--- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20935' abstract: - lang: eng text: In situ cryo-electron tomography (cryo-ET) has emerged as the method of choice to investigate the structures of biomolecules in their native context. However, challenges remain for the efficient production and sharing of large-scale cryo-ET datasets. Here, we combined cryogenic plasma-based focused ion beam (cryo-PFIB) milling with recent advances in cryo-ET acquisition and processing to generate a dataset of 1,829 annotated tomograms of the green alga Chlamydomonas reinhardtii, which we provide as a community resource to drive method development and inspire biological discovery. To assay data quality, we performed subtomogram averaging of both soluble and membrane-bound complexes ranging in size from >3 MDa to ∼200 kDa, including 80S ribosomes, Rubisco, nucleosomes, microtubules, clathrin, photosystem II, and mitochondrial ATP synthase. The majority of these density maps reached sub-nanometer resolution, demonstrating the potential of this C. reinhardtii dataset as well as the promise of modern cryo-ET workflows and open data sharing to empower visual proteomics. acknowledgement: Calculations were performed at the Max Planck Institute of Biochemistry and the Raven Supercomputer of the Max Planck Computing and Data Facility (MPCDF) in Garching, Germany; at the sciCORE (http://scicore.unibas.ch/) scientific computing center at the University of Basel, Switzerland; and at Thermo Fisher Scientific, in Eindhoven, the Netherlands. This work was supported by Thermo Fisher Scientific. All lamella preparations and tilt-series collections used in this work were conducted at Thermo Fisher R&D facilities in Brno and Eindhoven, utilizing Arctis and Krios microscopes. This work was also supported by the ERC consolidator grant “cryOcean” (fulfilled by the Swiss State Secretariat for Education, Research and Innovation, M822.00045) as well as a Swiss Nanoscience Institute PhD school grant to B.D.E. and P.V.d.S., an EMBO long-term postdoctoral fellowship (ALTF-383-2022) to G.T., an SNSF Postdoctoral Fellowship (project 210561) to F.W., a Boehringer Ingelheim Fonds fellowship to L.L., and by the Max Planck Society to J.A.G.B. and J.M.P. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Ron full_name: Kelley, Ron last_name: Kelley - first_name: Sagar full_name: Khavnekar, Sagar last_name: Khavnekar - first_name: Ricardo D. full_name: Righetto, Ricardo D. last_name: Righetto - first_name: Jessica full_name: Heebner, Jessica last_name: Heebner - first_name: Martin full_name: Obr, Martin id: 4741CA5A-F248-11E8-B48F-1D18A9856A87 last_name: Obr orcid: 0000-0003-1756-6564 - first_name: Xianjun full_name: Zhang, Xianjun last_name: Zhang - first_name: Saikat full_name: Chakraborty, Saikat last_name: Chakraborty - first_name: Grigory full_name: Tagiltsev, Grigory last_name: Tagiltsev - first_name: Alicia full_name: Michael, Alicia id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael orcid: 0000-0002-6080-839X - first_name: Sofie full_name: Van Dorst, Sofie last_name: Van Dorst - first_name: Florent full_name: Waltz, Florent last_name: Waltz - first_name: Caitlyn L. full_name: Mccafferty, Caitlyn L. last_name: Mccafferty - first_name: Lorenz full_name: Lamm, Lorenz last_name: Lamm - first_name: Simon full_name: Zufferey, Simon last_name: Zufferey - first_name: Philippe full_name: Van Der Stappen, Philippe last_name: Van Der Stappen - first_name: Hugo full_name: Van Den Hoek, Hugo last_name: Van Den Hoek - first_name: Wojciech full_name: Wietrzynski, Wojciech last_name: Wietrzynski - first_name: Pavol full_name: Harar, Pavol id: e03d953a-6e8c-11ef-99e4-f0717d385cd5 last_name: Harar orcid: 0000-0001-5206-1794 - first_name: William full_name: Wan, William last_name: Wan - first_name: John A.G. full_name: Briggs, John A.G. last_name: Briggs - first_name: Jürgen M. full_name: Plitzko, Jürgen M. last_name: Plitzko - first_name: Benjamin D. full_name: Engel, Benjamin D. last_name: Engel - first_name: Abhay full_name: Kotecha, Abhay last_name: Kotecha citation: ama: Kelley R, Khavnekar S, Righetto RD, et al. Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii. Molecular Cell. 2026;86(1):213-230.e7. doi:10.1016/j.molcel.2025.11.029 apa: Kelley, R., Khavnekar, S., Righetto, R. D., Heebner, J., Obr, M., Zhang, X., … Kotecha, A. (2026). Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii. Molecular Cell. Cell Press. https://doi.org/10.1016/j.molcel.2025.11.029 chicago: Kelley, Ron, Sagar Khavnekar, Ricardo D. Righetto, Jessica Heebner, Martin Obr, Xianjun Zhang, Saikat Chakraborty, et al. “Toward Community-Driven Visual Proteomics with Large-Scale Cryo-Electron Tomography of Chlamydomonas Reinhardtii.” Molecular Cell. Cell Press, 2026. https://doi.org/10.1016/j.molcel.2025.11.029. ieee: R. Kelley et al., “Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii,” Molecular Cell, vol. 86, no. 1. Cell Press, p. 213–230.e7, 2026. ista: Kelley R, Khavnekar S, Righetto RD, Heebner J, Obr M, Zhang X, Chakraborty S, Tagiltsev G, Michael AK, Van Dorst S, Waltz F, Mccafferty CL, Lamm L, Zufferey S, Van Der Stappen P, Van Den Hoek H, Wietrzynski W, Harar P, Wan W, Briggs JAG, Plitzko JM, Engel BD, Kotecha A. 2026. Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii. Molecular Cell. 86(1), 213–230.e7. mla: Kelley, Ron, et al. “Toward Community-Driven Visual Proteomics with Large-Scale Cryo-Electron Tomography of Chlamydomonas Reinhardtii.” Molecular Cell, vol. 86, no. 1, Cell Press, 2026, p. 213–230.e7, doi:10.1016/j.molcel.2025.11.029. short: R. Kelley, S. Khavnekar, R.D. Righetto, J. Heebner, M. Obr, X. Zhang, S. Chakraborty, G. Tagiltsev, A.K. Michael, S. Van Dorst, F. Waltz, C.L. Mccafferty, L. Lamm, S. Zufferey, P. Van Der Stappen, H. Van Den Hoek, W. Wietrzynski, P. Harar, W. Wan, J.A.G. Briggs, J.M. Plitzko, B.D. Engel, A. Kotecha, Molecular Cell 86 (2026) 213–230.e7. das_tickbox: '1' dataavailabilitystatement: "Raw EM data are available at the EMPIAR under accession code EMPIAR: EMPIAR-11830. Annotation and processing information for all 1,829 tomograms are provided in spreadsheet format.153 The following subtomogram averages have been deposited at the Electron Microscopy Data Bank (EMDB): 80S ribosome (EMDB: EMD-51847), nucleosome (EMDB: EMD-19906), PSII (EMDB: EMD-51731), Rubisco (EMDB: EMD-51848), microtubule (EMDB: EMD-51804), clathrin (EMDB: EMD-51789), and ATP synthase (EMDB: EMD-51802). Segmentations shown in Figures 2 and 3 are deposited on Zenodo (https://doi.org/10.5281/zenodo.15875785). Particle positions and orientations used for STA, along with all resources derived from this work, are available on GitHub (https://github.com/Chromatin-Structure-Rhythms-Lab/ChlamyAnnotations). Reconstructed tomograms and annotations are also available to explore interactively at the CZII Cryo-ET Data Portal (DS-10302, https://cryoetdataportal.czscience.com/datasets/10302/). Raw data for cryo-PFIB/SEM slice-and-view of a whole C. reinhardtii cell has also been deposited (EMPIAR: EMPIAR-11275).\r\n\r\nThis paper does not report original code.\r\n\r\nAny additional information required to reanalyze the data reported in this paper is available from the lead contact upon request." date_created: 2026-01-04T23:01:36Z date_published: 2026-01-08T00:00:00Z date_updated: 2026-10-20T09:02:52Z day: '08' ddc: - '570' department: - _id: AlMi doi: 10.1016/j.molcel.2025.11.029 file: - access_level: open_access checksum: 96a2f8519124d1a0d9de8d2594bf7147 content_type: application/pdf creator: dernst date_created: 2026-07-28T07:38:45Z date_updated: 2026-07-28T07:38:45Z file_id: '22599' file_name: 2026_MolecularCell_Kelley.pdf file_size: 26749637 relation: main_file success: 1 file_date_updated: 2026-07-28T07:38:45Z fulldoi: https://doi.org/10.1016/j.molcel.2025.11.029 has_accepted_license: '1' intvolume: ' 86' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 213-230.e7 publication: Molecular Cell publication_identifier: eissn: - 1097-4164 issn: - 1097-2765 publication_status: published publisher: Cell Press quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 86 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20986' abstract: - lang: eng text: During complex vocal interactions, different features of acoustic stimuli are integrated to produce appropriate vocal responses,1 such as copying sounds during vocal matching behavior in some animals.2,3,4,5,6,7,8,9,10,11,12 However, little is known about the interplay and possible trade-offs between the different temporal and spectral acoustic features during these vocal exchanges.2,13,14 Nightingales can flexibly match the pitch of their tonal “whistle songs” in real time during counter-singing duels.15,16 Here, we show that the syllable duration of whistle playbacks could alter the song responses of wild nightingales, causing their whistle duration distribution to shift toward the presented stimulus duration. When exposed to whistle playbacks featuring unnatural combinations of pitch and duration, nightingales demonstrate a flexible trade-off between pitch matching and temporal imitation, yet they are constrained by their vocal repertoire. They selectively adapted their vocal responses to approximate these novel stimuli, aligning them with their natural whistle repertoire. We developed a computational model of nightingale whistle-matching behavior that revealed a hierarchical organization of acoustic feature production. During whistle matching, the feature integration process is constrained by the duration of syllables, and pitch matching follows within this temporal framework, forcing a trade-off between the two features. Our findings reveal a complex interplay between the spectral and temporal domains that shapes song-matching behavior. acknowledgement: 'We would like to thank J. Benichov and N. Hein for their help with fieldwork; M. Ramadas for helping with the segmentation analysis; T. Eliav, C. Chintaluri, G. Tkacik, and A. Navas for providing helpful comments to the project and manuscript; and A. Costalunga for the drawings of nightingales. Funding sources: The Joachim Herz Stiftung Add-on Fellowships for Interdisciplinary Life Science, awarded to G.C.; the ERC Consolidator Grant 819603 SYNAPSEEK, awarded to T.P.V.; and DFG Research Unit 5768–532521431, DFG Research Grant-547921981, DFG SFB 1315–327654276, and the ERC Starting Grant 757459 MIDNIGHT, awarded to D.V.' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Juan Sebastian full_name: Calderon Garcia, Juan Sebastian id: 1271b54b-dbcd-11ea-9d1d-d92da838fe2c last_name: Calderon Garcia - first_name: Giacomo full_name: Costalunga, Giacomo last_name: Costalunga - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Daniela full_name: Vallentin, Daniela last_name: Vallentin citation: ama: Calderon Garcia JS, Costalunga G, Vogels TP, Vallentin D. Interplay between syllable duration and pitch during whistle matching in wild nightingales. Current Biology. 2026;36(3):791-798.e6. doi:10.1016/j.cub.2025.12.025 apa: Calderon Garcia, J. S., Costalunga, G., Vogels, T. P., & Vallentin, D. (2026). Interplay between syllable duration and pitch during whistle matching in wild nightingales. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2025.12.025 chicago: Calderon Garcia, Juan Sebastian, Giacomo Costalunga, Tim P Vogels, and Daniela Vallentin. “Interplay between Syllable Duration and Pitch during Whistle Matching in Wild Nightingales.” Current Biology. Cell Press, 2026. https://doi.org/10.1016/j.cub.2025.12.025. ieee: J. S. Calderon Garcia, G. Costalunga, T. P. Vogels, and D. Vallentin, “Interplay between syllable duration and pitch during whistle matching in wild nightingales,” Current Biology, vol. 36, no. 3. Cell Press, p. 791–798.e6, 2026. ista: Calderon Garcia JS, Costalunga G, Vogels TP, Vallentin D. 2026. Interplay between syllable duration and pitch during whistle matching in wild nightingales. Current Biology. 36(3), 791–798.e6. mla: Calderon Garcia, Juan Sebastian, et al. “Interplay between Syllable Duration and Pitch during Whistle Matching in Wild Nightingales.” Current Biology, vol. 36, no. 3, Cell Press, 2026, p. 791–798.e6, doi:10.1016/j.cub.2025.12.025. short: J.S. Calderon Garcia, G. Costalunga, T.P. Vogels, D. Vallentin, Current Biology 36 (2026) 791–798.e6. das_tickbox: '1' dataavailabilitystatement: "All data have been deposited at https://github.com/vallentinlab/NG-whistle-durations and are publicly available as of the date of publication.\r\nAll original code has been deposited at https://github.com/vallentinlab/NG-whistle-durations and is publicly available as of the date of publication.