[{"language":[{"iso":"eng"}],"citation":{"short":"S.M. Velasquez, X. Guo, M. Gallemi, B. Aryal, P. Venhuizen, E. Barbez, K.A. Dünser, M. Darino, A. Pӗnčík, O. Novák, M. Kalyna, G. Mouille, E. Benková, R.P. Bhalerao, J. Mravec, J. Kleine-Vehn, International Journal of Molecular Sciences 22 (2021).","ista":"Velasquez SM, Guo X, Gallemi M, Aryal B, Venhuizen P, Barbez E, Dünser KA, Darino M, Pӗnčík A, Novák O, Kalyna M, Mouille G, Benková E, Bhalerao RP, Mravec J, Kleine-Vehn J. 2021. Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. International Journal of Molecular Sciences. 22(17), 9222.","mla":"Velasquez, Silvia Melina, et al. “Xyloglucan Remodeling Defines Auxin-Dependent Differential Tissue Expansion in Plants.” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 17, 9222, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/ijms22179222\">10.3390/ijms22179222</a>.","ama":"Velasquez SM, Guo X, Gallemi M, et al. Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. <i>International Journal of Molecular Sciences</i>. 2021;22(17). doi:<a href=\"https://doi.org/10.3390/ijms22179222\">10.3390/ijms22179222</a>","chicago":"Velasquez, Silvia Melina, Xiaoyuan Guo, Marçal Gallemi, Bibek Aryal, Peter Venhuizen, Elke Barbez, Kai Alexander Dünser, et al. “Xyloglucan Remodeling Defines Auxin-Dependent Differential Tissue Expansion in Plants.” <i>International Journal of Molecular Sciences</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ijms22179222\">https://doi.org/10.3390/ijms22179222</a>.","ieee":"S. M. Velasquez <i>et al.</i>, “Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants,” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 17. MDPI, 2021.","apa":"Velasquez, S. M., Guo, X., Gallemi, M., Aryal, B., Venhuizen, P., Barbez, E., … Kleine-Vehn, J. (2021). Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms22179222\">https://doi.org/10.3390/ijms22179222</a>"},"doi":"10.3390/ijms22179222","oa_version":"Published Version","intvolume":"        22","_id":"9986","corr_author":"1","oa":1,"month":"08","date_created":"2021-09-05T22:01:24Z","publication":"International Journal of Molecular Sciences","pmid":1,"scopus_import":"1","abstract":[{"text":"Size control is a fundamental question in biology, showing incremental complexity in plants, whose cells possess a rigid cell wall. The phytohormone auxin is a vital growth regulator with central importance for differential growth control. Our results indicate that auxin-reliant growth programs affect the molecular complexity of xyloglucans, the major type of cell wall hemicellulose in eudicots. Auxin-dependent induction and repression of growth coincide with reduced and enhanced molecular complexity of xyloglucans, respectively. In agreement with a proposed function in growth control, genetic interference with xyloglucan side decorations distinctly modulates auxin-dependent differential growth rates. Our work proposes that auxin-dependent growth programs have a spatially defined effect on xyloglucan’s molecular structure, which in turn affects cell wall mechanics and specifies differential, gravitropic hypocotyl growth.","lang":"eng"}],"article_number":"9222","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-08-26T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_identifier":{"issn":["1661-6596"],"eissn":["1422-0067"]},"has_accepted_license":"1","issue":"17","date_updated":"2024-10-09T21:00:50Z","title":"Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants","department":[{"_id":"EvBe"}],"article_processing_charge":"Yes","file":[{"checksum":"6b7055cf89f1b7ed8594c3fdf56f000b","access_level":"open_access","date_updated":"2021-09-07T09:04:53Z","file_name":"2021_IntJMolecularSciences_Velasquez.pdf","content_type":"application/pdf","creator":"cchlebak","relation":"main_file","file_id":"9988","date_created":"2021-09-06T12:50:19Z","file_size":2162247}],"type":"journal_article","publication_status":"published","ddc":["575"],"publisher":"MDPI","quality_controlled":"1","author":[{"last_name":"Velasquez","first_name":"Silvia Melina","full_name":"Velasquez, Silvia Melina"},{"last_name":"Guo","first_name":"Xiaoyuan","full_name":"Guo, Xiaoyuan"},{"orcid":"0000-0003-4675-6893","last_name":"Gallemi","id":"460C6802-F248-11E8-B48F-1D18A9856A87","first_name":"Marçal","full_name":"Gallemi, Marçal"},{"first_name":"Bibek","full_name":"Aryal, Bibek","last_name":"Aryal"},{"first_name":"Peter","full_name":"Venhuizen, Peter","last_name":"Venhuizen"},{"full_name":"Barbez, Elke","first_name":"Elke","last_name":"Barbez"},{"last_name":"Dünser","first_name":"Kai Alexander","full_name":"Dünser, Kai Alexander"},{"last_name":"Darino","first_name":"Martin","full_name":"Darino, Martin"},{"last_name":"Pӗnčík","full_name":"Pӗnčík, Aleš","first_name":"Aleš"},{"full_name":"Novák, Ondřej","first_name":"Ondřej","last_name":"Novák"},{"last_name":"Kalyna","first_name":"Maria","full_name":"Kalyna, Maria"},{"first_name":"Gregory","full_name":"Mouille, Gregory","last_name":"Mouille"},{"first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bhalerao","first_name":"Rishikesh P.","full_name":"Bhalerao, Rishikesh P."},{"full_name":"Mravec, Jozef","first_name":"Jozef","last_name":"Mravec"},{"first_name":"Jürgen","full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine-Vehn"}],"keyword":["auxin","growth","cell wall","xyloglucans","hypocotyls","gravitropism"],"external_id":{"pmid":["34502129"],"isi":["000694347100001"]},"article_type":"original","file_date_updated":"2021-09-07T09:04:53Z","acknowledgement":"We are grateful to Paul Knox, Markus Pauly, Malcom O’Neill, and Ignacio Zarra for providing published material; the BOKU-VIBT Imaging Center for access and M. Debreczeny for expertise; J.I. Thaker and Georg Seifert for critical reading.\r\n","isi":1,"day":"26","volume":22,"year":"2021"},{"date_published":"2021-08-30T00:00:00Z","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"87","publication_identifier":{"eissn":["1420-9020"],"issn":["1022-1824"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        27","_id":"9998","citation":{"ista":"Koroteev P, Pushkar P, Smirnov AV, Zeitlin AM. 2021. Quantum K-theory of quiver varieties and many-body systems. Selecta Mathematica. 27(5), 87.","mla":"Koroteev, Peter, et al. “Quantum K-Theory of Quiver Varieties and Many-Body Systems.” <i>Selecta Mathematica</i>, vol. 27, no. 5, 87, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/s00029-021-00698-3\">10.1007/s00029-021-00698-3</a>.","short":"P. Koroteev, P. Pushkar, A.V. Smirnov, A.M. Zeitlin, Selecta Mathematica 27 (2021).","ama":"Koroteev P, Pushkar P, Smirnov AV, Zeitlin AM. Quantum K-theory of quiver varieties and many-body systems. <i>Selecta Mathematica</i>. 2021;27(5). doi:<a href=\"https://doi.org/10.1007/s00029-021-00698-3\">10.1007/s00029-021-00698-3</a>","chicago":"Koroteev, Peter, Petr Pushkar, Andrey V. Smirnov, and Anton M. Zeitlin. “Quantum K-Theory of Quiver Varieties and Many-Body Systems.” <i>Selecta Mathematica</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00029-021-00698-3\">https://doi.org/10.1007/s00029-021-00698-3</a>.","ieee":"P. Koroteev, P. Pushkar, A. V. Smirnov, and A. M. Zeitlin, “Quantum K-theory of quiver varieties and many-body systems,” <i>Selecta Mathematica</i>, vol. 27, no. 5. Springer Nature, 2021.","apa":"Koroteev, P., Pushkar, P., Smirnov, A. V., &#38; Zeitlin, A. M. (2021). Quantum K-theory of quiver varieties and many-body systems. <i>Selecta Mathematica</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00029-021-00698-3\">https://doi.org/10.1007/s00029-021-00698-3</a>"},"oa_version":"Published Version","doi":"10.1007/s00029-021-00698-3","language":[{"iso":"eng"}],"scopus_import":"1","abstract":[{"lang":"eng","text":"We define quantum equivariant K-theory of Nakajima quiver varieties. We discuss type A in detail as well as its connections with quantum XXZ spin chains and trigonometric Ruijsenaars-Schneider models. Finally we study a limit which produces a K-theoretic version of results of Givental and Kim, connecting quantum geometry of flag varieties and Toda lattice."}],"month":"08","date_created":"2021-09-12T22:01:22Z","publication":"Selecta Mathematica","oa":1,"file_date_updated":"2021-09-13T11:31:34Z","article_type":"original","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"external_id":{"isi":["000692795200001"]},"volume":27,"year":"2021","day":"30","isi":1,"acknowledgement":"First of all we would like to thank Andrei Okounkov for invaluable discussions, advises and sharing with us his fantastic viewpoint on modern quantum geometry. We are also grateful to D. Korb and Z. Zhou for their interest and comments. The work of A. Smirnov was supported in part by RFBR Grants under Numbers 15-02-04175 and 15-01-04217 and in part by NSF Grant DMS–2054527. The work of P. Koroteev, A.M. Zeitlin and A. Smirnov is supported in part by AMS Simons travel Grant. A. M. Zeitlin is partially supported by Simons Collaboration Grant, Award ID: 578501. Open access funding provided by Institute of Science and Technology (IST Austria).","type":"journal_article","publication_status":"published","file":[{"access_level":"open_access","checksum":"beadc5a722ffb48190e1e63ee2dbfee5","date_updated":"2021-09-13T11:31:34Z","relation":"main_file","content_type":"application/pdf","creator":"cchlebak","file_name":"2021_SelectaMath_Koroteev.pdf","success":1,"file_size":584648,"date_created":"2021-09-13T11:31:34Z","file_id":"10010"}],"title":"Quantum K-theory of quiver varieties and many-body systems","department":[{"_id":"TaHa"}],"article_processing_charge":"Yes (via OA deal)","issue":"5","has_accepted_license":"1","date_updated":"2025-04-15T06:53:09Z","quality_controlled":"1","author":[{"full_name":"Koroteev, Peter","first_name":"Peter","last_name":"Koroteev"},{"id":"151DCEB6-9EC3-11E9-8480-ABECE5697425","last_name":"Pushkar","full_name":"Pushkar, Petr","first_name":"Petr"},{"last_name":"Smirnov","full_name":"Smirnov, Andrey V.","first_name":"Andrey V."},{"last_name":"Zeitlin","full_name":"Zeitlin, Anton M.","first_name":"Anton M."}],"ddc":["530"],"publisher":"Springer Nature"},{"keyword":["cell delamination","apical constriction","dragging","mechanical forces","collective 18 locomotion","dorsal forerunner cells","zebrafish"],"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","grant_number":"742573"}],"external_id":{"pmid":["34448451"],"isi":["000700428500001"]},"article_type":"original","file_date_updated":"2022-05-13T08:03:37Z","isi":1,"day":"27","volume":10,"year":"2021","has_accepted_license":"1","date_updated":"2025-04-14T07:46:58Z","department":[{"_id":"CaHe"}],"title":"Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism","article_processing_charge":"Yes","file":[{"success":1,"file_size":9010446,"file_id":"11371","date_created":"2022-05-13T08:03:37Z","relation":"main_file","file_name":"2021_eLife_Pulgar.pdf","creator":"dernst","content_type":"application/pdf","date_updated":"2022-05-13T08:03:37Z","access_level":"open_access","checksum":"a3f82b0499cc822ac1eab48a01f3f57e"}],"type":"journal_article","publication_status":"published","ddc":["570"],"publisher":"eLife Sciences Publications","quality_controlled":"1","author":[{"first_name":"Eduardo","full_name":"Pulgar, Eduardo","last_name":"Pulgar"},{"first_name":"Cornelia","full_name":"Schwayer, Cornelia","orcid":"0000-0001-5130-2226","last_name":"Schwayer","id":"3436488C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guerrero","full_name":"Guerrero, Néstor","first_name":"Néstor"},{"last_name":"López","full_name":"López, Loreto","first_name":"Loreto"},{"last_name":"Márquez","first_name":"Susana","full_name":"Márquez, Susana"},{"first_name":"Steffen","full_name":"Härtel, Steffen","last_name":"Härtel"},{"last_name":"Soto","first_name":"Rodrigo","full_name":"Soto, Rodrigo"},{"first_name":"Carl Philipp","full_name":"Heisenberg, Carl Philipp","last_name":"Heisenberg"},{"last_name":"Concha","first_name":"Miguel L.","full_name":"Concha, Miguel L."}],"article_number":"e66483","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-08-27T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_identifier":{"eissn":["2050-084X"]},"language":[{"iso":"eng"}],"citation":{"chicago":"Pulgar, Eduardo, Cornelia Schwayer, Néstor Guerrero, Loreto López, Susana Márquez, Steffen Härtel, Rodrigo Soto, Carl Philipp Heisenberg, and Miguel L. Concha. “Apical Contacts Stemming from Incomplete Delamination Guide Progenitor Cell Allocation through a Dragging Mechanism.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.66483\">https://doi.org/10.7554/eLife.66483</a>.","ieee":"E. Pulgar <i>et al.</i>, “Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","apa":"Pulgar, E., Schwayer, C., Guerrero, N., López, L., Márquez, S., Härtel, S., … Concha, M. L. (2021). Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.66483\">https://doi.org/10.7554/eLife.66483</a>","ama":"Pulgar E, Schwayer C, Guerrero N, et al. Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.66483\">10.7554/eLife.66483</a>","mla":"Pulgar, Eduardo, et al. “Apical Contacts Stemming from Incomplete Delamination Guide Progenitor Cell Allocation through a Dragging Mechanism.” <i>ELife</i>, vol. 10, e66483, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.66483\">10.7554/eLife.66483</a>.","ista":"Pulgar E, Schwayer C, Guerrero N, López L, Márquez S, Härtel S, Soto R, Heisenberg CP, Concha ML. 2021. Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. eLife. 10, e66483.","short":"E. Pulgar, C. Schwayer, N. Guerrero, L. López, S. Márquez, S. Härtel, R. Soto, C.P. Heisenberg, M.L. Concha, ELife 10 (2021)."},"oa_version":"Published Version","doi":"10.7554/eLife.66483","intvolume":"        10","_id":"9999","oa":1,"publication":"eLife","date_created":"2021-09-12T22:01:23Z","month":"08","pmid":1,"scopus_import":"1","ec_funded":1,"abstract":[{"lang":"eng","text":"The developmental strategies used by progenitor cells to endure a safe journey from their induction place towards the site of terminal differentiation are still poorly understood. Here we uncovered a progenitor cell allocation mechanism that stems from an incomplete process of epithelial delamination that allows progenitors to coordinate their movement with adjacent extra-embryonic tissues. Progenitors of the zebrafish laterality organ originate from the surface epithelial enveloping layer by an apical constriction process of cell delamination. During this process, progenitors retain long-term apical contacts that enable the epithelial layer to pull a subset of progenitors along their way towards the vegetal pole. The remaining delaminated progenitors follow apically-attached progenitors’ movement by a co-attraction mechanism, avoiding sequestration by the adjacent endoderm, ensuring their fate and collective allocation at the differentiation site. Thus, we reveal that incomplete delamination serves as a cellular platform for coordinated tissue movements during development. Impact Statement: Incomplete delamination serves as a cellular platform for coordinated tissue movements during development, guiding newly formed progenitor cell groups to the differentiation site."}]},{"article_type":"original","keyword":["Multidisciplinary"],"external_id":{"pmid":["34210850"]},"volume":373,"year":"2021","day":"02","acknowledgement":"We thank the John Innes Centre Bioimaging Facility (S. Lopez, E. Wegel, and K. Findlay) for their assistance with microscopy and the Norwich BioScience Institute Partnership Computing Infrastructure for Science Group for high-performance computing resources. Funding: This work was funded by a European Research Council Starting Grant (“SexMeth” 804981; J.L., J.W., and X.F.), a Sainsbury Charitable Foundation studentship (J.W.), two Biotechnology and Biological Sciences Research Council (BBSRC) grants (BBS0096201 and BBP0135111; W.S., M.V., and X.F.), two John Innes Foundation studentships (B.A. and S.D.), and a BBSRC David Phillips Fellowship (BBL0250431; H.G. and X.F.). Author contributions: J.L., J.W., and X.F. designed the study and wrote the manuscript; J.L., W.S., B.A., H.G., and S.D. performed the experiments; and J.L., J.W., B.A., H.G., S.D., M.V., and X.F. analyzed the data. Competing interests: The authors declare no competing interests. Data and material availability: All sequencing data have been deposited in the Gene Expression Omnibus (GEO) under accession no. GSE161625. Accession nos. of published datasets used in this study are listed in table S6. Published software used in this study include Bowtie v1.2.2 (https://doi.org/10.1002/0471250953.bi1107s32), Bismark v0.22.2 (https://doi.org/10.1093/bioinformatics/btr167), Kallisto v0.43.0 (https://doi.org/10.1038/nbt0816-888d), Shortstack v3.8.5 (https://doi.org/10.1534/g3.116.030452), and Cutadapt v1.15 (https://doi.org/10.1089/cmb.2017.0096). TrimGalore v0.4.1 and MarkDuplicates v1.141 are available from https://github.com/FelixKrueger/TrimGalore and https://github.com/broadinstitute/picard, respectively. All remaining data are in the main paper or the supplementary materials.","type":"journal_article","publication_status":"published","extern":"1","department":[{"_id":"XiFe"}],"title":"Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis","article_processing_charge":"No","issue":"6550","date_updated":"2026-03-19T10:52:21Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2021.01.25.428150"}],"quality_controlled":"1","author":[{"full_name":"Long, Jincheng","first_name":"Jincheng","last_name":"Long"},{"last_name":"Walker","first_name":"James","full_name":"Walker, James"},{"full_name":"She, Wenjing","first_name":"Wenjing","last_name":"She"},{"first_name":"Billy","full_name":"Aldridge, Billy","last_name":"Aldridge"},{"first_name":"Hongbo","full_name":"Gao, Hongbo","last_name":"Gao"},{"full_name":"Deans, Samuel","first_name":"Samuel","last_name":"Deans"},{"first_name":"Martin","full_name":"Vickers, Martin","last_name":"Vickers"},{"first_name":"Xiaoqi","full_name":"Feng, Xiaoqi","last_name":"Feng","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"}],"publisher":"American Association for the Advancement of Science","date_published":"2021-07-02T00:00:00Z","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"OA_type":"green","intvolume":"       373","_id":"12187","citation":{"ama":"Long J, Walker J, She W, et al. Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis. <i>Science</i>. 2021;373(6550). doi:<a href=\"https://doi.org/10.1126/science.abh0556\">10.1126/science.abh0556</a>","chicago":"Long, Jincheng, James Walker, Wenjing She, Billy Aldridge, Hongbo Gao, Samuel Deans, Martin Vickers, and Xiaoqi Feng. “Nurse Cell-Derived Small RNAs Define Paternal Epigenetic Inheritance in Arabidopsis.” <i>Science</i>. American Association for the Advancement of Science, 2021. <a href=\"https://doi.org/10.1126/science.abh0556\">https://doi.org/10.1126/science.abh0556</a>.","ieee":"J. Long <i>et al.</i>, “Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis,” <i>Science</i>, vol. 373, no. 6550. American Association for the Advancement of Science, 2021.","apa":"Long, J., Walker, J., She, W., Aldridge, B., Gao, H., Deans, S., … Feng, X. (2021). Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.abh0556\">https://doi.org/10.1126/science.abh0556</a>","ista":"Long J, Walker J, She W, Aldridge B, Gao H, Deans S, Vickers M, Feng X. 2021. Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis. Science. 373(6550).","mla":"Long, Jincheng, et al. “Nurse Cell-Derived Small RNAs Define Paternal Epigenetic Inheritance in Arabidopsis.” <i>Science</i>, vol. 373, no. 6550, American Association for the Advancement of Science, 2021, doi:<a href=\"https://doi.org/10.1126/science.abh0556\">10.1126/science.abh0556</a>.","short":"J. Long, J. Walker, W. She, B. Aldridge, H. Gao, S. Deans, M. Vickers, X. Feng, Science 373 (2021)."},"oa_version":"Preprint","doi":"10.1126/science.abh0556","language":[{"iso":"eng"}],"OA_place":"repository","scopus_import":"1","abstract":[{"lang":"eng","text":"Genomes of germ cells present an existential vulnerability to organisms because germ cell mutations will propagate to future generations. Transposable elements are one source of such mutations. In the small flowering plant Arabidopsis, Long et al. found that genome methylation in the male germline is directed by small interfering RNAs (siRNAs) imperfectly transcribed from transposons (see the Perspective by Mosher). These germline siRNAs silence germline transposons and establish inherited methylation patterns in sperm, thus maintaining the integrity of the plant genome across generations."}],"date_created":"2023-01-16T09:15:14Z","publication":"Science","month":"07","pmid":1,"oa":1},{"volume":35,"year":"2021","day":"08","isi":1,"acknowledgement":"This work was supported by the program “Investissements d’avenir” ANR-10-IAIHU-06 , ICM , a Sorbonne Université Emergence grant, an Allen Distinguished Investigator Award , and the Roger De Spoelberch Foundation Prize (to B.A.H.); Armenise-Harvard Foundation , AIRC , and CARITRO (to L.T.); and the European Research Council under the European Union’s Horizon 2020 research and innovation programme grant agreement no. 725780 LinPro (to S.H.). T.Z. and T.L. were supported by doctoral fellowships from the China Scholarship Council and A.H.H. by a doctoral DOC fellowship of the Austrian Academy of Sciences ( 24812 ). All animal work was conducted at the PHENO-ICMice facility. The Core is supported by 2 “Investissements d’avenir” (ANR-10- IAIHU-06 and ANR-11-INBS-0011-NeurATRIS) and the “Fondation pour la Recherche Médicale.” Light microscopy work was carried out at ICM’s imaging core facility, ICM.Quant, and analysis of scRNA-seq data was carried out at ICM’s bioinformatics core facility, iCONICS. We thank Paulina Ejsmont, Natalia Danda, and Nathalie De Geest for technical support. We are grateful to Dr. Shahragim TAJBAKHSH for providing R26Rstop-NICD-nGFP transgenic mice, Dr. Bart De Strooper for Psn1-deficient mice, Dr. Jean-Christophe Marine for Gt(ROSA)26SortdTom reporter mice, and Dr. Martinez Barbera for Sox2CreERT2 mice. We also give thanks to Dr. Mikio Hoshino for providing Atoh1 and Ptf1a antibodies. B.A.H. is an Einstein Visiting Fellow of the Berlin Institute of Health .","file_date_updated":"2021-06-15T14:01:35Z","article_type":"original","project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"725780"},{"grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of radial neuronal migration"}],"external_id":{"pmid":["34107249 "],"isi":["000659894300001"]},"quality_controlled":"1","author":[{"first_name":"Tingting","full_name":"Zhang, Tingting","last_name":"Zhang"},{"last_name":"Liu","full_name":"Liu, Tengyuan","first_name":"Tengyuan"},{"last_name":"Mora","full_name":"Mora, Natalia","first_name":"Natalia"},{"first_name":"Justine","full_name":"Guegan, Justine","last_name":"Guegan"},{"full_name":"Bertrand, Mathilde","first_name":"Mathilde","last_name":"Bertrand"},{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","last_name":"Contreras","full_name":"Contreras, Ximena","first_name":"Ximena"},{"full_name":"Hansen, Andi H","first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","last_name":"Hansen"},{"full_name":"Streicher, Carmen","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher"},{"first_name":"Marica","full_name":"Anderle, Marica","last_name":"Anderle"},{"first_name":"Natasha","full_name":"Danda, Natasha","last_name":"Danda"},{"last_name":"Tiberi","full_name":"Tiberi, Luca","first_name":"Luca"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","first_name":"Simon"},{"first_name":"Bassem A.","full_name":"Hassan, Bassem A.","last_name":"Hassan"}],"ddc":["570"],"publisher":"Elsevier","type":"journal_article","publication_status":"published","file":[{"file_size":8900385,"success":1,"date_created":"2021-06-15T14:01:35Z","file_id":"9554","relation":"main_file","content_type":"application/pdf","creator":"cziletti","file_name":"2021_CellReports_Zhang.pdf","date_updated":"2021-06-15T14:01:35Z","access_level":"open_access","checksum":"7def3d42ebc8f5675efb6f38819e3e2e"}],"department":[{"_id":"SiHi"}],"title":"Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum","article_processing_charge":"No","has_accepted_license":"1","issue":"10","date_updated":"2026-04-02T11:52:30Z","publication_identifier":{"eissn":[" 2211-1247"]},"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"related_material":{"link":[{"url":"https://doi.org/10.1101/2020.03.18.997205","relation":"earlier_version"}]},"date_published":"2021-06-08T00:00:00Z","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_number":"109208","scopus_import":"1","ec_funded":1,"abstract":[{"lang":"eng","text":"Brain neurons arise from relatively few progenitors generating an enormous diversity of neuronal types. Nonetheless, a cardinal feature of mammalian brain neurogenesis is thought to be that excitatory and inhibitory neurons derive from separate, spatially segregated progenitors. Whether bi-potential progenitors with an intrinsic capacity to generate both lineages exist and how such a fate decision may be regulated are unknown. Using cerebellar development as a model, we discover that individual progenitors can give rise to both inhibitory and excitatory lineages. Gradations of Notch activity determine the fates of the progenitors and their daughters. Daughters with the highest levels of Notch activity retain the progenitor fate, while intermediate levels of Notch activity generate inhibitory neurons, and daughters with very low levels of Notch signaling adopt the excitatory fate. Therefore, Notch-mediated binary cell fate choice is a mechanism for regulating the ratio of excitatory to inhibitory neurons from common progenitors."}],"publication":"Cell Reports","month":"06","date_created":"2020-09-21T12:00:48Z","pmid":1,"oa":1,"intvolume":"        35","_id":"8546","citation":{"apa":"Zhang, T., Liu, T., Mora, N., Guegan, J., Bertrand, M., Contreras, X., … Hassan, B. A. (2021). Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2021.109208\">https://doi.org/10.1016/j.celrep.2021.109208</a>","chicago":"Zhang, Tingting, Tengyuan Liu, Natalia Mora, Justine Guegan, Mathilde Bertrand, Ximena Contreras, Andi H Hansen, et al. “Generation of Excitatory and Inhibitory Neurons from Common Progenitors via Notch Signaling in the Cerebellum.” <i>Cell Reports</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.celrep.2021.109208\">https://doi.org/10.1016/j.celrep.2021.109208</a>.","ieee":"T. Zhang <i>et al.</i>, “Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum,” <i>Cell Reports</i>, vol. 35, no. 10. Elsevier, 2021.","ama":"Zhang T, Liu T, Mora N, et al. Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum. <i>Cell Reports</i>. 