a vertical temperature gradient. An output power density of 33 μW cm−2 is generated at a temperature difference of 40 K, showing the potential application for low-grade wearable electronic devices.","lang":"eng"}],"author":[{"last_name":"Zhang","first_name":"Li","full_name":"Zhang, Li"},{"full_name":"Liu, Xingyu","first_name":"Xingyu","last_name":"Liu"},{"last_name":"Wu","first_name":"Ting","full_name":"Wu, Ting"},{"full_name":"Xu, Shengduo","id":"12ab8624-4c8a-11ec-9e11-e1ac2438f22f","first_name":"Shengduo","last_name":"Xu"},{"last_name":"Suo","full_name":"Suo, Guoquan","first_name":"Guoquan"},{"full_name":"Ye, Xiaohui","first_name":"Xiaohui","last_name":"Ye"},{"last_name":"Hou","first_name":"Xiaojiang","full_name":"Hou, Xiaojiang"},{"last_name":"Yang","first_name":"Yanling","full_name":"Yang, Yanling"},{"last_name":"Liu","first_name":"Qingfeng","full_name":"Liu, Qingfeng"},{"last_name":"Wang","first_name":"Hongqiang","full_name":"Wang, Hongqiang"}],"doi":"10.1016/j.apsusc.2022.156101","publisher":"Elsevier","fulldoi":"https://doi.org/10.1016/j.apsusc.2022.156101","day":"15","publication_identifier":{"issn":["0169-4332"]},"_id":"12113","status":"public","month":"03","year":"2023","publication":"Applied Surface Science","scopus_import":"1","title":"Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient","article_processing_charge":"No","citation":{"chicago":"Zhang, Li, Xingyu Liu, Ting Wu, Shengduo Xu, Guoquan Suo, Xiaohui Ye, Xiaojiang Hou, Yanling Yang, Qingfeng Liu, and Hongqiang Wang. “Two-Step Post-Treatment to Deliver High Performance Thermoelectric Device with Vertical Temperature Gradient.” <i>Applied Surface Science</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.apsusc.2022.156101\">https://doi.org/10.1016/j.apsusc.2022.156101</a>.","ieee":"L. Zhang <i>et al.</i>, “Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient,” <i>Applied Surface Science</i>, vol. 613. Elsevier, 2023.","short":"L. Zhang, X. Liu, T. Wu, S. Xu, G. Suo, X. Ye, X. Hou, Y. Yang, Q. Liu, H. Wang, Applied Surface Science 613 (2023).","ama":"Zhang L, Liu X, Wu T, et al. Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. <i>Applied Surface Science</i>. 2023;613. doi:<a href=\"https://doi.org/10.1016/j.apsusc.2022.156101\">10.1016/j.apsusc.2022.156101</a>","ista":"Zhang L, Liu X, Wu T, Xu S, Suo G, Ye X, Hou X, Yang Y, Liu Q, Wang H. 2023. Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. Applied Surface Science. 613, 156101.","apa":"Zhang, L., Liu, X., Wu, T., Xu, S., Suo, G., Ye, X., … Wang, H. (2023). Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. <i>Applied Surface Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.apsusc.2022.156101\">https://doi.org/10.1016/j.apsusc.2022.156101</a>","mla":"Zhang, Li, et al. “Two-Step Post-Treatment to Deliver High Performance Thermoelectric Device with Vertical Temperature Gradient.” <i>Applied Surface Science</i>, vol. 613, 156101, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.apsusc.2022.156101\">10.1016/j.apsusc.2022.156101</a>."},"external_id":{"isi":["000911497000001"]},"acknowledgement":"Scientific Research Program Funded by Shaanxi Provincial Education Department (Program No.22JY012), Natural Science Basic Research Program of Shaanxi (Grant No.2022JZ-31), Young Talent fund of University Association for Science and Technology in Shaanxi, China (Grant No.20210411), China Postdoctoral Science Foundation (Grant No. 2021M692621), the Foundation of Shaanxi University of Science & Technology (Grant No. 2017GBJ-03), Open Foundation of Key Laboratory of Auxiliary Chemistry and Technology for Chemical Industry, Ministry of Education, Shaanxi University of Science and Technology (Grant No. KFKT2022-15), and Open Foundation of Shaanxi Collaborative Innovation Center of Industrial Auxiliary Chemistry and Technology, Shaanxi University of Science and Technology (Grant No. KFKT2022-15).","volume":613,"article_type":"original","department":[{"_id":"MaIb"}],"publication_status":"published","date_updated":"2025-01-09T07:35:04Z","date_published":"2023-03-15T00:00:00Z","type":"journal_article","quality_controlled":"1","intvolume":"       613","language":[{"iso":"eng"}],"oa_version":"None","date_created":"2023-01-12T11:55:02Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"volume":30,"acknowledgement":"This work was supported by European Commission’s