\r\nAny additional information required to reanalyze the data reported in this paper is available from the lead contact upon request." date_created: 2026-01-14T12:00:29Z date_published: 2026-02-02T00:00:00Z date_updated: 2026-10-20T09:02:18Z day: '02' ddc: - '570' - '577' department: - _id: GradSch - _id: TiVo doi: 10.1016/j.cub.2025.12.025 ec_funded: 1 external_id: pmid: - '41529680' file: - access_level: open_access checksum: e17c3537193d5ab4886596d1a04f9b0e content_type: application/pdf creator: dernst date_created: 2026-07-27T10:47:55Z date_updated: 2026-07-27T10:47:55Z file_id: '22416' file_name: 2026_CurrentBiology_CalderonGarcia.pdf file_size: 7120959 relation: main_file success: 1 file_date_updated: 2026-07-27T10:47:55Z fulldoi: https://doi.org/10.1016/j.cub.2025.12.025 has_accepted_license: '1' intvolume: ' 36' issue: '3' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 791-798.e6 pmid: 1 project: - _id: 0aacfa84-070f-11eb-9043-d7eb2c709234 call_identifier: H2020 grant_number: '819603' name: Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning. publication: Current Biology publication_identifier: eissn: - 1879-0445 issn: - 0960-9822 publication_status: published publisher: Cell Press quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Interplay between syllable duration and pitch during whistle matching in wild nightingales tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '21502' abstract: - lang: eng text: The mammalian brain stores glucose, the main circulating energy substrate, as glycogen. In rodents, the cerebellum contains relatively high glycogen levels, yet its cellular and subcellular distribution remains poorly defined. Using monoclonal antibodies against glycogen, we examined its distribution in the mouse cerebellar cortex. Glycogen was predominantly localized to Bergmann glia (BG) processes in the molecular layer and was also detected in Purkinje cells (PCs), the principal cerebellar neurons. To assess the functional significance of cerebellar glycogen, we analyzed behavior in mice lacking glycogen synthase 1 (Gys1) in BG or PCs using a floxed Gys1 line. Gys1 deficiency in either PCs or GFAP-positive cells reduced anxiety-like behavior, whereas combined deletion caused PC degeneration and ataxia. These findings reveal a critical role for glycogen metabolism in both astrocytes and neurons in cerebellar function. acknowledgement: This work was supported by the Novo Nordisk Foundation (NNFOC0058058, H. Hirase), the Danmarks Frie Forskningsfond (0134-00107B and 5283-00069A, H.Hirase), the Lundbeck Foundation, Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research (KAKENHI) program (22K06454/24H01221, A.K.; 23K27482, H.Hirai), the Japan Agency for Medical Research and Development (AMED) Brain Mapping by Integrated Neurotechnologies for Disease Studies (Brain/MINDS) (JP21dm0207111, H. Hirai), AMED Brain/MINDS 2.0 (JP23wm0625001 and JP24wm0625103, H. Hirai), and grants from the Spanish Ministerio de Ciencia e Innovación (MCIU/FEDER/AEI) (PID2020-118699 GB-100, J.D.) and the Fundación Ramón Areces (J.D.). Sonam Akther has been supported by the RIKEN IPA fellowship. We are thankful to Dr. Yuki Oe for his support in the initial stage of this study and to Dan Xue for his help with the graphical abstract. We thank Dr. Pia Weikop for providing CTN research infrastructure. The authors declare no competing financial interests. article_number: '115192' article_processing_charge: Yes article_type: original author: - first_name: Sonam full_name: Akther, Sonam last_name: Akther - first_name: Ashley Bomin full_name: Lee, Ashley Bomin last_name: Lee - first_name: Ayumu full_name: Konno, Ayumu last_name: Konno - first_name: Antonis full_name: Asiminas, Antonis last_name: Asiminas - first_name: Marta full_name: Vittani, Marta last_name: Vittani - first_name: Tsuneko full_name: Mishima, Tsuneko last_name: Mishima - first_name: Hirokazu full_name: Hirai, Hirokazu last_name: Hirai - first_name: Claire Francesca full_name: Meehan, Claire Francesca last_name: Meehan - first_name: Jordi full_name: Duran, Jordi last_name: Duran - first_name: Joan full_name: Guinovart, Joan last_name: Guinovart - first_name: Hitoshi full_name: Ashida, Hitoshi last_name: Ashida - first_name: Tsuyoshi full_name: Morita, Tsuyoshi last_name: Morita - first_name: Otto full_name: Baba, Otto last_name: Baba - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Maiken full_name: Nedergaard, Maiken last_name: Nedergaard - first_name: Hajime full_name: Hirase, Hajime last_name: Hirase citation: ama: Akther S, Lee AB, Konno A, et al. Distribution and functional significance of rodent cerebellar glycogen. iScience. 2026;29(4). doi:10.1016/j.isci.2026.115192 apa: Akther, S., Lee, A. B., Konno, A., Asiminas, A., Vittani, M., Mishima, T., … Hirase, H. (2026). Distribution and functional significance of rodent cerebellar glycogen. IScience. Cell Press. https://doi.org/10.1016/j.isci.2026.115192 chicago: Akther, Sonam, Ashley Bomin Lee, Ayumu Konno, Antonis Asiminas, Marta Vittani, Tsuneko Mishima, Hirokazu Hirai, et al. “Distribution and Functional Significance of Rodent Cerebellar Glycogen.” IScience. Cell Press, 2026. https://doi.org/10.1016/j.isci.2026.115192. ieee: S. Akther et al., “Distribution and functional significance of rodent cerebellar glycogen,” iScience, vol. 29, no. 4. Cell Press, 2026. ista: Akther S, Lee AB, Konno A, Asiminas A, Vittani M, Mishima T, Hirai H, Meehan CF, Duran J, Guinovart J, Ashida H, Morita T, Baba O, Shigemoto R, Nedergaard M, Hirase H. 2026. Distribution and functional significance of rodent cerebellar glycogen. iScience. 29(4), 115192. mla: Akther, Sonam, et al. “Distribution and Functional Significance of Rodent Cerebellar Glycogen.” IScience, vol. 29, no. 4, 115192, Cell Press, 2026, doi:10.1016/j.isci.2026.115192. short: S. Akther, A.B. Lee, A. Konno, A. Asiminas, M. Vittani, T. Mishima, H. Hirai, C.F. Meehan, J. Duran, J. Guinovart, H. Ashida, T. Morita, O. Baba, R. Shigemoto, M. Nedergaard, H. Hirase, IScience 29 (2026). das_tickbox: '1' dataavailabilitystatement: "This study did not generate new materials or reagents.All data supporting the findings of this study are available from the lead contact upon reasonable request.\r\nThis study did not generate any new code.\r\nAdditional raw data can be obtained from the lead contact upon reasonable request." date_created: 2026-03-29T22:07:07Z date_published: 2026-04-17T00:00:00Z date_updated: 2026-10-20T09:02:33Z day: '17' ddc: - '570' department: - _id: RySh doi: 10.1016/j.isci.2026.115192 external_id: pmid: - '41890976' file: - access_level: open_access checksum: 9c9ccc87072d04808e4af407d647ed20 content_type: application/pdf creator: dernst date_created: 2026-07-27T12:03:23Z date_updated: 2026-07-27T12:03:23Z file_id: '22427' file_name: 2026_iScience_Akther.pdf file_size: 14469960 relation: main_file success: 1 file_date_updated: 2026-07-27T12:03:23Z fulldoi: https://doi.org/10.1016/j.isci.2026.115192 has_accepted_license: '1' intvolume: ' 29' issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 publication: iScience publication_identifier: eissn: - 2589-0042 publication_status: published publisher: Cell Press quality_controlled: '1' researchdata_availability: upon request scopus_import: '1' status: public supplementarymaterial: no title: Distribution and functional significance of rodent cerebellar glycogen tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '20924' abstract: - lang: eng text: "Pioneer transcription factors (TFs) possess the ability to read out DNA motifs embedded within nucleosomes, driving changes in gene expression during cellular differentiation and reprogramming. Here, we present selected engagement on nucleosome sequencing (SeEN-seq), a protocol designed to systematically identify potential TF-binding sites on the nucleosome. We describe steps for nucleosome library assembly, SeEN-seq assay, and cryoelectron microscopy (cryo-EM) sample preparation. This protocol facilitates the preparation of homogeneous pioneer TF-nucleosome complexes for cryo-EM structure determination using single-particle analysis.\r\nFor complete details on the use and execution of this protocol, please refer to Michael et al.1" acknowledgement: We thank R.H. Kim, A. Casper, and R. Gautsch for sequencing at the NGS facility (RRID:SCR_025746). K.T. is an Honorary Professor at the Department of Biology, Ludwig-Maximilians-University, Munich, Germany. This study was funded by European Research Council grant ERC-CoG-818556 TotipotentZygotChrom (K.T.), Max Planck Society (K.T.), and ERC Starting Grant “ChromaChrono” 101162145 (A.K.M.). article_number: '104295' article_processing_charge: Yes article_type: original author: - first_name: Wataru full_name: Kobayashi, Wataru last_name: Kobayashi - first_name: Alicia full_name: Michael, Alicia id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael orcid: 0000-0002-6080-839X - first_name: Siwat full_name: Ruangroengkulrith, Siwat last_name: Ruangroengkulrith - first_name: Maximilian full_name: Kümmecke, Maximilian last_name: Kümmecke - first_name: Kikuë full_name: Tachibana, Kikuë last_name: Tachibana citation: ama: Kobayashi W, Michael AK, Ruangroengkulrith S, Kümmecke M, Tachibana K. Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination. STAR Protocols. 2026;7(1). doi:10.1016/j.xpro.2025.104295 apa: Kobayashi, W., Michael, A. K., Ruangroengkulrith, S., Kümmecke, M., & Tachibana, K. (2026). Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination. STAR Protocols. Cell Press. https://doi.org/10.1016/j.xpro.2025.104295 chicago: Kobayashi, Wataru, Alicia K. Michael, Siwat Ruangroengkulrith, Maximilian Kümmecke, and Kikuë Tachibana. “Protocol for Integrative Analysis of Transcription Factor-Nucleosome Interactions Using SeEN-Seq and Cryo-EM Structure Determination.” STAR Protocols. Cell Press, 2026. https://doi.org/10.1016/j.xpro.2025.104295. ieee: W. Kobayashi, A. K. Michael, S. Ruangroengkulrith, M. Kümmecke, and K. Tachibana, “Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination,” STAR Protocols, vol. 7, no. 1. Cell Press, 2026. ista: Kobayashi W, Michael AK, Ruangroengkulrith S, Kümmecke M, Tachibana K. 2026. Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination. STAR Protocols. 7(1), 104295. mla: Kobayashi, Wataru, et al. “Protocol for Integrative Analysis of Transcription Factor-Nucleosome Interactions Using SeEN-Seq and Cryo-EM Structure Determination.” STAR Protocols, vol. 7, no. 1, 104295, Cell Press, 2026, doi:10.1016/j.xpro.2025.104295. short: W. Kobayashi, A.K. Michael, S. Ruangroengkulrith, M. Kümmecke, K. Tachibana, STAR Protocols 7 (2026). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: Raw SeEN-seq data of ESRRB nucleosome binding have been deposited on the Sequence Read Achieve database under the accession PRJNA1305216. Example analysis scripts and input files for SeEN-seq analysis can be found at https://doi.org/10.5281/zenodo.17665082. date_created: 2026-01-04T23:01:33Z date_published: 2026-03-20T00:00:00Z date_updated: 2026-10-20T09:01:26Z day: '20' ddc: - '570' department: - _id: AlMi doi: 10.1016/j.xpro.2025.104295 external_id: pmid: - '41455105' file: - access_level: open_access checksum: cf04b061a48548a649e6a2435bf120db content_type: application/pdf creator: dernst date_created: 2026-07-23T06:33:24Z date_updated: 2026-07-23T06:33:24Z file_id: '22389' file_name: 2026_StarProtocols_Kobayashi.pdf file_size: 5531906 relation: main_file success: 1 file_date_updated: 2026-07-23T06:33:24Z fulldoi: https://doi.org/10.1016/j.xpro.2025.104295 has_accepted_license: '1' intvolume: ' 7' issue: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 9136c684-16d5-11f0-9cad-91c0177b365f grant_number: '101162145' name: Circadian structural transitions of chromatin publication: STAR Protocols publication_identifier: eissn: - 2666-1667 publication_status: published publisher: Cell Press quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20725' abstract: - lang: eng text: The canonical mechanism by which the phytohormone auxin regulates transcription has been one of the cornerstones of plant signaling. The recent unexpected discovery of cyclic AMP (cAMP) as a second messenger in this pathway has revised its foundations while leaving many open questions and gaps in our understanding; these will be discussed in this forum article. acknowledgement: I apologize to colleagues whose relevant work I was unable to cite due to space limitations. This work was funded by the European Union (ERC, CYNIPS, 101142681) and Austrian Science Fund (FWF; 37051-B). I thank Drs Huihuang Chen, Yuanrong Pei, Jason Reed, Linlin Qi, and Dolf Weijers for inspiration and critical input. article_processing_charge: Yes (via OA deal) article_type: review author: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Friml J. Role of cAMP in TIR1/AFB auxin signaling: Open issues. Trends in Plant Science. 