[{"quality_controlled":"1","doi":"10.3847/1538-4357/ae089c","fulldoi":"https://doi.org/10.3847/1538-4357/ae089c","date_published":"2025-11-20T00:00:00Z","oa_version":"Published Version","author":[{"first_name":"Pierluigi","full_name":"Rinaldi, Pierluigi","last_name":"Rinaldi"},{"first_name":"Pablo G.","full_name":"Pérez-González, Pablo G.","last_name":"Pérez-González"},{"first_name":"George H.","full_name":"Rieke, George H.","last_name":"Rieke"},{"last_name":"Lyu","full_name":"Lyu, Jianwei","first_name":"Jianwei"},{"first_name":"Francesco","full_name":"D’Eugenio, Francesco","last_name":"D’Eugenio"},{"full_name":"Wu, Zihao","last_name":"Wu","first_name":"Zihao"},{"full_name":"Carniani, Stefano","last_name":"Carniani","first_name":"Stefano"},{"full_name":"Looser, Tobias J.","last_name":"Looser","first_name":"Tobias J."},{"first_name":"Irene","last_name":"Shivaei","full_name":"Shivaei, Irene"},{"first_name":"Leindert A.","full_name":"Boogaard, Leindert A.","last_name":"Boogaard"},{"last_name":"Diaz-Santos","full_name":"Diaz-Santos, Tanio","first_name":"Tanio"},{"last_name":"Colina","full_name":"Colina, Luis","first_name":"Luis"},{"last_name":"Östlin","full_name":"Östlin, Göran","first_name":"Göran"},{"full_name":"Alberts, Stacey","last_name":"Alberts","first_name":"Stacey"},{"first_name":"Javier","full_name":"Álvarez-Márquez, Javier","last_name":"Álvarez-Márquez"},{"first_name":"Marianna","full_name":"Annuziatella, Marianna","last_name":"Annuziatella"},{"full_name":"Aravena, Manuel","last_name":"Aravena","first_name":"Manuel"},{"first_name":"Rachana","full_name":"Bhatawdekar, Rachana","last_name":"Bhatawdekar"},{"first_name":"Andrew J.","last_name":"Bunker","full_name":"Bunker, Andrew J."},{"first_name":"Karina I.","last_name":"Caputi","full_name":"Caputi, Karina I."},{"last_name":"Charlot","full_name":"Charlot, Stéphane","first_name":"Stéphane"},{"last_name":"Crespo Gómez","full_name":"Crespo Gómez, Alejandro","first_name":"Alejandro"},{"first_name":"Mirko","last_name":"Curti","full_name":"Curti, Mirko"},{"first_name":"Andreas","last_name":"Eckart","full_name":"Eckart, Andreas"},{"first_name":"Steven","last_name":"Gillman","full_name":"Gillman, Steven"},{"last_name":"Hainline","full_name":"Hainline, Kevin","first_name":"Kevin"},{"first_name":"Nimisha","last_name":"Kumari","full_name":"Kumari, Nimisha"},{"last_name":"Hjorth","full_name":"Hjorth, Jens","first_name":"Jens"},{"full_name":"Iani, Edoardo","id":"4053390a-6b68-11ef-9828-a3b8adef8d0a","last_name":"Iani","orcid":"0000-0001-8386-3546","first_name":"Edoardo"},{"first_name":"Hanae","last_name":"Inami","full_name":"Inami, Hanae"},{"last_name":"Ji","full_name":"Ji, Zhiyuan","first_name":"Zhiyuan"},{"first_name":"Benjamin D.","last_name":"Johnson","full_name":"Johnson, Benjamin D."},{"last_name":"Jones","full_name":"Jones, Gareth C.","first_name":"Gareth C."},{"first_name":"Álvaro","last_name":"Labiano","full_name":"Labiano, Álvaro"},{"full_name":"Maiolino, Roberto","last_name":"Maiolino","first_name":"Roberto"},{"first_name":"Jens","last_name":"Melinder","full_name":"Melinder, Jens"},{"first_name":"Thibaud","last_name":"Moutard","full_name":"Moutard, Thibaud"},{"first_name":"Florian","last_name":"Peissker","full_name":"Peissker, Florian"},{"first_name":"Marcia","last_name":"Rieke","full_name":"Rieke, Marcia"},{"last_name":"Robertson","full_name":"Robertson, Brant","first_name":"Brant"},{"full_name":"Scholtz, Jan","last_name":"Scholtz","first_name":"Jan"},{"first_name":"Sandro","full_name":"Tacchella, Sandro","last_name":"Tacchella"},{"first_name":"Paul P.","last_name":"Van Der Werf","full_name":"Van Der Werf, Paul P."},{"first_name":"Fabian","last_name":"Walter","full_name":"Walter, Fabian"},{"first_name":"Christina C.","last_name":"Williams","full_name":"Williams, Christina C."},{"first_name":"Chris","last_name":"Willott","full_name":"Willott, Chris"},{"last_name":"Witstok","full_name":"Witstok, Joris","first_name":"Joris"},{"last_name":"Übler","full_name":"Übler, Hannah","first_name":"Hannah"},{"last_name":"Zhu","full_name":"Zhu, Yongda","first_name":"Yongda"}],"publication_status":"published","issue":"1","intvolume":"       994","abstract":[{"text":"We present a comprehensive analysis of the MIRI Extremely Red Object Virgil, a Lyα emitter at zspec = 6.6379 ± 0.0035 with the photometric properties of a Little Red Dot. Leveraging new JWST/MIRI imaging from the MIDIS and PAHSPECS programs, we confirm Virgil’s extraordinary nature among galaxies in JADES/GOODS-South, exhibiting a strikingly red NIRCam-to-MIRI color (F444W–F1500W = 2.84 ± 0.04 mag). Deep NIRSpec/PRISM spectroscopy from the OASIS program offers key insights into the host galaxy, revealing properties of an average star-forming galaxy during Cosmic Reionization, such as a subsolar metallicity, low-to-moderate dust content, and a relatively high ionization parameter and electron temperature. By estimating the star formation rate of Virgil from UV and Hα, we find evidence that the galaxy is either entering or fading out of a bursty episode. Although line-ratio diagnostics employed at high z would classify Virgil as an active galactic nucleus (AGN), this classification becomes ambiguous once redshift evolution is considered. Nonetheless, Virgil occupies the same parameter space as recently confirmed AGNs at similar redshifts. The new deep MIRI data at 15 μm reinforce the AGN nature of Virgil, as inferred from multiple spectral energy distribution (SED) fitting codes. Virgil’s rising infrared SED and UV excess resemble those of Dust-Obscured Galaxies (DOGs) studied with Spitzer at Cosmic Noon, particularly blue-excess HotDOGs. Our results highlight the need for a multiwavelength approach incorporating MIRI to uncover such extreme sources at z ≳ 6 and to shed light on the interplay between galaxy evolution and early black hole growth during Cosmic Reionization.","lang":"eng"}],"citation":{"ama":"Rinaldi P, Pérez-González PG, Rieke GH, et al. Deciphering the nature of Virgil: An obscured active galactic nucleus lurking within an apparently normal Lyα emitter during cosmic reionization. <i>The Astrophysical Journal</i>. 2025;994(1). doi:<a href=\"https://doi.org/10.3847/1538-4357/ae089c\">10.3847/1538-4357/ae089c</a>","ieee":"P. Rinaldi <i>et al.</i>, “Deciphering the nature of Virgil: An obscured active galactic nucleus lurking within an apparently normal Lyα emitter during cosmic reionization,” <i>The Astrophysical Journal</i>, vol. 994, no. 1. IOP Publishing, 2025.","ista":"Rinaldi P, Pérez-González PG, Rieke GH, Lyu J, D’Eugenio F, Wu Z, Carniani S, Looser TJ, Shivaei I, Boogaard LA, Diaz-Santos T, Colina L, Östlin G, Alberts S, Álvarez-Márquez J, Annuziatella M, Aravena M, Bhatawdekar R, Bunker AJ, Caputi KI, Charlot S, Crespo Gómez A, Curti M, Eckart A, Gillman S, Hainline K, Kumari N, Hjorth J, Iani E, Inami H, Ji Z, Johnson BD, Jones GC, Labiano Á, Maiolino R, Melinder J, Moutard T, Peissker F, Rieke M, Robertson B, Scholtz J, Tacchella S, Van Der Werf PP, Walter F, Williams CC, Willott C, Witstok J, Übler H, Zhu Y. 2025. Deciphering the nature of Virgil: An obscured active galactic nucleus lurking within an apparently normal Lyα emitter during cosmic reionization. The Astrophysical Journal. 994(1), 86.","apa":"Rinaldi, P., Pérez-González, P. G., Rieke, G. H., Lyu, J., D’Eugenio, F., Wu, Z., … Zhu, Y. (2025). Deciphering the nature of Virgil: An obscured active galactic nucleus lurking within an apparently normal Lyα emitter during cosmic reionization. <i>The Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/ae089c\">https://doi.org/10.3847/1538-4357/ae089c</a>","chicago":"Rinaldi, Pierluigi, Pablo G. Pérez-González, George H. Rieke, Jianwei Lyu, Francesco D’Eugenio, Zihao Wu, Stefano Carniani, et al. “Deciphering the Nature of Virgil: An Obscured Active Galactic Nucleus Lurking within an Apparently Normal Lyα Emitter during Cosmic Reionization.” <i>The Astrophysical Journal</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.3847/1538-4357/ae089c\">https://doi.org/10.3847/1538-4357/ae089c</a>.","mla":"Rinaldi, Pierluigi, et al. “Deciphering the Nature of Virgil: An Obscured Active Galactic Nucleus Lurking within an Apparently Normal Lyα Emitter during Cosmic Reionization.” <i>The Astrophysical Journal</i>, vol. 994, no. 1, 86, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.3847/1538-4357/ae089c\">10.3847/1538-4357/ae089c</a>.","short":"P. Rinaldi, P.G. Pérez-González, G.H. Rieke, J. Lyu, F. D’Eugenio, Z. Wu, S. Carniani, T.J. Looser, I. Shivaei, L.A. Boogaard, T. Diaz-Santos, L. Colina, G. Östlin, S. Alberts, J. Álvarez-Márquez, M. Annuziatella, M. Aravena, R. Bhatawdekar, A.J. Bunker, K.I. Caputi, S. Charlot, A. Crespo Gómez, M. Curti, A. Eckart, S. Gillman, K. Hainline, N. Kumari, J. Hjorth, E. Iani, H. Inami, Z. Ji, B.D. Johnson, G.C. Jones, Á. Labiano, R. Maiolino, J. Melinder, T. Moutard, F. Peissker, M. Rieke, B. Robertson, J. Scholtz, S. Tacchella, P.P. Van Der Werf, F. Walter, C.C. Williams, C. Willott, J. Witstok, H. Übler, Y. Zhu, The Astrophysical Journal 994 (2025)."},"article_processing_charge":"Yes","PlanS_conform":"1","publication":"The Astrophysical Journal","article_number":"86","year":"2025","_id":"21727","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"gold","scopus_import":"1","file_date_updated":"2026-04-13T07:53:00Z","OA_place":"publisher","has_accepted_license":"1","publisher":"IOP Publishing","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"month":"11","ddc":["520"],"type":"journal_article","date_created":"2026-04-12T22:01:53Z","acknowledgement":"The authors are deeply grateful to Antonello Calabrò for valuable insights on CLOUDY and pyCloudy, and for publicly sharing their SFG and AGN models, which were used as a reference to verify the consistency of our photoionization models. The authors also thank Adam Carnall for insightful input on bagpipes and for assistance with the implementation of the two-population model adopted in this work. Finally, they also thank Camilla Pacifici, Vasily Kokorev, and Cristian Vignali for their insightful discussions.\r\n\r\nThis work is based on observations made with the NASA/ESA/CSA JWST. The data were obtained from the Mikulski Archive for Space Telescopes (MAST) at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. These observations are associated with JWST programs GTO #1180, GO #1210, GTO#1283, GO #1963, GO #1895, GO# 3215, and GO#6511.\r\n\r\nThe authors acknowledge the FRESCO, JEMS, and #3215 teams led by co-PIs P. Oesch, C. C. Williams, M. Maseda, D. Eisenstein, and R. Maiolino for developing their observing program with a zero-exclusive-access period. Processing for the JADES NIRCam data release was performed on the lux cluster at the University of California, Santa Cruz, funded by NSF MRI grant AST 1828315. Also based on observations made with the NASA/ESA Hubble Space Telescope obtained from the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 526555. The data presented in this article were obtained from MAST at the Space Telescope Science Institute. The specific observations analyzed can be accessed via doi: 10.17909/1rq3-8048 P. Oesch & D. Magee (2023), C. Williams et al. (2023), G. Illingworth (2015), and M. Rieke et al. (2023).\r\n\r\nA.J.B. acknowledges funding from the “FirstGalaxies” Advanced Grant from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No. 789056).\r\n\r\nP.G.P.-G. acknowledges support from grant PID2022-139567NB-I00 funded by the Spanish Ministerio de Ciencia e Innovación MCIN/AEI/10.13039/501100011033, FEDER, UE.\r\n\r\nB.E.R. acknowledges support from the NIRCam Science Team contract to the University of Arizona, NAS5-02015, and JWST Program 3215.\r\n\r\nS.T. acknowledges support by the Royal Society Research Grant G125142.\r\n\r\nThe research of C.C.W. is supported by NOIRLab, which is managed by the Association of Universities for Research in Astronomy (AURA) under a cooperative agreement with the National Science Foundation.\r\n\r\nJ.W. gratefully acknowledges support from the Cosmic Dawn Center through the DAWN Fellowship. The Cosmic Dawn Center (DAWN) is funded by the Danish National Research Foundation under grant No. 140.\r\n\r\nY.Z., Z.J., and P.L. gratefully acknowledge the JWST/NIRCam contract to the University of Arizona NAS5-02015.\r\n\r\nThe work of G.H.R. and P.L. was also supported by grant 80NSSC18K0555, from the NASA Goddard Space Flight Center to the University of Arizona.\r\n\r\nH.Ü. acknowledges funding by the European Union (ERC APEX, 101164796). Views and opinions expressed are however those of the authors only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.\r\n\r\nG.C.J. acknowledges support by the Science and Technology Facilities Council (STFC), ERC Advanced grant 695671 “QUENCH.”\r\n\r\nA.C.G. acknowledges support by JWST contract B0215/JWST-GO-02926.\r\n\r\nG.O. acknowledges support from the Swedish National Space Agency (SNSA).\r\n\r\nH.I. acknowledges support from JSPS KAKENHI grant No. JP21H01129.\r\n\r\nM.A. gratefully acknowledges support from ANID Basal Project FB210003 and ANID MILENIO NCN2024_112.\r\n\r\nT.D.S. acknowledges the research project was supported by the Hellenic Foundation for Research and Innovation (HFRI) under the “2nd Call for HFRI Research Projects to Support Faculty Members and Researchers” (project No.: 03382).\r\n\r\nR.M. acknowledges support by the Science and Technology Facilities Council (STFC), by the ERC through Advanced grant 695671 “QUENCH,” and by the UKRI Frontier Research grant RISEandFALL. R.M. also acknowledges funding from a research professorship from the Royal Society.\r\n\r\nI.S. acknowledges funding from the Atraccíon de Talento grant No. 2022-T1/TIC-20472 of the Comunidad de Madrid, Spain, and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant No. 101117541, DistantDust).