Seventh Framework Programme under Grant Agreement No. 279113 (OCTIPS; www.octips.eu).","main_file_link":[{"url":"https://doi.org/10.1245/s10434-022-12681-z","open_access":"1"}],"page":"46-47","citation":{"chicago":"Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote, Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS) Consortium.” <i>Annals of Surgical Oncology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1245/s10434-022-12681-z\">https://doi.org/10.1245/s10434-022-12681-z</a>.","mla":"Glajzer, Jacek, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS) Consortium.” <i>Annals of Surgical Oncology</i>, vol. 30, Springer Nature, 2023, pp. 46–47, doi:<a href=\"https://doi.org/10.1245/s10434-022-12681-z\">10.1245/s10434-022-12681-z</a>.","apa":"Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele, A., … Braicu, E. I. (2023). ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. <i>Annals of Surgical Oncology</i>. Springer Nature. <a href=\"https://doi.org/10.1245/s10434-022-12681-z\">https://doi.org/10.1245/s10434-022-12681-z</a>","ista":"Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET, Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023. ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. 30, 46–47.","ama":"Glajzer J, Castillo-Tong DC, Richter R, et al. ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. <i>Annals of Surgical Oncology</i>. 2023;30:46-47. doi:<a href=\"https://doi.org/10.1245/s10434-022-12681-z\">10.1245/s10434-022-12681-z</a>","short":"J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele, I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T. Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I. Braicu, Annals of Surgical Oncology 30 (2023) 46–47.","ieee":"J. Glajzer <i>et al.</i>, “ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium,” <i>Annals of Surgical Oncology</i>, vol. 30. Springer Nature, pp. 46–47, 2023."},"external_id":{"isi":["000879151800001"]},"quality_controlled":"1","intvolume":"        30","language":[{"iso":"eng"}],"oa_version":"Published Version","date_created":"2023-01-12T11:56:22Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-01-01T00:00:00Z","type":"journal_article","publication_status":"published","department":[{"_id":"JoDa"}],"date_updated":"2026-06-18T17:21:25Z","article_type":"original","author":[{"first_name":"Jacek","full_name":"Glajzer, Jacek","last_name":"Glajzer"},{"first_name":"Dan Cacsire","full_name":"Castillo-Tong, Dan Cacsire","last_name":"Castillo-Tong"},{"last_name":"Richter","first_name":"Rolf","full_name":"Richter, Rolf"},{"last_name":"Vergote","full_name":"Vergote, Ignace","first_name":"Ignace"},{"last_name":"Kulbe","full_name":"Kulbe, Hagen","first_name":"Hagen"},{"first_name":"Adriaan","full_name":"Vanderstichele, Adriaan","last_name":"Vanderstichele"},{"first_name":"Ilary","full_name":"Ruscito, Ilary","last_name":"Ruscito"},{"full_name":"Trillsch, Fabian","first_name":"Fabian","last_name":"Trillsch"},{"last_name":"Mustea","full_name":"Mustea, Alexander","first_name":"Alexander"},{"last_name":"Kreuzinger","first_name":"Caroline","full_name":"Kreuzinger, Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gourley, Charlie","first_name":"Charlie","last_name":"Gourley"},{"first_name":"Hani","full_name":"Gabra, Hani","last_name":"Gabra"},{"last_name":"Taube","first_name":"Eliane T.","full_name":"Taube, Eliane T."},{"full_name":"Dorigo, Oliver","first_name":"Oliver","last_name":"Dorigo"},{"first_name":"David","full_name":"Horst, David","last_name":"Horst"},{"last_name":"Keunecke","full_name":"Keunecke, Carlotta","first_name":"Carlotta"},{"first_name":"Joanna","full_name":"Baum, Joanna","last_name":"Baum"},{"last_name":"Angelotti","full_name":"Angelotti, Timothy","first_name":"Timothy"},{"last_name":"Sehouli","first_name":"Jalid","full_name":"Sehouli, Jalid"},{"first_name":"Elena Ioana","full_name":"Braicu, Elena Ioana","last_name":"Braicu"}],"related_material":{"record":[{"status":"public","relation":"other","id":"12205"}]},"isi":1,"keyword":["Oncology","Surgery"],"scopus_import":"1","title":"ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium","article_processing_charge":"No","oa":1,"month":"01","_id":"12115","status":"public","year":"2023","publication":"Annals of Surgical Oncology","day":"01","publication_identifier":{"issn":["1068-9265"],"eissn":["1534-4681"]},"doi":"10.1245/s10434-022-12681-z","publisher":"Springer Nature","ddc":["570"],"fulldoi":"https://doi.org/10.1245/s10434-022-12681-z"},{"citation":{"ista":"Zeller P, Yeung J, Viñas Gaza H, de Barbanson BA, Bhardwaj V, Florescu M, van der Linden R, van Oudenaarden A. 2023. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 55, 333–345.","ama":"Zeller P, Yeung J, Viñas Gaza H, et al. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. <i>Nature Genetics</i>. 2023;55:333-345. doi:<a href=\"https://doi.org/10.1038/s41588-022-01260-3\">10.1038/s41588-022-01260-3</a>","mla":"Zeller, Peter, et al. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” <i>Nature Genetics</i>, vol. 55, Springer Nature, 2023, pp. 333–45, doi:<a href=\"https://doi.org/10.1038/s41588-022-01260-3\">10.1038/s41588-022-01260-3</a>.","apa":"Zeller, P., Yeung, J., Viñas Gaza, H., de Barbanson, B. A., Bhardwaj, V., Florescu, M., … van Oudenaarden, A. (2023). Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. <i>Nature Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41588-022-01260-3\">https://doi.org/10.1038/s41588-022-01260-3</a>","ieee":"P. Zeller <i>et al.</i>, “Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis,” <i>Nature Genetics</i>, vol. 55. Springer Nature, pp. 333–345, 2023.","short":"P. Zeller, J. Yeung, H. Viñas Gaza, B.A. de Barbanson, V. Bhardwaj, M. Florescu, R. van der Linden, A. van Oudenaarden, Nature Genetics 55 (2023) 333–345.","chicago":"Zeller, Peter, Jake Yeung, Helena Viñas Gaza, Buys Anton de Barbanson, Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, and Alexander van Oudenaarden. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” <i>Nature Genetics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41588-022-01260-3\">https://doi.org/10.1038/s41588-022-01260-3</a>."},"page":"333-345","external_id":{"pmid":["36539617"]},"acknowledgement":"We thank A. Giladi for sharing mRNA abundance tables of cell types together with J. van den Berg for critical reading of the manuscript. We thank M. Bartosovic for sharing method comparison data. pK19pA-MN was a gift from Ulrich Laemmli (Addgene plasmid 86973, http://n2t.net/addgene:86973; RRID:Addgene_86973). Figure 8 is adopted from Hematopoiesis (human) diagram by A. Rad and M. Häggström under CC-BY-SA 3.0 license. This work was supported by European Research Council Advanced under grant ERC-AdG 742225-IntScOmics and Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP award NWO-CW 714.016.001. The SNF (P2BSP3-174991), HFSP (LT000209/2018-L) and Marie Skłodowska-Curie Actions (798573) supported P.Z. The SNF (P2ELP3_184488) and HFSP (LT000097/2019-L) supported J.Y. and the EMBO LTF (ALTF 1197–2019) supported V.B. This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","volume":55,"article_type":"review","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_name":"2023_NatureGenetics_Zeller.pdf","content_type":"application/pdf","success":1,"date_updated":"2023-02-27T07:46:45Z","relation":"main_file","checksum":"6fdb8e34fbeea63edd0f2c6c2cc5823e","file_id":"12688","access_level":"open_access","date_created":"2023-02-27T07:46:45Z","creator":"dernst","file_size":21484855}],"publication_status":"published","department":[{"_id":"ScienComp"}],"date_updated":"2025-04-23T08:45:00Z","date_published":"2023-02-01T00:00:00Z","type":"journal_article","has_accepted_license":"1","intvolume":"        55","quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2023-01-12T12:09:09Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Genetics"],"abstract":[{"lang":"eng","text":"Post-translational histone modifications modulate chromatin activity to affect gene expression. How chromatin states underlie lineage choice in single cells is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in the mouse bone marrow. During differentiation, hematopoietic stem and progenitor cells (HSPCs) acquire active chromatin states mediated by cell-type-specifying transcription factors, which are unique for each lineage. By contrast, most alterations in repressive marks during differentiation occur independent of the final cell type. Chromatin trajectory analysis shows that lineage choice at the chromatin level occurs at the progenitor stage. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin states. This implies a hierarchical regulation of chromatin during hematopoiesis: heterochromatin dynamics distinguish differentiation trajectories and lineages, while euchromatin dynamics reflect cell types within lineages."