2026;31(2):136-138. doi:10.1016/j.tplants.2025.10.018' apa: 'Friml, J. (2026). Role of cAMP in TIR1/AFB auxin signaling: Open issues. Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2025.10.018' chicago: 'Friml, Jiří. “Role of CAMP in TIR1/AFB Auxin Signaling: Open Issues.” Trends in Plant Science. Cell Press, 2026. https://doi.org/10.1016/j.tplants.2025.10.018.' ieee: 'J. Friml, “Role of cAMP in TIR1/AFB auxin signaling: Open issues,” Trends in Plant Science, vol. 31, no. 2. Cell Press, pp. 136–138, 2026.' ista: 'Friml J. 2026. Role of cAMP in TIR1/AFB auxin signaling: Open issues. Trends in Plant Science. 31(2), 136–138.' mla: 'Friml, Jiří. “Role of CAMP in TIR1/AFB Auxin Signaling: Open Issues.” Trends in Plant Science, vol. 31, no. 2, Cell Press, 2026, pp. 136–38, doi:10.1016/j.tplants.2025.10.018.' short: J. Friml, Trends in Plant Science 31 (2026) 136–138. corr_author: '1' das_tickbox: '0' date_created: 2025-12-02T16:29:22Z date_published: 2026-02-01T00:00:00Z date_updated: 2026-10-20T09:01:46Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.tplants.2025.10.018 external_id: pmid: - '41249070' file: - access_level: open_access checksum: e60e903fb4b3e917dba763976ec652cd content_type: application/pdf creator: dernst date_created: 2026-07-27T08:26:40Z date_updated: 2026-07-27T08:26:40Z file_id: '22413' file_name: 2026_TrendsPlantScience_Friml.pdf file_size: 432792 relation: main_file success: 1 file_date_updated: 2026-07-27T08:26:40Z fulldoi: https://doi.org/10.1016/j.tplants.2025.10.018 has_accepted_license: '1' intvolume: ' 31' issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 136-138 pmid: 1 project: - _id: 8f347782-16d5-11f0-9cad-8c19706ee739 grant_number: '101142681' name: Cyclic nucleotides as second messengers in plants - _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6 grant_number: P37051 name: Guanylate cyclase activity of TIR1/AFBs auxin receptors publication: Trends in Plant Science publication_identifier: eissn: - 1878-4372 issn: - 1360-1385 publication_status: published publisher: Cell Press quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: 'Role of cAMP in TIR1/AFB auxin signaling: Open issues' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2026' ... --- OA_type: closed access _id: '20636' abstract: - lang: eng text: The versatile and pivotal roles of the phytohormone auxin in regulating plant growth and development are typically linked to its directional transport, relying on the polarized PIN-FORMED (PIN) auxin exporters at the plasma membrane (PM). For decades, auxin has been proposed to promote PIN polarization, generating self-regulatory feedback mediating much of plant development, but mechanistic insight into this regulation is lacking. Here, we uncover an auxin-induced protein complex at the PM, containing auxin co-receptors transmembrane kinases (TMKs) and PIN1 auxin exporter, as the core machinery that underlies this feedback regulation. Auxin promotes PIN1 phosphorylation by TMKs, modulating PIN1 polarization and transport activity. We also provide evidence that PIN1-exported extracellular auxin is crucial for TMK activation and cell elongation, thus forming the simplest two-element self-regulatory feedback circuit. Thus, these findings offer direct mechanistic insights into a potential self-organizing circuit for auxin signaling and transport to ensure proper plant development in Arabidopsis. acknowledgement: We thank Lukáš Fiedler‬ for helping with the writing. This work was supported by the National Key Research and Development Program of China (2023YFA0913500) to T.X., R.H., Y.Y., Y.X., and M.W. and by the National Natural Science Foundation of China grants to T.X. (32130010), Z.Y. (3241101698), and R.H. (32070309 and 32470276) and startup funds from the Fujian Agriculture and Forestry University and the Shanghai Plant Stress Biology Center, Chinese Academy of Sciences to T.X. article_processing_charge: No article_type: original author: - first_name: R full_name: Huang, R last_name: Huang - first_name: J full_name: Wang, J last_name: Wang - first_name: M full_name: Chang, M last_name: Chang - first_name: W full_name: Tang, W last_name: Tang - first_name: Y full_name: Yu, Y last_name: Yu - first_name: Y full_name: Zhang, Y last_name: Zhang - first_name: Y full_name: Peng, Y last_name: Peng - first_name: Y full_name: Wang, Y last_name: Wang - first_name: Y full_name: Guo, Y last_name: Guo - first_name: T full_name: Lu, T last_name: Lu - first_name: Y full_name: Cao, Y last_name: Cao - first_name: Y full_name: Zhou, Y last_name: Zhou - first_name: Q full_name: Zhang, Q last_name: Zhang - first_name: Y full_name: Huang, Y last_name: Huang - first_name: A full_name: Wu, A last_name: Wu - first_name: L full_name: Ren, L last_name: Ren - first_name: Michelle C full_name: Gallei, Michelle C id: 35A03822-F248-11E8-B48F-1D18A9856A87 last_name: Gallei orcid: 0000-0003-1286-7368 - first_name: J full_name: Dong, J last_name: Dong - first_name: H full_name: Chen, H last_name: Chen - first_name: J full_name: He, J last_name: He - first_name: M full_name: Wen, M last_name: Wen - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: L full_name: Sun, L last_name: Sun - first_name: Y full_name: Xiong, Y last_name: Xiong - first_name: Z full_name: Yang, Z last_name: Yang - first_name: T full_name: Xu, T last_name: Xu citation: ama: Huang R, Wang J, Chang M, et al. TMK-PIN1 drives a short self-organizing circuit for auxin export and signaling in Arabidopsis. Developmental Cell. 2026;61(1):73-84. doi:10.1016/j.devcel.2025.09.009 apa: Huang, R., Wang, J., Chang, M., Tang, W., Yu, Y., Zhang, Y., … Xu, T. (2026). TMK-PIN1 drives a short self-organizing circuit for auxin export and signaling in Arabidopsis. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2025.09.009 chicago: Huang, R, J Wang, M Chang, W Tang, Y Yu, Y Zhang, Y Peng, et al. “TMK-PIN1 Drives a Short Self-Organizing Circuit for Auxin Export and Signaling in Arabidopsis.” Developmental Cell. Cell Press, 2026. https://doi.org/10.1016/j.devcel.2025.09.009. ieee: R. Huang et al., “TMK-PIN1 drives a short self-organizing circuit for auxin export and signaling in Arabidopsis,” Developmental Cell, vol. 61, no. 1. Cell Press, pp. 73–84, 2026. ista: Huang R, Wang J, Chang M, Tang W, Yu Y, Zhang Y, Peng Y, Wang Y, Guo Y, Lu T, Cao Y, Zhou Y, Zhang Q, Huang Y, Wu A, Ren L, Gallei MC, Dong J, Chen H, He J, Wen M, Friml J, Sun L, Xiong Y, Yang Z, Xu T. 2026. TMK-PIN1 drives a short self-organizing circuit for auxin export and signaling in Arabidopsis. Developmental Cell. 61(1), 73–84. mla: Huang, R., et al. “TMK-PIN1 Drives a Short Self-Organizing Circuit for Auxin Export and Signaling in Arabidopsis.” Developmental Cell, vol. 61, no. 1, Cell Press, 2026, pp. 73–84, doi:10.1016/j.devcel.2025.09.009. short: R. Huang, J. Wang, M. Chang, W. Tang, Y. Yu, Y. Zhang, Y. Peng, Y. Wang, Y. Guo, T. Lu, Y. Cao, Y. Zhou, Q. Zhang, Y. Huang, A. Wu, L. Ren, M.C. Gallei, J. Dong, H. Chen, J. He, M. Wen, J. Friml, L. Sun, Y. Xiong, Z. Yang, T. Xu, Developmental Cell 61 (2026) 73–84. das_tickbox: '1' dataavailabilitystatement: "Plasmids and genetic materials generated in this study will be made available upon request from the lead contact.The mass spectrometry data reported in this work have been deposited at the iProX database. Original western blot gel images have been deposited to Mendeley Data. The accession code and the DOI are listed in the key resources table.\r\nThis paper does not report original code. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request." date_created: 2025-11-12T10:03:39Z date_published: 2026-01-14T00:00:00Z date_updated: 2026-10-20T09:02:01Z day: '14' department: - _id: JiFr doi: 10.1016/j.devcel.2025.09.009 external_id: pmid: - '41043435' fulldoi: https://doi.org/10.1016/j.devcel.2025.09.009 intvolume: ' 61' issue: '1' language: - iso: eng month: '01' oa_version: None page: 73-84 pmid: 1 publication: Developmental Cell publication_identifier: eissn: - 1878-1551 issn: - 1534-5807 publication_status: published publisher: Cell Press quality_controlled: '1' researchdata_availability: upon request scopus_import: '1' status: public supplementarymaterial: yes title: TMK-PIN1 drives a short self-organizing circuit for auxin export and signaling in Arabidopsis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 61 year: '2026' ... --- OA_type: closed access _id: '22286' abstract: - lang: eng text: Plants are remarkable organisms. Unlike animals, they cannot flee and, rooted in one place, they must cope with whatever challenges arise — nutrient scarcity, drought, shade, wind or obstacles in the soil. Their extraordinary ability to survive in such unstable environmental conditions lies in their capacity to adapt. In response to environmental signals, plants can rapidly adjust the rate of organ growth, change the direction of growth, bend toward resources, or remodel their body architecture by promoting or suppressing the formation of new organs such as lateral roots, branches, leaves, or flowers. This unique developmental plasticity depends on chemical signals, plant hormones that serve as regulators and coordinators of endogenous molecular and cellular processes. Chief among these signals is auxin, a plant hormone central to nearly every aspect of plant life. article_processing_charge: No article_type: original author: - first_name: Valentin full_name: Leitner, Valentin id: 4c665ce3-0016-11ec-bea0-e44de7a4fa3d last_name: Leitner - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Leitner V, Benková E. Auxin and the control of plant growth and development. Current Biology. 2026;36(13):R739-R744. doi:10.1016/j.cub.2026.04.047 apa: Leitner, V., & Benková, E. (2026). Auxin and the control of plant growth and development. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2026.04.047 chicago: Leitner, Valentin, and Eva Benková. “Auxin and the Control of Plant Growth and Development.” Current Biology. Cell Press, 2026. https://doi.org/10.1016/j.cub.2026.04.047. ieee: V. Leitner and E. Benková, “Auxin and the control of plant growth and development,” Current Biology, vol. 36, no. 13. Cell Press, pp. R739–R744, 2026. ista: Leitner V, Benková E. 2026. Auxin and the control of plant growth and development. Current Biology. 36(13), R739–R744. mla: Leitner, Valentin, and Eva Benková. “Auxin and the Control of Plant Growth and Development.” Current Biology, vol. 36, no. 13, Cell Press, 2026, pp. R739–44, doi:10.1016/j.cub.2026.04.047. short: V. Leitner, E. Benková, Current Biology 36 (2026) R739–R744. corr_author: '1' das_tickbox: '0' date_created: 2026-07-13T09:39:40Z date_published: 2026-07-06T00:00:00Z date_updated: 2026-10-20T09:00:35Z day: '06' department: - _id: EvBe - _id: GradSch doi: 10.1016/j.cub.2026.04.047 external_id: pmid: - '42407441' fulldoi: https://doi.org/10.1016/j.cub.2026.04.047 intvolume: ' 36' issue: '13' language: - iso: eng month: '07' oa_version: None page: R739-R744 pmid: 1 publication: Current Biology publication_identifier: issn: - 0960-9822 publication_status: published publisher: Cell Press quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Auxin and the control of plant growth and development type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2026' ... --- OA_type: closed access _id: '22305' abstract: - lang: eng text: Active dendrites enrich the repertoire of single-neuron computations. Whereas a lot is known about the function of dendrites in vitro, information about their in vivo properties is limited. A new study1 uses advanced imaging to study hippocampal CA1 pyramidal neuron dendrites in head-fixed, awake animals. article_processing_charge: No article_type: letter_note author: - first_name: Subhodeep full_name: Bhattacharya, Subhodeep id: 45f74010-66f6-11f0-a7d4-c441fa3685ff last_name: Bhattacharya orcid: 0009-0009-0334-9068 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Bhattacharya S, Jonas PM. Mission impossible? Quantitative analysis of dendritic computations in vivo. Neuron. 2026;114(10):1706-1708. doi:10.1016/j.neuron.2026.04.002 apa: Bhattacharya, S., & Jonas, P. M. (2026). Mission impossible? Quantitative analysis of dendritic computations in vivo. Neuron. Cell Press. https://doi.org/10.1016/j.neuron.2026.04.002 chicago: Bhattacharya, Subhodeep, and Peter M Jonas. “Mission Impossible? Quantitative Analysis of Dendritic Computations in Vivo.” Neuron. Cell Press, 2026. https://doi.org/10.1016/j.neuron.2026.04.002. ieee: S. Bhattacharya and P. M. Jonas, “Mission impossible? Quantitative analysis of dendritic computations in vivo,” Neuron, vol. 114, no. 10. Cell Press, pp. 1706–1708, 2026. ista: Bhattacharya S, Jonas PM. 2026. Mission impossible? Quantitative analysis of dendritic computations in vivo. Neuron. 