2021;35(10). doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109208\">10.1016/j.celrep.2021.109208</a>","mla":"Zhang, Tingting, et al. “Generation of Excitatory and Inhibitory Neurons from Common Progenitors via Notch Signaling in the Cerebellum.” <i>Cell Reports</i>, vol. 35, no. 10, 109208, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109208\">10.1016/j.celrep.2021.109208</a>.","ista":"Zhang T, Liu T, Mora N, Guegan J, Bertrand M, Contreras X, Hansen AH, Streicher C, Anderle M, Danda N, Tiberi L, Hippenmeyer S, Hassan BA. 2021. Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum. Cell Reports. 35(10), 109208.","short":"T. Zhang, T. Liu, N. Mora, J. Guegan, M. Bertrand, X. Contreras, A.H. Hansen, C. Streicher, M. Anderle, N. Danda, L. Tiberi, S. Hippenmeyer, B.A. Hassan, Cell Reports 35 (2021)."},"oa_version":"Published Version","doi":"10.1016/j.celrep.2021.109208","language":[{"iso":"eng"}]},{"article_number":"6094","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-10-19T00:00:00Z","related_material":{"link":[{"url":"https://doi.org/10.1101/2020.11.23.394171 ","description":"Preprint","relation":"earlier_version"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"citation":{"chicago":"Pradhan, Saurabh J., Puli Chandramouli Reddy, Michael Smutny, Ankita Sharma, Keisuke Sako, Meghana S. Oak, Rini Shah, et al. “Satb2 Acts as a Gatekeeper for Major Developmental Transitions during Early Vertebrate Embryogenesis.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-26234-7\">https://doi.org/10.1038/s41467-021-26234-7</a>.","apa":"Pradhan, S. J., Reddy, P. C., Smutny, M., Sharma, A., Sako, K., Oak, M. S., … Galande, S. (2021). Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-26234-7\">https://doi.org/10.1038/s41467-021-26234-7</a>","ieee":"S. J. Pradhan <i>et al.</i>, “Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","ama":"Pradhan SJ, Reddy PC, Smutny M, et al. Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-26234-7\">10.1038/s41467-021-26234-7</a>","ista":"Pradhan SJ, Reddy PC, Smutny M, Sharma A, Sako K, Oak MS, Shah R, Pal M, Deshpande O, Dsilva G, Tang Y, Mishra R, Deshpande G, Giraldez AJ, Sonawane M, Heisenberg C-PJ, Galande S. 2021. Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nature Communications. 12(1), 6094.","mla":"Pradhan, Saurabh J., et al. “Satb2 Acts as a Gatekeeper for Major Developmental Transitions during Early Vertebrate Embryogenesis.” <i>Nature Communications</i>, vol. 12, no. 1, 6094, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-26234-7\">10.1038/s41467-021-26234-7</a>.","short":"S.J. Pradhan, P.C. Reddy, M. Smutny, A. Sharma, K. Sako, M.S. Oak, R. Shah, M. Pal, O. Deshpande, G. Dsilva, Y. Tang, R. Mishra, G. Deshpande, A.J. Giraldez, M. Sonawane, C.-P.J. Heisenberg, S. Galande, Nature Communications 12 (2021)."},"oa_version":"Published Version","doi":"10.1038/s41467-021-26234-7","intvolume":"        12","corr_author":"1","_id":"10202","oa":1,"publication":"Nature Communications","date_created":"2021-10-31T23:01:29Z","month":"10","pmid":1,"abstract":[{"lang":"eng","text":"Zygotic genome activation (ZGA) initiates regionalized transcription underlying distinct cellular identities. ZGA is dependent upon dynamic chromatin architecture sculpted by conserved DNA-binding proteins. However, the direct mechanistic link between the onset of ZGA and the tissue-specific transcription remains unclear. Here, we have addressed the involvement of chromatin organizer Satb2 in orchestrating both processes during zebrafish embryogenesis. Integrative analysis of transcriptome, genome-wide occupancy and chromatin accessibility reveals contrasting molecular activities of maternally deposited and zygotically synthesized Satb2. Maternal Satb2 prevents premature transcription of zygotic genes by influencing the interplay between the pluripotency factors. By contrast, zygotic Satb2 activates transcription of the same group of genes during neural crest development and organogenesis. Thus, our comparative analysis of maternal versus zygotic function of Satb2 underscores how these antithetical activities are temporally coordinated and functionally implemented highlighting the evolutionary implications of the biphasic and bimodal regulation of landmark developmental transitions by a single determinant."}],"scopus_import":"1","external_id":{"isi":["000709050300016"],"pmid":["34667153"]},"article_type":"original","file_date_updated":"2021-11-09T13:59:26Z","acknowledgement":"We are grateful to the members of C.-P.H. and SG lab for discussions. Authors thank Shubha Tole for providing embryonic mouse tissues. Authors are grateful to Alessandro Mongera and Chetana Sachidanandan for generous help with Tg: Sox10: GFP line. Authors would like to thank Satyajeet Khare, Vanessa Barone, Jyothish S., Shalini Mishra, Yoshita Bhide, and Keshav Jha for assistance in experiments. We would also like to thank Chaitanya Dingare for valuable suggestions. We thank Diana Pinhiero and Alexandra Schauer for critical reading of early versions of the manuscript. This work was supported by the Centre of Excellence in Epigenetics program of the Department of Biotechnology, Government of India Phase I (BT/01/COE/09/07) to S.G. and R.K.M., and Phase II (BT/COE/34/SP17426/2016) to S.G. and JC Bose Fellowship (JCB/2019/000013) from Science and Engineering Research Board, Government of India to S.G., DST-BMWF Indo-Austrian bilateral program grant to S.G. and C.-P.H. The work using animal models was partly supported by the infrastructure support grants from the Department of Biotechnology (National Facility for Laboratory Model Organisms: BT/INF/22/SP17358/2016 and Establishment of a Pune Biotech Cluster, Model Organism to Human Disease: B-2 Whole Animal Imaging & Tissue Processing FacilityBT/Pune-Biocluster/01/2015). S.J.P. was supported by Fellowship from the Council of Scientific and Industrial Research, India and travel fellowship from the Company of Biologists, UK. P.C.R. was supported by the Early Career Fellowship of the Wellcome Trust-DBT India Alliance (IA/E/16/1/503057). A.S. was supported by UGC and R.S. was supported by CSIR India. M.S. was supported by core funding from the Tata Institute of Fundamental Research (TIFR 12P-121).","isi":1,"day":"19","volume":12,"year":"2021","has_accepted_license":"1","issue":"1","date_updated":"2026-04-02T11:57:41Z","title":"Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis","department":[{"_id":"CaHe"}],"article_processing_charge":"Yes","file":[{"date_updated":"2021-11-09T13:59:26Z","access_level":"open_access","checksum":"c40a69ae94435ecd3a30c9874a11ef2b","file_size":7144437,"success":1,"date_created":"2021-11-09T13:59:26Z","file_id":"10262","relation":"main_file","content_type":"application/pdf","creator":"cziletti","file_name":"2021_NatureComm_Pradhan.pdf"}],"type":"journal_article","publication_status":"published","publisher":"Springer Nature","ddc":["570"],"quality_controlled":"1","author":[{"first_name":"Saurabh J.","full_name":"Pradhan, Saurabh J.","last_name":"Pradhan"},{"last_name":"Reddy","full_name":"Reddy, Puli Chandramouli","first_name":"Puli Chandramouli"},{"first_name":"Michael","full_name":"Smutny, Michael","last_name":"Smutny","orcid":"0000-0002-5920-9090","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sharma","full_name":"Sharma, Ankita","first_name":"Ankita"},{"orcid":"0000-0002-6453-8075","last_name":"Sako","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","first_name":"Keisuke","full_name":"Sako, Keisuke"},{"last_name":"Oak","full_name":"Oak, Meghana S.","first_name":"Meghana S."},{"full_name":"Shah, Rini","first_name":"Rini","last_name":"Shah"},{"last_name":"Pal","full_name":"Pal, Mrinmoy","first_name":"Mrinmoy"},{"last_name":"Deshpande","full_name":"Deshpande, Ojas","first_name":"Ojas"},{"last_name":"Dsilva","first_name":"Greg","full_name":"Dsilva, Greg"},{"last_name":"Tang","full_name":"Tang, Yin","first_name":"Yin"},{"first_name":"Rakesh","full_name":"Mishra, Rakesh","last_name":"Mishra"},{"last_name":"Deshpande","full_name":"Deshpande, Girish","first_name":"Girish"},{"last_name":"Giraldez","first_name":"Antonio J.","full_name":"Giraldez, Antonio J."},{"full_name":"Sonawane, Mahendra","first_name":"Mahendra","last_name":"Sonawane"},{"first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Galande","full_name":"Galande, Sanjeev","first_name":"Sanjeev"}]},{"abstract":[{"text":"In mammalian genomes, differentially methylated regions (DMRs) and histone marks including trimethylation of histone 3 lysine 27 (H3K27me3) at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. However, neither parent-of-origin-specific transcription nor imprints have been comprehensively mapped at the blastocyst stage of preimplantation development. Here, we address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos. We find that seventy-one genes exhibit previously unreported parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expressed). Uniparental expression of nBiX genes disappears soon after implantation. Micro-whole-genome bisulfite sequencing (µWGBS) of individual uniparental blastocysts detects 859 DMRs. We further find that 16% of nBiX genes are associated with a DMR, whereas most are associated with parentally-biased H3K27me3, suggesting a role for Polycomb-mediated imprinting in blastocysts. nBiX genes are clustered: five clusters contained at least one published imprinted gene, and five clusters exclusively contained nBiX genes. These data suggest that early development undergoes a complex program of stage-specific imprinting involving different tiers of regulation.","lang":"eng"}],"scopus_import":"1","date_created":"2021-06-27T22:01:46Z","month":"07","publication":"Nature Communications","oa":1,"intvolume":"        12","_id":"9601","citation":{"ama":"Santini L, Halbritter F, Titz-Teixeira F, et al. Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23510-4\">10.1038/s41467-021-23510-4</a>","apa":"Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ma, X., … Leeb, M. (2021). Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-23510-4\">https://doi.org/10.1038/s41467-021-23510-4</a>","chicago":"Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki, Maki Asami, Xiaoyan Ma, Julia Ramesmayer, et al. “Genomic Imprinting in Mouse Blastocysts Is Predominantly Associated with H3K27me3.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23510-4\">https://doi.org/10.1038/s41467-021-23510-4</a>.","ieee":"L. Santini <i>et al.</i>, “Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","mla":"Santini, Laura, et al. “Genomic Imprinting in Mouse Blastocysts Is Predominantly Associated with H3K27me3.” <i>Nature Communications</i>, vol. 12, no. 1, 3804, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23510-4\">10.1038/s41467-021-23510-4</a>.","ista":"Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ma X, Ramesmayer J, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. 2021. Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. 12(1), 3804.","short":"L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, X. Ma, J. Ramesmayer, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, Nature Communications 12 (2021)."},"oa_version":"Published Version","doi":"10.1038/s41467-021-23510-4","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_published":"2021-07-12T00:00:00Z","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_number":"3804","quality_controlled":"1","author":[{"full_name":"Santini, Laura","first_name":"Laura","last_name":"Santini"},{"full_name":"Halbritter, Florian","first_name":"Florian","last_name":"Halbritter"},{"first_name":"Fabian","full_name":"Titz-Teixeira, Fabian","last_name":"Titz-Teixeira"},{"first_name":"Toru","full_name":"Suzuki, Toru","last_name":"Suzuki"},{"last_name":"Asami","first_name":"Maki","full_name":"Asami, Maki"},{"full_name":"Ma, Xiaoyan","first_name":"Xiaoyan","last_name":"Ma"},{"last_name":"Ramesmayer","first_name":"Julia","full_name":"Ramesmayer, Julia"},{"last_name":"Lackner","first_name":"Andreas","full_name":"Lackner, Andreas"},{"full_name":"Warr, Nick","first_name":"Nick","last_name":"Warr"},{"orcid":"0000-0002-7462-0048","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Pauler, Florian"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","first_name":"Simon"},{"last_name":"Laue","first_name":"Ernest","full_name":"Laue, Ernest"},{"full_name":"Farlik, Matthias","first_name":"Matthias","last_name":"Farlik"},{"first_name":"Christoph","full_name":"Bock, Christoph","last_name":"Bock"},{"first_name":"Andreas","full_name":"Beyer, Andreas","last_name":"Beyer"},{"last_name":"Perry","full_name":"Perry, Anthony C.F.","first_name":"Anthony C.F."