\r\n\r\nK.I.C. acknowledges funding from the Dutch Research Council (NWO) through the award of the Vici grant VI.C.212.036.\r\n\r\nFacilities: HST - Hubble Space Telescope satellite, JWST. -\r\n\r\nSoftware: Astropy (Astropy Collaboration et al. 2022), Bagpipes (A. C. Carnall et al. 2019), MSAEXP (G. Brammer 2023) NumPy (C. R. Harris et al. 2020), pandas (The pandas development team 2024) Photutils (L. Bradley et al. 2016), TOPCAT (M. Taylor 2022).","volume":994,"article_type":"original","department":[{"_id":"JoMa"}],"language":[{"iso":"eng"}],"file":[{"date_updated":"2026-04-13T07:53:00Z","success":1,"access_level":"open_access","date_created":"2026-04-13T07:53:00Z","file_name":"2025_AstrophysicalJournal_Rinaldi.pdf","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_id":"21731","file_size":10298729,"checksum":"5d13b0ad3e9f56cbe29c5de0ba5757c8"}],"oa":1,"day":"20","date_updated":"2026-04-13T07:54:11Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Deciphering the nature of Virgil: An obscured active galactic nucleus lurking within an apparently normal Lyα emitter during cosmic reionization","DOAJ_listed":"1"},{"citation":{"short":"T.A. Henzinger, in:, Proceedings of the 27th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, IEEE, 2025.","mla":"Henzinger, Thomas A. “Neural Certificates.” <i>Proceedings of the 27th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing</i>, IEEE, 2025, doi:<a href=\"https://doi.org/10.1109/SYNASC69064.2025.00008\">10.1109/SYNASC69064.2025.00008</a>.","chicago":"Henzinger, Thomas A. “Neural Certificates.” In <i>Proceedings of the 27th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing</i>. IEEE, 2025. <a href=\"https://doi.org/10.1109/SYNASC69064.2025.00008\">https://doi.org/10.1109/SYNASC69064.2025.00008</a>.","ista":"Henzinger TA. 2025. Neural Certificates. Proceedings of the 27th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing. SYNASC: Symposium on Symbolic and Numeric Algorithms for Scientific Computing.","ieee":"T. A. Henzinger, “Neural Certificates,” in <i>Proceedings of the 27th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing</i>, Timisoara, Romania, 2025.","apa":"Henzinger, T. A. (2025). Neural Certificates. In <i>Proceedings of the 27th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing</i>. Timisoara, Romania: IEEE. <a href=\"https://doi.org/10.1109/SYNASC69064.2025.00008\">https://doi.org/10.1109/SYNASC69064.2025.00008</a>","ama":"Henzinger TA. Neural Certificates. In: <i>Proceedings of the 27th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing</i>. IEEE; 2025. doi:<a href=\"https://doi.org/10.1109/SYNASC69064.2025.00008\">10.1109/SYNASC69064.2025.00008</a>"},"article_processing_charge":"No","publication":"Proceedings of the 27th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing","day":"01","date_updated":"2026-05-18T08:34:15Z","year":"2025","status":"public","title":"Neural Certificates","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"21885","OA_type":"closed access","scopus_import":"1","corr_author":"1","publisher":"IEEE","publication_identifier":{"eissn":["2470-881X"],"eisbn":["9798331590116"]},"conference":{"name":"SYNASC: Symposium on Symbolic and Numeric Algorithms for Scientific Computing","start_date":"2025-09-22","location":"Timisoara, Romania","end_date":"2025-09-25"},"doi":"10.1109/SYNASC69064.2025.00008","quality_controlled":"1","fulldoi":"https://doi.org/10.1109/SYNASC69064.2025.00008","oa_version":"None","date_published":"2025-10-01T00:00:00Z","month":"10","type":"conference","date_created":"2026-05-17T22:02:11Z","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0002-2985-7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"}],"publication_status":"published","department":[{"_id":"ToHe"}],"abstract":[{"text":"Symbolic datatypes have proved to be central for automated reasoning about dynamical systems. In its basic form, a symbolic datatype for a class of dynamical systems supports the representation of state and transition sets, boolean operations and emptiness checks on such sets, and the transformation of a state set by a transition set. Successful examples of symbolic datatypes include BDDs and SAT for reasoning about finitestate systems, as well as polyhedra and SMT for reasoning about discrete dynamical systems over multidimensional realvalued state spaces. Most automated verification engines are based on such symbolic datatypes.","lang":"eng"}]},{"citation":{"ista":"Ignatyev Y, Papadopoulos S, Soretić M, Yeung J, Lin T-Y, Tanaka EM, Peshkin L, Levine AJ, Gabitto MI, Sweeney LB. Innovations in spinal cord cell type heterogeneity across vertebrate evolution. bioRxiv, <a href=\"https://doi.org/10.1101/2025.10.09.680955\">10.1101/2025.10.09.680955</a>.","ieee":"Y. Ignatyev <i>et al.</i>, “Innovations in spinal cord cell type heterogeneity across vertebrate evolution,” <i>bioRxiv</i>. .","apa":"Ignatyev, Y., Papadopoulos, S., Soretić, M., Yeung, J., Lin, T.-Y., Tanaka, E. M., … Sweeney, L. B. (n.d.). Innovations in spinal cord cell type heterogeneity across vertebrate evolution. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.10.09.680955\">https://doi.org/10.1101/2025.10.09.680955</a>","short":"Y. Ignatyev, S. Papadopoulos, M. Soretić, J. Yeung, T.-Y. Lin, E.M. Tanaka, L. Peshkin, A.J. Levine, M.I. Gabitto, L.B. Sweeney, BioRxiv (n.d.).","chicago":"Ignatyev, Yuri, Stavros Papadopoulos, Mateja Soretić, Jake Yeung, Tzi-Yang Lin, Elly M Tanaka, Leonid Peshkin, Ariel J Levine, Mariano I Gabitto, and Lora B. Sweeney. “Innovations in Spinal Cord Cell Type Heterogeneity across Vertebrate Evolution.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.10.09.680955\">https://doi.org/10.1101/2025.10.09.680955</a>.","mla":"Ignatyev, Yuri, et al. “Innovations in Spinal Cord Cell Type Heterogeneity across Vertebrate Evolution.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.10.09.680955\">10.1101/2025.10.09.680955</a>.","ama":"Ignatyev Y, Papadopoulos S, Soretić M, et al. Innovations in spinal cord cell type heterogeneity across vertebrate evolution. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.10.09.680955\">10.1101/2025.10.09.680955</a>"},"oa":1,"article_processing_charge":"No","day":"11","publication":"bioRxiv","date_updated":"2026-05-27T07:25:41Z","year":"2025","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"_id":"21920","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","title":"Innovations in spinal cord cell type heterogeneity across vertebrate evolution","OA_type":"green","corr_author":"1","OA_place":"repository","doi":"10.1101/2025.10.09.680955","type":"preprint","month":"10","oa_version":"Preprint","fulldoi":"https://doi.org/10.1101/2025.10.09.680955","date_published":"2025-10-11T00:00:00Z","project":[{"grant_number":"101041551","name":"Development and Evolution of Tetrapod Motor Circuits","_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae"},{"_id":"907b765e-16d5-11f0-9cad-fef108a945b1","grant_number":"27229","name":"A Tale of Two Circuits: Rostrocaudal spinal cord patterning during the swim-to-limb transition of Xenopus metamorphosis"}],"date_created":"2026-05-27T06:54:04Z","acknowledgement":"We would like to thank the members of the Sweeney Lab for discussion and support; Andrey\r\nBydanov for technical assistance with single-cell sequencing processing; and Jay Bikoff,\r\nNikos Konstantinides, Maria Tosches, and Graziana Gatto for comments on the manuscript. \r\nThis research was supported by: Horizon Europe ERC Starting Grant 101041551 (L.B.S,\r\nY.I., S.P.); Special Research Program (SFB) of the Austrian Science Fund (FWF) F7814-B\r\n(L.B.S., S.P., E.M.T); Austrian Science Fund (FWF) 10.55776/COE16 (L.B.S., Y.I., E.M.T.);\r\nAustrian Academy of Sciences DOC Fellowship 27229 (S.P.); ERC Advanced Grant 742046\r\n(E.M.T.); NIH award R24 OD031956 (L.P.); and in part by the Intramural Research\r\nProgram of the National Institutes of Health (NIH) through 1ZIA NS003153 to A.J.L.\r\nThe contributions of the NIH author are considered Works of the United States\r\nGovernment. The findings and conclusions presented in this paper are those of\r\nthe authors and do not necessarily reflect the views of the NIH or the U.S. Department\r\nof Health and Human Services. ","publication_status":"submitted","main_file_link":[{"url":"https://doi.org/10.1101/2025.10.09.680955","open_access":"1"}],"department":[{"_id":"LoSw"},{"_id":"ScienComp"}],"author":[{"first_name":"Yuri","last_name":"Ignatyev","full_name":"Ignatyev, Yuri"},{"last_name":"Papadopoulos","full_name":"Papadopoulos, Stavros","id":"40606b92-f128-11eb-9611-bf66a98cfa5c","first_name":"Stavros"},{"first_name":"Mateja","full_name":"Soretić, Mateja","last_name":"Soretić"},{"orcid":"0000-0003-1732-1559","first_name":"Jake","full_name":"Yeung, Jake","id":"123012b2-db30-11eb-b4d8-a35840c0551b","last_name":"Yeung"},{"first_name":"Tzi-Yang","full_name":"Lin, Tzi-Yang","last_name":"Lin"},{"last_name":"Tanaka","full_name":"Tanaka, Elly M","first_name":"Elly M"},{"last_name":"Peshkin","full_name":"Peshkin, Leonid","first_name":"Leonid"},{"last_name":"Levine","full_name":"Levine, Ariel J","first_name":"Ariel J"},{"full_name":"Gabitto, Mariano I","last_name":"Gabitto","first_name":"Mariano I"},{"first_name":"Lora Beatrice Jaeger","orcid":"0000-0001-9242-5601","last_name":"Sweeney","full_name":"Sweeney, Lora Beatrice Jaeger","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Vertebrates display remarkable diversity of sensorimotor behaviors, each adapted to distinct ecological and survival demands. This diversity raises fundamental questions about the evolutionary origin of motor control: do conserved spinal circuits underlie these behaviors, and how have they diverged across species. Recent studies detail spinal cell-type architecture in mammals but comparable, high-resolution atlases of the non-mammalian spinal cord are lacking. Here, we compare spinal cord cell types between fish, frogs, mice and humans, spanning ∼450 million years of evolution. Across species, we define highly conserved programs of cell type specification that segregate spinal neurons into nearly identical cardinal classes during development. This contrasts with adult stages, when spinal cell-type composition selectively diverges for excitatory neuron subpopulations. Using spatial transcriptomics, we localize this species divergence to the superficial, dorsal spinal cord, where variant neuropeptide expression defines mammalian-specific cell types. The most dorsal spinal cord thus emerges as a recently evolved hub for sensory integration in mammals, a neospinal cord analogous to the neocortex.</jats:p>"}]},{"oa_version":"Published Version","fulldoi":"https://doi.org/10.7554/elife.101851.3","date_published":"2025-03-14T00:00:00Z","abstract":[{"lang":"eng","text":"In the developing vertebrate central nervous system, neurons and glia typically arise\r\nsequentially from common progenitors. Here, we report that the transcription factor Forkhead\r\nBox G1 (Foxg1) regulates gliogenesis in the mouse neocortex via distinct cell-autonomous roles in progenitors and postmitotic neurons that regulate different aspects of the gliogenic FGF signalling pathway. We demonstrate that loss of Foxg1 in cortical progenitors at neurogenic stages causes premature astrogliogenesis. We identify a novel FOXG1 target, the pro-gliogenic FGF pathway component Fgfr3, which is suppressed by FOXG1 cell-autonomously to maintain neurogenesis. Furthermore, FOXG1 can also suppress premature astrogliogenesis triggered by the augmentation of FGF signalling. We identify a second novel function of FOXG1 in regulating the expression of gliogenic cues in newborn neocortical upper-layer neurons. Loss of FOXG1 in postmitotic neurons non-autonomously enhances gliogenesis in the progenitors via FGF signalling. These results fit well with the model that newborn neurons secrete cues that trigger progenitors to produce the next wave of cell types, astrocytes. If FGF signalling is attenuated in Foxg1 null progenitors, they progress to oligodendrocyte production. Therefore, loss of FOXG1 transitions the progenitor to a gliogenic state, producing either astrocytes or oligodendrocytes depending on FGF signalling levels. Our results uncover how FOXG1 integrates extrinsic signalling via the FGF pathway to regulate the sequential generation of neurons, astrocytes, and oligodendrocytes in the cerebral cortex. "}],"intvolume":"        13","publication_status":"published","author":[{"first_name":"Mahima","full_name":"Bose, Mahima","last_name":"Bose"},{"last_name":"Suresh","full_name":"Suresh, Varun","first_name":"Varun"},{"last_name":"Mishra","full_name":"Mishra, Urvi","first_name":"Urvi"},{"last_name":"Talwar","full_name":"Talwar, Ishita","first_name":"Ishita"},{"full_name":"Yadav, Anuradha","last_name":"Yadav","first_name":"Anuradha"},{"first_name":"Shiona","full_name":"Biswas, Shiona","last_name":"Biswas"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061"},{"last_name":"Tole","full_name":"Tole, Shubha","first_name":"Shubha"}],"doi":"10.7554/elife.101851.3","quality_controlled":"1","year":"2025","OA_type":"gold","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","_id":"14647","external_id":{"pmid":["40085500"]},"article_processing_charge":"Yes","citation":{"short":"M. Bose, V. Suresh, U. Mishra, I. Talwar, A. Yadav, S. Biswas, S. Hippenmeyer, S. Tole, ELife 13 (2025).","mla":"Bose, Mahima, et al. “Dual Role of FOXG1 in Regulating Gliogenesis in the Developing Neocortex via the FGF Signalling Pathway.” <i>ELife</i>, vol. 13, 101851, eLife Sciences Publications, 2025, doi:<a href=\"https://doi.org/10.7554/elife.101851.3\">10.7554/elife.101851.3</a>.","chicago":"Bose, Mahima, Varun Suresh, Urvi Mishra, Ishita Talwar, Anuradha Yadav, Shiona Biswas, Simon Hippenmeyer, and Shubha Tole. “Dual Role of FOXG1 in Regulating Gliogenesis in the Developing Neocortex via the FGF Signalling Pathway.” <i>ELife</i>. eLife Sciences Publications, 2025. <a href=\"https://doi.org/10.7554/elife.101851.3\">https://doi.org/10.7554/elife.101851.3</a>.","ieee":"M. Bose <i>et al.