114(10), 1706–1708. mla: Bhattacharya, Subhodeep, and Peter M. Jonas. “Mission Impossible? Quantitative Analysis of Dendritic Computations in Vivo.” Neuron, vol. 114, no. 10, Cell Press, 2026, pp. 1706–08, doi:10.1016/j.neuron.2026.04.002. short: S. Bhattacharya, P.M. Jonas, Neuron 114 (2026) 1706–1708. corr_author: '1' das_tickbox: '0' date_created: 2026-07-13T10:51:27Z date_published: 2026-05-20T00:00:00Z date_updated: 2026-10-20T09:00:56Z day: '20' department: - _id: PeJo doi: 10.1016/j.neuron.2026.04.002 external_id: pmid: - '42161246' fulldoi: https://doi.org/10.1016/j.neuron.2026.04.002 intvolume: ' 114' issue: '10' language: - iso: eng month: '05' oa_version: None page: 1706-1708 pmid: 1 publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Cell Press quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Mission impossible? Quantitative analysis of dendritic computations in vivo type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '21746' abstract: - lang: eng text: As vertebrates transitioned from water to land, locomotion shifted from undulatory swimming to limb-based movement. How spinal circuits and their cell types evolved to support this transition remains unclear. We leverage frog metamorphosis, which recapitulates this transition within a single organism, to define how spinal circuits generate aquatic versus terrestrial motor patterns. At swim stages, spinal architecture is uniform, with a transcriptionally and anatomically homogeneous motor and interneurons. As limbs develop and their movement complexifies, spinal circuits expand in neuron number and subtype diversity. This expansion is most pronounced for V1 inhibitory neurons, which increase ∼70-fold and diversify into transcriptionally distinct subtypes. Disrupting transcription factors defining emerging motor and V1 populations reveals molecular segregation between swim and limb circuits, highlighting the role of subtype diversity in motor coordination. A multifold increase in inhibitory neuron diversity thus underlies the tail-to-limb locomotor transition, providing a framework for spinal circuit adaptation during vertebrate evolution. acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: 'We would like to thank the members of the Sweeney Lab, Mario de Bono, Michael Forsthofer, Katharina Lust, and Meital Oren, for comments on the manuscript. We are also grateful to Tom Jessell and Chris Kintner for their scientific insight and mentorship during the conception of this project. It would also have not been possible without the technical support of the Aquatics and Imaging and Optics Facility support teams (ISTA). We thank Martin Estermann for preparing the initial draft of the graphical abstract and Niki Barolini for the final version. In addition, we thank our funding sources for providing the resources to do these experiments: GFF NÖ FTI Strategy Lower Austria dissertation grant FT121-D-046 (to D.V.), Horizon Europe ERC starting grant 101041551 (to Y.I., L.B.S., F.A.T., and D.V.), Special Research Program (SFB) of the Austrian Science Fund (FWF) project F7814-B (to L.B.S.), Austrian Science Fund (FWF) 10.55776/COE16 (to Y.I. and L.B.S.), NINDS 5R35NS116858 (to J.S.D.), CZI grant DAF2020-225401 (DOI) 10.37921/120055ratwvi (to R.H.), NIH grant R01NS123116 (to J.B.B.), American Lebanese Syrian Associated Charities (ALSAC) (to J.B.B.), German Academic Exchange Service (DAAD) IFI grant 57515251-91853472 (to Z.H.), and Project A.L.S. (to S.B.-M.).' article_number: '117227' article_processing_charge: Yes article_type: original author: - first_name: David full_name: Vijatovic, David id: cf391e77-ec3c-11ea-a124-d69323410b58 last_name: Vijatovic orcid: 0000-0002-5494-0941 - first_name: 'Florina Alexandra ' full_name: 'Toma, Florina Alexandra ' id: 2f73f876-f128-11eb-9611-b96b5a30cb0e last_name: Toma - first_name: Y full_name: Ignatyev, Y last_name: Ignatyev - first_name: Zoe P full_name: Harrington, Zoe P id: a8144562-32c9-11ee-b5ce-d9800628bda2 last_name: Harrington orcid: 0009-0008-0158-4032 - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Matthijs Geert full_name: Smits, Matthijs Geert id: 7a231d52-e216-11ee-a0bb-8acd55f8f1f0 last_name: Smits - first_name: Marco full_name: Dalla Vecchia, Marco id: 02a7a869-ff06-11ed-a87f-86649d6077e5 last_name: Dalla Vecchia - first_name: Alexandra J. full_name: Trevisan, Alexandra J. last_name: Trevisan - first_name: Phillip full_name: Chapman, Phillip last_name: Chapman - first_name: Mara full_name: Julseth, Mara id: 1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1 last_name: Julseth - first_name: Susan full_name: Brenner-Morton, Susan last_name: Brenner-Morton - first_name: Mariano I. full_name: Gabitto, Mariano I. last_name: Gabitto - first_name: Jeremy S. full_name: Dasen, Jeremy S. last_name: Dasen - first_name: Jay B. full_name: Bikoff, Jay B. last_name: Bikoff - first_name: Lora Beatrice Jaeger full_name: Sweeney, Lora Beatrice Jaeger id: 56BE8254-C4F0-11E9-8E45-0B23E6697425 last_name: Sweeney orcid: 0000-0001-9242-5601 citation: ama: Vijatovic D, Toma FA, Ignatyev Y, et al. Multifold increase in spinal inhibitory cell types with emergence of limb movement. Cell Reports. 2026;45(4). doi:10.1016/j.celrep.2026.117227 apa: Vijatovic, D., Toma, F. A., Ignatyev, Y., Harrington, Z. P., Sommer, C. M., Hauschild, R., … Sweeney, L. B. (2026). Multifold increase in spinal inhibitory cell types with emergence of limb movement. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2026.117227 chicago: Vijatovic, David, Florina Alexandra Toma, Y Ignatyev, Zoe P Harrington, Christoph M Sommer, Robert Hauschild, Matthijs Geert Smits, et al. “Multifold Increase in Spinal Inhibitory Cell Types with Emergence of Limb Movement.” Cell Reports. Cell Press, 2026. https://doi.org/10.1016/j.celrep.2026.117227. ieee: D. Vijatovic et al., “Multifold increase in spinal inhibitory cell types with emergence of limb movement,” Cell Reports, vol. 45, no. 4. Cell Press, 2026. ista: Vijatovic D, Toma FA, Ignatyev Y, Harrington ZP, Sommer CM, Hauschild R, Smits MG, Dalla Vecchia M, Trevisan AJ, Chapman P, Julseth M, Brenner-Morton S, Gabitto MI, Dasen JS, Bikoff JB, Sweeney LB. 2026. Multifold increase in spinal inhibitory cell types with emergence of limb movement. Cell Reports. 45(4), 117227. mla: Vijatovic, David, et al. “Multifold Increase in Spinal Inhibitory Cell Types with Emergence of Limb Movement.” Cell Reports, vol. 45, no. 4, 117227, Cell Press, 2026, doi:10.1016/j.celrep.2026.117227. short: D. Vijatovic, F.A. Toma, Y. Ignatyev, Z.P. Harrington, C.M. Sommer, R. Hauschild, M.G. Smits, M. Dalla Vecchia, A.J. Trevisan, P. Chapman, M. Julseth, S. Brenner-Morton, M.I. Gabitto, J.S. Dasen, J.B. Bikoff, L.B. Sweeney, Cell Reports 45 (2026). corr_author: '1' date_created: 2026-04-19T22:07:43Z date_published: 2026-04-28T00:00:00Z date_updated: 2026-10-20T09:04:23Z day: '28' ddc: - '570' department: - _id: LoSw - _id: GradSch - _id: TiVo - _id: Bio - _id: NiBa doi: 10.1016/j.celrep.2026.117227 external_id: pmid: - '41964955 ' file: - access_level: open_access checksum: 0d26cdb5b8d8dec3a911d8261a65cdef content_type: application/pdf creator: dernst date_created: 2026-05-04T12:20:10Z date_updated: 2026-05-04T12:20:10Z file_id: '21795' file_name: 2026_CellReports_Vijatovic.pdf file_size: 14925958 relation: main_file success: 1 file_date_updated: 2026-05-04T12:20:10Z fulldoi: https://doi.org/10.1016/j.celrep.2026.117227 has_accepted_license: '1' intvolume: ' 45' issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 project: - _id: ebb66355-77a9-11ec-83b8-b8ac210a4dae grant_number: '101041551' name: Development and Evolution of Tetrapod Motor Circuits - _id: 8da85f50-16d5-11f0-9cad-eab8b0ff6c9e grant_number: F7814 name: 'Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb transition: cell type to connection diversity' - _id: c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473 grant_number: CZI01 name: Tools for automation and feedback microscopy - _id: bd73af52-d553-11ed-ba76-912049f0ac7a grant_number: FTI21-D-046 name: Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis - _id: cf428362-b037-11f1-b015-8277a8a2f63d grant_number: COE16 name: Neuronal circuits in health and disease (Sweeney) publication: Cell Reports publication_identifier: eissn: - 2211-1247 issn: - 2639-1856 publication_status: published publisher: Cell Press quality_controlled: '1' related_material: record: - id: '22667' relation: dissertation_contains status: public scopus_import: '1' status: public title: Multifold increase in spinal inhibitory cell types with emergence of limb movement tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '21987' abstract: - lang: eng text: 'We introduce JODIE, a genetic joint modeling approach that estimates how DNA loci influence human traits by partitioning genetic effects into four components: direct effects (from a child’s alleles), indirect maternal and paternal effects (from parents’ alleles), and parent-of-origin (PofO) effects (dependent on parental transmission of alleles), while uniquely accounting for assortative mating. We analyze 30,000 child-mother-father trios from the Estonian Biobank and the Norwegian Mother, Father, and Child Cohort, focusing on height, body mass index, and childhood educational test scores. We find direct effects to be the largest contributor to trait variation, but combined, indirect parental and PofO effects are similarly substantial. We support our results by within-family genome-wide association testing and identify 276 independently associated DNA regions with a complex interplay between direct, indirect, and PofO effects. By joint modeling, we show that direct, indirect, and PofO effects collectively shape human phenotypic variation across loci genome-wide.' acknowledged_ssus: - _id: ScienComp acknowledgement: "We thank Zoltan Kutalik, Peter Visscher, and members of the Robinson group at ISTA for their comments, which improved this manuscript. This work was funded by an SNSF Eccellenza Grant to M.R.R. (PCEGP3-181181) and by core funding from the Institute of Science and Technology Austria.\r\nThe Norwegian Mother, Father, and Child Cohort Study is supported by the Norwegian Ministry of Health and Care Services and the Ministry of Education and Research. We are grateful to all the participating families in Norway who take part in this on-going cohort study. We thank the Norwegian Institute of Public Health (NIPH) for generating high-quality genomic data. The research is part of the HARVEST collaboration, supported by the Research Council of Norway (#229624). We also thank the NORMENT Center for providing genotype data, funded by the Research Council of Norway (#223273), South East Norway Health Authorities, and Stiftelsen Kristian Gerhard Jebsen, and in collaboration with deCODE Genetics. We further thank the Center for Diabetes Research, the University of Bergen for providing genotype data funded by the ERC AdG project SELECTionPREDISPOSED, Stiftelsen Kristian Gerhard Jebsen, Trond Mohn Foundation, the Research Council of Norway, the Novo Nordisk Foundation, the University of Bergen, and the Western Norway Health Authorities. The MoBa work was performed on the TSD (Tjeneste for Sensitive Data) facilities, owned by the University of Oslo, operated and developed by the TSD service group at the University of Oslo, IT Department (USIT, tsd-drift@usit.uio.no). E.Y. is supported by the European Union (grant numbers 101045526 and 101073237) and the Research Council of Norway (grant numbers 336078, 288083, and 331640).\r\nWe would like to acknowledge the participants and investigators of the Generation Scotland Cohort study. Generation Scotland received core support from the Chief Scientist Office of the Scottish Government Health Directorates (CZD/16/6) and the Scottish Funding Council (HR03006). Genotyping and methylation typing of the GS:SFHS samples was carried out by the Genetics Core Laboratory at the Wellcome Trust Clinical Research Facility, Edinburgh, Scotland and was funded by the Medical Research Council UK and the Wellcome Trust (Wellcome Trust Strategic Award “STratifying Resilience and Depression Longitudinally” [STRADL] ref. 104036/Z/14/Z).\r\nWe would like to thank and acknowledge the participants and investigators of the Estonian Biobank (EstBB) study. The research was conducted using the Estonian Center of Genomics/Roadmap II funded by the Estonian Research Council (project number TT17).