}],"author":[{"last_name":"Zeller","full_name":"Zeller, Peter","first_name":"Peter"},{"orcid":"0000-0003-1732-1559","first_name":"Jake","id":"123012b2-db30-11eb-b4d8-a35840c0551b","full_name":"Yeung, Jake","last_name":"Yeung"},{"last_name":"Viñas Gaza","first_name":"Helena","full_name":"Viñas Gaza, Helena"},{"last_name":"de Barbanson","full_name":"de Barbanson, Buys Anton","first_name":"Buys Anton"},{"full_name":"Bhardwaj, Vivek","first_name":"Vivek","last_name":"Bhardwaj"},{"full_name":"Florescu, Maria","first_name":"Maria","last_name":"Florescu"},{"first_name":"Reinier","full_name":"van der Linden, Reinier","last_name":"van der Linden"},{"full_name":"van Oudenaarden, Alexander","first_name":"Alexander","last_name":"van Oudenaarden"}],"pmid":1,"doi":"10.1038/s41588-022-01260-3","file_date_updated":"2023-02-27T07:46:45Z","publisher":"Springer Nature","fulldoi":"https://doi.org/10.1038/s41588-022-01260-3","ddc":["570","000"],"day":"01","publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"status":"public","_id":"12158","month":"02","year":"2023","publication":"Nature Genetics","scopus_import":"1","title":"Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis","article_processing_charge":"No","oa":1},{"volume":"150-151","acknowledgement":"This work received funding from the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 851288 to E.H.).\r\nB. C-M wants to acknowledge the support of the field of excellence Complexity of Life, in Basic Research and Innovation of the University of Graz.","project":[{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"citation":{"chicago":"Corominas-Murtra, Bernat, and Edouard B Hannezo. “Modelling the Dynamics of Mammalian Gut Homeostasis.” <i>Seminars in Cell &#38; Developmental Biology</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.semcdb.2022.11.005\">https://doi.org/10.1016/j.semcdb.2022.11.005</a>.","mla":"Corominas-Murtra, Bernat, and Edouard B. Hannezo. “Modelling the Dynamics of Mammalian Gut Homeostasis.” <i>Seminars in Cell &#38; Developmental Biology</i>, vol. 150–151, Elsevier, 2023, pp. 58–65, doi:<a href=\"https://doi.org/10.1016/j.semcdb.2022.11.005\">10.1016/j.semcdb.2022.11.005</a>.","apa":"Corominas-Murtra, B., &#38; Hannezo, E. B. (2023). Modelling the dynamics of mammalian gut homeostasis. <i>Seminars in Cell &#38; Developmental Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.semcdb.2022.11.005\">https://doi.org/10.1016/j.semcdb.2022.11.005</a>","ista":"Corominas-Murtra B, Hannezo EB. 2023. Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell &#38; Developmental Biology. 150–151, 58–65.","ama":"Corominas-Murtra B, Hannezo EB. Modelling the dynamics of mammalian gut homeostasis. <i>Seminars in Cell &#38; Developmental Biology</i>. 2023;150-151:58-65. doi:<a href=\"https://doi.org/10.1016/j.semcdb.2022.11.005\">10.1016/j.semcdb.2022.11.005</a>","short":"B. Corominas-Murtra, E.B. Hannezo, Seminars in Cell &#38; Developmental Biology 150–151 (2023) 58–65.","ieee":"B. Corominas-Murtra and E. B. Hannezo, “Modelling the dynamics of mammalian gut homeostasis,” <i>Seminars in Cell &#38; Developmental Biology</i>, vol. 150–151. Elsevier, pp. 58–65, 2023."},"page":"58-65","external_id":{"pmid":["36470715"],"isi":["001053522200001"]},"ec_funded":1,"type":"journal_article","has_accepted_license":"1","date_published":"2023-12-02T00:00:00Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-01-12T12:09:47Z","oa_version":"Published Version","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"access_level":"open_access","file_size":1343750,"creator":"dernst","date_created":"2024-01-08T10:16:04Z","success":1,"content_type":"application/pdf","file_name":"2023_SeminarsCellDevBiology_CorominasMurtra.pdf","file_id":"14741","checksum":"c619887cf130f4649bf3035417186004","relation":"main_file","date_updated":"2024-01-08T10:16:04Z"}],"article_type":"review","date_updated":"2025-04-14T07:52:27Z","department":[{"_id":"EdHa"}],"publication_status":"published","abstract":[{"text":"Homeostatic balance in the intestinal epithelium relies on a fast cellular turnover, which is coordinated by an intricate interplay between biochemical signalling, mechanical forces and organ geometry. We review recent modelling approaches