</i>, “Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway,” <i>eLife</i>, vol. 13. eLife Sciences Publications, 2025.","ista":"Bose M, Suresh V, Mishra U, Talwar I, Yadav A, Biswas S, Hippenmeyer S, Tole S. 2025. Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway. eLife. 13, 101851.","apa":"Bose, M., Suresh, V., Mishra, U., Talwar, I., Yadav, A., Biswas, S., … Tole, S. (2025). Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.101851.3\">https://doi.org/10.7554/elife.101851.3</a>","ama":"Bose M, Suresh V, Mishra U, et al. Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway. <i>eLife</i>. 2025;13. doi:<a href=\"https://doi.org/10.7554/elife.101851.3\">10.7554/elife.101851.3</a>"},"article_number":"101851","publication":"eLife","acknowledgement":"We thank the animal house staff of the Tata Institute of Fundamental Research, Mumbai (TIFR), for their excellent support; Gordon Fishell (Harvard Medical School, USA), and Goichi Miyoshi (Gunma University, Japan) for the Foxg1 floxed mouse line; Hiroshi Kawasaki (Kanazawa University, Japan) for the plasmids pCAG-FGF8 and pCAG-sFgfr3c; Soo Kyung Lee (University at Buffalo, The State University of New York, USA) for the Foxg1lox/lox genotyping primers and protocol. We thank Deepak Modi and Vainav Patel (National Institute for Research in Reproductive and Child Health, NIRRCH, Mumbai, India) for the use of the NIRRCH FACS Facility, and the staff of the NIRRCH and TIFR FACS facilities for their assistance. We thank Denis Jabaudon (University of Geneva, Switzerland) for his critical comments on the manuscript and members of the Jabaudon lab for helpful discussions. This work was funded by the Department of Atomic Energy (DAE), Govt. of India (Project Identification no. RTI4003,\r\nDAE OM no. 1303/2/2019/R&D-II/DAE/2079). ","article_type":"original","volume":13,"pmid":1,"date_created":"2023-12-06T13:07:01Z","month":"03","type":"journal_article","ddc":["570"],"file":[{"file_name":"2025_eLife_Bose.pdf","creator":"dernst","success":1,"date_updated":"2025-04-03T11:19:26Z","access_level":"open_access","date_created":"2025-04-03T11:19:26Z","file_size":17462771,"file_id":"19467","checksum":"64a6a6f86e24b21fe72c7a7fd6056fed","content_type":"application/pdf","relation":"main_file"}],"language":[{"iso":"eng"}],"department":[{"_id":"SiHi"}],"has_accepted_license":"1","file_date_updated":"2025-04-03T11:19:26Z","scopus_import":"1","OA_place":"publisher","publication_identifier":{"eissn":["2050-084X"]},"publisher":"eLife Sciences Publications","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2025-05-14T11:41:52Z","title":"Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway","oa":1,"day":"14"},{"year":"2025","OA_type":"green","_id":"15128","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","article_processing_charge":"No","external_id":{"arxiv":["2301.01712"],"isi":["001427953600004"]},"citation":{"ama":"Riabov V. Mesoscopic eigenvalue statistics for Wigner-type matrices. <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. 2025;61(1):129-154. doi:<a href=\"https://doi.org/10.1214/23-AIHP1438\">10.1214/23-AIHP1438</a>","ieee":"V. Riabov, “Mesoscopic eigenvalue statistics for Wigner-type matrices,” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>, vol. 61, no. 1. Institute of Mathematical Statistics, pp. 129–154, 2025.","apa":"Riabov, V. (2025). Mesoscopic eigenvalue statistics for Wigner-type matrices. <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/23-AIHP1438\">https://doi.org/10.1214/23-AIHP1438</a>","ista":"Riabov V. 2025. Mesoscopic eigenvalue statistics for Wigner-type matrices. Annales de l’institut Henri Poincare (B) Probability and Statistics. 61(1), 129–154.","mla":"Riabov, Volodymyr. “Mesoscopic Eigenvalue Statistics for Wigner-Type Matrices.” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>, vol. 61, no. 1, Institute of Mathematical Statistics, 2025, pp. 129–54, doi:<a href=\"https://doi.org/10.1214/23-AIHP1438\">10.1214/23-AIHP1438</a>.","chicago":"Riabov, Volodymyr. “Mesoscopic Eigenvalue Statistics for Wigner-Type Matrices.” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. Institute of Mathematical Statistics, 2025. <a href=\"https://doi.org/10.1214/23-AIHP1438\">https://doi.org/10.1214/23-AIHP1438</a>.","short":"V. Riabov, Annales de l’institut Henri Poincare (B) Probability and Statistics 61 (2025) 129–154."},"publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","fulldoi":"https://doi.org/10.1214/23-AIHP1438","date_published":"2025-02-01T00:00:00Z","oa_version":"Preprint","isi":1,"project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331"}],"intvolume":"        61","abstract":[{"lang":"eng","text":"We prove a universal mesoscopic central limit theorem for linear eigenvalue statistics of a Wigner-type matrix inside the bulk of the spectrum with compactly supported twice continuously differentiable test functions. The main novel ingredient is an optimal local law for the two-point function $T(z,\\zeta)$  and a general class of related quantities involving two resolvents at nearby spectral parameters."},{"text":"On établit un théorème limite central universel pour les statistiques linéaires mésoscopiques des valeurs propres d’une matrice de type Wigner au milieu du spectre, avec des fonctions de classe \r\n et à support compact. La principale nouveauté de cette approche est qu’elle repose sur une loi locale optimale pour la fonction à deux points $T(z,\\zeta)$ , ainsi que pour une classe plus générale d’observables impliquant deux résolvantes évaluées en des paramètres proches.","lang":"fre"}],"publication_status":"published","author":[{"first_name":"Volodymyr","id":"1949f904-edfb-11eb-afb5-e2dfddabb93b","full_name":"Riabov, Volodymyr","last_name":"Riabov"}],"issue":"1","quality_controlled":"1","doi":"10.1214/23-AIHP1438","date_updated":"2025-05-19T13:54:31Z","title":"Mesoscopic eigenvalue statistics for Wigner-type matrices","oa":1,"day":"01","page":"129-154","date_created":"2024-03-20T09:41:04Z","acknowledgement":"I would like to express my gratitude to László Erdős for suggesting the project and supervising my work. I am also thankful to Yuanyuan Xu and Oleksii Kolupaiev for many helpful discussions. Furthermore, I am grateful to Guillaume Dubach for translating the abstract into French.\r\nThe author was supported by the ERC Advanced Grant “RMTBeyond” No. 101020331.","article_type":"original","volume":61,"month":"02","type":"journal_article","department":[{"_id":"GradSch"},{"_id":"LaEr"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.01712","open_access":"1"}],"arxiv":1,"language":[{"iso":"eng"}],"corr_author":"1","OA_place":"repository","scopus_import":"1","ec_funded":1,"publication_identifier":{"issn":["0246-0203"]},"publisher":"Institute of Mathematical Statistics"},{"publication":"Discrete Applied Mathematics","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["001343647000001"],"arxiv":["2404.05542"]},"citation":{"ieee":"M. Anastos, S. Boyadzhiyska, S. Rathke, and J. Rué, “On the chromatic number of powers of subdivisions of graphs,” <i>Discrete Applied Mathematics</i>, vol. 360. Elsevier, pp. 506–511, 2025.","ista":"Anastos M, Boyadzhiyska S, Rathke S, Rué J. 2025. On the chromatic number of powers of subdivisions of graphs. Discrete Applied Mathematics. 360, 506–511.","apa":"Anastos, M., Boyadzhiyska, S., Rathke, S., &#38; Rué, J. (2025). On the chromatic number of powers of subdivisions of graphs. <i>Discrete Applied Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.dam.2024.10.002\">https://doi.org/10.1016/j.dam.2024.10.002</a>","short":"M. Anastos, S. Boyadzhiyska, S. Rathke, J. Rué, Discrete Applied Mathematics 360 (2025) 506–511.","mla":"Anastos, Michael, et al. “On the Chromatic Number of Powers of Subdivisions of Graphs.” <i>Discrete Applied Mathematics</i>, vol. 360, Elsevier, 2025, pp. 506–11, doi:<a href=\"https://doi.org/10.1016/j.dam.2024.10.002\">10.1016/j.dam.2024.10.002</a>.","chicago":"Anastos, Michael, Simona Boyadzhiyska, Silas Rathke, and Juanjo Rué. “On the Chromatic Number of Powers of Subdivisions of Graphs.” <i>Discrete Applied Mathematics</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.dam.2024.10.002\">https://doi.org/10.1016/j.dam.2024.10.002</a>.","ama":"Anastos M, Boyadzhiyska S, Rathke S, Rué J. On the chromatic number of powers of subdivisions of graphs. <i>Discrete Applied Mathematics</i>. 2025;360:506-511. doi:<a href=\"https://doi.org/10.1016/j.dam.2024.10.002\">10.1016/j.dam.2024.10.002</a>"},"OA_type":"hybrid","_id":"18478","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","year":"2025","quality_controlled":"1","doi":"10.1016/j.dam.2024.10.002","intvolume":"       360","abstract":[{"text":"For a given graph G=(V,E), we define its \\emph{nth subdivision} as the graph obtained from G by replacing every edge by a path of length n. We also define the \\emph{mth power} of G as the graph on vertex set V where we connect every pair of vertices at distance at most m in G. In this paper, we study the chromatic number of powers of subdivisions of graphs and resolve the case m=n asymptotically. In particular, our result confirms a conjecture of Mozafari-Nia and Iradmusa in the case m=n=3 in a strong sense.","lang":"eng"}],"author":[{"first_name":"Michael","last_name":"Anastos","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","full_name":"Anastos, Michael"},{"first_name":"Simona","full_name":"Boyadzhiyska, Simona","last_name":"Boyadzhiyska"},{"first_name":"Silas","full_name":"Rathke, Silas","last_name":"Rathke"},{"first_name":"Juanjo","last_name":"Rué","full_name":"Rué, Juanjo"}],"publication_status":"published","fulldoi":"https://doi.org/10.1016/j.dam.2024.10.002","isi":1,"oa_version":"Published Version","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"date_published":"2025-01-15T00:00:00Z","day":"15","oa":1,"title":"On the chromatic number of powers of subdivisions of graphs","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2025-04-14T07:54:56Z","ec_funded":1,"publication_identifier":{"issn":["0166-218X"]},"publisher":"Elsevier","has_accepted_license":"1","corr_author":"1","scopus_import":"1","file_date_updated":"2025-01-13T09:25:59Z","OA_place":"publisher","file":[{"checksum":"bd20a13e56b3ea01daf5e7aca5247c60","file_size":441060,"file_id":"18836","relation":"main_file","content_type":"application/pdf","creator":"dernst","file_name":"2025_DiscreteApplMath_Anastos.pdf","date_created":"2025-01-13T09:25:59Z","access_level":"open_access","date_updated":"2025-01-13T09:25:59Z","success":1}],"department":[{"_id":"MaKw"}],"arxiv":1,"language":[{"iso":"eng"}],"page":"506-511","date_created":"2024-10-27T23:01:44Z","article_type":"original","acknowledgement":"This work was initiated at the annual workshop of the Combinatorics and Graph Theory group of Freie Universität Berlin in Wilhelmsaue in September 2023. The authors would like to thank the institution for enabling this research. Finally, the fourth author would like to thank Tibor Szabó and the Combinatorics and Graph Theory group at Freie Universität Berlin for their hospitality during the research visit. Additionally, we thank Moharram Iradmusa for bringing the papers [5], [7] to our attention. Finally, we thank the anonymous referees for their suggestions on the manuscript, which have improved the quality of the document.\r\nM.A.: This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413 .\r\nS.B.: The research leading to these results was supported by EPSRC, UK, grant no. EP/V048287/1. There are no additional data beyond that contained within the main manuscript.\r\nS.R.: Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – The Berlin Mathematics Research Center MATH+ (EXC-2046/1, project ID: 390685689).\r\nJ.R. acknowledges the support of the Grant PID2020-113082GB-I00 funded by MICIU/AEI/10.13039/501100011033, Spain, and the Severo Ochoa and María de Maeztu Program for Centers and Units of Excellence in R&D, Spain (CEX2020-001084-M).","volume":360,"ddc":["510"],"month":"01","type":"journal_article"},{"publication":"IEEE Transactions on Network Science and Engineering","citation":{"ama":"Zhang Y, Wang J, Wen G, et al. Limitation of time promotes cooperation in structured collaboration systems. <i>IEEE Transactions on Network Science and Engineering</i>. 2025;12(1):4-12. doi:<a href=\"https://doi.org/10.1109/TNSE.2024.3481434\">10.1109/TNSE.2024.3481434</a>","ieee":"Y. Zhang <i>et al.</i>, “Limitation of time promotes cooperation in structured collaboration systems,” <i>IEEE Transactions on Network Science and Engineering</i>, vol. 12, no. 1. IEEE, pp. 4–12, 2025.","ista":"Zhang Y, Wang J, Wen G, Guan J, Zhou S, Chen G, Chatterjee K, Perc M. 2025. Limitation of time promotes cooperation in structured collaboration systems. IEEE Transactions on Network Science and Engineering. 12(1), 4–12.","apa":"Zhang, Y., Wang, J., Wen, G., Guan, J., Zhou, S., Chen, G., … Perc, M. (2025). Limitation of time promotes cooperation in structured collaboration systems. <i>IEEE Transactions on Network Science and Engineering</i>. IEEE. <a href=\"https://doi.org/10.1109/TNSE.2024.3481434\">https://doi.org/10.1109/TNSE.2024.3481434</a>","short":"Y. Zhang, J. Wang, G. Wen, J. Guan, S. Zhou, G. Chen, K. Chatterjee, M. Perc, IEEE Transactions on Network Science and Engineering 12 (2025) 4–12.","chicago":"Zhang, Yichao, Jiasheng Wang, Guanghui Wen, Jihong Guan, Shuigeng Zhou, Guanrong Chen, Krishnendu Chatterjee, and Matjaz Perc. “Limitation of Time Promotes Cooperation in Structured Collaboration Systems.” <i>IEEE Transactions on Network Science and Engineering</i>. IEEE, 2025. <a href=\"https://doi.org/10.1109/TNSE.2024.3481434\">https://doi.org/10.1109/TNSE.2024.3481434</a>.","mla":"Zhang, Yichao, et al. “Limitation of Time Promotes Cooperation in Structured Collaboration Systems.” <i>IEEE Transactions on Network Science and Engineering</i>, vol. 12, no. 1, IEEE, 2025, pp. 4–12, doi:<a href=\"https://doi.org/10.1109/TNSE.2024.3481434\">10.1109/TNSE.2024.3481434</a>."},"external_id":{"isi":["001385382200040"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","_id":"18529","OA_type":"closed access","year":"2025","doi":"10.1109/TNSE.2024.3481434","quality_controlled":"1","author":[{"first_name":"Yichao","last_name":"Zhang","full_name":"Zhang, Yichao"},{"full_name":"Wang, Jiasheng","last_name":"Wang","first_name":"Jiasheng"},{"first_name":"Guanghui","last_name":"Wen","full_name":"Wen, Guanghui"},{"full_name":"Guan, Jihong","last_name":"Guan","first_name":"Jihong"},{"first_name":"Shuigeng","full_name":"Zhou, Shuigeng","last_name":"Zhou"},{"first_name":"Guanrong","last_name":"Chen","full_name":"Chen, Guanrong"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"first_name":"Matjaz","last_name":"Perc","full_name":"Perc, Matjaz"}],"publication_status":"published","issue":"1","abstract":[{"lang":"eng","text":"Temporal networks are obtained from time-dependent interactions among individuals, whereas the interactions can be emails, phone calls, face-to-face meetings, or work collaboration. In this article, a temporal game framework is established, in which interactions among rational individuals are embedded into two-player games in a time-dependent manner. This allows studying the time-dependent complexity and variability of interactions, and the way they affect prosocial behaviors. Based on this simple mathematical model, it is found that the level of cooperation is promoted when the time of collaboration is equally limited for every individual. This observation is confirmed by a series of systematic human experiments on over 1,400 subjects, forming a foundation for comprehensively describing human temporal interactions in collaboration. The research results reveal an important incentive for human cooperation, leading to a better understanding of a fascinating aspect of human nature in society."}],"intvolume":"        12","fulldoi":"https://doi.org/10.1109/TNSE.2024.3481434","oa_version":"None","isi":1,"date_published":"2025-01-01T00:00:00Z","day":"01","title":"Limitation of time promotes cooperation in structured collaboration systems","date_updated":"2025-02-27T12:35:48Z","publisher":"IEEE","publication_identifier":{"eissn":["2327-4697"]},"scopus_import":"1","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"month":"01","type":"journal_article","article_type":"original","volume":12,"page":"4-12","date_created":"2024-11-10T23:02:00Z"},{"OA_place":"publisher","scopus_import":"1","file_date_updated":"2024-11-28T06:52:38Z","corr_author":"1","has_accepted_license":"1","publisher":"Springer Nature","publication_identifier":{"eissn":["1662-3592"],"issn":["1575-5460"]},"ec_funded":1,"month":"02","type":"journal_article","ddc":["514","510"],"acknowledgement":"M.L. acknowledge support by the Dioscuri program initiated by the Max Planck Society, jointly managed with the National Science Centre (Poland), and mutually funded by the Polish Ministry of Science and Higher Education and the German Federal Ministry of Education and Research. M.L. also acknowledges that this project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413. Research of M.M. is partially supported by the Polish National Science Center under Opus Grant No. 2019/35/B/ST1/00874. The work of K.M. was partially supported by the National Science Foundation under awards DMS-1839294 and HDR TRIPODS award CCF-1934924, DARPA contract HR0011-16-2-0033, National Institutes of Health award R01 GM126555, Air Force Office of Scientific Research under award numbers FA9550-23-1-0011, AWD00010853-MOD002 and MURI FA9550-23-1-0400. K.M. was also supported by a grant from the Simons Foundation. Open access funding provided by Institute of Science and Technology (IST Austria). ","article_type":"original","volume":24,"date_created":"2024-11-24T23:01:47Z","language":[{"iso":"eng"}],"arxiv":1,"department":[{"_id":"UlWa"}],"file":[{"file_size":1483668,"file_id":"18595","checksum":"73309a57cc798d696caa57b6aa1467d8","content_type":"application/pdf","relation":"main_file","file_name":"2025_predecomposition.pdf","creator":"mlipinsk","date_updated":"2024-11-28T06:52:38Z","success":1,"access_level":"open_access","date_created":"2024-11-28T06:52:38Z"}],"oa":1,"day":"01","date_updated":"2025-04-14T07:54:56Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Morse predecomposition of an invariant set","doi":"10.1007/s12346-024-01144-3","quality_controlled":"1","oa_version":"Published Version","fulldoi":"https://doi.org/10.1007/s12346-024-01144-3","date_published":"2025-02-01T00:00:00Z","project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"isi":1,"publication_status":"published","author":[{"orcid":"0000-0001-9789-9750","first_name":"Michał","full_name":"Lipiński, Michał","id":"dfffb474-4317-11ee-8f5c-fe3fc95a425e","last_name":"Lipiński"},{"full_name":"Mischaikow, Konstantin","last_name":"Mischaikow","first_name":"Konstantin"},{"first_name":"Marian","last_name":"Mrozek","full_name":"Mrozek, Marian"}],"issue":"1","intvolume":"        24","abstract":[{"text":"Motivated by the study of recurrent orbits and dynamics within a Morse set of a Morse decomposition we introduce the concept of Morse predecomposition of an isolated invariant set within the setting of both combinatorial and classical dynamical systems. While Morse decomposition summarizes solely the gradient part of a dynamical system, the developed generalization extends to the recurrent component as well. In particular, a chain recurrent set, which is indecomposable in terms of Morse decomposition, can be represented more finely in the Morse predecomposition framework. This generalization is achieved by forgoing the poset structure inherent to Morse decomposition and relaxing the notion of connection between Morse sets (elements of Morse decomposition) in favor of what we term ’links’. We prove that a Morse decomposition is a special case of Morse predecomposition indexed by a poset. Additionally, we show how a Morse predecomposition may be condensed back to retrieve a Morse decomposition.","lang":"eng"}],"citation":{"ama":"Lipiński M, Mischaikow K, Mrozek M. Morse predecomposition of an invariant set. <i>Qualitative Theory of Dynamical Systems</i>. 2025;24(1). doi:<a href=\"https://doi.org/10.1007/s12346-024-01144-3\">10.1007/s12346-024-01144-3</a>","short":"M. Lipiński, K. Mischaikow, M. Mrozek, Qualitative Theory of Dynamical Systems 24 (2025).","chicago":"Lipiński, Michał, Konstantin Mischaikow, and Marian Mrozek. “Morse Predecomposition of an Invariant Set.” <i>Qualitative Theory of Dynamical Systems</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s12346-024-01144-3\">https://doi.org/10.1007/s12346-024-01144-3</a>.","mla":"Lipiński, Michał, et al. “Morse Predecomposition of an Invariant Set.” <i>Qualitative Theory of Dynamical Systems</i>, vol. 24, no. 1, 5, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1007/s12346-024-01144-3\">10.1007/s12346-024-01144-3</a>.","ista":"Lipiński M, Mischaikow K, Mrozek M. 2025. Morse predecomposition of an invariant set. Qualitative Theory of Dynamical Systems. 24(1), 5.","ieee":"M. Lipiński, K. Mischaikow, and M. Mrozek, “Morse predecomposition of an invariant set,” <i>Qualitative Theory of Dynamical Systems</i>, vol. 24, no. 1. Springer Nature, 2025.","apa":"Lipiński, M., Mischaikow, K., &#38; Mrozek, M. (2025). Morse predecomposition of an invariant set. <i>Qualitative Theory of Dynamical Systems</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s12346-024-01144-3\">https://doi.org/10.1007/s12346-024-01144-3</a>"},"external_id":{"isi":["001356000500005"],"arxiv":["2312.08013"]},"article_processing_charge":"Yes (via OA deal)","publication":"Qualitative Theory of Dynamical Systems","article_number":"5","year":"2025","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","_id":"18580","OA_type":"hybrid"},{"_id":"18626","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"green","year":"2025","publication":"Advances in Mathematics","article_number":"110055","citation":{"mla":"Edelsbrunner, Herbert, et al. “Order-2 Delaunay Triangulations Optimize Angles.” <i>Advances in Mathematics</i>, vol. 461, 110055, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.aim.2024.110055\">10.1016/j.aim.2024.110055</a>.","chicago":"Edelsbrunner, Herbert, Alexey Garber, and Morteza Saghafian. “Order-2 Delaunay Triangulations Optimize Angles.” <i>Advances in Mathematics</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.aim.2024.110055\">https://doi.org/10.1016/j.aim.2024.110055</a>.","short":"H. Edelsbrunner, A. Garber, M. Saghafian, Advances in Mathematics 461 (2025).","ista":"Edelsbrunner H, Garber A, Saghafian M. 2025. Order-2 Delaunay triangulations optimize angles. Advances in Mathematics. 461, 110055.","apa":"Edelsbrunner, H., Garber, A., &#38; Saghafian, M. (2025). Order-2 Delaunay triangulations optimize angles. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2024.110055\">https://doi.org/10.1016/j.aim.2024.110055</a>","ieee":"H. Edelsbrunner, A. Garber, and M. Saghafian, “Order-2 Delaunay triangulations optimize angles,” <i>Advances in Mathematics</i>, vol. 461. Elsevier, 2025.","ama":"Edelsbrunner H, Garber A, Saghafian M. Order-2 Delaunay triangulations optimize angles. <i>Advances in Mathematics</i>. 2025;461. doi:<a href=\"https://doi.org/10.1016/j.aim.2024.110055\">10.1016/j.aim.2024.110055</a>"},"article_processing_charge":"No","external_id":{"arxiv":["2310.18238"],"isi":["001370682500001"]},"publication_status":"published","author":[{"orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"first_name":"Alexey","last_name":"Garber","full_name":"Garber, Alexey"},{"first_name":"Morteza","last_name":"Saghafian","id":"f86f7148-b140-11ec-9577-95435b8df824","full_name":"Saghafian, Morteza"}],"abstract":[{"text":"The local angle property of the (order-1) Delaunay triangulations of a generic set in R2\r\n asserts that the sum of two angles opposite a common edge is less than π. This paper extends this property to higher order and uses it to generalize two classic properties from order-1 to order-2: (1) among the complete level-2 hypertriangulations of a generic point set in R2, the order-2 Delaunay triangulation lexicographically maximizes the sorted angle vector; (2) among the maximal level-2 hypertriangulations of a generic point set in R2, the order-2 Delaunay triangulation is the only one that has the local angle property. We also use our method of establishing (2) to give a new short proof of the angle vector optimality for the (order-1) Delaunay triangulation. For order-1, both properties have been instrumental in numerous applications of Delaunay triangulations, and we expect that their generalization will make order-2 Delaunay triangulations more attractive to applications as well.","lang":"eng"}],"intvolume":"       461","isi":1,"fulldoi":"https://doi.org/10.1016/j.aim.2024.110055","date_published":"2025-02-01T00:00:00Z","project":[{"name":"Alpha Shape Theory Extended","grant_number":"788183","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science","grant_number":"Z00342"},{"name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"oa_version":"Preprint","quality_controlled":"1","doi":"10.1016/j.aim.2024.110055","title":"Order-2 Delaunay triangulations optimize angles","date_updated":"2025-04-15T07:16:53Z","day":"01","oa":1,"department":[{"_id":"HeEd"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2310.18238"}],"language":[{"iso":"eng"}],"arxiv":1,"type":"journal_article","month":"02","date_created":"2024-12-08T23:01:54Z","volume":461,"article_type":"original","acknowledgement":"Work by the first and third authors is partially supported by the European Research Council (ERC), grant no. 788183, by the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, Austrian Science Fund (FWF), grant no. I 02979-N35. Work by the second author is partially supported by the Alexander von Humboldt Foundation.","publisher":"Elsevier","ec_funded":1,"publication_identifier":{"eissn":["1090-2082"],"issn":["0001-8708"]},"corr_author":"1","OA_place":"repository","scopus_import":"1"},{"file_date_updated":"2025-01-13T10:34:42Z","scopus_import":"1","OA_place":"publisher","has_accepted_license":"1","publisher":"Wiley","publication_identifier":{"issn":["0025-584X"],"eissn":["1522-2616"]},"ec_funded":1,"month":"01","type":"journal_article","ddc":["510"],"article_type":"original","volume":298,"acknowledgement":"KTS is grateful to Christoph Thiele for valuable discussions and helpful references. LDS is grateful to Nathanaël Berestycki for valuable discussions on Gaussian Multiplicative Chaoses. The authors are grateful to an anonymous reviewer for suggestions which improved the presentation.\r\nThe authors gratefully acknowledge funding by the Deutsche Forschungsgemeinschaft through the project ‘Random Riemannian Geometry’ within the SPP 2265 ‘Random Geometric Systems.'\r\nLDS gratefully acknowledges financial support from the European Research Council (grant agreement No. 716117, awarded to J. Maas) and from the Austrian Science Fund (FWF). His research was funded by the Austrian Science Fund (FWF) project 10.55776/F65 and project 10.55776/ESP208.\r\nRH, EK, and KTS gratefully acknowledge funding by the Hausdorff Center for Mathematics (project ID 390685813), and through project B03 within the CRC 1060 (project ID 211504053). RH and KTS also gratefully acknowledges financial support from the European Research Council through the ERC AdG ‘RicciBounds’ (grant agreement 694405).\r\nOpen access funding enabled and organized by Projekt DEAL.","date_created":"2024-12-08T23:01:56Z","page":"244-281","arxiv":1,"language":[{"iso":"eng"}],"department":[{"_id":"JaMa"}],"file":[{"date_created":"2025-01-13T10:34:42Z","access_level":"open_access","success":1,"date_updated":"2025-01-13T10:34:42Z","creator":"dernst","file_name":"2025_MathNachrichten_DelloSchiavo.pdf","relation":"main_file","content_type":"application/pdf","checksum":"1dc50d156feb777c86d779fb1c9ac875","file_id":"18838","file_size":1734511}],"oa":1,"day":"01","date_updated":"2025-04-14T07:27:49Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Polyharmonic fields and Liouville quantum gravity measures on tori of arbitrary dimension: From discrete to continuous","doi":"10.1002/mana.202400169","quality_controlled":"1","isi":1,"fulldoi":"https://doi.org/10.1002/mana.202400169","project":[{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"},{"_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c","grant_number":"E208","name":"Configuration Spaces over Non-Smooth Spaces"}],"oa_version":"Published Version","date_published":"2025-01-01T00:00:00Z","issue":"1","publication_status":"published","author":[{"id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","full_name":"Dello Schiavo, Lorenzo","last_name":"Dello Schiavo","orcid":"0000-0002-9881-6870","first_name":"Lorenzo"},{"full_name":"Herry, Ronan","last_name":"Herry","first_name":"Ronan"},{"full_name":"Kopfer, Eva","last_name":"Kopfer","first_name":"Eva"},{"first_name":"Karl Theodor","full_name":"Sturm, Karl Theodor","last_name":"Sturm"}],"abstract":[{"text":"For an arbitrary dimension (Formula presented.), we study: the polyharmonic Gaussian field (Formula presented.) on the discrete torus (Formula presented.), that is the random field whose law on (Formula presented.) given by (Formula presented.) where (Formula presented.) is the Lebesgue measure and (Formula presented.) is the discrete Laplacian; the associated discrete Liouville quantum gravity (LQG) measure associated with it, that is, the random measure on (Formula presented.) (Formula presented.) where (Formula presented.) is a regularity parameter. As (Formula presented.), we prove convergence of the fields (Formula presented.) to the polyharmonic Gaussian field (Formula presented.) on the continuous torus (Formula presented.), as well as convergence of the random measures (Formula presented.) to the LQG measure (Formula presented.) on (Formula presented.), for all (Formula presented.). ","lang":"eng"}],"intvolume":"       298","citation":{"ieee":"L. Dello Schiavo, R. Herry, E. Kopfer, and K. T. Sturm, “Polyharmonic fields and Liouville quantum gravity measures on tori of arbitrary dimension: From discrete to continuous,” <i>Mathematische Nachrichten</i>, vol. 298, no. 1. Wiley, pp. 244–281, 2025.","ista":"Dello Schiavo L, Herry R, Kopfer E, Sturm KT. 2025. Polyharmonic fields and Liouville quantum gravity measures on tori of arbitrary dimension: From discrete to continuous. Mathematische Nachrichten. 298(1), 244–281.","apa":"Dello Schiavo, L., Herry, R., Kopfer, E., &#38; Sturm, K. T. (2025). Polyharmonic fields and Liouville quantum gravity measures on tori of arbitrary dimension: From discrete to continuous. <i>Mathematische Nachrichten</i>. Wiley. <a href=\"https://doi.org/10.1002/mana.202400169\">https://doi.org/10.1002/mana.202400169</a>","mla":"Dello Schiavo, Lorenzo, et al. “Polyharmonic Fields and Liouville Quantum Gravity Measures on Tori of Arbitrary Dimension: From Discrete to Continuous.” <i>Mathematische Nachrichten</i>, vol. 298, no. 1, Wiley, 2025, pp. 244–81, doi:<a href=\"https://doi.org/10.1002/mana.202400169\">10.1002/mana.202400169</a>.","chicago":"Dello Schiavo, Lorenzo, Ronan Herry, Eva Kopfer, and Karl Theodor Sturm. “Polyharmonic Fields and Liouville Quantum Gravity Measures on Tori of Arbitrary Dimension: From Discrete to Continuous.” <i>Mathematische Nachrichten</i>. Wiley, 2025. <a href=\"https://doi.org/10.1002/mana.202400169\">https://doi.org/10.1002/mana.202400169</a>.","short":"L. Dello Schiavo, R. Herry, E. Kopfer, K.T. Sturm, Mathematische Nachrichten 298 (2025) 244–281.","ama":"Dello Schiavo L, Herry R, Kopfer E, Sturm KT. Polyharmonic fields and Liouville quantum gravity measures on tori of arbitrary dimension: From discrete to continuous. <i>Mathematische Nachrichten</i>. 2025;298(1):244-281. doi:<a href=\"https://doi.org/10.1002/mana.202400169\">10.1002/mana.202400169</a>"},"external_id":{"arxiv":["2302.02963"],"isi":["001366948500001"]},"article_processing_charge":"Yes (via OA deal)","publication":"Mathematische Nachrichten","year":"2025","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"18632","OA_type":"hybrid"},{"doi":"10.15479/AT:ISTA:18697","abstract":[{"lang":"eng","text":"The information-processing capability of the brain’s cellular network depends on the physical wiring pattern between neurons and their molecular and functional characteristics. Mapping neurons and resolving their individual synaptic connections can be achieved by volumetric imaging at nanoscale resolution with dense cellular labelling. Light microscopy is uniquely positioned to visualize specific molecules but dense, synapse-level circuit reconstruction by light microscopy has been out of reach due to limitations in resolution, contrast, and volumetric imaging capability. Here we developed light-microscopy based connectomics (LICONN). We integrated specifically engineered hydrogel embedding and expansion with comprehensive deep-learning based segmentation and analysis of connectivity, thus directly incorporating molecular information in synapse-level brain tissue reconstructions. LICONN will allow synapse-level brain tissue phenotyping in biological experiments in a readily adoptable manner."}],"author":[{"first_name":"Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Julia","last_name":"Lyudchik","full_name":"Lyudchik, Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Caroline","last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline"}],"fulldoi":"https://doi.org/10.15479/AT:ISTA:18697","oa_version":"Published Version","date_published":"2025-03-03T00:00:00Z","contributor":[{"first_name":"Mojtaba","contributor_type":"researcher","orcid":"0000-0002-7667-6854","last_name":"Tavakoli","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Julia","contributor_type":"researcher","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik"},{"contributor_type":"researcher","first_name":"Michal","last_name":"Januszewski"},{"last_name":"Vistunou","id":"7e146587-8972-11ed-ae7b-d7a32ea86a81","first_name":"Vitali","contributor_type":"researcher"},{"contributor_type":"researcher","first_name":"Nathalie","id":"40E7F008-F248-11E8-B48F-1D18A9856A87","last_name":"Agudelo Duenas"},{"first_name":"Jakob","contributor_type":"researcher","last_name":"Vorlaufer","id":"937696FA-C996-11E9-8C7C-CF13E6697425"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","orcid":"0000-0003-1216-9105","first_name":"Christoph M","contributor_type":"researcher"},{"contributor_type":"researcher","first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kreuzinger"},{"contributor_type":"researcher","first_name":"Bárbara","id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87","last_name":"Oliveira"},{"contributor_type":"researcher","first_name":"Alban","last_name":"Cenameri"},{"first_name":"Gaia","contributor_type":"researcher","orcid":"0000-0002-7673-7178","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jain","contributor_type":"researcher","first_name":"Viren"},{"last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Johann G","orcid":"0000-0001-8559-3973"}],"article_processing_charge":"No","citation":{"ama":"Danzl JG, Lyudchik J, Kreuzinger C. Light-microscopy based connectomic reconstruction of mammalian brain tissue. 2025. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18697\">10.15479/AT:ISTA:18697</a>","short":"J.G. Danzl, J. Lyudchik, C. Kreuzinger, (2025).","mla":"Danzl, Johann G., et al. <i>Light-Microscopy Based Connectomic Reconstruction of Mammalian Brain Tissue</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18697\">10.15479/AT:ISTA:18697</a>.","chicago":"Danzl, Johann G, Julia Lyudchik, and Caroline Kreuzinger. “Light-Microscopy Based Connectomic Reconstruction of Mammalian Brain Tissue.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT:ISTA:18697\">https://doi.org/10.15479/AT:ISTA:18697</a>.","apa":"Danzl, J. G., Lyudchik, J., &#38; Kreuzinger, C. (2025). Light-microscopy based connectomic reconstruction of mammalian brain tissue. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:18697\">https://doi.org/10.15479/AT:ISTA:18697</a>","ieee":"J. G. Danzl, J. Lyudchik, and C. Kreuzinger, “Light-microscopy based connectomic reconstruction of mammalian brain tissue.” Institute of Science and Technology Austria, 2025.","ista":"Danzl JG, Lyudchik J, Kreuzinger C. 2025. 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datasets of large size (>10GB) and datasets in zarr/n5/ims/npz format are provided via this external link.","url":"https://pub.ista.ac.at/group_danzl/data/LICONN/","relation":"research_data"}],"record":[{"status":"public","relation":"used_in_publication","id":"19704"}]},"day":"03","oa":1,"title":"Light-microscopy based connectomic reconstruction of mammalian brain tissue","tmp":{"short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png"},"date_updated":"2026-04-28T13:33:34Z"},{"doi":"10.15479/AT:ISTA:17344","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","file_date_updated":"2025-01-02T12:30:39Z","acknowledged_ssus":[{"_id":"ScienComp"}],"corr_author":"1","abstract":[{"lang":"eng","text":"This file contains the code associated with the manuscript 'Effect of assortative 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"}],"file":[{"checksum":"9c5f91876014706990a0728c3675cd2a","file_size":326835,"file_id":"18722","relation":"main_file","content_type":"application/zip","creator":"psurendr","file_name":"Codes.zip","date_created":"2025-01-02T12:30:27Z","access_level":"open_access","date_updated":"2025-01-02T12:30:27Z","success":1},{"content_type":"text/plain","relation":"main_file","file_size":620,"file_id":"18723","checksum":"47fe98b7cc526e634e42de58f5eae288","date_updated":"2025-01-02T12:30:39Z","success":1,"access_level":"open_access","date_created":"2025-01-02T12:30:39Z","file_name":"ReadMe.txt","creator":"psurendr"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"author":[{"orcid":"0000-0001-6395-386X","first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","full_name":"Surendranadh, Parvathy","last_name":"Surendranadh"},{"first_name":"Himani","full_name":"Sachdeva, Himani","last_name":"Sachdeva"}],"date_created":"2025-01-01T15:28:27Z","fulldoi":"https://doi.org/10.15479/AT:ISTA:17344","date_published":"2025-01-07T00:00:00Z","oa_version":"Published Version","ddc":["576"],"month":"01","type":"research_data","related_material":{"record":[{"id":"19876","relation":"used_in_publication","status":"public"}]},"day":"07","article_processing_charge":"No","citation":{"ama":"Surendranadh P, Sachdeva H. Mathematica notebook and Fortran code for “Effect of assortative mating and sexual selection on polygenic barriers to gene flow.” 2025. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17344\">10.15479/AT:ISTA:17344</a>","mla":"Surendranadh, Parvathy, and Himani Sachdeva. <i>Mathematica Notebook and Fortran Code for “Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.”</i> Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17344\">10.15479/AT:ISTA:17344</a>.","chicago":"Surendranadh, Parvathy, and Himani Sachdeva. “Mathematica Notebook and Fortran Code for ‘Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.’” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT:ISTA:17344\">https://doi.org/10.15479/AT:ISTA:17344</a>.","short":"P. Surendranadh, H. Sachdeva, (2025).","ista":"Surendranadh P, Sachdeva H. 2025. Mathematica notebook and Fortran code for ‘Effect of assortative mating and sexual selection on polygenic barriers to gene flow’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:17344\">10.15479/AT:ISTA:17344</a>.","ieee":"P. Surendranadh and H. Sachdeva, “Mathematica notebook and Fortran code for ‘Effect of assortative mating and sexual selection on polygenic barriers to gene flow.’” Institute of Science and Technology Austria, 2025.","apa":"Surendranadh, P., &#38; Sachdeva, H. (2025). Mathematica notebook and Fortran code for “Effect of assortative mating and sexual selection on polygenic barriers to gene flow.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:17344\">https://doi.org/10.15479/AT:ISTA:17344</a>"},"oa":1,"status":"public","user_id":"9947682f-b9fa-11ee-9c4a-b3ffaafe6614","title":"Mathematica notebook and Fortran code for 'Effect of assortative mating and sexual selection on polygenic barriers to gene flow'","_id":"18712","year":"2025","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2025-12-30T08:44:12Z"},{"quality_controlled":"1","doi":"10.1007/978-1-0716-4310-5_7","intvolume":"      2886","abstract":[{"text":"Mosaic Analysis with Double Markers (MADM) represents a mouse genetic approach coupling differential fluorescent labeling to genetic manipulations in dividing cells and their lineages. MADM uniquely enables the generation and visualization of individual control or homozygous mutant cells in a heterozygous genetic environment. Among its diverse applications, MADM has been used to dissect cell-autonomous gene functions important for cortical development and neural development in general. The high cellular resolution offered by MADM also permits the analysis of transcriptomic changes of individual cells upon genetic manipulations. In this chapter, we describe an experimental protocol combining the generation and isolation of MADM-labeled cells with downstream single-cell RNA-sequencing technologies to probe cell-type specific phenotypes due to genetic mutations at single-cell resolution.","lang":"eng"}],"publication_status":"published","author":[{"last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87","full_name":"Cheung, Giselle T","first_name":"Giselle T","orcid":"0000-0001-8457-2572"},{"orcid":"0000-0002-7462-0048","first_name":"Florian","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler"},{"orcid":"0000-0003-2279-1061","first_name":"Simon","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer"}],"fulldoi":"https://doi.org/10.1007/978-1-0716-4310-5_7","oa_version":"None","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"date_published":"2025-01-03T00:00:00Z","publication":"Lineage Tracing","article_processing_charge":"No","external_id":{"pmid":["39745639"]},"series_title":"MIMB","citation":{"mla":"Cheung, Giselle T., et al. “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).” <i>Lineage Tracing</i>, edited by Jorge Garcia-Marques and Tzumin Lee, vol. 2886, Springer Nature, 2025, pp. 139–51, doi:<a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">10.1007/978-1-0716-4310-5_7</a>.","chicago":"Cheung, Giselle T, Florian Pauler, and Simon Hippenmeyer. “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).” In <i>Lineage Tracing</i>, edited by Jorge Garcia-Marques and Tzumin Lee, 2886:139–51. MIMB. New York, NY: Springer Nature, 2025. <a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">https://doi.org/10.1007/978-1-0716-4310-5_7</a>.","short":"G.T. Cheung, F. Pauler, S. Hippenmeyer, in:, J. Garcia-Marques, T. Lee (Eds.), Lineage Tracing, Springer Nature, New York, NY, 2025, pp. 139–151.","ieee":"G. T. Cheung, F. Pauler, and S. Hippenmeyer, “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM),” in <i>Lineage Tracing</i>, vol. 2886, J. Garcia-Marques and T. Lee, Eds. New York, NY: Springer Nature, 2025, pp. 139–151.","apa":"Cheung, G. T., Pauler, F., &#38; Hippenmeyer, S. (2025). Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In J. Garcia-Marques &#38; T. Lee (Eds.), <i>Lineage Tracing</i> (Vol. 2886, pp. 139–151). New York, NY: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">https://doi.org/10.1007/978-1-0716-4310-5_7</a>","ista":"Cheung GT, Pauler F, Hippenmeyer S. 2025.Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In: Lineage Tracing. Methods in Molecular Biology, vol. 2886, 139–151.","ama":"Cheung GT, Pauler F, Hippenmeyer S. Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In: Garcia-Marques J, Lee T, eds. <i>Lineage Tracing</i>. Vol 2886. MIMB. New York, NY: Springer Nature; 2025:139-151. doi:<a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">10.1007/978-1-0716-4310-5_7</a>"},"OA_type":"closed access","_id":"18765","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2025","ec_funded":1,"publication_identifier":{"eissn":["1940-6029"],"issn":["1064-3745"],"eisbn":["9781071643105"],"isbn":["9781071643099"]},"publisher":"Springer Nature","alternative_title":["Methods in Molecular Biology"],"acknowledged_ssus":[{"_id":"Bio"}],"corr_author":"1","scopus_import":"1","department":[{"_id":"SiHi"}],"language":[{"iso":"eng"}],"page":"139-151","pmid":1,"date_created":"2025-01-07T08:36:47Z","volume":2886,"acknowledgement":"We thank all Hippenmeyer lab members for support and discussions. Experimental steps described were optimized with support provided by the Imaging & Optics Facility (IOF) and Preclinical Facility (PCF) at ISTA, Vienna BioCenter Core Facilities (VBCF), and Christoph Bock lab at Center for Molecular Medicine (CeMM). G.C. received funding from European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional funds: The Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H.","type":"book_chapter","month":"01","editor":[{"full_name":"Garcia-Marques, Jorge","last_name":"Garcia-Marques","first_name":"Jorge"},{"last_name":"Lee","full_name":"Lee, Tzumin","first_name":"Tzumin"}],"day":"03","title":"Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM)","place":"New York, NY","date_updated":"2025-04-14T07:43:46Z"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"APC_amount":"12348 EUR","date_updated":"2025-11-20T10:28:36Z","title":"Mechanism of mammalian transcriptional repression by noncoding RNA","oa":1,"related_material":{"record":[{"relation":"earlier_version","id":"14644","status":"public"}]},"day":"01","page":"607-612","date_created":"2025-01-08T11:20:20Z","pmid":1,"volume":32,"acknowledgement":"We thank the members of the Bernecky laboratory for helpful discussions and A. Hlavata for providing Pol II for use in the fluorescence anisotropy binding assay. We thank V.-V. Hodirnau for SerialEM data collection and support with EPU data collection. We thank D. Slade (Max Perutz Laboratories and Medical University of Vienna, Vienna, Austria) for the wild-type TFIIF expression plasmid. We thank N. Thompson and R. Burgess (McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, USA) for the 8WG16 hybridoma cell line. We thank C. Plaschka and M. Loose for critical reading of the manuscript. This work was supported by Austrian Science Fund (FWF) grant no. P34185 (DOI 10.55776/P34185) (C.B.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. This research was further supported by the Scientific Service Units of ISTA through resources provided by the Laboratory Support Facility, Electron Microscopy Facility, Scientific Computing and the Preclinical Facility.","article_type":"original","month":"04","ddc":["570"],"type":"journal_article","file":[{"relation":"main_file","content_type":"application/pdf","checksum":"2919b30b271f395888e880076a680d73","file_size":9306639,"file_id":"19573","access_level":"open_access","date_created":"2025-04-16T08:17:27Z","success":1,"date_updated":"2025-04-16T08:17:27Z","creator":"dernst","file_name":"2025_NatureStrucMolBiol_Tluckova.pdf"}],"department":[{"_id":"CaBe"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","corr_author":"1","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"},{"_id":"PreCl"}],"OA_place":"publisher","scopus_import":"1","file_date_updated":"2025-04-16T08:17:27Z","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"publisher":"Springer Nature","year":"2025","OA_type":"hybrid","_id":"18778","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["001390268000001"],"pmid":["39762629"]},"citation":{"apa":"Tluckova, K., Kaczmarek, B. M., Testa Salmazo, A. P., &#38; Bernecky, C. (2025). Mechanism of mammalian transcriptional repression by noncoding RNA. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-024-01448-7\">https://doi.org/10.1038/s41594-024-01448-7</a>","ieee":"K. Tluckova, B. M. Kaczmarek, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian transcriptional repression by noncoding RNA,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 32. Springer Nature, pp. 607–612, 2025.","ista":"Tluckova K, Kaczmarek BM, Testa Salmazo AP, Bernecky C. 2025. Mechanism of mammalian transcriptional repression by noncoding RNA. Nature Structural &#38; Molecular Biology. 32, 607–612.","short":"K. Tluckova, B.M. Kaczmarek, A.P. Testa Salmazo, C. Bernecky, Nature Structural &#38; Molecular Biology 32 (2025) 607–612.","mla":"Tluckova, Katarina, et al. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 32, Springer Nature, 2025, pp. 607–12, doi:<a href=\"https://doi.org/10.1038/s41594-024-01448-7\">10.1038/s41594-024-01448-7</a>.","chicago":"Tluckova, Katarina, Beata M Kaczmarek, Anita P Testa Salmazo, and Carrie Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41594-024-01448-7\">https://doi.org/10.1038/s41594-024-01448-7</a>.","ama":"Tluckova K, Kaczmarek BM, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. <i>Nature Structural &#38; Molecular Biology</i>. 2025;32:607-612. doi:<a href=\"https://doi.org/10.1038/s41594-024-01448-7\">10.1038/s41594-024-01448-7</a>"},"publication":"Nature Structural & Molecular Biology","fulldoi":"https://doi.org/10.1038/s41594-024-01448-7","oa_version":"Published Version","isi":1,"project":[{"name":"Regulation of mammalian transcription by noncoding RNA","grant_number":"P34185","_id":"c08a6700-5a5b-11eb-8a69-82a722b2bc30"}],"date_published":"2025-04-01T00:00:00Z","intvolume":"        32","abstract":[{"text":"Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryogenic-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how distinct domains of the general transcription factor TFIIF control repressive activity. Together, we reveal how a noncoding RNA can regulate mammalian gene expression.","lang":"eng"}],"publication_status":"published","author":[{"first_name":"Katarina","full_name":"Tluckova, Katarina","id":"4AC7D980-F248-11E8-B48F-1D18A9856A87","last_name":"Tluckova"},{"full_name":"Kaczmarek, Beata M","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87","last_name":"Kaczmarek","first_name":"Beata M"},{"last_name":"Testa Salmazo","full_name":"Testa Salmazo, Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","first_name":"Anita P"},{"last_name":"Bernecky","full_name":"Bernecky, Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","orcid":"0000-0003-0893-7036"}],"quality_controlled":"1","doi":"10.1038/s41594-024-01448-7"},{"department":[{"_id":"MiLe"}],"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2408.10052","open_access":"1"}],"language":[{"iso":"eng"}],"arxiv":1,"month":"01","type":"journal_article","date_created":"2025-01-12T23:04:00Z","article_type":"original","volume":111,"acknowledgement":"We thank J. Cremon and J. Bjerlin for earlier contributions to the configuration-interaction calculations used in this work (see Refs. [49,50]). F.B. and S.M.R. acknowledge helpful discussions with Carl Heintze, Sandra Brandstetter, and Lila Chergui. We further want to thank Lila Chergui for helpful comments on the paper. This research was financially supported by the Knut and Alice Wallenberg Foundation (Grant No. KAW 2018.0217) and the Swedish Research Council (Grant No. 2022-03654 VR).","publisher":"American Physical Society","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"OA_place":"repository","scopus_import":"1","title":"Comparison of renormalized interactions using one-dimensional few-body systems as a testbed","date_updated":"2025-02-27T12:41:58Z","day":"03","oa":1,"publication_status":"published","author":[{"first_name":"Fabian","last_name":"Brauneis","full_name":"Brauneis, Fabian"},{"full_name":"Hammer, Hans Werner","last_name":"Hammer","first_name":"Hans Werner"},{"first_name":"Stephanie M.","full_name":"Reimann, Stephanie M.","last_name":"Reimann"},{"first_name":"Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem"}],"issue":"1","intvolume":"       111","abstract":[{"lang":"eng","text":"Even though the one-dimensional contact interaction requires no regularization, renormalization methods have been shown to improve the convergence of numerical calculations considerably. In this work, we compare and contrast these methods: “the running coupling constant” where the two-body ground-state energy is used as a renormalization condition, and two effective interaction approaches that include information about the ground as well as excited states. In particular, we calculate the energies and densities of few-fermion systems in a harmonic oscillator with the configuration-interaction method and compare the results based upon renormalized and bare interactions. We find that the use of the running coupling constant instead of the bare interaction improves convergence significantly. A comparison with an effective interaction, which is designed to reproduce the relative part of the energy spectrum of two particles, showed a similar improvement. The effective interaction provides an additional improvement if the center-of-mass excitations are included in the construction. Finally, we discuss the transformation of observables alongside the renormalization of the potential, and demonstrate that this might be an essential ingredient for accurate numerical calculations."}],"isi":1,"fulldoi":"https://doi.org/10.1103/PhysRevA.111.013303","date_published":"2025-01-03T00:00:00Z","oa_version":"Preprint","quality_controlled":"1","doi":"10.1103/PhysRevA.111.013303","_id":"18821","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"green","year":"2025","publication":"Physical Review A","article_number":"013303","citation":{"chicago":"Brauneis, Fabian, Hans Werner Hammer, Stephanie M. Reimann, and Artem Volosniev. “Comparison of Renormalized Interactions Using One-Dimensional Few-Body Systems as a Testbed.” <i>Physical Review A</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/PhysRevA.111.013303\">https://doi.org/10.1103/PhysRevA.111.013303</a>.","mla":"Brauneis, Fabian, et al. “Comparison of Renormalized Interactions Using One-Dimensional Few-Body Systems as a Testbed.” <i>Physical Review A</i>, vol. 111, no. 1, 013303, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/PhysRevA.111.013303\">10.1103/PhysRevA.111.013303</a>.","short":"F. Brauneis, H.W. Hammer, S.M. Reimann, A. Volosniev, Physical Review A 111 (2025).","ieee":"F. Brauneis, H. W. Hammer, S. M. Reimann, and A. Volosniev, “Comparison of renormalized interactions using one-dimensional few-body systems as a testbed,” <i>Physical Review A</i>, vol. 111, no. 1. American Physical Society, 2025.","ista":"Brauneis F, Hammer HW, Reimann SM, Volosniev A. 2025. Comparison of renormalized interactions using one-dimensional few-body systems as a testbed. Physical Review A. 111(1), 013303.","apa":"Brauneis, F., Hammer, H. W., Reimann, S. M., &#38; Volosniev, A. (2025). Comparison of renormalized interactions using one-dimensional few-body systems as a testbed. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.111.013303\">https://doi.org/10.1103/PhysRevA.111.013303</a>","ama":"Brauneis F, Hammer HW, Reimann SM, Volosniev A. Comparison of renormalized interactions using one-dimensional few-body systems as a testbed. <i>Physical Review A</i>. 