\r\nNorwegian analyses were performed on resources provided by Sigma2 - the National Infrastructure for High-Performance Computing and Data Storage in Norway. Estonian Data analysis was carried out in the High-Performance Computing Center cloud provided by University of Tartu. Analysis of the Generation Scotland data and the summary statistics obtained from the other analyses was conducted at IST Austria and is supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp)." article_number: '101277' article_processing_charge: Yes article_type: original author: - first_name: Ilse full_name: Krätschmer, Ilse id: 30d4014e-7753-11eb-b44b-db6d61112e73 last_name: Krätschmer orcid: 0000-0002-5636-9259 - first_name: Laura full_name: Hegemann, Laura last_name: Hegemann - first_name: Robin J. full_name: Hofmeister, Robin J. last_name: Hofmeister - first_name: Elizabeth C. full_name: Corfield, Elizabeth C. last_name: Corfield - first_name: Mahdi full_name: Mahmoudi, Mahdi last_name: Mahmoudi - first_name: Olivier full_name: Delaneau, Olivier last_name: Delaneau - first_name: Ole A. full_name: Andreassen, Ole A. last_name: Andreassen - first_name: Archie full_name: Campbell, Archie last_name: Campbell - first_name: Caroline full_name: Hayward, Caroline last_name: Hayward - first_name: Riccardo E. full_name: Marioni, Riccardo E. last_name: Marioni - first_name: Eivind full_name: Ystrom, Eivind last_name: Ystrom - first_name: Alexandra full_name: Havdahl, Alexandra last_name: Havdahl - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 citation: ama: Krätschmer I, Hegemann L, Hofmeister RJ, et al. Separating direct, indirect, and parent-of-origin genetic effects in the human population. Cell Genomics. 2026;6(7). doi:10.1016/j.xgen.2026.101277 apa: Krätschmer, I., Hegemann, L., Hofmeister, R. J., Corfield, E. C., Mahmoudi, M., Delaneau, O., … Robinson, M. R. (2026). Separating direct, indirect, and parent-of-origin genetic effects in the human population. Cell Genomics. Cell Press. https://doi.org/10.1016/j.xgen.2026.101277 chicago: Krätschmer, Ilse, Laura Hegemann, Robin J. Hofmeister, Elizabeth C. Corfield, Mahdi Mahmoudi, Olivier Delaneau, Ole A. Andreassen, et al. “Separating Direct, Indirect, and Parent-of-Origin Genetic Effects in the Human Population.” Cell Genomics. Cell Press, 2026. https://doi.org/10.1016/j.xgen.2026.101277. ieee: I. Krätschmer et al., “Separating direct, indirect, and parent-of-origin genetic effects in the human population,” Cell Genomics, vol. 6, no. 7. Cell Press, 2026. ista: Krätschmer I, Hegemann L, Hofmeister RJ, Corfield EC, Mahmoudi M, Delaneau O, Andreassen OA, Campbell A, Hayward C, Marioni RE, Ystrom E, Havdahl A, Robinson MR. 2026. Separating direct, indirect, and parent-of-origin genetic effects in the human population. Cell Genomics. 6(7), 101277. mla: Krätschmer, Ilse, et al. “Separating Direct, Indirect, and Parent-of-Origin Genetic Effects in the Human Population.” Cell Genomics, vol. 6, no. 7, 101277, Cell Press, 2026, doi:10.1016/j.xgen.2026.101277. short: I. Krätschmer, L. Hegemann, R.J. Hofmeister, E.C. Corfield, M. Mahmoudi, O. Delaneau, O.A. Andreassen, A. Campbell, C. Hayward, R.E. Marioni, E. Ystrom, A. Havdahl, M.R. Robinson, Cell Genomics 6 (2026). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: "Information on how to access the MoBaPsychGen post-imputation QC data are available here: https://www.fhi.no/en/me/the-psychgen-centre-for-genetic-epidemiology-and-mental-health/access-to-genetic-data-after-quality-control-by-the-mobapsychgen-pipeline-v/.\r\nEstonian Biobank data (https://genomics.ut.ee/en/content/estonian-biobank) were used in this project. For access to be granted to the Estonian Biobank genotypic and corresponding phenotypic data, a preliminary application must be presented to the oversight committee, who must first approve the project. Ethics permission must then be obtained from the Estonian Committee on Bioethics and Human Research. Finally, a full project must be submitted and approved by the Estonian Biobank.\r\nAccess to the Generation Scotland data is available with appropriate permission from the Generation Scotland Access Committee. Applications should be made to access@generationscotland.org (https://genscot.ed.ac.uk/).\r\nThe code for JODIE developed in this work is open source and is publicly available on zenodo (https://doi.org/10.5281/zenodo.19593928) and GitHub (https://github.com/medical-genomics-group/JODIE).\r\nHaplotype Reference Consortium Release 1.1 data (https://ega-archive.org/datasets/EGAD00001002729) are available by application to a Data Access Committee (DAC) of the Wellcome Trust Sanger Institute.\r\nThe Common Metabolic Diseases Atlas can be accessed here: https://cmdga.org." date_created: 2026-06-10T07:39:08Z date_published: 2026-07-08T00:00:00Z date_updated: 2026-10-20T09:03:50Z day: '08' ddc: - '570' department: - _id: MaRo doi: 10.1016/j.xgen.2026.101277 external_id: pmid: - '40909755' file: - access_level: open_access checksum: f896b510480d2d4e4a7fd46c2e2761f4 content_type: application/pdf creator: dernst date_created: 2026-07-28T07:24:50Z date_updated: 2026-07-28T07:24:50Z file_id: '22597' file_name: 2026_CellGenomics_Kraetschmer.pdf file_size: 3679297 relation: main_file success: 1 file_date_updated: 2026-07-28T07:24:50Z fulldoi: https://doi.org/10.1016/j.xgen.2026.101277 has_accepted_license: '1' intvolume: ' 6' issue: '7' keyword: - direct genetic effects - DGE - indirect genetic effects - IGE - parent-of-origin effects - phenotypic variation - assortative mating - within-family GWAS - MoBa - EstBB language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 9B8D11D6-BA93-11EA-9121-9846C619BF3A grant_number: PCEGP3_181181 name: Improving estimation and prediction of common complex disease risk publication: Cell Genomics publication_identifier: eissn: - 2666-979X publication_status: published publisher: Cell Press quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/human-traits-beyond-inherited-genes/ researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Separating direct, indirect, and parent-of-origin genetic effects in the human population tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2026' ... --- OA_place: publisher _id: '22258' abstract: - lang: eng text: "Uncovering the genetic architecture of complex traits and pinpointing causal molecular drivers require the ability to distinguish true signals from noise within massive, high-dimensional omics datasets. To extract meaningful biological insights from these datasets, such as identifying causal genetic variants and proteins, scalable and accurate inference methods are essential. To this end, this thesis develops novel Bayesian inference frameworks based on Vector Approximate Message Passing and demonstrates their effectiveness in the modeling of disease onset times and quantitative physical and clinical measures.\r\n\r\nFirst, we introduce gVAMP, a Bayesian framework tailored for Genome-Wide Association Studies that enables the joint modeling of quantitative complex traits across millions of genetic variants. gVAMP demonstrates superior accuracy in variable selection and out-of-sample polygenic risk prediction compared to state-of-the-art approaches. We model human height using 17 million whole-genome sequence variants from the UK Biobank, incorporating a vast number of rare variants and revealing novel associations. gVAMP achieves a prediction accuracy of approximately 46% for human height, representing the highest reported performance for this trait to date. \r\n\r\nSecond, we present vampW, a Bayesian framework for survival analysis applied to proteomic data. By effectively handling right-censoring and complex protein dependencies within the UK Biobank Pharma Proteomics Project dataset, vampW identifies 219 protein associations across 24 disease outcomes, the majority of which are not among the top marginal discoveries. We further adjust protein levels for exponential age effects, yielding 1,308 associations and highlighting the sensitivity of the analysis to the chosen age-correction methodology. Finally, vampW improves upon the variable selection capabilities of the commonly used (penalized) variants of the Cox proportional hazards model and delivers state-of-the-art out-of-sample prediction of disease onset times.\r\n\r\nCollectively, these methods provide powerful tools for dissecting the genetic architecture of complex traits and the proteomic drivers of disease onset. Furthermore, by delivering accurate polygenic risk scores and precise predictions of onset times, this work advances the capabilities of personalized medicine and clinical risk stratification." acknowledged_ssus: - _id: ScienComp acknowledgement: "This work was supported in part by the Swiss National Science Foundation through the\r\nEccellenza Grant \"Improving estimation and prediction of common complex disease risk\"\r\n(grant number PCEGP3_181181); the European Research Council through the grant\r\n\"Inference in High Dimensions: Light-speed Algorithms and Information Limits\" (grant\r\nnumber 101161364); and the Fondation Jean-Jacques et Felicia Lopez-Loreta through the\r\nPrix Lopez-Loretta 2019.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Al full_name: Depope, Al id: 0b77531d-dbcd-11ea-9d1d-a8eee0bf3830 last_name: Depope citation: ama: 'Depope A. From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics. 2026. doi:10.15479/AT-ISTA-22258' apa: 'Depope, A. (2026). From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22258' chicago: 'Depope, Al. “From Sparse Selection to Risk Prediction: Approximate Message Passing for Proteomic Survival Models and Large-Scale Genomics.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22258.' ieee: 'A. Depope, “From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics,” Institute of Science and Technology Austria, 2026.' ista: 'Depope A. 2026. From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics. Institute of Science and Technology Austria.' mla: 'Depope, Al. From Sparse Selection to Risk Prediction: Approximate Message Passing for Proteomic Survival Models and Large-Scale Genomics. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22258.' short: 'A. Depope, From Sparse Selection to Risk Prediction: Approximate Message Passing for Proteomic Survival Models and Large-Scale Genomics, Institute of Science and Technology Austria, 2026.' corr_author: '1' das_tickbox: '1' date_created: 2026-07-10T13:27:20Z date_published: 2026-07-11T00:00:00Z date_updated: 2026-10-20T09:03:21Z day: '11' ddc: - '576' - '610' - '006' degree_awarded: PhD department: - _id: GradSch - _id: MaRo - _id: MaMo doi: 10.15479/AT-ISTA-22258 doi_confirm: '1' file: - access_level: open_access checksum: 9ab386790515628d957a194f30a7ccb4 content_type: application/pdf creator: adepope date_created: 2026-07-13T14:52:19Z date_updated: 2026-07-13T14:52:19Z file_id: '22316' file_name: 2026_Depope_Al_Thesis.pdf file_size: 25109878 relation: main_file - access_level: closed checksum: 8ed8fb63f76a695d5b6fec35343f4b90 content_type: application/zip creator: adepope date_created: 2026-07-13T14:56:41Z date_updated: 2026-07-13T14:56:41Z file_id: '22317' file_name: 2026_Depope_Al_Thesis.zip file_size: 1203199939 relation: source_file file_date_updated: 2026-07-13T14:56:41Z fulldoi: https://doi.org/10.15479/AT-ISTA-22258 has_accepted_license: '1' keyword: - Approximate Message Passing - GWAS - Genomics - Proteomics - Survival modeling language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '169' project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli - _id: 911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf grant_number: '101161364' name: 'Inference in High Dimensions: Light-speed Algorithms and Information Limits' - _id: 9B8D11D6-BA93-11EA-9121-9846C619BF3A grant_number: PCEGP3_181181 name: Improving estimation and prediction of common complex disease risk publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '21488' relation: part_of_dissertation status: public status: public supervisor: - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 title: 'From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '21488' abstract: - lang: eng text: Human height is a model for the genetic analysis of complex traits, and recent studies suggest the presence of thousands of common genetic variant associations and hundreds of low-frequency/rare variants. Here, we develop a new algorithmic paradigm based on approximate message passing (genomic vector approximate message passing [gVAMP]) for identifying DNA sequence variants associated with complex traits and common diseases in large-scale whole-genome sequencing (WGS) data. We show that gVAMP accurately localizes associations to variants with the correct frequency and position in the DNA, outperforming existing fine-mapping methods in selecting the appropriate genetic variants within WGS data. We then apply gVAMP to jointly model the relationship of tens of millions of WGS variants with human height in hundreds of thousands of UK Biobank individuals. We identify 59 rare variants and gene burden scores alongside many hundreds of DNA regions containing common variant associations and show that understanding the genetic basis of complex traits will require the