},{"last_name":"Leeb","full_name":"Leeb, Martin","first_name":"Martin"}],"ddc":["570"],"publisher":"Springer Nature","type":"journal_article","publication_status":"published","file":[{"date_updated":"2021-06-28T08:04:22Z","checksum":"75dd89d09945185b2d14b2434a0bcb50","access_level":"open_access","file_id":"9608","date_created":"2021-06-28T08:04:22Z","success":1,"file_size":2156554,"file_name":"2021_NatureCommunications_Santini.pdf","creator":"asandaue","content_type":"application/pdf","relation":"main_file"}],"title":"Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3","department":[{"_id":"SiHi"}],"article_processing_charge":"No","has_accepted_license":"1","issue":"1","date_updated":"2026-04-02T13:55:23Z","volume":12,"year":"2021","day":"12","isi":1,"acknowledgement":"The authors thank Robert Feil and Anton Wutz for helpful discussions and comments, Samuel Collombet and Peter Fraser for sharing embryo TAD coordinates, and Andy Riddel at the Cambridge Stem Cell Institute and Thomas Sauer at the Max Perutz Laboratories FACS facility for flow-sorting. We thank the team of the Biomedical Sequencing Facility at the CeMM and the Vienna Biocenter Core Facilities (VBCF) for support with next-generation sequencing. We are grateful to animal care teams at the University of Bath and MRC Harwell. A.C.F.P. acknowledges support from the UK Medical Research Council (MR/N000080/1 and MR/N020294/1) and Biotechnology and Biological Sciences Research Council (BB/P009506/1). L.S. is part of the FWF doctoral programme SMICH and supported by an Austrian Academy of Sciences DOC Fellowship. M.L. is funded by a Vienna Research Group for Young Investigators grant (VRG14-006) by the Vienna Science and Technology Fund (WWTF) and by the Austrian Science Fund FWF (I3786 and P31334).","file_date_updated":"2021-06-28T08:04:22Z","article_type":"original","external_id":{"isi":["000667248600005"]}},{"language":[{"iso":"eng"}],"doi":"10.3390/cells10071593","oa_version":"Published Version","citation":{"ieee":"N. A. Muench, S. Patel, M. E. Maes, R. J. Donahue, A. Ikeda, and R. W. Nickells, “The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease,” <i>Cells</i>, vol. 10, no. 7. MDPI, 2021.","chicago":"Muench, Nicole A., Sonia Patel, Margaret E Maes, Ryan J. Donahue, Akihiro Ikeda, and Robert W. Nickells. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” <i>Cells</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/cells10071593\">https://doi.org/10.3390/cells10071593</a>.","apa":"Muench, N. A., Patel, S., Maes, M. E., Donahue, R. J., Ikeda, A., &#38; Nickells, R. W. (2021). The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells10071593\">https://doi.org/10.3390/cells10071593</a>","ama":"Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. <i>Cells</i>. 2021;10(7). doi:<a href=\"https://doi.org/10.3390/cells10071593\">10.3390/cells10071593</a>","short":"N.A. Muench, S. Patel, M.E. Maes, R.J. Donahue, A. Ikeda, R.W. Nickells, Cells 10 (2021).","ista":"Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. 2021. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. 10(7), 1593.","mla":"Muench, Nicole A., et al. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” <i>Cells</i>, vol. 10, no. 7, 1593, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/cells10071593\">10.3390/cells10071593</a>."},"_id":"9761","intvolume":"        10","oa":1,"pmid":1,"date_created":"2021-08-01T22:01:22Z","publication":"Cells","month":"06","scopus_import":"1","abstract":[{"text":"The important roles of mitochondrial function and dysfunction in the process of neurodegeneration are widely acknowledged. Retinal ganglion cells (RGCs) appear to be a highly vulnerable neuronal cell type in the central nervous system with respect to mitochondrial dysfunction but the actual reasons for this are still incompletely understood. These cells have a unique circumstance where unmyelinated axons must bend nearly 90° to exit the eye and then cross a translaminar pressure gradient before becoming myelinated in the optic nerve. This region, the optic nerve head, contains some of the highest density of mitochondria present in these cells. Glaucoma represents a perfect storm of events occurring at this location, with a combination of changes in the translaminar pressure gradient and reassignment of the metabolic support functions of supporting glia, which appears to apply increased metabolic stress to the RGC axons leading to a failure of axonal transport mechanisms. However, RGCs themselves are also extremely sensitive to genetic mutations, particularly in genes affecting mitochondrial dynamics and mitochondrial clearance. These mutations, which systemically affect the mitochondria in every cell, often lead to an optic neuropathy as the sole pathologic defect in affected patients. This review summarizes knowledge of mitochondrial structure and function, the known energy demands of neurons in general, and places these in the context of normal and pathological characteristics of mitochondria attributed to RGCs. ","lang":"eng"}],"article_number":"1593","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","date_published":"2021-06-25T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_identifier":{"eissn":["2073-4409"]},"date_updated":"2026-04-02T13:56:24Z","has_accepted_license":"1","issue":"7","article_processing_charge":"Yes","department":[{"_id":"SaSi"}],"title":"The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease","file":[{"date_updated":"2021-08-04T14:01:30Z","access_level":"open_access","checksum":"e0497ce5c77fa3b65a538c7d6e0f6c66","success":1,"file_size":4555611,"date_created":"2021-08-04T14:01:30Z","file_id":"9768","relation":"main_file","creator":"cziletti","content_type":"application/pdf","file_name":"2021_Cells_Muench.pdf"}],"publication_status":"published","type":"journal_article","publisher":"MDPI","ddc":["570"],"author":[{"first_name":"Nicole A.","full_name":"Muench, Nicole A.","last_name":"Muench"},{"last_name":"Patel","first_name":"Sonia","full_name":"Patel, Sonia"},{"first_name":"Margaret E","full_name":"Maes, Margaret E","last_name":"Maes","orcid":"0000-0001-9642-1085","id":"3838F452-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Donahue, Ryan J.","first_name":"Ryan J.","last_name":"Donahue"},{"last_name":"Ikeda","full_name":"Ikeda, Akihiro","first_name":"Akihiro"},{"last_name":"Nickells","first_name":"Robert W.","full_name":"Nickells, Robert W."}],"quality_controlled":"1","external_id":{"pmid":["34201955"],"isi":["000678193300001"]},"article_type":"original","file_date_updated":"2021-08-04T14:01:30Z","acknowledgement":"The authors are grateful to Kazuya Oikawa and Gillian McLellan for generously sharing some of their data for this review, and to Janis Eells for helpful comments on the manuscript.","isi":1,"day":"25","year":"2021","volume":10},{"quality_controlled":"1","author":[{"last_name":"Hu","full_name":"Hu, Yangjie","first_name":"Yangjie"},{"first_name":"Moutasem","full_name":"Omary, Moutasem","last_name":"Omary"},{"last_name":"Hu","first_name":"Yun","full_name":"Hu, Yun"},{"first_name":"Ohad","full_name":"Doron, Ohad","last_name":"Doron"},{"orcid":"0000-0001-8295-2926","last_name":"Hörmayer","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas","full_name":"Hörmayer, Lukas"},{"last_name":"Chen","full_name":"Chen, Qingguo","first_name":"Qingguo"},{"last_name":"Megides","full_name":"Megides, Or","first_name":"Or"},{"last_name":"Chekli","first_name":"Ori","full_name":"Chekli, Ori"},{"first_name":"Zhaojun","full_name":"Ding, Zhaojun","last_name":"Ding"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří"},{"last_name":"Zhao","full_name":"Zhao, Yunde","first_name":"Yunde"},{"full_name":"Tsarfaty, Ilan","first_name":"Ilan","last_name":"Tsarfaty"},{"last_name":"Shani","first_name":"Eilon","full_name":"Shani, Eilon"}],"publisher":"Springer Nature","ddc":["580"],"type":"journal_article","publication_status":"published","file":[{"relation":"main_file","creator":"dernst","content_type":"application/pdf","file_name":"2021_NatureComm_Hu.pdf","file_size":8602096,"success":1,"date_created":"2021-03-22T11:18:58Z","file_id":"9275","access_level":"open_access","checksum":"e1022f3aee349853ded2b2b3e092362d","date_updated":"2021-03-22T11:18:58Z"}],"title":"Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing","department":[{"_id":"JiFr"}],"article_processing_charge":"No","has_accepted_license":"1","date_updated":"2026-04-02T13:57:40Z","volume":12,"year":"2021","day":"12","isi":1,"acknowledgement":"This work was supported by grants from the Israel Science Foundation (2378/19 to E.S.), the Joint NSFC-ISF Research Grant (3419/20 to E.S. and Z.D.), the Human Frontier Science Program (HFSP—LIY000540/2020 to E.S.), the European Research Council Starting Grant (757683- RobustHormoneTrans to E.S.), PBC postdoctoral fellowships (to Y.H. and M.O.), NIH (GM114660 to Y.Z.), Breast Cancer Research Foundation (BCRF to I.T.).","file_date_updated":"2021-03-22T11:18:58Z","article_type":"original","external_id":{"isi":["000630419400048"],"pmid":["33712581"]},"scopus_import":"1","abstract":[{"text":"Auxin is a key regulator of plant growth and development. Local auxin biosynthesis and intercellular transport generates regional gradients in the root that are instructive for processes such as specification of developmental zones that maintain root growth and tropic responses. Here we present a toolbox to study auxin-mediated root development that features: (i) the ability to control auxin synthesis with high spatio-temporal resolution and (ii) single-cell nucleus tracking and morphokinetic analysis infrastructure. Integration of these two features enables cutting-edge analysis of root development at single-cell resolution based on morphokinetic parameters under normal growth conditions and during cell-type-specific induction of auxin biosynthesis. We show directional auxin flow in the root and refine the contributions of key players in this process. In addition, we determine the quantitative kinetics of Arabidopsis root meristem skewing, which depends on local auxin gradients but does not require PIN2 and AUX1 auxin transporter activities. Beyond the mechanistic insights into root development, the tools developed here will enable biologists to study kinetics and morphology of various critical processes at the single cell-level in whole organisms.","lang":"eng"}],"date_created":"2021-03-21T23:01:19Z","month":"03","publication":"Nature Communications","pmid":1,"oa":1,"intvolume":"        12","_id":"9254","citation":{"short":"Y. Hu, M. Omary, Y. Hu, O. Doron, L. Hörmayer, Q. Chen, O. Megides, O. Chekli, Z. Ding, J. Friml, Y. Zhao, I. Tsarfaty, E. Shani, Nature Communications 12 (2021).","mla":"Hu, Yangjie, et al. “Cell Kinetics of Auxin Transport and Activity in Arabidopsis Root Growth and Skewing.” <i>Nature Communications</i>, vol. 12, 1657, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-21802-3\">10.1038/s41467-021-21802-3</a>.","ista":"Hu Y, Omary M, Hu Y, Doron O, Hörmayer L, Chen Q, Megides O, Chekli O, Ding Z, Friml J, Zhao Y, Tsarfaty I, Shani E. 2021. Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing. Nature Communications. 12, 1657.","ama":"Hu Y, Omary M, Hu Y, et al. Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing. <i>Nature Communications</i>. 2021;12. doi:<a href=\"https://doi.org/10.1038/s41467-021-21802-3\">10.1038/s41467-021-21802-3</a>","ieee":"Y. Hu <i>et al.</i>, “Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing,” <i>Nature Communications</i>, vol. 12. Springer Nature, 2021.","apa":"Hu, Y., Omary, M., Hu, Y., Doron, O., Hörmayer, L., Chen, Q., … Shani, E. (2021). Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-21802-3\">https://doi.org/10.1038/s41467-021-21802-3</a>","chicago":"Hu, Yangjie, Moutasem Omary, Yun Hu, Ohad Doron, Lukas Hörmayer, Qingguo Chen, Or Megides, et al. “Cell Kinetics of Auxin Transport and Activity in Arabidopsis Root Growth and Skewing.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-21802-3\">https://doi.org/10.1038/s41467-021-21802-3</a>."},"oa_version":"Published Version","doi":"10.1038/s41467-021-21802-3","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_published":"2021-03-12T00:00:00Z","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_number":"1657"},{"publication_status":"published","type":"journal_article","file":[{"date_updated":"2021-08-09T09:25:41Z","access_level":"open_access","checksum":"0277aa155d5db1febd2cb384768bba5f","file_size":2706919,"success":1,"date_created":"2021-08-09T09:25:41Z","file_id":"9832","relation":"main_file","creator":"asandaue","content_type":"application/pdf","file_name":"2021_PLoSONE_Graff.pdf"}],"article_processing_charge":"Yes","department":[{"_id":"HeEd"}],"title":"Persistent homology as a new method of the assessment of heart rate variability","date_updated":"2026-04-02T13:56:42Z","issue":"7","has_accepted_license":"1","author":[{"last_name":"Graff","first_name":"Grzegorz","full_name":"Graff, Grzegorz"},{"full_name":"Graff, Beata","first_name":"Beata","last_name":"Graff"},{"first_name":"Pawel","full_name":"Pilarczyk, Pawel","last_name":"Pilarczyk","id":"3768D56A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jablonski, Grzegorz","first_name":"Grzegorz","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","last_name":"Jablonski","orcid":"0000-0002-3536-9866"},{"full_name":"Gąsecki, Dariusz","first_name":"Dariusz","last_name":"Gąsecki"},{"full_name":"Narkiewicz, Krzysztof","first_name":"Krzysztof","last_name":"Narkiewicz"}],"quality_controlled":"1","publisher":"Public Library of Science","ddc":["006"],"file_date_updated":"2021-08-09T09:25:41Z","article_type":"original","external_id":{"isi":["000678124900050"],"pmid":["34292957"]},"year":"2021","volume":16,"day":"01","isi":1,"acknowledgement":"We express our gratitude to the anonymous referees who provided constructive comments that helped us improve the quality of the paper.","_id":"9821","intvolume":"        16","doi":"10.1371/journal.pone.0253851","oa_version":"Published Version","citation":{"ama":"Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. Persistent homology as a new method of the assessment of heart rate variability. <i>PLoS ONE</i>. 2021;16(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0253851\">10.1371/journal.pone.0253851</a>","ieee":"G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, and K. Narkiewicz, “Persistent homology as a new method of the assessment of heart rate variability,” <i>PLoS ONE</i>, vol. 16, no. 7. Public Library of Science, 2021.","apa":"Graff, G., Graff, B., Pilarczyk, P., Jablonski, G., Gąsecki, D., &#38; Narkiewicz, K. (2021). Persistent homology as a new method of the assessment of heart rate variability. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0253851\">https://doi.org/10.1371/journal.pone.0253851</a>","chicago":"Graff, Grzegorz, Beata Graff, Pawel Pilarczyk, Grzegorz Jablonski, Dariusz Gąsecki, and Krzysztof Narkiewicz. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” <i>PLoS ONE</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pone.0253851\">https://doi.org/10.1371/journal.pone.0253851</a>.","mla":"Graff, Grzegorz, et al. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” <i>PLoS ONE</i>, vol. 16, no. 7, e0253851, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pone.0253851\">10.1371/journal.pone.0253851</a>.","ista":"Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. 2021. Persistent homology as a new method of the assessment of heart rate variability. PLoS ONE. 16(7), e0253851.","short":"G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, K. Narkiewicz, PLoS ONE 16 (2021)."},"language":[{"iso":"eng"}],"scopus_import":"1","abstract":[{"text":"Heart rate variability (hrv) is a physiological phenomenon of the variation in the length of the time interval between consecutive heartbeats. In many cases it could be an indicator of the development of pathological states. The classical approach to the analysis of hrv includes time domain methods and frequency domain methods. However, attempts are still being made to define new and more effective hrv assessment tools. Persistent homology is a novel data analysis tool developed in the recent decades that is rooted at algebraic topology. The Topological Data Analysis (TDA) approach focuses on examining the shape of the data in terms of connectedness and holes, and has recently proved to be very effective in various fields of research. In this paper we propose the use of persistent homology to the hrv analysis. We recall selected topological descriptors used in the literature and we introduce some new topological descriptors that reflect the specificity of hrv, and we discuss their relation to the standard hrv measures. In particular, we show that this novel approach provides a collection of indices that might be at least as useful as the classical parameters in differentiating between series of beat-to-beat intervals (RR-intervals) in healthy subjects and patients suffering from a stroke episode.","lang":"eng"}],"pmid":1,"publication":"PLoS ONE","month":"07","date_created":"2021-08-08T22:01:28Z","oa":1,"date_published":"2021-07-01T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","article_number":"e0253851","publication_identifier":{"eissn":["1932-6203"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"}},{"file_date_updated":"2021-10-28T12:06:01Z","article_type":"original","external_id":{"arxiv":["2102.05397"],"isi":["000702042400001"]},"volume":23,"year":"2021","day":"29","isi":1,"acknowledgement":"We thank Paula Sanematsu, Matthias Merkel, Daniel Sussman, Cristina Marchetti and Edouard Hannezo for helpful discussions, and M Merkel for developing and sharing the original version of the 3D Voronoi code. This work was primarily funded by NSF-PHY-1607416, NSF-PHY-2014192 , and are in the division of physics at the National Science Foundation. PS and MLM acknowledge additional support from Simons Grant No. 454947.\r\n","type":"journal_article","publication_status":"published","file":[{"access_level":"open_access","checksum":"ace603e8f0962b3ba55f23fa34f57764","date_updated":"2021-10-28T12:06:01Z","relation":"main_file","creator":"cziletti","content_type":"application/pdf","file_name":"2021_NewJPhys_Sahu.pdf","file_size":2215016,"success":1,"date_created":"2021-10-28T12:06:01Z","file_id":"10193"}],"title":"Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue","department":[{"_id":"EdHa"}],"article_processing_charge":"Yes","has_accepted_license":"1","issue":"9","date_updated":"2026-04-02T13:54:56Z","quality_controlled":"1","author":[{"id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E","last_name":"Sahu","full_name":"Sahu, Preeti","first_name":"Preeti"},{"last_name":"Schwarz","full_name":"Schwarz, J. M.","first_name":"J. M."},{"full_name":"Manning, M. Lisa","first_name":"M. Lisa","last_name":"Manning"}],"publisher":"IOP Publishing","ddc":["570"],"date_published":"2021-09-29T00:00:00Z","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_number":"093043","arxiv":1,"publication_identifier":{"eissn":["1367-2630"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        23","_id":"10178","citation":{"ama":"Sahu P, Schwarz JM, Manning ML. Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. <i>New Journal of Physics</i>. 2021;23(9). doi:<a href=\"https://doi.org/10.1088/1367-2630/ac23f1\">10.1088/1367-2630/ac23f1</a>","chicago":"Sahu, Preeti, J. M. Schwarz, and M. Lisa Manning. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” <i>New Journal of Physics</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/1367-2630/ac23f1\">https://doi.org/10.1088/1367-2630/ac23f1</a>.","apa":"Sahu, P., Schwarz, J. M., &#38; Manning, M. L. (2021). Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/ac23f1\">https://doi.org/10.1088/1367-2630/ac23f1</a>","ieee":"P. Sahu, J. M. Schwarz, and M. L. Manning, “Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue,” <i>New Journal of Physics</i>, vol. 23, no. 9. IOP Publishing, 2021.","ista":"Sahu P, Schwarz JM, Manning ML. 2021. Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. New Journal of Physics. 23(9), 093043.","mla":"Sahu, Preeti, et al. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” <i>New Journal of Physics</i>, vol. 23, no. 9, 093043, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/1367-2630/ac23f1\">10.1088/1367-2630/ac23f1</a>.","short":"P. Sahu, J.M. Schwarz, M.L. Manning, New Journal of Physics 23 (2021)."},"oa_version":"Published Version","doi":"10.1088/1367-2630/ac23f1","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"In dense biological tissues, cell types performing different roles remain segregated by maintaining sharp interfaces. To better understand the mechanisms for such sharp compartmentalization, we study the effect of an imposed heterotypic tension at the interface between two distinct cell types in a fully 3D Voronoi model for confluent tissues. We find that cells rapidly sort and self-organize to generate a tissue-scale interface between cell types, and cells adjacent to this interface exhibit signature geometric features including nematic-like ordering, bimodal facet areas, and registration, or alignment, of cell centers on either side of the two-tissue interface. The magnitude of these features scales directly with the magnitude of the imposed tension, suggesting that biologists can estimate the magnitude of tissue surface tension between two tissue types simply by segmenting a 3D tissue. To uncover the underlying physical mechanisms driving these geometric features, we develop two minimal, ordered models using two different underlying lattices that identify an energetic competition between bulk cell shapes and tissue interface area. When the interface area dominates, changes to neighbor topology are costly and occur less frequently, which generates the observed geometric features."}],"scopus_import":"1","month":"09","date_created":"2021-10-24T22:01:34Z","publication":"New Journal of Physics","oa":1},{"quality_controlled":"1","author":[{"last_name":"Zeng","full_name":"Zeng, Yinwei","first_name":"Yinwei"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","last_name":"Verstraeten","full_name":"Verstraeten, Inge","first_name":"Inge"},{"last_name":"Trinh","first_name":"Hoang Khai","full_name":"Trinh, Hoang Khai"},{"last_name":"Heugebaert","full_name":"Heugebaert, Thomas","first_name":"Thomas"},{"last_name":"Stevens","first_name":"Christian V.","full_name":"Stevens, Christian V."},{"full_name":"Garcia-Maquilon, Irene","first_name":"Irene","last_name":"Garcia-Maquilon"},{"last_name":"Rodriguez","first_name":"Pedro L.","full_name":"Rodriguez, Pedro L."},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"last_name":"Geelen","first_name":"Danny","full_name":"Geelen, Danny"}],"publisher":"MDPI","ddc":["580","570"],"type":"journal_article","publication_status":"published","file":[{"checksum":"3d99535618cf9a5b14d264408fa52e97","access_level":"open_access","date_updated":"2021-08-16T09:02:40Z","content_type":"application/pdf","creator":"asandaue","file_name":"2021_Genes_Zeng.pdf","relation":"main_file","date_created":"2021-08-16T09:02:40Z","file_id":"9919","success":1,"file_size":1340305}],"department":[{"_id":"JiFr"}],"title":"Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling","article_processing_charge":"Yes","has_accepted_license":"1","issue":"8","date_updated":"2026-04-02T13:57:06Z","volume":12,"year":"2021","day":"27","isi":1,"acknowledgement":"We thank S. Cutler (Riverside, USA) for providing the ABA biosynthesis mutants and ABA signaling mutants.","file_date_updated":"2021-08-16T09:02:40Z","article_type":"original","external_id":{"isi":["000690558000001"]},"abstract":[{"lang":"eng","text":"Roots are composed of different root types and, in the dicotyledonous Arabidopsis, typically consist of a primary root that branches into lateral roots. Adventitious roots emerge from non-root tissue and are formed upon wounding or other types of abiotic stress. Here, we investigated adventitious root (AR) formation in Arabidopsis hypocotyls under conditions of altered abscisic acid (ABA) signaling. Exogenously applied ABA suppressed AR formation at 0.25 µM or higher doses. AR formation was less sensitive to the synthetic ABA analog pyrabactin (PB). However, PB was a more potent inhibitor at concentrations above 1 µM, suggesting that it was more selective in triggering a root inhibition response. Analysis of a series of phosphonamide and phosphonate pyrabactin analogs suggested that adventitious root formation and lateral root branching are differentially regulated by ABA signaling. ABA biosynthesis and signaling mutants affirmed a general inhibitory role of ABA and point to PYL1 and PYL2 as candidate ABA receptors that regulate AR inhibition."}],"scopus_import":"1","month":"07","date_created":"2021-08-15T22:01:28Z","publication":"Genes","oa":1,"intvolume":"        12","_id":"9909","citation":{"ama":"Zeng Y, Verstraeten I, Trinh HK, et al. Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. <i>Genes</i>. 2021;12(8). doi:<a href=\"https://doi.org/10.3390/genes12081141\">10.3390/genes12081141</a>","ieee":"Y. Zeng <i>et al.</i>, “Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling,” <i>Genes</i>, vol. 12, no. 8. MDPI, 2021.","chicago":"Zeng, Yinwei, Inge Verstraeten, Hoang Khai Trinh, Thomas Heugebaert, Christian V. Stevens, Irene Garcia-Maquilon, Pedro L. Rodriguez, Steffen Vanneste, and Danny Geelen. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling.” <i>Genes</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/genes12081141\">https://doi.org/10.3390/genes12081141</a>.","apa":"Zeng, Y., Verstraeten, I., Trinh, H. K., Heugebaert, T., Stevens, C. V., Garcia-Maquilon, I., … Geelen, D. (2021). Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. <i>Genes</i>. MDPI. <a href=\"https://doi.org/10.3390/genes12081141\">https://doi.org/10.3390/genes12081141</a>","ista":"Zeng Y, Verstraeten I, Trinh HK, Heugebaert T, Stevens CV, Garcia-Maquilon I, Rodriguez PL, Vanneste S, Geelen D. 2021. Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. Genes. 12(8), 1141.","mla":"Zeng, Yinwei, et al. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling.” <i>Genes</i>, vol. 12, no. 8, 1141, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/genes12081141\">10.3390/genes12081141</a>.","short":"Y. Zeng, I. Verstraeten, H.K. Trinh, T. Heugebaert, C.V. Stevens, I. Garcia-Maquilon, P.L. Rodriguez, S. Vanneste, D. Geelen, Genes 12 (2021)."},"doi":"10.3390/genes12081141","oa_version":"Published Version","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2073-4425"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_published":"2021-07-27T00:00:00Z","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_number":"1141"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_identifier":{"eissn":["1573-0530"],"issn":["0377-9017"]},"article_number":"45","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","date_published":"2021-04-05T00:00:00Z","oa":1,"date_created":"2021-04-18T22:01:41Z","month":"04","publication":"Letters in Mathematical Physics","abstract":[{"lang":"eng","text":"We revise a previous result about the Fröhlich dynamics in the strong coupling limit obtained in Griesemer (Rev Math Phys 29(10):1750030, 2017). In the latter it was shown that the Fröhlich time evolution applied to the initial state φ0⊗ξα, where φ0 is the electron ground state of the Pekar energy functional and ξα the associated coherent state of the phonons, can be approximated by a global phase for times small compared to α2. In the present note we prove that a similar approximation holds for t=O(α2) if one includes a nontrivial effective dynamics for the phonons that is generated by an operator proportional to α−2 and quadratic in creation and annihilation operators. Our result implies that the electron ground state remains close to its initial state for times of order α2, while the phonon fluctuations around the coherent state ξα can be described by a time-dependent Bogoliubov transformation."}],"scopus_import":"1","language":[{"iso":"eng"}],"doi":"10.1007/s11005-021-01380-7","oa_version":"Published Version","citation":{"ama":"Mitrouskas DJ. A note on the Fröhlich dynamics in the strong coupling limit. <i>Letters in Mathematical Physics</i>. 2021;111. doi:<a href=\"https://doi.org/10.1007/s11005-021-01380-7\">10.1007/s11005-021-01380-7</a>","ieee":"D. J. Mitrouskas, “A note on the Fröhlich dynamics in the strong coupling limit,” <i>Letters in Mathematical Physics</i>, vol. 111. Springer Nature, 2021.","chicago":"Mitrouskas, David Johannes. “A Note on the Fröhlich Dynamics in the Strong Coupling Limit.” <i>Letters in Mathematical Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s11005-021-01380-7\">https://doi.org/10.1007/s11005-021-01380-7</a>.","apa":"Mitrouskas, D. J. (2021). A note on the Fröhlich dynamics in the strong coupling limit. <i>Letters in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11005-021-01380-7\">https://doi.org/10.1007/s11005-021-01380-7</a>","mla":"Mitrouskas, David Johannes. “A Note on the Fröhlich Dynamics in the Strong Coupling Limit.” <i>Letters in Mathematical Physics</i>, vol. 111, 45, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/s11005-021-01380-7\">10.1007/s11005-021-01380-7</a>.","ista":"Mitrouskas DJ. 2021. A note on the Fröhlich dynamics in the strong coupling limit. Letters in Mathematical Physics. 111, 45.","short":"D.J. Mitrouskas, Letters in Mathematical Physics 111 (2021)."},"_id":"9333","intvolume":"       111","acknowledgement":"I thank Marcel Griesemer for many interesting discussions about the Fröhlich polaron and also for valuable comments on this manuscript. Helpful discussions with Nikolai Leopold and Robert Seiringer are also gratefully acknowledged. This work was partially supported by the Deutsche Forschungsgemeinschaft (DFG) through the Research Training Group 1838: Spectral Theory and Dynamics of Quantum Systems. Open Access funding enabled and organized by Projekt DEAL.","isi":1,"day":"05","year":"2021","volume":111,"external_id":{"isi":["000637359300002"]},"article_type":"original","file_date_updated":"2021-04-19T10:40:01Z","publisher":"Springer Nature","ddc":["510"],"author":[{"id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","last_name":"Mitrouskas","full_name":"Mitrouskas, David Johannes","first_name":"David Johannes"}],"quality_controlled":"1","date_updated":"2026-04-02T13:58:00Z","has_accepted_license":"1","article_processing_charge":"No","title":"A note on the Fröhlich dynamics in the strong coupling limit","department":[{"_id":"RoSe"}],"file":[{"access_level":"open_access","checksum":"be56c0845a43c0c5c772ee0b5053f7d7","date_updated":"2021-04-19T10:40:01Z","relation":"main_file","file_name":"2021_LettersMathPhysics_Mitrouskas.pdf","content_type":"application/pdf","creator":"dernst","file_size":438084,"success":1,"file_id":"9341","date_created":"2021-04-19T10:40:01Z"}],"publication_status":"published","type":"journal_article"},{"day":"26","volume":10,"year":"2021","acknowledgement":"Work in ERA lab is supported by the Swedish Research Council, the Center of Innovative Medicine (CIMED) Grant, Karolinska Institutet, and the Heart and Lung Foundation, and\r\nthe Daniel Alagille Award from the European Association for the Study of the Liver. One project in ERA lab is funded by ModeRNA, unrelated to this project. The funders have no role in the design or interpretation of the work. SH has been supported by a KI-MU PhD student program, and by a Wera Ekstro¨m Foundation Scholarship. We are grateful for support from Tornspiran foundation to NVH. JK: This research was carried out under the project CEITEC 2020 (LQ1601) with financial support from the Ministry of Education, Youth and Sports of the Czech Republic under the National Sustainability Programme II and CzechNanoLab Research Infrastructure supported by MEYS CR (LM2018110) . UL: The financial support from the Swedish Research Council and ICMC (Integrated CardioMetabolic Center) is acknowledged. JJ: The work was supported by the Grant Agency of Masaryk University (project no. MUNI/A/1565/2018). We thank Kari Huppert and Stacey Huppert for their expertise and help regarding bile duct cannulation and their laboratory hospitality. We also thank Nadja Schultz and Charlotte L Mattsson for their help with common bile duct cannulation. We thank Daniel Holl for his help with trachea cannulation. We thank Nikos Papadogiannakis for his assistance with mild Alagille biopsy samples and discussion. We thank Karolinska Biomedicum Imaging Core, especially Shigeaki Kanatani for his help with image analysis. We thank Jan Masek and Carolina Gutierrez for their scientific input in manuscript writing. We thank Peter Ranefall and the BioImage Informatics (SciLife national facility) for their help writing parts of the MATLAB pipeline.\r\nThe TROMA-III antibody developed by Rolf Kemler was obtained from the Developmental Studies Hybridoma (DSHB) Bank developed under the auspices of NICHD and maintained by The University of Iowa, Department of Biological Sciences, Iowa City, IA52242. We thank Goncalo M Brito for all illustrations. This work was supported by the European Union (European Research Council Starting grant 851288 to E.H.).","isi":1,"file_date_updated":"2021-03-22T08:50:33Z","project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","grant_number":"851288"}],"external_id":{"isi":["000625357100001"],"pmid":["33635272"]},"article_type":"original","quality_controlled":"1","author":[{"full_name":"Hankeova, Simona","first_name":"Simona","last_name":"Hankeova"},{"first_name":"Jakub","full_name":"Salplachta, Jakub","last_name":"Salplachta"},{"full_name":"Zikmund, Tomas","first_name":"Tomas","last_name":"Zikmund"},{"first_name":"Michaela","full_name":"Kavkova, Michaela","last_name":"Kavkova"},{"first_name":"Noémi","full_name":"Van Hul, Noémi","last_name":"Van Hul"},{"last_name":"Brinek","first_name":"Adam","full_name":"Brinek, Adam"},{"first_name":"Veronika","full_name":"Smekalova, Veronika","last_name":"Smekalova"},{"full_name":"Laznovsky, Jakub","first_name":"Jakub","last_name":"Laznovsky"},{"last_name":"Dawit","full_name":"Dawit, Feven","first_name":"Feven"},{"last_name":"Jaros","full_name":"Jaros, Josef","first_name":"Josef"},{"full_name":"Bryja, Vítězslav","first_name":"Vítězslav","last_name":"Bryja"},{"last_name":"Lendahl","full_name":"Lendahl, Urban","first_name":"Urban"},{"full_name":"Ellis, Ewa","first_name":"Ewa","last_name":"Ellis"},{"full_name":"Nemeth, Antal","first_name":"Antal","last_name":"Nemeth"},{"full_name":"Fischler, Björn","first_name":"Björn","last_name":"Fischler"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"last_name":"Kaiser","first_name":"Jozef","full_name":"Kaiser, Jozef"},{"last_name":"Andersson","first_name":"Emma Rachel","full_name":"Andersson, Emma Rachel"}],"ddc":["570"],"publisher":"eLife Sciences Publications","file":[{"checksum":"20ccf4dfe46c48cf986794c8bf4fd1cb","access_level":"open_access","date_updated":"2021-03-22T08:50:33Z","content_type":"application/pdf","creator":"dernst","file_name":"2021_eLife_Hankeova.pdf","relation":"main_file","date_created":"2021-03-22T08:50:33Z","file_id":"9271","success":1,"file_size":9259690}],"type":"journal_article","publication_status":"published","has_accepted_license":"1","date_updated":"2026-04-02T14:00:00Z","title":"DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome","department":[{"_id":"EdHa"}],"article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_identifier":{"eissn":["2050-084X"]},"status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-02-26T00:00:00Z","article_number":"e60916","abstract":[{"text":"Organ function depends on tissues adopting the correct architecture. However, insights into organ architecture are currently hampered by an absence of standardized quantitative 3D analysis. We aimed to develop a robust technology to visualize, digitalize, and segment the architecture of two tubular systems in 3D: double resin casting micro computed tomography (DUCT). As proof of principle, we applied DUCT to a mouse model for Alagille syndrome (Jag1Ndr/Ndr mice), characterized by intrahepatic bile duct paucity, that can spontaneously generate a biliary system in adulthood. DUCT identified increased central biliary branching and peripheral bile duct tortuosity as two compensatory processes occurring in distinct regions of Jag1Ndr/Ndr liver, leading to full reconstitution of wild-type biliary volume and phenotypic recovery. DUCT is thus a powerful new technology for 3D analysis, which can reveal novel phenotypes and provide a standardized method of defining liver architecture in mouse models.","lang":"eng"}],"ec_funded":1,"scopus_import":"1","oa":1,"publication":"eLife","date_created":"2021-03-14T23:01:34Z","month":"02","pmid":1,"citation":{"apa":"Hankeova, S., Salplachta, J., Zikmund, T., Kavkova, M., Van Hul, N., Brinek, A., … Andersson, E. R. (2021). DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.60916\">https://doi.org/10.7554/eLife.60916</a>","ieee":"S. Hankeova <i>et al.</i>, “DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","chicago":"Hankeova, Simona, Jakub Salplachta, Tomas Zikmund, Michaela Kavkova, Noémi Van Hul, Adam Brinek, Veronika Smekalova, et al. “DUCT Reveals Architectural Mechanisms Contributing to Bile Duct Recovery in a Mouse Model for Alagille Syndrome.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.60916\">https://doi.org/10.7554/eLife.60916</a>.","ama":"Hankeova S, Salplachta J, Zikmund T, et al. DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.60916\">10.7554/eLife.60916</a>","short":"S. Hankeova, J. Salplachta, T. Zikmund, M. Kavkova, N. Van Hul, A. Brinek, V. Smekalova, J. Laznovsky, F. Dawit, J. Jaros, V. Bryja, U. Lendahl, E. Ellis, A. Nemeth, B. Fischler, E.B. Hannezo, J. Kaiser, E.R. Andersson, ELife 10 (2021).","mla":"Hankeova, Simona, et al. “DUCT Reveals Architectural Mechanisms Contributing to Bile Duct Recovery in a Mouse Model for Alagille Syndrome.” <i>ELife</i>, vol. 10, e60916, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.60916\">10.7554/eLife.60916</a>.","ista":"Hankeova S, Salplachta J, Zikmund T, Kavkova M, Van Hul N, Brinek A, Smekalova V, Laznovsky J, Dawit F, Jaros J, Bryja V, Lendahl U, Ellis E, Nemeth A, Fischler B, Hannezo EB, Kaiser J, Andersson ER. 2021. DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome. eLife. 10, e60916."},"oa_version":"Published Version","doi":"10.7554/eLife.60916","intvolume":"        10","_id":"9244","language":[{"iso":"eng"}]},{"file_date_updated":"2021-04-06T10:39:08Z","external_id":{"pmid":["33740033"],"isi":["000663160600002"]},"project":[{"name":"Active mechano-chemical description of the cell cytoskeleton","_id":"268294B6-B435-11E9-9278-68D0E5697425","grant_number":"P31639","call_identifier":"FWF"}],"article_type":"original","day":"19","year":"2021","volume":220,"acknowledgement":"This work was supported by European Research Council grant 281971, Wellcome Trust Research Career Development Fellowship WT095829AIA and Wellcome Trust Senior Research\r\nFellowship 219482/Z/19/Z to J.L. Gallop, a Wellcome Trust Senior Investigator Award 098357 to B.D. Simons, and an Austrian Science Fund grant (P31639) to E. Hannezo. We acknowledge\r\ncore funding by the Wellcome Trust (092096) and Cancer Research UK (C6946/A14492). U. Dobramysl was supported by a Wellcome Trust Junior Interdisciplinary Fellowship grant\r\n(105602/Z/14/Z) and a Herchel Smith Postdoctoral Fellowship. H. Shimo was supported by a Funai Foundation Overseas scholarship.","isi":1,"file":[{"date_updated":"2021-04-06T10:39:08Z","checksum":"4739ffd90f2c7e05ac5b00f057c58aa2","access_level":"open_access","date_created":"2021-04-06T10:39:08Z","file_id":"9310","success":1,"file_size":9019720,"content_type":"application/pdf","creator":"dernst","file_name":"2021_JCB_Dobramysl.pdf","relation":"main_file"}],"publication_status":"published","type":"journal_article","date_updated":"2026-04-02T13:59:43Z","has_accepted_license":"1","issue":"4","article_processing_charge":"No","department":[{"_id":"EdHa"}],"title":"Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation","author":[{"last_name":"Dobramysl","first_name":"Ulrich","full_name":"Dobramysl, Ulrich"},{"first_name":"Iris Katharina","full_name":"Jarsch, Iris Katharina","last_name":"Jarsch"},{"first_name":"Yoshiko","full_name":"Inoue, Yoshiko","last_name":"Inoue"},{"full_name":"Shimo, Hanae","first_name":"Hanae","last_name":"Shimo"},{"first_name":"Benjamin","full_name":"Richier, Benjamin","last_name":"Richier"},{"last_name":"Gadsby","full_name":"Gadsby, Jonathan R.","first_name":"Jonathan R."