2025;111(1). doi:<a href=\"https://doi.org/10.1103/PhysRevA.111.013303\">10.1103/PhysRevA.111.013303</a>"},"article_processing_charge":"No","external_id":{"isi":["001398791400004"],"arxiv":["2408.10052"]}},{"publication_status":"published","issue":"1","author":[{"last_name":"Cao","full_name":"Cao, Dechang","first_name":"Dechang"},{"id":"26bd38d3-c59a-11ee-a1af-d7a988cafcc5","full_name":"De Jaeger-Braet, Joke G","last_name":"De Jaeger-Braet","first_name":"Joke G"}],"intvolume":"       197","isi":1,"fulldoi":"https://doi.org/10.1093/plphys/kiae651","date_published":"2025-01-01T00:00:00Z","oa_version":"Published Version","quality_controlled":"1","doi":"10.1093/plphys/kiae651","_id":"18823","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"hybrid","year":"2025","publication":"Plant Physiology","article_number":"kiae651","citation":{"chicago":"Cao, Dechang, and Joke G De Jaeger-Braet. “Memory of Maternal Temperatures: DNA Methylation Alterations across Generations.” <i>Plant Physiology</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/plphys/kiae651\">https://doi.org/10.1093/plphys/kiae651</a>.","mla":"Cao, Dechang, and Joke G. De Jaeger-Braet. “Memory of Maternal Temperatures: DNA Methylation Alterations across Generations.” <i>Plant Physiology</i>, vol. 197, no. 1, kiae651, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/plphys/kiae651\">10.1093/plphys/kiae651</a>.","short":"D. Cao, J.G. De Jaeger-Braet, Plant Physiology 197 (2025).","apa":"Cao, D., &#38; De Jaeger-Braet, J. G. (2025). Memory of maternal temperatures: DNA methylation alterations across generations. <i>Plant Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plphys/kiae651\">https://doi.org/10.1093/plphys/kiae651</a>","ista":"Cao D, De Jaeger-Braet JG. 2025. Memory of maternal temperatures: DNA methylation alterations across generations. Plant Physiology. 197(1), kiae651.","ieee":"D. Cao and J. G. De Jaeger-Braet, “Memory of maternal temperatures: DNA methylation alterations across generations,” <i>Plant Physiology</i>, vol. 197, no. 1. Oxford University Press, 2025.","ama":"Cao D, De Jaeger-Braet JG. Memory of maternal temperatures: DNA methylation alterations across generations. <i>Plant Physiology</i>. 2025;197(1). doi:<a href=\"https://doi.org/10.1093/plphys/kiae651\">10.1093/plphys/kiae651</a>"},"article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["001382979900001"],"pmid":["39691053"]},"department":[{"_id":"XiFe"}],"language":[{"iso":"eng"}],"file":[{"file_name":"2025_PlantPhysiology_Cao.pdf","creator":"dernst","success":1,"date_updated":"2025-07-15T08:17:25Z","date_created":"2025-07-15T08:17:25Z","access_level":"open_access","file_id":"20023","file_size":1214018,"checksum":"a9b2a12d7bc6174f27e28413e9c77a9c","content_type":"application/pdf","relation":"main_file"}],"month":"01","type":"journal_article","ddc":["580"],"pmid":1,"date_created":"2025-01-12T23:04:02Z","article_type":"original","volume":197,"publisher":"Oxford University Press","publication_identifier":{"eissn":["1532-2548"]},"corr_author":"1","OA_place":"publisher","scopus_import":"1","file_date_updated":"2025-07-15T08:17:25Z","has_accepted_license":"1","title":"Memory of maternal temperatures: DNA methylation alterations across generations","date_updated":"2025-07-15T08:18:19Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","oa":1},{"status":"public","title":"Research Data for the publication \"Super-resolution expansion microscopy in plant roots\"","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","_id":"18837","year":"2025","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png"},"date_updated":"2026-06-10T08:30:20Z","related_material":{"record":[{"status":"public","id":"19003","relation":"used_in_publication"}]},"contributor":[{"orcid":"0000-0003-1286-7368","first_name":"Michelle C","contributor_type":"researcher","id":"35A03822-F248-11E8-B48F-1D18A9856A87","last_name":"Gallei"},{"id":"45812BD4-F248-11E8-B48F-1D18A9856A87","last_name":"Truckenbrodt","first_name":"Sven M","contributor_type":"researcher"},{"last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Caroline"},{"contributor_type":"researcher","first_name":"Syamala","last_name":"Inumella","id":"F8660870-D756-11E9-98C5-34DFE5697425"},{"first_name":"Vitali","contributor_type":"researcher","id":"7e146587-8972-11ed-ae7b-d7a32ea86a81","last_name":"Vistunou"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","orcid":"0000-0003-1216-9105","first_name":"Christoph M","contributor_type":"researcher"},{"last_name":"Tavakoli","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Mojtaba","orcid":"0000-0002-7667-6854"},{"first_name":"Nathalie","contributor_type":"researcher","id":"40E7F008-F248-11E8-B48F-1D18A9856A87","last_name":"Agudelo Duenas"},{"id":"937696FA-C996-11E9-8C7C-CF13E6697425","last_name":"Vorlaufer","contributor_type":"researcher","first_name":"Jakob"},{"contributor_type":"researcher","first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","last_name":"Jahr"},{"first_name":"Marek","contributor_type":"researcher","last_name":"Randuch","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae"},{"last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","contributor_type":"researcher","orcid":"0000-0002-2739-8843"},{"first_name":"Eva","contributor_type":"researcher","orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","contributor_type":"researcher","first_name":"Jiří"},{"orcid":"0000-0001-8559-3973","first_name":"Johann G","contributor_type":"researcher","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl"}],"article_processing_charge":"No","oa":1,"citation":{"ieee":"J. G. Danzl and C. Kreuzinger, “Research Data for the publication ‘Super-resolution expansion microscopy in plant roots.’” Institute of Science and Technology Austria, 2025.","apa":"Danzl, J. G., &#38; Kreuzinger, C. (2025). Research Data for the publication “Super-resolution expansion microscopy in plant roots.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:18837\">https://doi.org/10.15479/AT:ISTA:18837</a>","ista":"Danzl JG, Kreuzinger C. 2025. Research Data for the publication ‘Super-resolution expansion microscopy in plant roots’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:18837\">10.15479/AT:ISTA:18837</a>.","chicago":"Danzl, Johann G, and Caroline Kreuzinger. “Research Data for the Publication ‘Super-Resolution Expansion Microscopy in Plant Roots.’” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT:ISTA:18837\">https://doi.org/10.15479/AT:ISTA:18837</a>.","mla":"Danzl, Johann G., and Caroline Kreuzinger. <i>Research Data for the Publication “Super-Resolution Expansion Microscopy in Plant Roots.”</i> Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18837\">10.15479/AT:ISTA:18837</a>.","short":"J.G. Danzl, C. Kreuzinger, (2025).","ama":"Danzl JG, Kreuzinger C. Research Data for the publication “Super-resolution expansion microscopy in plant roots.” 2025. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18837\">10.15479/AT:ISTA:18837</a>"},"abstract":[{"text":"Super-resolution methods provide far better spatial resolution than the optical diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless, they have yet to attain widespread use in plants, largely due to plants’ challenging optical properties. Expansion microscopy improves effective resolution by isotropically increasing the physical distances between sample structures while preserving relative spatial arrangements and clearing the sample. However, its application to plants has been hindered by the rigid, mechanically cohesive structure of plant tissues. Here, we report on whole-mount expansion microscopy of thale cress (Arabidopsis thaliana) root tissues (PlantEx), achieving a four-fold resolution increase over conventional microscopy. Our results highlight the microtubule cytoskeleton organization and interaction between molecularly defined cellular constituents. Combining PlantEx with stimulated emission depletion (STED) microscopy, we increase nanoscale resolution and visualize the complex organization of subcellular organelles from intact tissues by example of the densely packed COPI-coated vesicles associated with the Golgi apparatus and put these into a cellular structural context. Our results show that expansion microscopy can be applied to increase effective imaging resolution in Arabidopsis root specimens.","lang":"eng"}],"file":[{"creator":"ckreuzin","file_name":"Fig 1D+2D PlantEx.tif","date_created":"2025-03-07T10:09:15Z","access_level":"open_access","date_updated":"2025-03-07T10:09:15Z","success":1,"checksum":"a522d476ca1106163abb403ee156f6d0","file_size":588707932,"file_id":"19312","relation":"main_file","content_type":"image/tiff"},{"relation":"main_file","content_type":"image/tiff","checksum":"2d0e8279e85821de946fa8dbc4ed8134","file_size":786998434,"file_id":"19313","date_created":"2025-03-07T10:29:22Z","access_level":"open_access","date_updated":"2025-03-07T10:29:22Z","success":1,"creator":"ckreuzin","file_name":"Fig 1D+2D 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G","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl"},{"first_name":"Caroline","last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline"}],"date_created":"2025-01-13T09:51:29Z","date_published":"2025-04-01T00:00:00Z","fulldoi":"https://doi.org/10.15479/AT:ISTA:18837","oa_version":"Published Version","type":"research_data","month":"04","doi":"10.15479/AT:ISTA:18837","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","file_date_updated":"2025-03-07T11:09:13Z","corr_author":"1"},{"oa":1,"day":"07","date_updated":"2025-07-03T11:58:22Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"DNA targeting by compact Cas9d and its resurrected ancestor","DOAJ_listed":"1","OA_place":"publisher","scopus_import":"1","file_date_updated":"2025-01-22T14:35:22Z","has_accepted_license":"1","publisher":"Springer Nature","publication_identifier":{"eissn":["2041-1723"]},"month":"01","type":"journal_article","ddc":["570"],"volume":16,"acknowledgement":"We would like to thank M. Ocampo Camacho and M.F. Canedo Ocampo for assistance with the figures. We thank M. Hooper for assistance developing the GFP assay and operating the CE machine for in vitro cleavage analysis. We thank E. Schwartz and A. Brilot for expert cryo-EM support in the Sauer Structural Biology Laboratory at UT Austin. This work was funded, in part, by a sponsored research agreement with Metagenomi, Inc. (to D.W.T), a Welch Foundation Research Grant F-1938 (to D.W.T), and the Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation Medical Research Grant (to D.W.T), and a grant from the National Institute of Allergy and Infectious Diseases (NIAID 1R01AI110577 to K.A.J.).","article_type":"original","pmid":1,"date_created":"2025-01-19T23:01:50Z","language":[{"iso":"eng"}],"department":[{"_id":"JaBr"}],"file":[{"date_created":"2025-01-22T14:35:22Z","access_level":"open_access","success":1,"date_updated":"2025-01-22T14:35:22Z","creator":"dernst","file_name":"2025_NatureComm_Ocampo.pdf","relation":"main_file","content_type":"application/pdf","checksum":"885e96690620790d5c9f188a1587b4cd","file_id":"18869","file_size":5450660}],"citation":{"chicago":"Ocampo, Rodrigo Fregoso, Jack Peter Kelly Bravo, Tyler L. Dangerfield, Isabel Nocedal, Samatar A. Jirde, Lisa M. Alexander, Nicole C. Thomas, et al. “DNA Targeting by Compact Cas9d and Its Resurrected Ancestor.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-024-55573-4\">https://doi.org/10.1038/s41467-024-55573-4</a>.","mla":"Ocampo, Rodrigo Fregoso, et al. “DNA Targeting by Compact Cas9d and Its Resurrected Ancestor.” <i>Nature Communications</i>, vol. 16, 457, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-024-55573-4\">10.1038/s41467-024-55573-4</a>.","short":"R.F. Ocampo, J.P.K. Bravo, T.L. Dangerfield, I. Nocedal, S.A. Jirde, L.M. Alexander, N.C. Thomas, A. Das, S. Nielson, K.A. Johnson, C.T. Brown, C.N. Butterfield, D.S.A. Goltsman, D.W. Taylor, Nature Communications 16 (2025).","ieee":"R. F. Ocampo <i>et al.</i>, “DNA targeting by compact Cas9d and its resurrected ancestor,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","apa":"Ocampo, R. F., Bravo, J. P. K., Dangerfield, T. L., Nocedal, I., Jirde, S. A., Alexander, L. M., … Taylor, D. W. (2025). DNA targeting by compact Cas9d and its resurrected ancestor. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-55573-4\">https://doi.org/10.1038/s41467-024-55573-4</a>","ista":"Ocampo RF, Bravo JPK, Dangerfield TL, Nocedal I, Jirde SA, Alexander LM, Thomas NC, Das A, Nielson S, Johnson KA, Brown CT, Butterfield CN, Goltsman DSA, Taylor DW. 2025. DNA targeting by compact Cas9d and its resurrected ancestor. Nature Communications. 16, 457.","ama":"Ocampo RF, Bravo JPK, Dangerfield TL, et al. DNA targeting by compact Cas9d and its resurrected ancestor. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-024-55573-4\">10.1038/s41467-024-55573-4</a>"},"external_id":{"pmid":["39774105"]},"article_processing_charge":"Yes","publication":"Nature Communications","article_number":"457","year":"2025","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"18848","OA_type":"gold","doi":"10.1038/s41467-024-55573-4","quality_controlled":"1","date_published":"2025-01-07T00:00:00Z","fulldoi":"https://doi.org/10.1038/s41467-024-55573-4","oa_version":"Published Version","publication_status":"published","author":[{"full_name":"Ocampo, Rodrigo Fregoso","last_name":"Ocampo","first_name":"Rodrigo Fregoso"},{"id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","full_name":"Bravo, Jack Peter Kelly","last_name":"Bravo","orcid":"0000-0003-0456-0753","first_name":"Jack Peter Kelly"},{"first_name":"Tyler L.","full_name":"Dangerfield, Tyler L.","last_name":"Dangerfield"},{"first_name":"Isabel","last_name":"Nocedal","full_name":"Nocedal, Isabel"},{"last_name":"Jirde","full_name":"Jirde, Samatar A.","first_name":"Samatar A."