joint analysis of hundreds of millions of variables measured on millions of people. The polygenic risk scores obtained from gVAMP have high accuracy (including a prediction accuracy of ∼46% for human height) and outperform current methods for downstream tasks such as mixed linear model association testing across 13 UK Biobank traits. In conclusion, gVAMP offers a scalable foundation for a wider range of analyses in WGS data. acknowledgement: We thank Malgorzata Borczyk for creating the gene burden scores. We thank Robin Beaumont, Amedeo Roberto Esposito, Gareth Hawkes, Philip Schniter, Matthew Stephens, Pragya Sur, Peter Visscher, Michael Weedon, and Harry Wright for providing valuable suggestions and comments on earlier versions of the work. This project was funded by a Lopez-Loreta Prize to M.M., an SNSF Eccellenza Grant to M.R.R. (PCEGP3-181181), an ERC Starting Grant to M.M. (INF2, project number 101161364), and core funding from ISTA. High-performance computing was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp). We would like to acknowledge the participants and investigators of the UK Biobank study. We gratefully acknowledge the All of Us participants for their contributions, without whom this research would not have been possible. We also thank the National Institutes of Health All of Us Research Program for making available the participant data (and/or samples and/or cohort) examined in this study. article_number: '101162' article_processing_charge: Yes article_type: original author: - first_name: Al full_name: Depope, Al id: 0b77531d-dbcd-11ea-9d1d-a8eee0bf3830 last_name: Depope - first_name: Jakub full_name: Bajzik, Jakub id: b995e25b-8c4b-11ed-a6d8-f71b7bcd6122 last_name: Bajzik - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 citation: ama: Depope A, Bajzik J, Mondelli M, Robinson MR. Joint modeling of whole-genome sequencing data for human height via approximate message passing. Cell Genomics. 2026;6(5). doi:10.1016/j.xgen.2026.101162 apa: Depope, A., Bajzik, J., Mondelli, M., & Robinson, M. R. (2026). Joint modeling of whole-genome sequencing data for human height via approximate message passing. Cell Genomics. Cell Press. https://doi.org/10.1016/j.xgen.2026.101162 chicago: Depope, Al, Jakub Bajzik, Marco Mondelli, and Matthew Richard Robinson. “Joint Modeling of Whole-Genome Sequencing Data for Human Height via Approximate Message Passing.” Cell Genomics. Cell Press, 2026. https://doi.org/10.1016/j.xgen.2026.101162. ieee: A. Depope, J. Bajzik, M. Mondelli, and M. R. Robinson, “Joint modeling of whole-genome sequencing data for human height via approximate message passing,” Cell Genomics, vol. 6, no. 5. Cell Press, 2026. ista: Depope A, Bajzik J, Mondelli M, Robinson MR. 2026. Joint modeling of whole-genome sequencing data for human height via approximate message passing. Cell Genomics. 6(5), 101162. mla: Depope, Al, et al. “Joint Modeling of Whole-Genome Sequencing Data for Human Height via Approximate Message Passing.” Cell Genomics, vol. 6, no. 5, 101162, Cell Press, 2026, doi:10.1016/j.xgen.2026.101162. short: A. Depope, J. Bajzik, M. Mondelli, M.R. Robinson, Cell Genomics 6 (2026). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: "This project uses the UK Biobank data under project number 35520. UK Biobank genotypic and phenotypic data are available through a formal request at http://www.ukbiobank.ac.uk. It also uses genotypic and phenotypic data from the All of Us study, which are also available through a formal request at https://www.researchallofus.org/data-tools/data-access/. All summary statistic estimates are released publicly on Dryad: https://doi.org/10.5061/dryad.cz8w9gjjc.\r\n•\r\nThe gVAMP code developed in this work is open source and has been deposited on GitHub, where it is publicly available at https://github.com/medical-genomics-group/gVAMP, and the code used to generate the data in the manuscript are available from Zenodo https://doi.org/10.5281/zenodo.17935521. The URLs of other software used are listed in the key resources table." date_created: 2026-03-23T15:10:03Z date_published: 2026-05-13T00:00:00Z date_updated: 2026-10-20T09:03:22Z day: '13' ddc: - '000' - '570' department: - _id: MaMo - _id: MaRo doi: 10.1016/j.xgen.2026.101162 external_id: pmid: - '41713425' file: - access_level: open_access checksum: 6b59686f8d9733add4f23d23f3dd9df0 content_type: application/pdf creator: dernst date_created: 2026-07-28T07:06:26Z date_updated: 2026-07-28T07:06:26Z file_id: '22596' file_name: 2026_CellGenomics_Depope.pdf file_size: 3736705 relation: main_file success: 1 file_date_updated: 2026-07-28T07:06:26Z fulldoi: https://doi.org/10.1016/j.xgen.2026.101162 has_accepted_license: '1' intvolume: ' 6' issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli - _id: 911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf grant_number: '101161364' name: 'Inference in High Dimensions: Light-speed Algorithms and Information Limits' - _id: 9B8D11D6-BA93-11EA-9121-9846C619BF3A grant_number: PCEGP3_181181 name: Improving estimation and prediction of common complex disease risk publication: Cell Genomics publication_identifier: eissn: - 2666-979X publication_status: published publisher: Cell Press quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/big-data-and-human-height/ record: - id: '22258' relation: dissertation_contains status: public researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Joint modeling of whole-genome sequencing data for human height via approximate message passing tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2026' ... --- OA_place: publisher OA_type: hybrid _id: '22267' abstract: - lang: eng text: Thermal pollution, whether local or driven by global warming, threatens biodiversity in part through its detrimental effects on reproduction. Non-coding small RNAs (sRNAs) are crucial for maintaining germline developmental robustness under heat stress. Remarkably, we uncovered that neuronal sRNAs regulate germ cells’ thermotolerance, affecting both spermatogenic and oogenic germlines in a cell-non-autonomous manner. Furthermore, we demonstrate that, in RNAi mutants, an oxygen-sensing neural circuit, modulated by neuropeptide signaling, antagonizes germline maintenance, likely reflecting the nematode’s innate association of reduced oxygen levels with food availability and reproductive permissive environments. Finally, we provide evidence that laboratory-domesticated alleles of oxygen-response genes encoding neuropeptide receptor NPR-1 and hexacoordinated globin GLB-5 compromise germline thermotolerance. Hence, our findings raise the possibility that sensory perception, independent of direct environmental change, modulates germline integrity, highlighting a novel mechanism by which neural circuits integrate environmental information to safeguard reproductive fitness in fluctuating environments. acknowledgement: We thank Itai Reiger for their assistance with experiments. We thank Cori Bargmann (Rockefeller University) for providing introgressed strains carrying HW alleles of npr-1 and glb-5. Some graphics were created with Biorender.com. We are grateful to WormBase for providing valuable data and resources. Some strains were provided by the Caenorhabditis Genetics Center (CGC), which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). O.R. is grateful for the support of the Morris Kahn Foundation. C.K.E. was supported by an EMBO fellowship ALTF 6-2022. This work is funded by Eric and Wendy Schmidt Fund for Strategic Innovation Polymath Award 0140001000 (O.R.); European Research Council grant 335624 (O.R.); Israel Science Foundation 979/21 (Y.B.T.); and the US-Israel Binational Science Foundation 2023036 (Y.B.T.). article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Chee Kiang full_name: Ewe, Chee Kiang last_name: Ewe - first_name: Hanna full_name: Achache, Hanna last_name: Achache - first_name: Hanna full_name: Schön, Hanna id: C8E17EDC-D7AA-11E9-B7B7-45ECE5697425 last_name: Schön - first_name: Leonid full_name: Kontorovich, Leonid last_name: Kontorovich - first_name: Guy full_name: Teichman, Guy last_name: Teichman - first_name: Shir full_name: Weiss, Shir last_name: Weiss - first_name: Anna full_name: Mogilevskaya, Anna last_name: Mogilevskaya - first_name: Myriam full_name: Valenski, Myriam last_name: Valenski - first_name: Sarit full_name: Anava, Sarit last_name: Anava - first_name: Rutwik full_name: Bardapurkar, Rutwik last_name: Bardapurkar - first_name: Hila full_name: Gingold, Hila last_name: Gingold - first_name: Rachel full_name: Posner, Rachel last_name: Posner - first_name: Olga full_name: Antonova, Olga last_name: Antonova - first_name: Mario full_name: De Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: De Bono orcid: 0000-0001-8347-0443 - first_name: Yonatan B. full_name: Tzur, Yonatan B. last_name: Tzur - first_name: Oded full_name: Rechavi, Oded last_name: Rechavi citation: ama: Ewe CK, Achache H, Schön H, et al. Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress. Current Biology. 2026;36(14):3566-3579.e5. doi:10.1016/j.cub.2026.06.016 apa: Ewe, C. K., Achache, H., Schön, H., Kontorovich, L., Teichman, G., Weiss, S., … Rechavi, O. (2026). Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2026.06.016 chicago: Ewe, Chee Kiang, Hanna Achache, Hanna Schön, Leonid Kontorovich, Guy Teichman, Shir Weiss, Anna Mogilevskaya, et al. “Neuronal RNAi and Oxygen-Sensing Circuit Shape Germline Resilience to Heat Stress.” Current Biology. Cell Press, 2026. https://doi.org/10.1016/j.cub.2026.06.016. ieee: C. K. Ewe et al., “Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress,” Current Biology, vol. 36, no. 14. Cell Press, p. 3566–3579.e5, 2026. ista: Ewe CK, Achache H, Schön H, Kontorovich L, Teichman G, Weiss S, Mogilevskaya A, Valenski M, Anava S, Bardapurkar R, Gingold H, Posner R, Antonova O, de Bono M, Tzur YB, Rechavi O. 2026. Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress. Current Biology. 36(14), 3566–3579.e5. mla: Ewe, Chee Kiang, et al. “Neuronal RNAi and Oxygen-Sensing Circuit Shape Germline Resilience to Heat Stress.” Current Biology, vol. 36, no. 14, Cell Press, 2026, p. 3566–3579.e5, doi:10.1016/j.cub.2026.06.016. short: C.K. Ewe, H. Achache, H. Schön, L. Kontorovich, G. Teichman, S. Weiss, A. Mogilevskaya, M. Valenski, S. Anava, R. Bardapurkar, H. Gingold, R. Posner, O. Antonova, M. de Bono, Y.B. Tzur, O. Rechavi, Current Biology 36 (2026) 3566–3579.e5. das_tickbox: '1' dataavailabilitystatement: "* All NGS data are available through GEO under accession number GSE331410.\r\n* This paper does not report original code.\r\n* Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request." date_created: 2026-07-12T22:02:18Z date_published: 2026-07-20T00:00:00Z date_updated: 2026-10-20T09:03:35Z day: '20' ddc: - '570' department: - _id: MaDe doi: 10.1016/j.cub.2026.06.016 external_id: pmid: - '42409014' file: - access_level: open_access checksum: 5ec4472d81fd44de03ccb92b1eb690a6 content_type: application/pdf creator: dernst date_created: 2026-07-28T07:31:44Z date_updated: 2026-07-28T07:31:44Z file_id: '22598' file_name: 2026_CurrentBiology_KiangEwe.pdf file_size: 6795092 relation: main_file success: 1 file_date_updated: 2026-07-28T07:31:44Z fulldoi: https://doi.org/10.1016/j.cub.2026.06.016 has_accepted_license: '1' intvolume: ' 36' issue: '14' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 3566-3579.e5 pmid: 1 publication: Current Biology publication_identifier: eissn: - 1879-0445 issn: - 0960-9822 publication_status: published publisher: Cell Press quality_controlled: '1' researchdata_availability: upon request scopus_import: '1' status: public supplementarymaterial: yes title: Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2026' ... --- OA_place: publisher OA_type: hybrid _id: '22148' abstract: - lang: eng text: 'How the twin-arginine translocase (Tat) system transports fully folded substrate proteins across cellular membranes without disrupting membrane integrity has been a fundamental question in cell biology for decades. The Tat system, found in prokaryotes and plant organelles, recognizes a cargo signal peptide via a conserved twin-arginine motif. The multi-subunit Tat complex facilitates the proton-motive-force-dependent translocation process, yet its overall architecture has remained unknown. Here, we present the cryo-electron microscopy (cryo-EM) structure of the Escherichia coli (E. coli) trimeric TatB₃C₃ complex with bound substrate SufI, assembled in vivo. The complex adopts an unusual, wide-open, bowl-shaped architecture with a polar inner cavity. Unexpectedly, the cargo is engaged in a dual-contact mode: while the signal peptide binds inside one TatBC unit, the folded domain docks tightly onto an adjacent unit, possibly performing a proofreading function. This structure provides a mechanistic framework for substrate engagement and suggests the direct involvement of the entire Tat complex in substrate translocation.' acknowledged_ssus: - _id: EM-Fac - _id: ScienComp acknowledgement: We thank IST Austria for providing the funding. We thank IST Austria EM facility for the use of Titan Krios TEM. Data processing was performed using IST high-performance computer cluster. We thank Dr. R. Roemhild and Professor C. Guet (ISTA) for help in constructing Tat deletion strains and Dr. A. Charnagalov (ISTA) for technical help. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Ziyu full_name: Zhao, Ziyu id: a63fe682-9f3a-11ee-bf8c-cfdf919b9850 last_name: Zhao - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 biorxivid: 1 citation: ama: Zhao Z, Sazanov LA. Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo. Molecular Cell. doi:10.1016/j.molcel.2026.05.026 apa: Zhao, Z., & Sazanov, L. A. (n.d.). Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo. Molecular Cell. Cell Press. https://doi.org/10.1016/j.molcel.2026.05.026 chicago: Zhao, Ziyu, and Leonid A Sazanov. “Structure of E. Coli Twin-Arginine Translocase (Tat) Complex with Bound Cargo.” Molecular Cell. Cell Press, n.d. https://doi.org/10.1016/j.molcel.2026.05.026. ieee: Z. Zhao and L. A. Sazanov, “Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo,” Molecular Cell. Cell Press. ista: Zhao Z, Sazanov LA. Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo. Molecular Cell. mla: Zhao, Ziyu, and Leonid A. Sazanov. “Structure of E. Coli Twin-Arginine Translocase (Tat) Complex with Bound Cargo.” Molecular Cell, Cell Press, doi:10.1016/j.molcel.2026.05.026. short: Z. Zhao, L.A. Sazanov, Molecular Cell (n.d.). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: "This study did not generate new unique reagents. Strains and plasmids generated in this study are available from the lead contact without restrictions.\r\n• Source data are provided within this paper. The cryo-EM map is deposited in the Electron Microscopy Data Bank under accession number EMD-53848. The model is deposited in the Protein Data Bank under accession number 9R91. The structural data are publicly available as of the date of publication. Raw images of spot assays, SDS-PAGE and BN-PAGE gels with Coomassie staining and immunoblot images are available at Mendeley Data (https://doi.org/10.17632/v2g3p9n985.1).\r\n• This paper does not report original code.\r\n• Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request." date_created: 2026-06-28T22:01:35Z date_published: 2026-06-22T00:00:00Z date_updated: 2026-10-20T09:04:07Z day: '22' ddc: - '570' department: - _id: LeSa doi: 10.1016/j.molcel.2026.05.026 external_id: biorxivid: - 10.1101/2025.09.16.676506 fulldoi: https://doi.org/10.1016/j.molcel.2026.05.026 has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.molcel.2026.05.026 month: '06' oa: 1 oa_version: Published Version publication: Molecular Cell publication_identifier: eissn: - 1097-4164 issn: - 1097-2765 publication_status: inpress publisher: Cell Press quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/the-gate-for-bulky-cargo/ record: - id: '22189' relation: research_data status: public researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- OA_place: publisher _id: '22667' acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: "I am also grateful for the financial support that made this work possible, including the\r\nEuropean Research Council (ERC Starting Grant 101041551), the Austrian Science\r\nFund (FWF, Cluster of Excellence 10.55776/COE16), the GFF Lower Austria FTI\r\nStrategy Dissertation Fellowship (FTI21-D-046), and the FENS/IBRO-PERC\r\nExchange Fellowship. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: David full_name: Vijatovic, David id: cf391e77-ec3c-11ea-a124-d69323410b58 last_name: Vijatovic orcid: 0000-0002-5494-0941 citation: ama: Vijatovic D. Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis. 2026. doi:10.15479/AT-ISTA-22667 apa: Vijatovic, D. (2026). Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22667 chicago: Vijatovic, David. “Dissecting the Molecular and Functional Basis of Motor Control in the Frog Xenopus Laevis.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22667. ieee: D. Vijatovic, “Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis,” Institute of Science and Technology Austria, 2026. ista: Vijatovic D. 2026. Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis. Institute of Science and Technology Austria. mla: Vijatovic, David. Dissecting the Molecular and Functional Basis of Motor Control in the Frog Xenopus Laevis. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22667. short: D. Vijatovic, Dissecting the Molecular and Functional Basis of Motor Control in the Frog Xenopus Laevis, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-08-10T13:44:30Z date_published: 2026-08-10T00:00:00Z date_updated: 2026-10-20T09:04:22Z day: '10' ddc: - '573' degree_awarded: PhD department: - _id: GradSch - _id: LoSw doi: 10.15479/AT-ISTA-22667 doi_confirm: '1' file: - access_level: closed checksum: e3acfea4b1a3abf99e74224656740a15 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dvijatov date_created: 2026-08-10T13:35:39Z date_updated: 2026-08-10T13:35:39Z file_id: '22669' file_name: 2026_Vijatovic_David_Thesis.docx file_size: 14322760 relation: source_file - access_level: closed checksum: dc8c78ae14f69e54faa41e65db5c6402 content_type: application/pdf creator: dvijatov date_created: 2026-08-12T13:44:36Z date_updated: 2026-08-12T13:44:36Z embargo: 2027-08-10 embargo_to: open_access file_id: '22695' file_name: 2026_Vijatovic_David_Thesis.pdf file_size: 116926375 relation: main_file file_date_updated: 2026-08-12T13:44:36Z fulldoi: https://doi.org/10.15479/AT-ISTA-22667 has_accepted_license: '1' language: - iso: eng month: '08' oa_version: Published Version page: '172' project: - _id: ebb66355-77a9-11ec-83b8-b8ac210a4dae grant_number: '101041551' name: Development and Evolution of Tetrapod Motor Circuits - _id: bd73af52-d553-11ed-ba76-912049f0ac7a grant_number: FTI21-D-046 name: Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis - _id: 34a02c70-11ca-11ed-8bc3-fbfd2c86c88f grant_number: 3(GG016346-01) name: Development of Viral Vectors for Amphibian Gene Delivery and Manipulation publication_identifier: isbn: - 978-3-99078-082-4 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '15016' relation: part_of_dissertation status: public - id: '21746' relation: part_of_dissertation status: public status: public supervisor: - first_name: Lora Beatrice Jaeger full_name: Sweeney, Lora Beatrice Jaeger id: 56BE8254-C4F0-11E9-8E45-0B23E6697425 last_name: Sweeney orcid: 0000-0001-9242-5601 title: Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: publisher OA_type: gold _id: '22189' abstract: - lang: eng text: Raw images for SDS and Blue Native gels, western blots and spot growth assays, related to figures S1 and S2. article_processing_charge: No author: - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Sazanov LA. Structure of E. coli twin-arginine translocase (Tat) complex with bound cargo. Zhao et al. 2026. doi:10.17632/V2G3P9N985.1 apa: Sazanov, L. A. (2026). Structure of E. coli twin-arginine translocase (Tat) complex with bound cargo. Zhao et al. Mendeley Data. https://doi.org/10.17632/V2G3P9N985.1 chicago: Sazanov, Leonid A. “Structure of E. Coli Twin-Arginine Translocase (Tat) Complex with Bound Cargo. Zhao et Al.” Mendeley Data, 2026. https://doi.org/10.17632/V2G3P9N985.1. ieee: L. A. Sazanov, “Structure of E. coli twin-arginine translocase (Tat) complex with bound cargo. Zhao et al.” Mendeley Data, 2026. ista: Sazanov LA. 2026. Structure of E. coli twin-arginine translocase (Tat) complex with bound cargo. Zhao et al., Mendeley Data, 10.17632/V2G3P9N985.1. mla: Sazanov, Leonid A. Structure of E. Coli Twin-Arginine Translocase (Tat) Complex with Bound Cargo. Zhao et Al. Mendeley Data, 2026, doi:10.17632/V2G3P9N985.1. short: L.A. Sazanov, (2026). corr_author: '1' date_created: 2026-06-29T12:54:45Z date_published: 2026-05-15T00:00:00Z date_updated: 2026-10-20T09:04:06Z day: '15' ddc: - '570' department: - _id: LeSa doi: 10.17632/V2G3P9N985.1 fulldoi: https://doi.org/10.17632/V2G3P9N985.1 has_accepted_license: '1' keyword: - Protein Purification main_file_link: - open_access: '1' url: https://doi.org/10.17632/v2g3p9n985.1 month: '05' oa: 1 oa_version: Published Version publisher: Mendeley Data related_material: record: - id: '22148' relation: used_in_publication status: public status: public title: Structure of E. coli twin-arginine translocase (Tat) complex with bound cargo. Zhao et al. tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '22955' abstract: - lang: eng text: The regulation of 3D cell shape is a fundamental problem of life. In multicellular tissues, cell shape emerges through the balance of forces inside and outside the cell. In epithelia, the basement membrane (BM) is the first extracellular barrier that cells sense biochemically and mechanically. Despite this, little is known about how BM mechanical properties are regulated and how they impact cell shape. Through mathematical modeling, we show that the stress relaxation time of the BM can regulate cell shape. Using molecular dynamics simulations, we show that the stress relaxation time of a collagen IV network can be inferred from the lifetime of collagen IV molecules. To measure collagen IV lifetime in vivo, we develop a fluorescent timer reporter for collagen IV and show that perlecan modifies collagen IV lifetime. This cross-disciplinary approach establishes a multiscale framework to probe matrix turnover, and its regulation and function in cell shape control. acknowledgement: "We thank all members of the Mao lab for insightful discussions throughout the project, and we thank Giulia Paci and Nargess Khalilgharibi for critical reading of the manuscript. We thank Jonathan Chubb for molecular biology guidance and WellGenetics for generating the timer protein fly lines.\r\nR.B. was funded by a UCL COMPLEX PhD studentship and a Leverhulme Trust project grant RPG-2020-068 awarded to Y.M. B.M. and A.S. were funded by the European Union Horizon 2020 research and innovation programme (ERC starting grant no. 802960). S.B. was funded by NIH R35 GM143042. G.C. was funded by EPSRC Physics of Life, grants EP/W023806 and EP/W023865. B.J.S.S. and B.M.S. are funded by the Wellcome Trust (grant no. 301803/Z/23/Z to B.M.S.). E.K.P. was funded by the Medical Research Council UK (MRC programme award MC_UU_12018/5). Y.M. was funded by MRC award MR/W027437/1, a Lister Institute Research Prize, and the EMBO Young Investigator Programme." article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Ricardo full_name: Barrientos, Ricardo last_name: Barrientos - first_name: Billie full_name: Meadowcroft, Billie id: a4725fd6-932b-11ed-81e2-c098c7f37ae1 last_name: Meadowcroft orcid: 0000-0003-3441-1337 - first_name: Besaiz J. full_name: Sánchez-Sánchez, Besaiz J. last_name: Sánchez-Sánchez - first_name: Brian M. full_name: Stramer, Brian M. last_name: Stramer - first_name: Ewa K. full_name: Paluch, Ewa K. last_name: Paluch - first_name: Guillaume full_name: Charras, Guillaume last_name: Charras - first_name: Shiladitya full_name: Banerjee, Shiladitya last_name: Banerjee - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Yanlan full_name: Mao, Yanlan last_name: Mao citation: ama: Barrientos R, Meadowcroft B, Sánchez-Sánchez BJ, et al. Basement membrane turnover controls cell shape. Cell. 2026;189(18):5611-5624.e4. doi:10.1016/j.cell.2026.07.010 apa: Barrientos, R., Meadowcroft, B., Sánchez-Sánchez, B. J., Stramer, B. M., Paluch, E. K., Charras, G., … Mao, Y. (2026). Basement membrane turnover controls cell shape. Cell. Cell Press. https://doi.org/10.1016/j.cell.2026.07.010 chicago: Barrientos, Ricardo, Billie Meadowcroft, Besaiz J. Sánchez-Sánchez, Brian M. Stramer, Ewa K. Paluch, Guillaume Charras, Shiladitya Banerjee, Anđela Šarić, and Yanlan Mao. “Basement Membrane Turnover Controls Cell Shape.” Cell. Cell Press, 2026. https://doi.org/10.1016/j.cell.2026.07.010. ieee: R. Barrientos et al., “Basement membrane turnover controls cell shape,” Cell, vol. 189, no. 18. Cell Press, p. 5611–5624.e4, 2026. ista: Barrientos R, Meadowcroft B, Sánchez-Sánchez BJ, Stramer BM, Paluch EK, Charras G, Banerjee S, Šarić A, Mao Y. 2026. Basement membrane turnover controls cell shape. Cell. 189(18), 5611–5624.e4. mla: Barrientos, Ricardo, et al. “Basement Membrane Turnover Controls Cell Shape.” Cell, vol. 189, no. 18, Cell Press, 2026, p. 5611–5624.e4, doi:10.1016/j.cell.2026.07.010. short: R. Barrientos, B. Meadowcroft, B.J. Sánchez-Sánchez, B.M. Stramer, E.K. Paluch, G. Charras, S. Banerjee, A. Šarić, Y. Mao, Cell 189 (2026) 5611–5624.e4. das_tickbox: '1' dataavailabilitystatement: "The fly line generated in this study is available from the lead contact without restriction.