that have been developed to understand different facets of this remarkable homeostatic equilibrium. Existing models offer different, albeit complementary, perspectives on the problem. First, biomechanical models aim to explain the local and global mechanical stresses driving cell renewal as well as tissue shape maintenance. Second, compartmental models provide insights into the conditions necessary to keep a constant flow of cells with well-defined ratios of cell types, and how perturbations can lead to an unbalance of relative compartment sizes. A third family of models address, at the cellular level, the nature and regulation of stem fate choices that are necessary to fuel cellular turnover. We also review how these different approaches are starting to be integrated together across scales, to provide quantitative predictions and new conceptual frameworks to think about the dynamics of cell renewal in complex tissues.","lang":"eng"}],"pmid":1,"author":[{"last_name":"Corominas-Murtra","first_name":"Bernat","orcid":"0000-0001-9806-5643","full_name":"Corominas-Murtra, Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","last_name":"Hannezo"}],"keyword":["Cell Biology","Developmental Biology"],"isi":1,"corr_author":"1","publication":"Seminars in Cell & Developmental Biology","status":"public","_id":"12162","month":"12","year":"2023","article_processing_charge":"Yes (via OA deal)","oa":1,"scopus_import":"1","title":"Modelling the dynamics of mammalian gut homeostasis","ddc":["570"],"fulldoi":"https://doi.org/10.1016/j.semcdb.2022.11.005","file_date_updated":"2024-01-08T10:16:04Z","doi":"10.1016/j.semcdb.2022.11.005","publisher":"Elsevier","publication_identifier":{"issn":["1084-9521"]},"day":"02"},{"quality_controlled":"1","intvolume":"       597","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-01-12T12:09:58Z","language":[{"iso":"eng"}],"date_published":"2023-03-01T00:00:00Z","has_accepted_license":"1","type":"journal_article","department":[{"_id":"MaLo"}],"publication_status":"published","date_updated":"2024-10-09T21:03:42Z","article_type":"review","file":[{"file_id":"14063","relation":"main_file","checksum":"7492244d3f9c5faa1347ef03f6e5bc84","date_updated":"2023-08-16T08:31:04Z","success":1,"content_type":"application/pdf","file_name":"2023_FEBSLetters_Loose.pdf","file_size":3148143,"creator":"dernst","date_created":"2023-08-16T08:31:04Z","access_level":"open_access"}],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"acknowledgement":"The authors acknowledge support from IST Austria and helpful comments from the anonymous reviewers that helped to improve this manuscript. We apologize to the authors of primary literature and outstanding research not cited here due to space restraints.","volume":597,"issue":"6","external_id":{"isi":["000891573000001"],"pmid":["36448231"]},"citation":{"chicago":"Loose, Martin, Albert Auer, Gabriel Brognara, Hanifatul R Budiman, Lukasz M Kowalski, and Ivana Matijevic. “In Vitro Reconstitution of Small GTPase Regulation.” <i>FEBS Letters</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/1873-3468.14540\">https://doi.org/10.1002/1873-3468.14540</a>.","ama":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. In vitro reconstitution of small GTPase regulation. <i>FEBS Letters</i>. 2023;597(6):762-777. doi:<a href=\"https://doi.org/10.1002/1873-3468.14540\">10.1002/1873-3468.14540</a>","ista":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. 2023. In vitro reconstitution of small GTPase regulation. FEBS Letters. 597(6), 762–777.","mla":"Loose, Martin, et al. “In Vitro Reconstitution of Small GTPase Regulation.” <i>FEBS Letters</i>, vol. 597, no. 6, Wiley, 2023, pp. 762–77, doi:<a href=\"https://doi.org/10.1002/1873-3468.14540\">10.1002/1873-3468.14540</a>.","apa":"Loose, M., Auer, A., Brognara, G., Budiman, H. R., Kowalski, L. M., &#38; Matijevic, I. (2023). In vitro reconstitution of small GTPase regulation. <i>FEBS Letters</i>. Wiley. <a href=\"https://doi.org/10.1002/1873-3468.14540\">https://doi.org/10.1002/1873-3468.14540</a>","ieee":"M. Loose, A. Auer, G. Brognara, H. R. Budiman, L. M. Kowalski, and I. Matijevic, “In vitro reconstitution of small GTPase regulation,” <i>FEBS Letters</i>, vol. 597, no. 6. Wiley, pp. 762–777, 2023.","short":"M. Loose, A. Auer, G. Brognara, H.R. Budiman, L.M. Kowalski, I. Matijevic, FEBS Letters 597 (2023) 762–777."},"page":"762-777","title":"In vitro reconstitution of small GTPase regulation","scopus_import":"1","oa":1,"article_processing_charge":"Yes (via OA deal)","year":"2023","month":"03","_id":"12163","status":"public","publication":"FEBS Letters","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","day":"01","publication_identifier":{"issn":["0014-5793"],"eissn":["1873-3468"]},"publisher":"Wiley","file_date_updated":"2023-08-16T08:31:04Z","doi":"10.1002/1873-3468.14540","ddc":["570"],"fulldoi":"https://doi.org/10.1002/1873-3468.14540","author":[{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0000-0001-7309-9724","last_name":"Loose"},{"id":"3018E8C2-F248-11E8-B48F-1D18A9856A87","full_name":"Auer, Albert","first_name":"Albert","orcid":"0000-0002-3580-2906","last_name":"Auer"},{"id":"D96FFDA0-A884-11E9-9968-DC26E6697425","full_name":"Brognara, Gabriel","first_name":"Gabriel","last_name":"Brognara"},{"id":"55380f95-15b2-11ec-abd3-aff8e230696b","full_name":"Budiman, Hanifatul R","first_name":"Hanifatul R","last_name":"Budiman"},{"last_name":"Kowalski","id":"e3a512e2-4bbe-11eb-a68a-e3857a7844c2","full_name":"Kowalski, Lukasz M","first_name":"Lukasz M"},{"last_name":"Matijevic","full_name":"Matijevic, Ivana","id":"83c17ce3-15b2-11ec-abd3-f486545870bd","first_name":"Ivana"}],"pmid":1,"abstract":[{"text":"Small GTPases play essential roles in the organization of eukaryotic cells. In recent years, it has become clear that their intracellular functions result from intricate biochemical networks of the GTPase and their regulators that dynamically bind to a membrane surface. Due to the inherent complexities of their interactions, however, revealing the underlying mechanisms of action is often difficult to achieve from in vivo studies. This review summarizes in vitro reconstitution approaches developed to obtain a better mechanistic understanding of how small GTPase activities are regulated in space and time.","lang":"eng"}],"isi":1,"corr_author":"1","keyword":["Cell Biology","Genetics","Molecular Biology","Biochemistry","Structural Biology","Biophysics"]},{"page":"29-43","citation":{"apa":"Baig, M. A., Hendler, D., Milani, A., &#38; Travers, C. (2023). Long-lived counters with polylogarithmic amortized step complexity. <i>Distributed Computing</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00446-022-00439-5\">https://doi.org/10.1007/s00446-022-00439-5</a>","mla":"Baig, Mirza Ahad, et al. “Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” <i>Distributed Computing</i>, vol. 36, Springer Nature, 2023, pp. 29–43, doi:<a href=\"https://doi.org/10.1007/s00446-022-00439-5\">10.1007/s00446-022-00439-5</a>.","ama":"Baig MA, Hendler D, Milani A, Travers C. Long-lived counters with polylogarithmic amortized step complexity. <i>Distributed Computing</i>. 2023;36:29-43. doi:<a href=\"https://doi.org/10.1007/s00446-022-00439-5\">10.1007/s00446-022-00439-5</a>","ista":"Baig MA, Hendler D, Milani A, Travers C. 2023. Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. 36, 29–43.","short":"M.A. Baig, D. Hendler, A. Milani, C. Travers, Distributed Computing 36 (2023) 29–43.","ieee":"M. A. Baig, D. Hendler, A. Milani, and C. Travers, “Long-lived counters with polylogarithmic amortized step complexity,” <i>Distributed Computing</i>, vol. 36. Springer Nature, pp. 29–43, 2023.","chicago":"Baig, Mirza Ahad, Danny Hendler, Alessia Milani, and Corentin Travers. “Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” <i>Distributed Computing</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00446-022-00439-5\">https://doi.org/10.1007/s00446-022-00439-5</a>."},"external_id":{"isi":["000890138700001"]},"main_file_link":[{"open_access":"1","url":"https://drops.dagstuhl.de/opus/volltexte/2019/11310/"}],"volume":36,"acknowledgement":"A preliminary version of this work appeared in DISC’19. Mirza Ahad Baig, Alessia Milani and Corentin Travers are supported by ANR projects Descartes and FREDDA. Mirza Ahad Baig is supported by UMI Relax. Danny Hendler is supported by the Israel Science Foundation (Grants 380/18 and 1425/22).","article_type":"original","date_updated":"2023-08-16T08:39:36Z","publication_status":"published","department":[{"_id":"KrPi"}],"type":"journal_article","date_published":"2023-03-01T00:00:00Z","language":[{"iso":"eng"}],"date_created":"2023-01-12T12:10:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","intvolume":"        36","quality_controlled":"1","keyword":["Computational Theory and Mathematics","Computer Networks and Communications","Hardware and Architecture","Theoretical Computer Science"],"isi":1,"abstract":[{"lang":"eng","text":"A shared-memory counter is a widely-used and well-studied concurrent object. It supports two operations: An Inc operation that increases its value by 1 and a Read operation that returns its current value. In Jayanti et al (SIAM J Comput, 30(2), 2000), Jayanti, Tan and Toueg proved a linear lower bound on the worst-case step complexity of obstruction-free implementations, from read-write registers, of a large class of shared objects that includes counters. The lower bound leaves open the question of finding counter implementations with sub-linear amortized step complexity. In this work, we address this gap. We show that n-process, wait-free and linearizable counters can be implemented from read-write registers with O(log2n) amortized step complexity. This is the first counter algorithm from read-write registers that provides sub-linear amortized step complexity in executions of arbitrary length. Since a logarithmic lower bound on the amortized step complexity of obstruction-free counter implementations exists, our upper bound is within a logarithmic factor of the optimal. The worst-case step complexity of the construction remains linear, which is optimal. This is obtained thanks to a new max register construction with O(logn) amortized step complexity in executions of arbitrary length in which the value stored in the register does not grow too quickly. We then leverage an existing counter algorithm by Aspnes, Attiya and Censor-Hillel [1] in which we “plug” our max register implementation to show that it remains linearizable while achieving O(log2n) amortized step complexity."}],"author":[{"id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","full_name":"Baig, Mirza Ahad","first_name":"Mirza Ahad","last_name":"Baig"},{"last_name":"Hendler","first_name":"Danny","full_name":"Hendler, Danny"},{"last_name":"Milani","first_name":"Alessia","full_name":"Milani, Alessia"},{"last_name":"Travers","first_name":"Corentin","full_name":"Travers, Corentin"}],"fulldoi":"https://doi.org/10.1007/s00446-022-00439-5","doi":"10.1007/s00446-022-00439-5","publisher":"Springer Nature","publication_identifier":{"issn":["0178-2770"],"eissn":["1432-0452"]},"day":"01","publication":"Distributed Computing","_id":"12164","month":"03","status":"public","year":"2023","article_processing_charge":"No","oa":1,"scopus_import":"1","title":"Long-lived counters with polylogarithmic amortized step complexity"},{"volume":5,"citation":{"apa":"Hof, B. (2023). Directed percolation and the transition to turbulence. <i>Nature Reviews Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42254-022-00539-y\">https://doi.org/10.1038/s42254-022-00539-y</a>","mla":"Hof, Björn. “Directed Percolation and the Transition to Turbulence.” <i>Nature Reviews Physics</i>, vol. 5, Springer Nature, 2023, pp. 62–72, doi:<a href=\"https://doi.org/10.1038/s42254-022-00539-y\">10.1038/s42254-022-00539-y</a>.","ista":"Hof B. 2023. Directed percolation and the transition to turbulence. Nature Reviews Physics. 5, 62–72.","ama":"Hof B. Directed percolation and the transition to turbulence. <i>Nature Reviews Physics</i>. 2023;5:62-72. doi:<a href=\"https://doi.org/10.1038/s42254-022-00539-y\">10.1038/s42254-022-00539-y</a>","short":"B. Hof, Nature Reviews Physics 5 (2023) 62–72.","ieee":"B. Hof, “Directed percolation and the transition to turbulence,” <i>Nature Reviews Physics</i>, vol. 5. Springer Nature, pp. 62–72, 2023.","chicago":"Hof, Björn. “Directed Percolation and the Transition to Turbulence.” <i>Nature Reviews Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s42254-022-00539-y\">https://doi.org/10.1038/s42254-022-00539-y</a>."},"page":"62-72","external_id":{"isi":["000890148700002"]},"date_published":"2023-01-01T00:00:00Z","type":"journal_article","quality_controlled":"1","intvolume":"         5","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2023-01-12T12:10:18Z","oa_version":"None","article_type":"original","publication_status":"published","department":[{"_id":"BjHo"}],"date_updated":"2024-10-09T21:04:02Z","abstract":[{"text":"It may come as a surprise that a phenomenon as ubiquitous and prominent as the transition from laminar to turbulent flow has resisted combined efforts by physicists, engineers and mathematicians, and remained unresolved for almost one and a half centuries. In recent years, various studies have proposed analogies to directed percolation, a well-known universality class in statistical mechanics, which describes a non-equilibrium phase transition from a fluctuating active phase into an absorbing state. It is this unlikely relation between the multiscale, high-dimensional dynamics that signify the transition process in virtually all flows of practical relevance, and the arguably most basic non-equilibrium phase transition, that so far has mainly been the subject of model studies, which I review in this Perspective.","lang":"eng"}],"author":[{"orcid":"0000-0003-2057-2754","first_name":"Björn","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof"}],"isi":1,"corr_author":"1","keyword":["General Physics and Astronomy"],"month":"01","_id":"12165","status":"public","year":"2023","publication":"Nature Reviews Physics","scopus_import":"1","title":"Directed percolation and the transition to turbulence","article_processing_charge":"No","doi":"10.1038/s42254-022-00539-y","publisher":"Springer Nature","fulldoi":"https://doi.org/10.1038/s42254-022-00539-y","day":"01","publication_identifier":{"eissn":["2522-5820"]}},{"volume":32,"main_file_link":[{"url":"https://doi.org/10.1111/mec.16779","open_access":"1"}],"page":"26-29","citation":{"ieee":"A. M. Westram and R. Butlin, “Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize,” <i>Molecular Ecology</i>, vol. 32, no. 1. Wiley, pp. 26–29, 2023.","short":"A.M. Westram, R. Butlin, Molecular Ecology 32 (2023) 26–29.","ista":"Westram AM, Butlin R. 2023. Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. Molecular Ecology. 32(1), 26–29.","ama":"Westram AM, Butlin R. Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. <i>Molecular Ecology</i>. 2023;32(1):26-29. doi:<a href=\"https://doi.org/10.1111/mec.16779\">10.1111/mec.16779</a>","apa":"Westram, A. M., &#38; Butlin, R. (2023). Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.16779\">https://doi.org/10.1111/mec.16779</a>","mla":"Westram, Anja M., and Roger Butlin. “Professor Kerstin Johannesson–Winner of the 2022 Molecular Ecology Prize.” <i>Molecular Ecology</i>, vol. 32, no. 1, Wiley, 2023, pp. 26–29, doi:<a href=\"https://doi.org/10.1111/mec.16779\">10.1111/mec.16779</a>.","chicago":"Westram, Anja M, and Roger Butlin. “Professor Kerstin Johannesson–Winner of the 2022 Molecular Ecology Prize.” <i>Molecular Ecology</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/mec.16779\">https://doi.org/10.1111/mec.16779</a>."},"external_id":{"pmid":["36443277"],"isi":["000892168800001"]},"issue":"1","date_published":"2023-01-01T00:00:00Z","type":"journal_article","quality_controlled":"1","intvolume":"        32","language":[{"iso":"eng"}],"oa_version":"Published Version","date_created":"2023-01-12T12:10:28Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"editorial","publication_status":"published","department":[{"_id":"NiBa"}],"date_updated":"2026-06-18T17:24:18Z","abstract":[{"lang":"eng","text":"Kerstin Johannesson is a marine ecologist and evolutionary biologist based at the Tjärnö Marine Laboratory of the University of Gothenburg, which is situated in the beautiful Kosterhavet National Park on the Swedish west coast. Her work, using marine periwinkles (especially Littorina saxatilis and L. fabalis) as main model systems, has made a remarkable contribution to marine evolutionary biology and our understanding of local adaptation and its genetic underpinnings."}],"author":[{"orcid":"0000-0003-1050-4969","first_name":"Anja M","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram"},{"last_name":"Butlin","first_name":"Roger","full_name":"Butlin, Roger"}],"pmid":1,"isi":1,"corr_author":"1","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"OA_type":"free access","_id":"12166","month":"01","status":"public","year":"2023","publication":"Molecular Ecology","scopus_import":"1","title":"Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize","article_processing_charge":"No","oa":1,"doi":"10.1111/mec.16779","publisher":"Wiley","fulldoi":"https://doi.org/10.1111/mec.16779","ddc":["570"],"day":"01","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]}}]