},{"full_name":"Alexander, Lisa M.","last_name":"Alexander","first_name":"Lisa M."},{"last_name":"Thomas","full_name":"Thomas, Nicole C.","first_name":"Nicole C."},{"full_name":"Das, Anjali","last_name":"Das","first_name":"Anjali"},{"full_name":"Nielson, Sarah","last_name":"Nielson","first_name":"Sarah"},{"first_name":"Kenneth A.","full_name":"Johnson, Kenneth A.","last_name":"Johnson"},{"last_name":"Brown","full_name":"Brown, Christopher T.","first_name":"Christopher T."},{"full_name":"Butterfield, Cristina N.","last_name":"Butterfield","first_name":"Cristina N."},{"full_name":"Goltsman, Daniela S.A.","last_name":"Goltsman","first_name":"Daniela S.A."},{"first_name":"David W.","full_name":"Taylor, David W.","last_name":"Taylor"}],"intvolume":"        16","abstract":[{"text":"Type II CRISPR endonucleases are widely used programmable genome editing tools. Recently, CRISPR-Cas systems with highly compact nucleases have been discovered, including Cas9d (a type II-D nuclease). Here, we report the cryo-EM structures of a Cas9d nuclease (747 amino acids in length) in multiple functional states, revealing a stepwise process of DNA targeting involving a conformational switch in a REC2 domain insertion. Our structures provide insights into the intricately folded guide RNA which acts as a structural scaffold to anchor small, flexible protein domains for DNA recognition. The sgRNA can be truncated by up to ~25% yet still retain activity in vivo. Using ancestral sequence reconstruction, we generated compact nucleases capable of efficient genome editing in mammalian cells. Collectively, our results provide mechanistic insights into the evolution and DNA targeting of diverse type II CRISPR-Cas systems, providing a blueprint for future re-engineering of minimal RNA-guided DNA endonucleases.","lang":"eng"}]},{"doi":"10.1073/pnas.2402925121","quality_controlled":"1","author":[{"id":"3E999752-F248-11E8-B48F-1D18A9856A87","full_name":"Sokolowski, Thomas R","last_name":"Sokolowski","orcid":"0000-0002-1287-3779","first_name":"Thomas R"},{"full_name":"Gregor, Thomas","last_name":"Gregor","first_name":"Thomas"},{"first_name":"William","full_name":"Bialek, William","last_name":"Bialek"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","first_name":"Gašper"}],"issue":"1","publication_status":"published","abstract":[{"lang":"eng","text":"Many biological systems operate near the physical limits to their performance, suggesting that aspects of their behavior and underlying mechanisms could be derived from optimization principles. However, such principles have often been applied only in simplified models. Here, we explore a detailed mechanistic model of the gap gene network in the Drosophila embryo, optimizing its 50+ parameters to maximize the information that gene expression levels provide about nuclear positions. This optimization is conducted under realistic constraints, such as limits on the number of available molecules. Remarkably, the optimal networks we derive closely match the architecture and spatial gene expression profiles observed in the real organism. Our framework quantifies the tradeoffs involved in maximizing functional performance and allows for the exploration of alternative network configurations, addressing the question of which features are necessary and which are contingent. Our results suggest that multiple solutions to the optimization problem might exist across closely related organisms, offering insights into the evolution of gene regulatory networks."}],"intvolume":"       122","isi":1,"fulldoi":"https://doi.org/10.1073/pnas.2402925121","project":[{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"},{"name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos","grant_number":"101118866","_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9"},{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","grant_number":"RGP0034/2018"}],"oa_version":"Published Version","date_published":"2025-01-07T00:00:00Z","publication":"Proceedings of the National Academy of Sciences","article_number":"e2402925121","citation":{"ama":"Sokolowski TR, Gregor T, Bialek W, Tkačik G. Deriving a genetic regulatory network from an optimization principle. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(1). doi:<a href=\"https://doi.org/10.1073/pnas.2402925121\">10.1073/pnas.2402925121</a>","apa":"Sokolowski, T. R., Gregor, T., Bialek, W., &#38; Tkačik, G. (2025). Deriving a genetic regulatory network from an optimization principle. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2402925121\">https://doi.org/10.1073/pnas.2402925121</a>","ieee":"T. R. Sokolowski, T. Gregor, W. Bialek, and G. Tkačik, “Deriving a genetic regulatory network from an optimization principle,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 1. National Academy of Sciences, 2025.","ista":"Sokolowski TR, Gregor T, Bialek W, Tkačik G. 2025. Deriving a genetic regulatory network from an optimization principle. Proceedings of the National Academy of Sciences. 122(1), e2402925121.","chicago":"Sokolowski, Thomas R, Thomas Gregor, William Bialek, and Gašper Tkačik. “Deriving a Genetic Regulatory Network from an Optimization Principle.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2402925121\">https://doi.org/10.1073/pnas.2402925121</a>.","mla":"Sokolowski, Thomas R., et al. “Deriving a Genetic Regulatory Network from an Optimization Principle.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 1, e2402925121, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2402925121\">10.1073/pnas.2402925121</a>.","short":"T.R. Sokolowski, T. Gregor, W. Bialek, G. Tkačik, Proceedings of the National Academy of Sciences 122 (2025)."},"external_id":{"isi":["001392772400001"],"pmid":["39752518"]},"article_processing_charge":"Yes (in subscription journal)","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"18849","OA_type":"hybrid","year":"2025","publisher":"National Academy of Sciences","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"OA_place":"publisher","scopus_import":"1","file_date_updated":"2025-01-20T10:10:04Z","corr_author":"1","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"}],"file":[{"access_level":"open_access","date_created":"2025-01-20T10:10:04Z","date_updated":"2025-01-20T10:10:04Z","success":1,"creator":"dernst","file_name":"2025_PNAS_Sokolowski.pdf","relation":"main_file","content_type":"application/pdf","checksum":"8dbfc7d495413340225ebfae69b0cf9a","file_id":"18862","file_size":19073585}],"month":"01","ddc":["570"],"type":"journal_article","volume":122,"article_type":"original","acknowledgement":"We thank Nicholas H. Barton for his comments on the manuscript, Benjamin Zoller for helpful discussions, and Aleksandra Walczak and Curtis Callan for early collaborations that shaped this work. Special thanks to Eric F. Wieschaus for many persistently inspiring conversations. This work was supported in part by the Human Frontiers Science Program; the Austrian Science Fund (FWF P28844); by the European Research Council grant DynaTrans (101118866); by U.S. NSF, through the Center for the Physics of Biological Function (PHY–1734030); by NIH Grants R01GM097275, U01DA047730, and U01DK127429; by the John Simon Guggenheim Memorial Foundation; and by the LOEWE priority program “Center for Multiscale Modeling in Life Sciences” (CMMS), sponsored by the Hessian Ministry for Science and Research, Arts and Culture (HMWK).","date_created":"2025-01-19T23:01:50Z","pmid":1,"day":"07","oa":1,"title":"Deriving a genetic regulatory network from an optimization principle","date_updated":"2026-02-16T12:26:51Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"}},{"doi":"10.1073/pnas.2411887121","quality_controlled":"1","fulldoi":"https://doi.org/10.1073/pnas.2411887121","project":[{"name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos","grant_number":"101118866","_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9"}],"isi":1,"oa_version":"Published Version","date_published":"2025-01-07T00:00:00Z","publication_status":"published","author":[{"full_name":"Perkins, Mindy Liu","last_name":"Perkins","first_name":"Mindy Liu"},{"first_name":"Justin","last_name":"Crocker","full_name":"Crocker, Justin"},{"orcid":"0000-0002-6699-1455","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","last_name":"Tkačik"}],"issue":"1","abstract":[{"text":"Biophysical constraints limit the specificity with which transcription factors (TFs) can target regulatory DNA. While individual nontarget binding events may be low affinity, the sheer number of such interactions could present a challenge for gene regulation by degrading its precision or possibly leading to an erroneous induction state. Chromatin can prevent nontarget binding by rendering DNA physically inaccessible to TFs, at the cost of energy-consuming remodeling orchestrated by pioneer factors (PFs). Under what conditions and by how much can chromatin reduce regulatory errors on a global scale? We use a theoretical approach to compare two scenarios for gene regulation: one that relies on TF binding to free DNA alone and one that uses a combination of TFs and chromatin-regulating PFs to achieve desired gene expression patterns. We find, first, that chromatin effectively silences groups of genes that should be simultaneously OFF, thereby allowing more accurate graded control of expression for the remaining ON genes. Second, chromatin buffers the deleterious consequences of nontarget binding as the number of OFF genes grows, permitting a substantial expansion in regulatory complexity. Third, chromatin-based regulation productively co-opts nontarget TF binding for ON genes in order to establish a “leaky” baseline expression level, which targeted activator or repressor binding subsequently up- or down-modulates. Thus, on a global scale, using chromatin simultaneously alleviates pressure for high specificity of regulatory interactions and enables an increase in genome size with minimal impact on global expression error.","lang":"eng"}],"intvolume":"       122","citation":{"ama":"Perkins ML, Crocker J, Tkačik G. Chromatin enables precise and scalable gene regulation with factors of limited specificity. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(1). doi:<a href=\"https://doi.org/10.1073/pnas.2411887121\">10.1073/pnas.2411887121</a>","apa":"Perkins, M. L., Crocker, J., &#38; Tkačik, G. (2025). Chromatin enables precise and scalable gene regulation with factors of limited specificity. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2411887121\">https://doi.org/10.1073/pnas.2411887121</a>","ista":"Perkins ML, Crocker J, Tkačik G. 2025. Chromatin enables precise and scalable gene regulation with factors of limited specificity. Proceedings of the National Academy of Sciences. 122(1), e2411887121.","ieee":"M. L. Perkins, J. Crocker, and G. Tkačik, “Chromatin enables precise and scalable gene regulation with factors of limited specificity,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 1. National Academy of Sciences, 2025.","chicago":"Perkins, Mindy Liu, Justin Crocker, and Gašper Tkačik. “Chromatin Enables Precise and Scalable Gene Regulation with Factors of Limited Specificity.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2411887121\">https://doi.org/10.1073/pnas.2411887121</a>.","mla":"Perkins, Mindy Liu, et al. “Chromatin Enables Precise and Scalable Gene Regulation with Factors of Limited Specificity.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 1, e2411887121, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2411887121\">10.1073/pnas.2411887121</a>.","short":"M.L. Perkins, J. Crocker, G. Tkačik, Proceedings of the National Academy of Sciences 122 (2025)."},"external_id":{"pmid":["39793086"],"isi":["001392765300001"]},"article_processing_charge":"No","publication":"Proceedings of the National Academy of Sciences","article_number":"e2411887121","year":"2025","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"18850","OA_type":"hybrid","scopus_import":"1","OA_place":"publisher","file_date_updated":"2025-01-20T09:38:32Z","corr_author":"1","has_accepted_license":"1","publisher":"National Academy of Sciences","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"type":"journal_article","ddc":["570"],"month":"01","acknowledgement":"M.L.P. was supported by the European Molecular Biology Laboratory (EMBL) Interdisciplinary Postdoc Programme (EIPOD4 fellowships), cofunded by Marie SkÅ‚odowska-Curie Actions (Grant Agreement No. 847543). J.C. and M.L.P. were supported by EMBL Core Funding and Theory@EMBL. This work is supported by European Research Council Grant DynaTrans (101118866) to G.T. We would like to thank the members of the J.C. and G.T. groups, especially Natalia Misunou, Michal Hledík, and Réka Borbély, for helpful feedback and discussion. We also thank EMBL IT Services for the use of high performance computing resources.","article_type":"original","volume":122,"pmid":1,"date_created":"2025-01-19T23:01:51Z","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"}],"file":[{"content_type":"application/pdf","relation":"main_file","file_id":"18859","file_size":30943709,"checksum":"86a8d25a6e282aeb4128f1d0b86ff911","date_updated":"2025-01-20T09:38:32Z","success":1,"date_created":"2025-01-20T09:38:32Z","access_level":"open_access","file_name":"2025_PNAS_Perkins.pdf","creator":"dernst"}],"oa":1,"day":"07","related_material":{"link":[{"relation":"software","url":"https://github.com/officerredshirt/network_crosstalk"}]},"date_updated":"2026-05-06T12:43:59Z","APC_amount":"3261,23 EUR","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"Chromatin enables precise and scalable gene regulation with factors of limited specificity"}]