},{"full_name":"Mason, Julia","first_name":"Julia","last_name":"Mason"},{"first_name":"Alicja","full_name":"Szałapak, Alicja","last_name":"Szałapak"},{"full_name":"Ioannou, Pantelis Savvas","first_name":"Pantelis Savvas","last_name":"Ioannou"},{"first_name":"Guilherme Pereira","full_name":"Correia, Guilherme Pereira","last_name":"Correia"},{"last_name":"Walrant","full_name":"Walrant, Astrid","first_name":"Astrid"},{"last_name":"Butler","full_name":"Butler, Richard","first_name":"Richard"},{"first_name":"Edouard B","full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Simons","first_name":"Benjamin D.","full_name":"Simons, Benjamin D."},{"last_name":"Gallop","first_name":"Jennifer L.","full_name":"Gallop, Jennifer L."}],"quality_controlled":"1","publisher":"Rockefeller University Press","ddc":["576"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","date_published":"2021-03-19T00:00:00Z","article_number":"e202003052","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_identifier":{"eissn":["1540-8140"]},"oa_version":"Published Version","doi":"10.1083/jcb.202003052","citation":{"short":"U. Dobramysl, I.K. Jarsch, Y. Inoue, H. Shimo, B. Richier, J.R. Gadsby, J. Mason, A. Szałapak, P.S. Ioannou, G.P. Correia, A. Walrant, R. Butler, E.B. Hannezo, B.D. Simons, J.L. Gallop, Journal of Cell Biology 220 (2021).","mla":"Dobramysl, Ulrich, et al. “Stochastic Combinations of Actin Regulatory Proteins Are Sufficient to Drive Filopodia Formation.” <i>Journal of Cell Biology</i>, vol. 220, no. 4, e202003052, Rockefeller University Press, 2021, doi:<a href=\"https://doi.org/10.1083/jcb.202003052\">10.1083/jcb.202003052</a>.","ista":"Dobramysl U, Jarsch IK, Inoue Y, Shimo H, Richier B, Gadsby JR, Mason J, Szałapak A, Ioannou PS, Correia GP, Walrant A, Butler R, Hannezo EB, Simons BD, Gallop JL. 2021. Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation. Journal of Cell Biology. 220(4), e202003052.","ama":"Dobramysl U, Jarsch IK, Inoue Y, et al. Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation. <i>Journal of Cell Biology</i>. 2021;220(4). doi:<a href=\"https://doi.org/10.1083/jcb.202003052\">10.1083/jcb.202003052</a>","chicago":"Dobramysl, Ulrich, Iris Katharina Jarsch, Yoshiko Inoue, Hanae Shimo, Benjamin Richier, Jonathan R. Gadsby, Julia Mason, et al. “Stochastic Combinations of Actin Regulatory Proteins Are Sufficient to Drive Filopodia Formation.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2021. <a href=\"https://doi.org/10.1083/jcb.202003052\">https://doi.org/10.1083/jcb.202003052</a>.","ieee":"U. Dobramysl <i>et al.</i>, “Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation,” <i>Journal of Cell Biology</i>, vol. 220, no. 4. Rockefeller University Press, 2021.","apa":"Dobramysl, U., Jarsch, I. K., Inoue, Y., Shimo, H., Richier, B., Gadsby, J. R., … Gallop, J. L. (2021). Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202003052\">https://doi.org/10.1083/jcb.202003052</a>"},"_id":"9306","intvolume":"       220","language":[{"iso":"eng"}],"scopus_import":"1","abstract":[{"lang":"eng","text":"Assemblies of actin and its regulators underlie the dynamic morphology of all eukaryotic cells. To understand how actin regulatory proteins work together to generate actin-rich structures such as filopodia, we analyzed the localization of diverse actin regulators within filopodia in Drosophila embryos and in a complementary in vitro system of filopodia-like structures (FLSs). We found that the composition of the regulatory protein complex where actin is incorporated (the filopodial tip complex) is remarkably heterogeneous both in vivo and in vitro. Our data reveal that different pairs of proteins correlate with each other and with actin bundle length, suggesting the presence of functional subcomplexes. This is consistent with a theoretical framework where three or more redundant subcomplexes join the tip complex stochastically, with any two being sufficient to drive filopodia formation. We provide an explanation for the observed heterogeneity and suggest that a mechanism based on multiple components allows stereotypical filopodial dynamics to arise from diverse upstream signaling pathways."}],"oa":1,"pmid":1,"date_created":"2021-04-04T22:01:21Z","publication":"Journal of Cell Biology","month":"03"},{"language":[{"iso":"eng"}],"citation":{"ama":"Kampjut D, Steiner J, Sazanov LA. Cryo-EM grid optimization for membrane proteins. <i>iScience</i>. 2021;24(3). doi:<a href=\"https://doi.org/10.1016/j.isci.2021.102139\">10.1016/j.isci.2021.102139</a>","ieee":"D. Kampjut, J. Steiner, and L. A. Sazanov, “Cryo-EM grid optimization for membrane proteins,” <i>iScience</i>, vol. 24, no. 3. Elsevier, 2021.","apa":"Kampjut, D., Steiner, J., &#38; Sazanov, L. A. (2021). Cryo-EM grid optimization for membrane proteins. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2021.102139\">https://doi.org/10.1016/j.isci.2021.102139</a>","chicago":"Kampjut, Domen, Julia Steiner, and Leonid A Sazanov. “Cryo-EM Grid Optimization for Membrane Proteins.” <i>IScience</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.isci.2021.102139\">https://doi.org/10.1016/j.isci.2021.102139</a>.","short":"D. Kampjut, J. Steiner, L.A. Sazanov, IScience 24 (2021).","mla":"Kampjut, Domen, et al. “Cryo-EM Grid Optimization for Membrane Proteins.” <i>IScience</i>, vol. 24, no. 3, 102139, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.isci.2021.102139\">10.1016/j.isci.2021.102139</a>.","ista":"Kampjut D, Steiner J, Sazanov LA. 2021. Cryo-EM grid optimization for membrane proteins. iScience. 24(3), 102139."},"oa_version":"Published Version","doi":"10.1016/j.isci.2021.102139","intvolume":"        24","_id":"9205","oa":1,"publication":"iScience","date_created":"2021-02-28T23:01:24Z","month":"03","pmid":1,"ec_funded":1,"scopus_import":"1","abstract":[{"lang":"eng","text":"Cryo-EM grid preparation is an important bottleneck in protein structure determination, especially for membrane proteins, typically requiring screening of a large number of conditions. We systematically investigated the effects of buffer components, blotting conditions and grid types on the outcome of grid preparation of five different membrane protein samples. Aggregation was the most common type of problem which was addressed by changing detergents, salt concentration or reconstitution of proteins into nanodiscs or amphipols. We show that the optimal concentration of detergent is between 0.05 and 0.4% and that the presence of a low concentration of detergent with a high critical micellar concentration protects the proteins from denaturation at the air-water interface. Furthermore, we discuss the strategies for achieving an adequate ice thickness, particle coverage and orientation distribution on free ice and on support films. Our findings provide a clear roadmap for comprehensive screening of conditions for cryo-EM grid preparation of membrane proteins."}],"article_number":"102139","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-03-19T00:00:00Z","acknowledged_ssus":[{"_id":"EM-Fac"}],"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"publication_identifier":{"eissn":["2589-0042"]},"issue":"3","has_accepted_license":"1","date_updated":"2026-04-02T14:00:19Z","title":"Cryo-EM grid optimization for membrane proteins","department":[{"_id":"LeSa"}],"article_processing_charge":"No","file":[{"relation":"main_file","file_name":"2021_iScience_Kampjut.pdf","content_type":"application/pdf","creator":"dernst","file_size":7431411,"success":1,"file_id":"9219","date_created":"2021-03-03T07:38:14Z","access_level":"open_access","checksum":"50585447386fe5842f07ab9b3a66e7e9","date_updated":"2021-03-03T07:38:14Z"}],"type":"journal_article","publication_status":"published","ddc":["570"],"publisher":"Elsevier","quality_controlled":"1","author":[{"first_name":"Domen","full_name":"Kampjut, Domen","last_name":"Kampjut","orcid":"0000-0002-6018-3422","id":"37233050-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Steiner, Julia","first_name":"Julia","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","last_name":"Steiner","orcid":"0000-0003-0493-3775"},{"full_name":"Sazanov, Leonid A","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","orcid":"0000-0002-0977-7989"}],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"}],"external_id":{"pmid":["33665558"],"isi":["000631646000012"]},"article_type":"original","file_date_updated":"2021-03-03T07:38:14Z","acknowledgement":"We thank the Electron Microscopy Facilities at the Institute of Science and Technology Austria and at the Vienna Biocenter for providing access and training for the electron microscopes. This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement no. 665385 .","isi":1,"day":"19","volume":24,"year":"2021"},{"citation":{"ama":"Cipolloni G, Erdös L, Schröder DJ. Fluctuation around the circular law for random matrices with real entries. <i>Electronic Journal of Probability</i>. 2021;26. doi:<a href=\"https://doi.org/10.1214/21-EJP591\">10.1214/21-EJP591</a>","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Fluctuation around the Circular Law for Random Matrices with Real Entries.” <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics, 2021. <a href=\"https://doi.org/10.1214/21-EJP591\">https://doi.org/10.1214/21-EJP591</a>.","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2021). Fluctuation around the circular law for random matrices with real entries. <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/21-EJP591\">https://doi.org/10.1214/21-EJP591</a>","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Fluctuation around the circular law for random matrices with real entries,” <i>Electronic Journal of Probability</i>, vol. 26. Institute of Mathematical Statistics, 2021.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Electronic Journal of Probability 26 (2021).","ista":"Cipolloni G, Erdös L, Schröder DJ. 2021. Fluctuation around the circular law for random matrices with real entries. Electronic Journal of Probability. 26, 24.","mla":"Cipolloni, Giorgio, et al. “Fluctuation around the Circular Law for Random Matrices with Real Entries.” <i>Electronic Journal of Probability</i>, vol. 26, 24, Institute of Mathematical Statistics, 2021, doi:<a href=\"https://doi.org/10.1214/21-EJP591\">10.1214/21-EJP591</a>."},"oa_version":"Published Version","doi":"10.1214/21-EJP591","intvolume":"        26","_id":"9412","language":[{"iso":"eng"}],"scopus_import":"1","ec_funded":1,"abstract":[{"lang":"eng","text":"We extend our recent result [22] on the central limit theorem for the linear eigenvalue statistics of non-Hermitian matrices X with independent, identically distributed complex entries to the real symmetry class. We find that the expectation and variance substantially differ from their complex counterparts, reflecting (i) the special spectral symmetry of real matrices onto the real axis; and (ii) the fact that real i.i.d. matrices have many real eigenvalues. Our result generalizes the previously known special cases where either the test function is analytic [49] or the first four moments of the matrix elements match the real Gaussian [59, 44]. The key element of the proof is the analysis of several weakly dependent Dyson Brownian motions (DBMs). The conceptual novelty of the real case compared with [22] is that the correlation structure of the stochastic differentials in each individual DBM is non-trivial, potentially even jeopardising its well-posedness."}],"oa":1,"date_created":"2021-05-23T22:01:44Z","publication":"Electronic Journal of Probability","month":"03","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-03-23T00:00:00Z","article_number":"24","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"arxiv":1,"publication_identifier":{"eissn":["1083-6489"]},"file":[{"success":1,"file_size":865148,"file_id":"9423","date_created":"2021-05-25T13:24:19Z","relation":"main_file","file_name":"2021_EJP_Cipolloni.pdf","content_type":"application/pdf","creator":"kschuh","date_updated":"2021-05-25T13:24:19Z","access_level":"open_access","checksum":"864ab003ad4cffea783f65aa8c2ba69f"}],"type":"journal_article","publication_status":"published","has_accepted_license":"1","date_updated":"2026-04-02T14:00:37Z","title":"Fluctuation around the circular law for random matrices with real entries","department":[{"_id":"LaEr"}],"article_processing_charge":"No","quality_controlled":"1","author":[{"full_name":"Cipolloni, Giorgio","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","last_name":"Cipolloni","orcid":"0000-0002-4901-7992"},{"last_name":"Erdös","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","full_name":"Erdös, László"},{"last_name":"Schröder","orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J","full_name":"Schröder, Dominik J"}],"ddc":["510"],"publisher":"Institute of Mathematical Statistics","file_date_updated":"2021-05-25T13:24:19Z","project":[{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"external_id":{"arxiv":["2002.02438"],"isi":["000641855600001"]},"day":"23","volume":26,"year":"2021","isi":1},{"acknowledgement":"The authors would like to thank Ulisse Ferrari for useful discussions and feedback.","isi":1,"day":"15","volume":16,"year":"2021","external_id":{"isi":["000641474900072"],"pmid":["33857170"]},"article_type":"original","file_date_updated":"2021-05-04T13:22:19Z","ddc":["570"],"publisher":"Public Library of Science","quality_controlled":"1","author":[{"full_name":"Chalk, Matthew J","first_name":"Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7782-4436","last_name":"Chalk"},{"first_name":"Gašper","full_name":"Tkačik, Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Marre, Olivier","first_name":"Olivier","last_name":"Marre"}],"issue":"4","has_accepted_license":"1","date_updated":"2026-04-02T13:58:56Z","department":[{"_id":"GaTk"}],"title":"Inferring the function performed by a recurrent neural network","article_processing_charge":"No","file":[{"checksum":"c52da133850307d2031f552d998f00e8","access_level":"open_access","date_updated":"2021-05-04T13:22:19Z","file_name":"2021_pone_Chalk.pdf","content_type":"application/pdf","creator":"kschuh","relation":"main_file","file_id":"9371","date_created":"2021-05-04T13:22:19Z","file_size":2768282,"success":1}],"type":"journal_article","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_identifier":{"eissn":["1932-6203"]},"article_number":"e0248940","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-04-15T00:00:00Z","oa":1,"date_created":"2021-05-02T22:01:28Z","publication":"PLoS ONE","month":"04","pmid":1,"abstract":[{"lang":"eng","text":"A central goal in systems neuroscience is to understand the functions performed by neural circuits. Previous top-down models addressed this question by comparing the behaviour of an ideal model circuit, optimised to perform a given function, with neural recordings. However, this requires guessing in advance what function is being performed, which may not be possible for many neural systems. To address this, we propose an inverse reinforcement learning (RL) framework for inferring the function performed by a neural network from data. We assume that the responses of each neuron in a network are optimised so as to drive the network towards ‘rewarded’ states, that are desirable for performing a given function. We then show how one can use inverse RL to infer the reward function optimised by the network from observing its responses. This inferred reward function can be used to predict how the neural network should adapt its dynamics to perform the same function when the external environment or network structure changes. This could lead to theoretical predictions about how neural network dynamics adapt to deal with cell death and/or varying sensory stimulus statistics."}],"scopus_import":"1","language":[{"iso":"eng"}],"citation":{"short":"M.J. Chalk, G. Tkačik, O. Marre, PLoS ONE 16 (2021).","mla":"Chalk, Matthew J., et al. “Inferring the Function Performed by a Recurrent Neural Network.” <i>PLoS ONE</i>, vol. 16, no. 4, e0248940, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pone.0248940\">10.1371/journal.pone.0248940</a>.","ista":"Chalk MJ, Tkačik G, Marre O. 2021. Inferring the function performed by a recurrent neural network. PLoS ONE. 16(4), e0248940.","ieee":"M. J. Chalk, G. Tkačik, and O. Marre, “Inferring the function performed by a recurrent neural network,” <i>PLoS ONE</i>, vol. 16, no. 4. Public Library of Science, 2021.","apa":"Chalk, M. J., Tkačik, G., &#38; Marre, O. (2021). Inferring the function performed by a recurrent neural network. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0248940\">https://doi.org/10.1371/journal.pone.0248940</a>","chicago":"Chalk, Matthew J, Gašper Tkačik, and Olivier Marre. “Inferring the Function Performed by a Recurrent Neural Network.” <i>PLoS ONE</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pone.0248940\">https://doi.org/10.1371/journal.pone.0248940</a>.","ama":"Chalk MJ, Tkačik G, Marre O. Inferring the function performed by a recurrent neural network. <i>PLoS ONE</i>. 2021;16(4). doi:<a href=\"https://doi.org/10.1371/journal.pone.0248940\">10.1371/journal.pone.0248940</a>"},"oa_version":"Published Version","doi":"10.1371/journal.pone.0248940","intvolume":"        16","_id":"9362"},{"abstract":[{"text":"Humans conceptualize the diversity of life by classifying individuals into types we call ‘species’1. The species we recognize influence political and financial decisions and guide our understanding of how units of diversity evolve and interact. Although the idea of species may seem intuitive, a debate about the best way to define them has raged even before Darwin2. So much energy has been devoted to the so-called ‘species problem’ that no amount of discourse will ever likely solve it2,3. Dozens of species concepts are currently recognized3, but we lack a concrete understanding of how much researchers actually disagree and the factors that cause them to think differently1,2. To address this, we used a survey to quantify the species problem for the first time. The results indicate that the disagreement is extensive: two randomly chosen respondents will most likely disagree on the nature of species. The probability of disagreement is not predicted by researcher experience or broad study system, but tended to be lower among researchers with similar focus, training and who study the same organism. Should we see this diversity of perspectives as a problem? We argue that we should not.","lang":"eng"}],"scopus_import":"1","oa":1,"pmid":1,"month":"05","date_created":"2021-05-16T22:01:46Z","publication":"Current Biology","oa_version":"Published Version","doi":"10.1016/j.cub.2021.03.060","citation":{"short":"S. Stankowski, M. Ravinet, Current Biology 31 (2021) R428–R429.","ista":"Stankowski S, Ravinet M. 2021. Quantifying the use of species concepts. Current Biology. 31(9), R428–R429.","mla":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” <i>Current Biology</i>, vol. 31, no. 9, Cell Press, 2021, pp. R428–29, doi:<a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">10.1016/j.cub.2021.03.060</a>.","ieee":"S. Stankowski and M. Ravinet, “Quantifying the use of species concepts,” <i>Current Biology</i>, vol. 31, no. 9. Cell Press, pp. R428–R429, 2021.","chicago":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” <i>Current Biology</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">https://doi.org/10.1016/j.cub.2021.03.060</a>.","apa":"Stankowski, S., &#38; Ravinet, M. (2021). Quantifying the use of species concepts. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">https://doi.org/10.1016/j.cub.2021.03.060</a>","ama":"Stankowski S, Ravinet M. Quantifying the use of species concepts. <i>Current Biology</i>. 2021;31(9):R428-R429. doi:<a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">10.1016/j.cub.2021.03.060</a>"},"_id":"9392","corr_author":"1","intvolume":"        31","language":[{"iso":"eng"}],"page":"R428-R429","publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","date_published":"2021-05-10T00:00:00Z","author":[{"last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","full_name":"Stankowski, Sean"},{"first_name":"Mark","full_name":"Ravinet, Mark","last_name":"Ravinet"}],"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2021.03.060","open_access":"1"}],"publisher":"Cell Press","publication_status":"published","type":"journal_article","date_updated":"2026-04-02T13:59:25Z","issue":"9","article_processing_charge":"No","department":[{"_id":"NiBa"}],"title":"Quantifying the use of species concepts","day":"10","year":"2021","volume":31,"acknowledgement":"We thank Christopher Cooney, Martin Garlovsky, Anja M. Westram, Carina Baskett, Stefanie Belohlavy, Michal Hledik, Arka Pal, Nicholas H. Barton, Roger K. Butlin and members of the University of Sheffield Speciation Journal Club for feedback on draft survey questions and/or comments on a draft manuscript. Three anonymous reviewers gave thoughtful feedback that improved the manuscript. We thank Ahmad Nadeem, who was paid to build the Shiny app. We are especially grateful to everyone who took part in the survey. Ethical approval for the survey was obtained through the University of Sheffield Ethics Review Procedure (Application 029768). S.S. was supported by a NERC grant awarded to Roger K. Butlin.","isi":1,"external_id":{"isi":["000654741200004"],"pmid":["33974865"]},"article_type":"original"},{"department":[{"_id":"MiLe"}],"title":"Morphology of three-body quantum states from machine learning","article_processing_charge":"Yes","issue":"6","has_accepted_license":"1","date_updated":"2026-04-02T14:01:49Z","type":"journal_article","publication_status":"published","file":[{"date_updated":"2021-07-19T11:47:16Z","access_level":"open_access","checksum":"e39164ce7ea228d287cf8924e1a0f9fe","success":1,"file_size":3868445,"file_id":"9690","date_created":"2021-07-19T11:47:16Z","relation":"main_file","file_name":"2021_NewJPhys_Huber.pdf","creator":"cziletti","content_type":"application/pdf"}],"ddc":["530"],"publisher":"IOP Publishing","quality_controlled":"1","author":[{"first_name":"David","full_name":"Huber, David","last_name":"Huber"},{"first_name":"Oleksandr V.","full_name":"Marchukov, Oleksandr V.","last_name":"Marchukov"},{"full_name":"Hammer, Hans Werner","first_name":"Hans Werner","last_name":"Hammer"},{"full_name":"Volosniev, Artem","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","last_name":"Volosniev"}],"article_type":"original","project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"external_id":{"arxiv":["2102.04961"],"isi":["000664736300001"]},"file_date_updated":"2021-07-19T11:47:16Z","isi":1,"acknowledgement":"We thank Aidan Tracy for his input during the initial stages of this project. We thank Nathan Harshman, Achim Richter, Wojciech Rzadkowski, and Dane Hudson Smith for helpful discussions and comments on the manuscript. This work has been supported by European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411 (AGV); by the German Aeronautics and Space Administration (DLR) through Grant No. 50 WM 1957 (OVM); by the Deutsche Forschungsgemeinschaft through Project VO 2437/1-1 (Project No. 413495248) (AGV and HWH); by the Deutsche Forschungsgemeinschaft through Collaborative Research Center SFB 1245 (Project No. 279384907) and by the Bundesministerium für Bildung und Forschung under Contract 05P18RDFN1 (HWH). HWH also thanks the ECT* for hospitality during the workshop 'Universal physics in Many-Body Quantum Systems—From Atoms to Quarks'. This infrastructure is part of a project that has received funding from the European Union's Horizon 2020 research and innovation program under Grant Agreement No. 824093. We acknowledge support by the Deutsche Forschungsgemeinschaft and the Open Access Publishing Fund of Technische Universität Darmstadt.","volume":23,"year":"2021","day":"23","language":[{"iso":"eng"}],"intvolume":"        23","_id":"9679","citation":{"ama":"Huber D, Marchukov OV, Hammer HW, Volosniev A. Morphology of three-body quantum states from machine learning. <i>New Journal of Physics</i>. 2021;23(6). doi:<a href=\"https://doi.org/10.1088/1367-2630/ac0576\">10.1088/1367-2630/ac0576</a>","ieee":"D. Huber, O. V. Marchukov, H. W. Hammer, and A. Volosniev, “Morphology of three-body quantum states from machine learning,” <i>New Journal of Physics</i>, vol. 23, no. 6. IOP Publishing, 2021.","apa":"Huber, D., Marchukov, O. V., Hammer, H. W., &#38; Volosniev, A. (2021). Morphology of three-body quantum states from machine learning. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/ac0576\">https://doi.org/10.1088/1367-2630/ac0576</a>","chicago":"Huber, David, Oleksandr V. Marchukov, Hans Werner Hammer, and Artem Volosniev. “Morphology of Three-Body Quantum States from Machine Learning.” <i>New Journal of Physics</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/1367-2630/ac0576\">https://doi.org/10.1088/1367-2630/ac0576</a>.","short":"D. Huber, O.V. Marchukov, H.W. Hammer, A. Volosniev, New Journal of Physics 23 (2021).","mla":"Huber, David, et al. “Morphology of Three-Body Quantum States from Machine Learning.” <i>New Journal of Physics</i>, vol. 23, no. 6, 065009, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/1367-2630/ac0576\">10.1088/1367-2630/ac0576</a>.","ista":"Huber D, Marchukov OV, Hammer HW, Volosniev A. 2021. Morphology of three-body quantum states from machine learning. New Journal of Physics. 23(6), 065009."},"doi":"10.1088/1367-2630/ac0576","oa_version":"Published Version","date_created":"2021-07-18T22:01:22Z","publication":"New Journal of Physics","month":"06","oa":1,"scopus_import":"1","abstract":[{"text":"The relative motion of three impenetrable particles on a ring, in our case two identical fermions and one impurity, is isomorphic to a triangular quantum billiard. Depending on the ratio κ of the impurity and fermion masses, the billiards can be integrable or non-integrable (also referred to in the main text as chaotic). To set the stage, we first investigate the energy level distributions of the billiards as a function of 1/κ ∈ [0, 1] and find no evidence of integrable cases beyond the limiting values 1/κ = 1 and 1/κ = 0. Then, we use machine learning tools to analyze properties of probability distributions of individual quantum states. We find that convolutional neural networks can correctly classify integrable and non-integrable states. The decisive features of the wave functions are the normalization and a large number of zero elements, corresponding to the existence of a nodal line. The network achieves typical accuracies of 97%, suggesting that machine learning tools can be used to analyze and classify the morphology of probability densities obtained in theory or experiment.","lang":"eng"}],"ec_funded":1,"article_number":"065009","date_published":"2021-06-23T00:00:00Z","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","arxiv":1,"publication_identifier":{"eissn":["1367-2630"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"}}]