\r\nData and code availability\r\n•\r\nCollagen IV fluorescent timer image data and associated data analysis code have been deposited in the UCL Research Data Repository at https://doi.org/10.5522/04/32647191 and are publicly available as of the date of publication.\r\n•\r\nAll original code associated with the tissue mechanics model has also been deposited in the UCL Research Data Repository at https://doi.org/10.5522/04/32647191 and is publicly available as of the date of publication.\r\n•\r\nAll original code associated with the collagen IV network model has been deposited on Zenodo at https://doi.org/10.5281/zenodo.20719515 and is publicly available as of the date of publication.\r\n•\r\nAny additional information reported in this paper is available from the lead contact upon request." date_created: 2026-09-17T11:06:06Z date_published: 2026-09-03T00:00:00Z date_updated: 2026-10-20T09:04:52Z day: '03' ddc: - '570' department: - _id: AnSa doi: 10.1016/j.cell.2026.07.010 ec_funded: 1 external_id: pmid: - '42532043' file: - access_level: open_access checksum: 01e74f866223ca9ea8680b617d4aa4e3 content_type: application/pdf creator: dernst date_created: 2026-09-24T12:35:11Z date_updated: 2026-09-24T12:35:11Z file_id: '22990' file_name: 2026_Cell_Barrientos.pdf file_size: 5642382 relation: main_file success: 1 file_date_updated: 2026-09-24T12:35:11Z fulldoi: https://doi.org/10.1016/j.cell.2026.07.010 has_accepted_license: '1' intvolume: ' 189' issue: '18' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 5611-5624.e4 pmid: 1 project: - _id: eba2549b-77a9-11ec-83b8-a81e493eae4e call_identifier: H2020 grant_number: '802960' name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines' publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Cell Press quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: Basement membrane turnover controls cell shape tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 189 year: '2026' ... --- OA_type: closed access _id: '21996' abstract: - lang: eng text: In this issue of Cell Host & Microbe, Osterman et al. discover aRES,1 a new family of bacterial immune proteins that deplete cellular NAD+, generating cleavage products that cannot be utilized by canonical phage NAD+ regeneration pathways. They identify the invader-specific trigger for aRES and characterize two distinct evolutionary countermeasures employed by phages to resist aRES. acknowledgement: This work was supported by the Austrian Science Fund (FWF) (10.55776/PAT1617625). article_processing_charge: No article_type: original author: - first_name: Daniel full_name: Williams-Jones, Daniel id: 128eaab9-b327-11f0-bdbe-e02d5abac73b last_name: Williams-Jones - first_name: Jack Peter Kelly full_name: Bravo, Jack Peter Kelly id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e last_name: Bravo orcid: 0000-0003-0456-0753 citation: ama: 'Williams-Jones D, Bravo JPK. NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back. Cell Host & Microbe. 2026;34(6):978-980. doi:10.1016/j.chom.2026.05.013' apa: 'Williams-Jones, D., & Bravo, J. P. K. (2026). NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back. Cell Host & Microbe. Cell Press. https://doi.org/10.1016/j.chom.2026.05.013' chicago: 'Williams-Jones, Daniel, and Jack Peter Kelly Bravo. “NAD to the Bone: How Bacteria Put Phages under ARES-t … and How Phages Fight Back.” Cell Host & Microbe. Cell Press, 2026. https://doi.org/10.1016/j.chom.2026.05.013.' ieee: 'D. Williams-Jones and J. P. K. Bravo, “NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back,” Cell Host & Microbe, vol. 34, no. 6. Cell Press, pp. 978–980, 2026.' ista: 'Williams-Jones D, Bravo JPK. 2026. NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back. Cell Host & Microbe. 34(6), 978–980.' mla: 'Williams-Jones, Daniel, and Jack Peter Kelly Bravo. “NAD to the Bone: How Bacteria Put Phages under ARES-t … and How Phages Fight Back.” Cell Host & Microbe, vol. 34, no. 6, Cell Press, 2026, pp. 978–80, doi:10.1016/j.chom.2026.05.013.' short: D. Williams-Jones, J.P.K. Bravo, Cell Host & Microbe 34 (2026) 978–980. corr_author: '1' das_tickbox: '1' date_created: 2026-06-14T22:01:42Z date_published: 2026-06-10T00:00:00Z date_updated: 2026-10-20T09:04:35Z day: '10' department: - _id: JaBr doi: 10.1016/j.chom.2026.05.013 external_id: pmid: - '42269584' fulldoi: https://doi.org/10.1016/j.chom.2026.05.013 intvolume: ' 34' issue: '6' language: - iso: eng month: '06' oa_version: None page: 978-980 pmid: 1 project: - _id: 9f295cab-ad08-11f1-bc83-9e197d0f6d50 grant_number: PAT1617625 name: 'Search & Destroy: Mechanisms of anti-plasmid immunity' publication: Cell Host & Microbe publication_identifier: eissn: - 1934-6069 issn: - 1931-3128 publication_status: published publisher: Cell Press quality_controlled: '1' scopus_import: '1' status: public title: 'NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2026' ... --- OA_place: repository OA_type: green _id: '22104' abstract: - lang: eng text: ' Modern computer systems store vast amounts of personal data, enabling advances in AI and ML but risking user privacy and trust. For privacy reasons, it is sometimes desired for an ML model to forget part of the data it was trained on. In this paper, we introduce a novel unlearning approach based on Forgetting Neural Networks (FNNs), a neuroscience-inspired architecture that explicitly encodes forgetting through multiplicative decay factors. While FNNs had previously been studied as a theoretical construct, we provide the first concrete implementation and demonstrate their effectiveness for targeted unlearning. We propose several variants with per-neuron forgetting factors, including rank-based assignments guided by activation levels, and evaluate them on MNIST and Fashion-MNIST benchmarks. Our method systematically removes information associated with forget sets while preserving performance on retained data. Membership inference attacks confirm the effectiveness of FNN-based unlearning in erasing information about the training data from the neural network. These results establish FNNs as a promising foundation for efficient and interpretable unlearning.' acknowledgement: "This work has been supported by the European Research\r\nCouncil under Grant No.: ERC-2020-AdG\r\n101020093. We thank Brian Subirana for the original\r\nideation of the concept of forgetting neural networks\r\nand his belief in their potential." article_processing_charge: No arxiv: 1 author: - first_name: Amartya full_name: Hatua, Amartya last_name: Hatua - first_name: Trung T. full_name: Nguyen, Trung T. last_name: Nguyen - first_name: Filip full_name: Cano Cordoba, Filip id: 708cad98-e86a-11ef-8098-bdae2d7c6af1 last_name: Cano Cordoba orcid: 0000-0002-0783-904X - first_name: Andrew H. full_name: Sung, Andrew H. last_name: Sung citation: ama: 'Hatua A, Nguyen TT, Cano Cordoba F, Sung AH. Machine unlearning using forgetting neural networks. In: Proceedings of the 18th International Conference on Agents and Artificial Intelligence. Vol 2. Science and Technology Publications; 2026:1536-1546. doi:10.5220/0014326500004052' apa: 'Hatua, A., Nguyen, T. T., Cano Cordoba, F., & Sung, A. H. (2026). Machine unlearning using forgetting neural networks. In Proceedings of the 18th International Conference on Agents and Artificial Intelligence (Vol. 2, pp. 1536–1546). Marbella, Spain: Science and Technology Publications. https://doi.org/10.5220/0014326500004052' chicago: Hatua, Amartya, Trung T. Nguyen, Filip Cano Cordoba, and Andrew H. Sung. “Machine Unlearning Using Forgetting Neural Networks.” In Proceedings of the 18th International Conference on Agents and Artificial Intelligence, 2:1536–46. Science and Technology Publications, 2026. https://doi.org/10.5220/0014326500004052. ieee: A. Hatua, T. T. Nguyen, F. Cano Cordoba, and A. H. Sung, “Machine unlearning using forgetting neural networks,” in Proceedings of the 18th International Conference on Agents and Artificial Intelligence, Marbella, Spain, 2026, vol. 2, pp. 1536–1546. ista: 'Hatua A, Nguyen TT, Cano Cordoba F, Sung AH. 2026. Machine unlearning using forgetting neural networks. Proceedings of the 18th International Conference on Agents and Artificial Intelligence. ICAART: International Conference on Agents and Artificial Intelligence vol. 2, 1536–1546.' mla: Hatua, Amartya, et al. “Machine Unlearning Using Forgetting Neural Networks.” Proceedings of the 18th International Conference on Agents and Artificial Intelligence, vol. 2, Science and Technology Publications, 2026, pp. 1536–46, doi:10.5220/0014326500004052. short: A. Hatua, T.T. Nguyen, F. Cano Cordoba, A.H. Sung, in:, Proceedings of the 18th International Conference on Agents and Artificial Intelligence, Science and Technology Publications, 2026, pp. 1536–1546. conference: end_date: 2026-03-08 location: Marbella, Spain name: 'ICAART: International Conference on Agents and Artificial Intelligence' start_date: 2026-03-05 das_tickbox: '0' date_created: 2026-06-21T22:03:01Z date_published: 2026-04-01T00:00:00Z date_updated: 2026-10-20T14:05:02Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.5220/0014326500004052 ec_funded: 1 external_id: arxiv: - '2410.22374' file: - access_level: open_access checksum: d0f5212846c8f3129509b081648465cb content_type: application/pdf creator: dernst date_created: 2026-10-20T14:00:27Z date_updated: 2026-10-20T14:00:27Z file_id: '23178' file_name: 2026_CAART_Hatua.pdf file_size: 779692 relation: main_file success: 1 file_date_updated: 2026-10-20T14:00:27Z fulldoi: https://doi.org/10.5220/0014326500004052 has_accepted_license: '1' intvolume: ' 2' keyword: - Machine Unlearning - Neuroscience-Inspired Machine Learning - Membership Inference Attacks language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1536-1546 project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: Proceedings of the 18th International Conference on Agents and Artificial Intelligence publication_identifier: eissn: - 2184-433X isbn: - '9789897587962' issn: - 2184-3589 publication_status: published publisher: Science and Technology Publications quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Machine unlearning using forgetting neural networks tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2026' ... --- OA_place: repository OA_type: green _id: '22359' abstract: - lang: eng text: We prove a mesoscopic central limit theorem for linear eigenvalue statistics of correlated Hermitian random matrices. The class considered here includes Wigner and Wigner-type matrices, as well as models whose entry correlations decay polynomially in the distance between index pairs. The proof combines a multivariate cumulant expansion with multi-resolvent local laws and a detailed analysis of the resulting variance kernel on the operator-level. acknowledgement: Supported by ERC Advanced Grant “RMTBeyond” No. 101020331 article_number: '2607.05848' article_processing_charge: No arxiv: 1 author: - first_name: Jaehun full_name: Lee, Jaehun id: 96155047-f36a-11ef-b766-8b5ae7cecd49 last_name: Lee - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 citation: ama: Lee J, Erdös L. Mesoscopic eigenvalue statistics for correlated random matrices. arXiv. doi:10.48550/arXiv.2607.05848 apa: Lee, J., & Erdös, L. (n.d.). Mesoscopic eigenvalue statistics for correlated random matrices. arXiv. https://doi.org/10.48550/arXiv.2607.05848 chicago: Lee, Jaehun, and László Erdös. “Mesoscopic Eigenvalue Statistics for Correlated Random Matrices.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2607.05848. ieee: J. Lee and L. Erdös, “Mesoscopic eigenvalue statistics for correlated random matrices,” arXiv. . ista: Lee J, Erdös L. Mesoscopic eigenvalue statistics for correlated random matrices. arXiv, 2607.05848. mla: Lee, Jaehun, and László Erdös. “Mesoscopic Eigenvalue Statistics for Correlated Random Matrices.” ArXiv, 2607.05848, doi:10.48550/arXiv.2607.05848. short: J. Lee, L. Erdös, ArXiv (n.d.). corr_author: '1' das_tickbox: '1' date_created: 2026-07-18T08:59:02Z date_published: 2026-07-07T00:00:00Z date_updated: 2026-10-20T10:06:12Z day: '07' department: - _id: LaEr doi: 10.48550/arXiv.2607.05848 ec_funded: 1 external_id: arxiv: - '2607.05848' fulldoi: https://doi.org/10.48550/arXiv.2607.05848 keyword: - Central limit theorem - universality - matrix Dyson equation - multi-resolvent local law language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2607.05848 month: '07' oa: 1 oa_version: Preprint project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: arXiv publication_status: submitted status: public title: Mesoscopic eigenvalue statistics for correlated random matrices type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ...