[{"type":"dissertation","supervisor":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X"}],"OA_place":"publisher","alternative_title":["ISTA Thesis"],"file":[{"relation":"source_file","content_type":"application/x-zip-compressed","checksum":"dc15958f6400b5bdaa28bf58fc7a4056","embargo_to":"open_access","file_size":156207943,"file_id":"18130","date_updated":"2025-05-23T22:30:09Z","access_level":"closed","creator":"mjanik","file_name":"janik_thesis.zip","date_created":"2024-09-23T17:15:09Z"},{"file_id":"18131","embargo":"2025-05-23","file_size":96195684,"checksum":"74737aee285dc1f491643327350efe9c","relation":"main_file","content_type":"application/pdf","file_name":"janik_thesis_pdfa.pdf","date_created":"2024-09-23T17:15:30Z","access_level":"open_access","creator":"mjanik","date_updated":"2025-05-23T22:30:09Z"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ista":"Janik M. 2024. Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors. Institute of Science and Technology Austria.","mla":"Janik, Marian. Strong Charge-Photon Coupling in Germanium Enabled by Granular Aluminium Superinductors. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18129.","ama":"Janik M. Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors. 2024. doi:10.15479/at:ista:18129","ieee":"M. Janik, “Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors,” Institute of Science and Technology Austria, 2024.","short":"M. Janik, Strong Charge-Photon Coupling in Germanium Enabled by Granular Aluminium Superinductors, Institute of Science and Technology Austria, 2024.","chicago":"Janik, Marian. “Strong Charge-Photon Coupling in Germanium Enabled by Granular Aluminium Superinductors.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18129.","apa":"Janik, M. (2024). Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18129"},"publication_identifier":{"issn":["2663-337X"]},"corr_author":"1","degree_awarded":"PhD","abstract":[{"lang":"eng","text":"State-of-the-art quantum computers, with roughly a thousand qubits, face a crucial technological challenge of scaling up. Spins confined in quantum dots (QDs) are a promising candidate\r\nfor qubits due to their long coherence, tunability, control, and readout. However, their natural\r\ncoupling is the short-ranged (∼ 100 nm) exchange interaction, limited to nearest neighbours.\r\nLong-ranged (∼ 1 mm) qubit interactions mediated by a photon could be engineered through a\r\ncoherent spin-photon coupling. Achieving a strong coupling to a photon is inherently challenging in QDs due to the small dipole moment of the confined charge. However, the potential of\r\nhigh-impedance resonators to compensate for this has gained significant attention in the past\r\ndecade. Nevertheless, previous QD circuit quantum electrodynamics implementations have not\r\nexceeded the impedance of ∼ 3.8 kΩ, leaving opportunities for significant improvement. The\r\nlarge kinetic inductance of granular aluminium (grAl) could provide an order-of-magnitude\r\nenhancement. However, fully exploiting the potential of disordered or granular superconductors\r\nis challenging as their impedances close to the superconductor-to-insulator transition are\r\ndifficult to control reproducibly. We report on the realization of a wireless ohmmeter which\r\nallows in situ resistance measurements during film deposition and, therefore, indirect control\r\nof the kinetic inductance of grAl films. This allows us to reproducibly fabricate resonators\r\nwith characteristic impedance exceeding the resistance quantum, even reaching 22.3 kW, due\r\nto the large sheet kinetic inductance of up to 3 nH □−1\r\n. By integrating an 8 kW resonator\r\nwith a germanium double QD, we demonstrate a strong charge-photon coupling with the\r\nhighest rate reported, 566 MHz. The demonstrated method and grAl properties make these\r\nresonators suitable for boosting the spin-photon coupling strength, a crucial requirement for\r\nfast, high-fidelity, long-distance two-qubit gates.\r\n"}],"date_published":"2024-09-24T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_updated":"2026-04-07T13:23:25Z","publication_status":"published","project":[{"grant_number":"I05060","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","name":"High impedance circuit quantum electrodynamics with hole spins"},{"_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","name":"Merging spin and superconducting qubits in planar Ge","grant_number":"P36507"},{"grant_number":"P32235","name":"Towards scalable hut wire quantum devices","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","call_identifier":"FWF"},{"grant_number":"101069515","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","name":"Integrated Germanium Quantum Technology"},{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"}],"title":"Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"has_accepted_license":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"article_processing_charge":"No","day":"24","publisher":"Institute of Science and Technology Austria","page":"164","license":"https://creativecommons.org/licenses/by/4.0/","language":[{"iso":"eng"}],"year":"2024","oa_version":"Published Version","status":"public","_id":"18129","ddc":["539"],"file_date_updated":"2025-05-23T22:30:09Z","month":"09","oa":1,"date_created":"2024-09-23T17:25:43Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"18144","status":"public"}]},"author":[{"id":"396A1950-F248-11E8-B48F-1D18A9856A87","first_name":"Marian","last_name":"Janik","full_name":"Janik, Marian","orcid":"0009-0003-9037-8831"}],"doi":"10.15479/at:ista:18129"},{"abstract":[{"lang":"eng","text":"Recent advancements in molecular diagnostic techniques have enabled the collection of\r\nmultiple types of omics data from patients, including genomics, epigenomics, proteomics,\r\nand transcriptomics. However, we lack effective methods for integrating all these different\r\ndata types and combining them with clinical outcomes to study the molecular mechanisms\r\nthat govern pathological phenotypes. We present multi-omics BayesW, a penalized Bayesian\r\nregression method that can handle general omics data for survival analysis of time-to-event\r\nphenotypes. Our method can: (1) accommodate incomplete data by allowing censored\r\nindividuals, (2) use continuous time-to-event data to test associations of markers with a\r\nphenotype and (3) estimate effects jointly while allowing for independent groups of biological\r\nmarkers. Extensive simulations using planted signals on real data demonstrate that our model\r\naccurately retrieves the true parameters of the model while controlling for false discoveries\r\nand maintaining the expected prediction accuracy. We address data correlations by estimating\r\nthe effects jointly, even between omic groups, while also estimating the individual variance\r\nexplained by each group. We apply our model to two datasets. Using 18,000 individuals from\r\nthe Generation Scotland study we model the association of time at onset of Type 2 Diabetes,\r\nStroke, Ischemic Disease, and Osteoarthritis from baseline study entry, with 831,724 CpG\r\nmethylation probes. We find that large proportions of variation in disease onset times can\r\nbe attributed to methylation as measured in whole blood at baseline in individuals without\r\ndisease symptoms. We then apply our model to The Cancer Genome Atlas (TCGA) pan-cancer\r\ndataset, in which we use 5 types of omics: copy number variation, epigenetics, somatic\r\nmutations, miRNA, and gene expression. For cancer survival age-at-onset we find that, when\r\nfitting the 5 groups together, almost all variation attributable to \"omics\" data is explained by\r\nDNA methylation. When considering progression times, both methylation and gene expression\r\nexplain a large part of the variance. We found 2 genes that are significantly associated (95%\r\nposterior inclusion probability) with cancer survival time, conditional on all other genome-wide\r\nomics data variation. Owing to the vast variability of mechanisms characterizing different\r\ncancers, there are likely few specific genes with a strong signal in a pan-cancer setting. Taken\r\ntogether, we showed the applicability of our multi-omics BayesW model to a wide-range of\r\nbiological questions in multi-omics data.\r\n"}],"degree_awarded":"MS","date_updated":"2026-04-07T13:03:41Z","title":"Bayesian linear regression for analyzing general omics data with time-to-event phenotypes","publication_status":"published","date_published":"2024-08-13T00:00:00Z","tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"publication_identifier":{"issn":["2791-4585"]},"corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ista":"Villanueva Marijuan A. 2024. Bayesian linear regression for analyzing general omics data with time-to-event phenotypes. Institute of Science and Technology Austria.","mla":"Villanueva Marijuan, Ariadna. Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17368.","ieee":"A. Villanueva Marijuan, “Bayesian linear regression for analyzing general omics data with time-to-event phenotypes,” Institute of Science and Technology Austria, 2024.","ama":"Villanueva Marijuan A. Bayesian linear regression for analyzing general omics data with time-to-event phenotypes. 2024. doi:10.15479/at:ista:17368","short":"A. Villanueva Marijuan, Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes, Institute of Science and Technology Austria, 2024.","apa":"Villanueva Marijuan, A. (2024). Bayesian linear regression for analyzing general omics data with time-to-event phenotypes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17368","chicago":"Villanueva Marijuan, Ariadna. “Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17368."},"supervisor":[{"first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","last_name":"Robinson","full_name":"Robinson, Matthew Richard"}],"type":"dissertation","OA_place":"publisher","file":[{"creator":"avillanu","access_level":"open_access","date_updated":"2025-02-14T23:30:03Z","file_name":"Masters_thesis_AriadnaVillanueva.pdf","date_created":"2024-08-14T11:51:24Z","checksum":"0c2daa174609f0c00919dccc5701d375","relation":"main_file","content_type":"application/pdf","file_id":"17433","file_size":13052436,"embargo":"2025-02-14"},{"file_size":45642547,"file_id":"17434","embargo_to":"open_access","checksum":"e9ed4465dfa539ac4c3a8d4d0b6271a1","content_type":"application/zip","relation":"source_file","date_created":"2024-08-14T11:51:57Z","file_name":"Masters thesis-AriadnaVillanueva.zip","creator":"avillanu","access_level":"closed","date_updated":"2025-02-14T23:30:03Z"}],"alternative_title":["ISTA Master's Thesis"],"author":[{"full_name":"Villanueva Marijuan, Ariadna","last_name":"Villanueva Marijuan","first_name":"Ariadna","id":"e0ae4864-133f-11ed-8f02-adaa8dd27540"}],"date_created":"2024-08-02T10:52:40Z","doi":"10.15479/at:ista:17368","oa_version":"Published Version","status":"public","_id":"17368","ddc":["610"],"file_date_updated":"2025-02-14T23:30:03Z","oa":1,"month":"08","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","page":"60","keyword":["Epigenetics","Multi-omics","Bayesian regression"],"language":[{"iso":"eng"}],"year":"2024","has_accepted_license":"1","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"MaRo"}],"publisher":"Institute of Science and Technology Austria","day":"13"},{"department":[{"_id":"GeKa"},{"_id":"GradSch"},{"_id":"JoFi"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"article_processing_charge":"No","day":"03","language":[{"iso":"eng"}],"year":"2024","article_number":"2407.03079","oa_version":"Preprint","status":"public","_id":"18144","month":"07","oa":1,"related_material":{"record":[{"status":"public","id":"18886","relation":"research_data"},{"id":"19401","relation":"later_version","status":"public"},{"id":"18129","relation":"dissertation_contains","status":"public"}]},"date_created":"2024-09-26T09:50:43Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2407.03079","open_access":"1"}],"author":[{"full_name":"Janik, Marian","last_name":"Janik","orcid":"0009-0003-9037-8831","id":"396A1950-F248-11E8-B48F-1D18A9856A87","first_name":"Marian"},{"full_name":"Roux, Kevin Etienne Robert","last_name":"Roux","id":"53f93ea2-803f-11ed-ab7e-b283135794ef","first_name":"Kevin Etienne Robert"},{"full_name":"Borja Espinosa, Carla N","last_name":"Borja Espinosa","first_name":"Carla N","id":"18777c01-896a-11ed-bdf8-e4851dc07d16"},{"first_name":"Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","full_name":"Sagi, Oliver","last_name":"Sagi"},{"last_name":"Baghdadi","full_name":"Baghdadi, Abdulhamid","first_name":"Abdulhamid","id":"160D87FA-96B5-11E9-BF77-7626E6697425"},{"full_name":"Adletzberger, Thomas","last_name":"Adletzberger","id":"38756BB2-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"first_name":"Stefano","last_name":"Calcaterra","full_name":"Calcaterra, Stefano"},{"last_name":"Botifoll","full_name":"Botifoll, Marc","first_name":"Marc"},{"first_name":"Alba Garzón","last_name":"Manjón","full_name":"Manjón, Alba Garzón"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"first_name":"Daniel","full_name":"Chrastina, Daniel","last_name":"Chrastina"},{"first_name":"Giovanni","full_name":"Isella, Giovanni","last_name":"Isella"},{"first_name":"Ioan M.","full_name":"Pop, Ioan M.","last_name":"Pop"},{"first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","last_name":"Katsaros"}],"doi":"10.48550/arXiv.2407.03079","acknowledgement":"We acknowledge Franco De Palma, Mahya Khorramshahi, Fabian Oppliger, Thomas Reisinger, Pasquale Scarlino and Xiao Xue for helpful discussions. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the Nanofabrication facility. This research and related results were made possible with the support of the NOMIS Foundation, the HORIZON-RIA 101069515 project, the FWF Projects with DOI:10.55776/P32235, DOI:10.55776/I5060 and DOI:10.55776/P36507. IMP acknowledges funding from the Deutsche Forschungsgemeinschaft (DFG – German Research Foundation) under project number 450396347 (GeHoldeQED). ICN2 acknowledges funding from Generalitat de Catalunya 2021SGR00457. We acknowledge support from CSIC Interdisciplinary Thematic Platform (PTI+) on Quantum Technologies (PTI-QTEP+). This research work has been funded by the European Commission – NextGenerationEU (Regulation EU 2020/2094), through CSIC’s\r\nQuantum Technologies Platform (QTEP). ICN2 is supported by the Severo Ochoa program from Spanish MCIN/AEI (Grant No.: CEX2021-001214-S) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autònoma de Barcelona Materials Science PhD program. AGM has received funding from Grant RYC2021-033479-I funded by MCIN/AEI/10.13039/501100011033 and by European Union NextGenerationEU/PRTR. M.B. acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020 FI 00103. The authors\r\nacknowledge the use of instrumentation and the technical advice provided by the Joint Electron Microscopy Center at ALBA (JEMCA). ICN2 acknowledges funding from Grant IU16-014206 (METCAM-FIB) funded by the European Union through the European Regional Development\r\nFund (ERDF), with the support of the Ministry of Research and Universities, Generalitat de Catalunya. ICN2 is a founding member of e-DREAM [60].","type":"preprint","OA_place":"repository","publication":"arXiv","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Janik, M., Roux, K. E. R., Borja Espinosa, C. N., Sagi, O., Baghdadi, A., Adletzberger, T., … Katsaros, G. (n.d.). Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors. arXiv. https://doi.org/10.48550/arXiv.2407.03079","chicago":"Janik, Marian, Kevin Etienne Robert Roux, Carla N Borja Espinosa, Oliver Sagi, Abdulhamid Baghdadi, Thomas Adletzberger, Stefano Calcaterra, et al. “Strong Charge-Photon Coupling in Planar Germanium Enabled by Granular Aluminium Superinductors.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2407.03079.","short":"M. Janik, K.E.R. Roux, C.N. Borja Espinosa, O. Sagi, A. Baghdadi, T. Adletzberger, S. Calcaterra, M. Botifoll, A.G. Manjón, J. Arbiol, D. Chrastina, G. Isella, I.M. Pop, G. Katsaros, ArXiv (n.d.).","ieee":"M. Janik et al., “Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors,” arXiv. .","ama":"Janik M, Roux KER, Borja Espinosa CN, et al. Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors. arXiv. doi:10.48550/arXiv.2407.03079","ista":"Janik M, Roux KER, Borja Espinosa CN, Sagi O, Baghdadi A, Adletzberger T, Calcaterra S, Botifoll M, Manjón AG, Arbiol J, Chrastina D, Isella G, Pop IM, Katsaros G. Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors. arXiv, 2407.03079.","mla":"Janik, Marian, et al. “Strong Charge-Photon Coupling in Planar Germanium Enabled by Granular Aluminium Superinductors.” ArXiv, 2407.03079, doi:10.48550/arXiv.2407.03079."},"arxiv":1,"corr_author":"1","abstract":[{"text":"High kinetic inductance superconductors are gaining increasing interest for\r\nthe realisation of qubits, amplifiers and detectors. Moreover, thanks to their\r\nhigh impedance, quantum buses made of such materials enable large zero-point\r\nfluctuations of the voltage, boosting the coupling rates to spin and charge\r\nqubits. However, fully exploiting the potential of disordered or granular\r\nsuperconductors is challenging, as their inductance and, therefore, impedance\r\nat high values are difficult to control. Here we have integrated a granular\r\naluminium resonator, having a characteristic impedance exceeding the resistance\r\nquantum, with a germanium double quantum dot and demonstrate strong\r\ncharge-photon coupling with a rate of $g_\\text{c}/2\\pi= (566 \\pm 2)$ MHz. This\r\nwas achieved due to the realisation of a wireless ohmmeter, which allows\r\n\\emph{in situ} measurements during film deposition and, therefore, control of\r\nthe kinetic inductance of granular aluminium films. Reproducible fabrication of\r\ncircuits with impedances (inductances) exceeding 13 k$\\Omega$ (1 nH per square)\r\nis now possible. This broadly applicable method opens the path for novel qubits\r\nand high-fidelity, long-distance two-qubit gates.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2024-07-03T00:00:00Z","external_id":{"arxiv":["2407.03079"]},"date_updated":"2026-05-27T22:30:24Z","publication_status":"draft","title":"Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors","project":[{"name":"Integrated Germanium Quantum Technology","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","grant_number":"101069515"},{"grant_number":"P32235","call_identifier":"FWF","name":"Towards scalable hut wire quantum devices","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a"},{"_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","name":"High impedance circuit quantum electrodynamics with hole spins","grant_number":"I05060"}]},{"language":[{"iso":"eng"}],"year":"2024","OA_type":"hybrid","page":"755-771.e9","day":"06","issue":"5","publisher":"Elsevier","article_type":"original","department":[{"_id":"PeJo"},{"_id":"EM-Fac"},{"_id":"RySh"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"M-Shop"}],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","intvolume":" 112","scopus_import":"1","doi":"10.1016/j.neuron.2023.12.002","related_material":{"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/synapses-brought-to-the-point/"}],"record":[{"status":"public","relation":"dissertation_contains","id":"15101"}]},"date_created":"2024-01-21T23:00:56Z","volume":112,"author":[{"last_name":"Chen","full_name":"Chen, JingJing","first_name":"JingJing","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","full_name":"Kaufmann, Walter"},{"first_name":"Chong","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","full_name":"Chen, Chong"},{"first_name":"Itaru","id":"32A73F6C-F248-11E8-B48F-1D18A9856A87","last_name":"Arai","full_name":"Arai, Itaru"},{"id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","first_name":"Olena","full_name":"Kim, Olena","last_name":"Kim","orcid":"0000-0003-2344-1039"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","last_name":"Jonas","full_name":"Jonas, Peter M"}],"month":"03","oa":1,"oa_version":"Published Version","status":"public","ddc":["570"],"_id":"14843","file_date_updated":"2025-04-23T14:02:08Z","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Chen J, Kaufmann W, Chen C, et al. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. 2024;112(5):755-771.e9. doi:10.1016/j.neuron.2023.12.002","ieee":"J. Chen et al., “Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse,” Neuron, vol. 112, no. 5. Elsevier, p. 755–771.e9, 2024.","mla":"Chen, JingJing, et al. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” Neuron, vol. 112, no. 5, Elsevier, 2024, p. 755–771.e9, doi:10.1016/j.neuron.2023.12.002.","ista":"Chen J, Kaufmann W, Chen C, Arai itaru, Kim O, Shigemoto R, Jonas PM. 2024. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. 112(5), 755–771.e9.","apa":"Chen, J., Kaufmann, W., Chen, C., Arai, itaru, Kim, O., Shigemoto, R., & Jonas, P. M. (2024). Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.12.002","chicago":"Chen, JingJing, Walter Kaufmann, Chong Chen, itaru Arai, Olena Kim, Ryuichi Shigemoto, and Peter M Jonas. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” Neuron. Elsevier, 2024. https://doi.org/10.1016/j.neuron.2023.12.002.","short":"J. Chen, W. Kaufmann, C. Chen, itaru Arai, O. Kim, R. Shigemoto, P.M. Jonas, Neuron 112 (2024) 755–771.e9."},"publication":"Neuron","file":[{"creator":"dernst","access_level":"open_access","date_updated":"2025-04-23T14:02:08Z","success":1,"date_created":"2025-04-23T14:02:08Z","file_name":"2024_Neuron_Chen.pdf","checksum":"30098b4f0209556ddfb3540a23d07ca5","content_type":"application/pdf","relation":"main_file","file_size":8192355,"file_id":"19614"}],"acknowledgement":"We thank Drs. David DiGregorio and Erwin Neher for critically reading an earlier version of the manuscript, Ralf Schneggenburger for helpful discussions, Benjamin Suter and Katharina Lichter for support with image analysis, Chris Wojtan for advice on numerical solution of partial differential equations, Maria Reva for help with Ripley analysis, Alois Schlögl for programming, and Akari Hagiwara and Toshihisa Ohtsuka for anti-ELKS antibody. We are grateful to Florian Marr, Christina Altmutter, and Vanessa Zheden for excellent technical assistance and to Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA (Electron Microscopy Facility, Preclinical Facility, and Machine Shop). The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 692692), the Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award; P 36232-B), all to P.J., and a DOC fellowship of the Austrian Academy of Sciences to J.-J.C.","type":"journal_article","OA_place":"publisher","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2024-03-06T00:00:00Z","isi":1,"external_id":{"pmid":["38215739"],"isi":["001202925700001"]},"date_updated":"2026-05-27T22:30:26Z","publication_status":"published","project":[{"grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"grant_number":"Z00312","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits"},{"_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232"},{"grant_number":"25383","name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","_id":"26B66A3E-B435-11E9-9278-68D0E5697425"}],"title":"Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse","abstract":[{"text":"The coupling between Ca2+ channels and release sensors is a key factor defining the signaling properties of a synapse. However, the coupling nanotopography at many synapses remains unknown, and it is unclear how it changes during development. To address these questions, we examined coupling at the cerebellar inhibitory basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission by paired recording and intracellular pipette perfusion revealed that the effects of exogenous Ca2+ chelators decreased during development, despite constant reliance of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked vesicles were only clustered at later developmental stages. Modeling suggested a developmental transformation from a more random to a more clustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic transmission.","lang":"eng"}],"quality_controlled":"1","PlanS_conform":"1","publication_identifier":{"issn":["0896-6273"],"eissn":["1097-4199"]},"corr_author":"1","ec_funded":1},{"citation":{"ista":"Chen J. 2024. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria.","mla":"Chen, JingJing. Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15101.","ama":"Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. 2024. doi:10.15479/at:ista:15101","ieee":"J. Chen, “Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse,” Institute of Science and Technology Austria, 2024.","short":"J. Chen, Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse, Institute of Science and Technology Austria, 2024.","chicago":"Chen, JingJing. “Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15101.","apa":"Chen, J. (2024). Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15101"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"date_created":"2024-03-11T14:10:58Z","file_name":"Thesis_Jingjing CHEN.docx","creator":"jchen","access_level":"closed","date_updated":"2024-04-02T22:30:03Z","file_id":"15104","file_size":11271363,"embargo_to":"open_access","checksum":"db4947474ffa271e66c254b6fe876a55","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file"},{"content_type":"application/pdf","relation":"main_file","checksum":"a5eeae8b5702cd540f5d03469bc33dde","file_size":16627311,"embargo":"2024-04-01","file_id":"15105","date_updated":"2024-04-02T22:30:03Z","access_level":"open_access","creator":"jchen","date_created":"2024-03-11T14:11:06Z","file_name":"Thesis_Jingjing CHEN_merged.pdf"}],"alternative_title":["ISTA Thesis"],"OA_place":"publisher","type":"dissertation","supervisor":[{"full_name":"Jonas, Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"project":[{"call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692"},{"grant_number":"Z00312","call_identifier":"FWF","name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"grant_number":"P36232","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits"},{"grant_number":"25383","name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","_id":"26B66A3E-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","title":"Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse","date_updated":"2026-04-07T13:24:22Z","date_published":"2024-03-11T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"abstract":[{"lang":"eng","text":"The coupling between presynaptic Ca2+ channels and release sensors is a key factor that\r\ndetermines speed and efficacy of synapse transmission. At some excitatory synapses,\r\nchannel–sensor coupling becomes tighter during development, and tightening is often\r\nassociated with a switch in the reliance on different Ca2+ channel subtypes. However, the\r\ncoupling topography at many synapses remains unknown, and it is unclear how it changes\r\nduring development. To address this question, we analyzed the coupling configuration at the\r\ncerebellar basket cell (BC) to Purkinje cell (PC) synapse at different developmental stages,\r\ncombining biophysical analysis, structural analysis, and modeling.\r\nQuantal analysis of BC–PC indicated that release probability decreased, while the\r\nnumber of functional sites increased during development. Although transmitter release\r\npersistently relied on P/Q-type Ca2+ channels in the time period postnatal day 7–23, effects\r\nof the Ca2+ chelator EGTA and BAPTA applied by intracellular pipette perfusion decreased\r\nduring development, indicative of tightening of source-sensor coupling. Furthermore,\r\npresynaptic action potentials became shorter during development, suggesting reduced\r\nefficacy of Ca2+ channel activation.\r\nStructural analysis by freeze-fracture replica labeling (FRL) and transmission electron\r\nmicroscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters\r\nthroughout development, whereas docked vesicles were only clustered at later\r\ndevelopmental stages. The number of functional release sites correlated better with the AZ\r\nnumber early in development, but match better with the Ca2+ channel cluster number at later\r\nstages.\r\nModeling suggested a developmental transformation from a more random to a more\r\nclustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches\r\na point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic\r\ntransmission."}],"degree_awarded":"PhD","corr_author":"1","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"year":"2024","language":[{"iso":"eng"}],"page":"84","publisher":"Institute of Science and Technology Austria","day":"11","article_processing_charge":"No","acknowledged_ssus":[{"_id":"EM-Fac"}],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"PeJo"}],"doi":"10.15479/at:ista:15101","author":[{"first_name":"JingJing","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","full_name":"Chen, JingJing"}],"related_material":{"record":[{"id":"14843","relation":"part_of_dissertation","status":"public"}]},"date_created":"2024-03-11T10:09:54Z","oa":1,"month":"03","_id":"15101","ddc":["570"],"file_date_updated":"2024-04-02T22:30:03Z","status":"public","oa_version":"Published Version"},{"corr_author":"1","publication_identifier":{"isbn":["978-3-99078-043-5"],"issn":["2663-337X"]},"date_published":"2024-09-10T00:00:00Z","title":"Thermal effects in one dimensional Josephson chains","publication_status":"published","project":[{"grant_number":"P33692","name":"Cavity electromechanics across a quantum phase transition","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931"}],"date_updated":"2026-04-07T13:04:06Z","degree_awarded":"PhD","abstract":[{"text":"This work can be broadly classified into the study of critical phenomena in a one dimensional\r\narray of Josephson junctions. While we study quantum criticality when the array is in thermal\r\nequilibrium at zero bias, the non-equilibrium study involves understanding the bistability of the\r\narray at a critical non-zero bias. This work furthers our knowledge in understanding quantum\r\ncritical behaviour at finite temperatures in a one dimensional Josephson array, while also\r\nestablishing relaxation behaviour dual to that observed in a single Josephson junction.\r\nChapter 1 briefly introduces the model to understand superconductor-insulator phase transition\r\nin a one dimensional Josephson array and points out the state of the field from where we\r\nstarted our zero-bias experiments. In this context it discusses the phase-charge duality observed\r\nin a Josephson array and its dual hysteretic behaviour to that of a single junction, setting the\r\nground for our non-equilibrium study of the array.\r\nChapter 2 shows the experimental setup and the chip layout of the device we measured.\r\nIn chapter 3 we show that, unlike the typical quantum-critical broadening scenario, in one dimensional Josephson arrays temperature dramatically shifts the critical region. This shift leads\r\nto a regime of superconductivity at high temperature, arising from the melted zero-temperature\r\ninsulator. Our results quantitatively explain the low-temperature onset of superconductivity in\r\nnominally insulating regimes, and the transition to the strongly insulating phase. We further\r\npresent, to our knowledge, the first understanding of the onset of anomalous-metallic resistance\r\nsaturation [30]. This work demonstrates a non-trivial interplay between thermal effects and\r\nquantum criticality. A practical consequence is that, counterintuitively, the coherence of\r\nhigh-impedance quantum circuits is expected to be stabilized by thermal fluctuations.\r\nIn chapter 4, we show relaxation oscillations in a current-biased one dimensional array of\r\nJosephson junctions. These oscillations are well described by a circuit model, dual to the\r\nordinary Josephson relaxation oscillations [72]. Injection locking these oscillations results in\r\ncurrent plateaux. The relaxation step is found to obey a characteristic self-consistent relation,\r\nsuggesting that it is governed by overheating effects.\r\nChapter 5 describes the various checks and analysis we performed to support our conclusions\r\nmade in chapters 3 and 4.\r\nFinally, chapter 6 describes the nanofabrication steps and the finite element electromagnetic\r\nsimulations we performed to fabricate our devices.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"file":[{"date_created":"2024-09-12T10:46:04Z","file_name":"PhD_Thesis_Soham_Mukhopadhyay.pdf","access_level":"open_access","creator":"smukhopa","date_updated":"2025-03-13T23:30:04Z","file_size":10297052,"file_id":"18059","embargo":"2025-03-13","checksum":"ed7763c3bbd59e1d7e1b664de3a26f3c","content_type":"application/pdf","relation":"main_file"},{"checksum":"e352667482701dd18a9a0e7418aef465","content_type":"application/zip","relation":"source_file","file_size":29178634,"file_id":"18060","embargo_to":"open_access","creator":"smukhopa","access_level":"closed","date_updated":"2025-03-13T23:30:04Z","date_created":"2024-09-12T10:50:58Z","file_name":"PhD_Thesis_Soham_Mukhopadhyay_source.zip"}],"OA_place":"publisher","supervisor":[{"first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","last_name":"Higginbotham"}],"type":"dissertation","citation":{"short":"S. Mukhopadhyay, Thermal Effects in One Dimensional Josephson Chains, Institute of Science and Technology Austria, 2024.","chicago":"Mukhopadhyay, Soham. “Thermal Effects in One Dimensional Josephson Chains.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17881.","apa":"Mukhopadhyay, S. (2024). Thermal effects in one dimensional Josephson chains. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17881","ista":"Mukhopadhyay S. 2024. Thermal effects in one dimensional Josephson chains. Institute of Science and Technology Austria.","mla":"Mukhopadhyay, Soham. Thermal Effects in One Dimensional Josephson Chains. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17881.","ieee":"S. Mukhopadhyay, “Thermal effects in one dimensional Josephson chains,” Institute of Science and Technology Austria, 2024.","ama":"Mukhopadhyay S. Thermal effects in one dimensional Josephson chains. 2024. doi:10.15479/at:ista:17881"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"09","oa":1,"ddc":["539"],"_id":"17881","file_date_updated":"2025-03-13T23:30:04Z","oa_version":"Published Version","status":"public","doi":"10.15479/at:ista:17881","date_created":"2024-09-08T10:23:25Z","related_material":{"record":[{"id":"14032","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"18057","status":"public"}]},"author":[{"first_name":"Soham","id":"FDE60288-A89D-11E9-947F-1AF6E5697425","orcid":"0000-0001-5263-5559","last_name":"Mukhopadhyay","full_name":"Mukhopadhyay, Soham"}],"day":"10","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"AnHi"}],"article_processing_charge":"No","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"has_accepted_license":"1","year":"2024","language":[{"iso":"eng"}],"page":"82"},{"day":"14","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"article_processing_charge":"No","department":[{"_id":"AnHi"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"year":"2024","oa":1,"month":"08","status":"public","oa_version":"Preprint","_id":"18057","article_number":"2408.07829","doi":"10.48550/arXiv.2408.07829","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2408.07829"}],"author":[{"first_name":"Soham","id":"FDE60288-A89D-11E9-947F-1AF6E5697425","orcid":"0000-0001-5263-5559","last_name":"Mukhopadhyay","full_name":"Mukhopadhyay, Soham"},{"id":"6c55e976-15b2-11ec-abd3-d790e8937fde","first_name":"Diego A","last_name":"Lancheros Naranjo","full_name":"Lancheros Naranjo, Diego A"},{"last_name":"Senior","full_name":"Senior, Jorden L","orcid":"0000-0002-0672-9295","id":"5479D234-2D30-11EA-89CC-40953DDC885E","first_name":"Jorden L"},{"first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"20324"},{"id":"17881","relation":"dissertation_contains","status":"public"}]},"date_created":"2024-09-11T09:25:22Z","acknowledgement":"We gratefully acknowledge support from the MIBA machine shop and Nanofabrication Facility at IST Austria. Work was supported by Austrian FWF grant P33692-N (S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and Innovation program under the Marie Sk lodowska-Curie Grant Agreement No. 754411 (J.S.), and a NOMIS foundation research grant (A.P.H.).\r\n","type":"preprint","OA_place":"repository","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"S. Mukhopadhyay, D.A. Lancheros Naranjo, J.L. Senior, A.P. Higginbotham, ArXiv (n.d.).","apa":"Mukhopadhyay, S., Lancheros Naranjo, D. A., Senior, J. L., & Higginbotham, A. P. (n.d.). Dual relaxation oscillations in a Josephson junction array. arXiv. https://doi.org/10.48550/arXiv.2408.07829","chicago":"Mukhopadhyay, Soham, Diego A Lancheros Naranjo, Jorden L Senior, and Andrew P Higginbotham. “Dual Relaxation Oscillations in a Josephson Junction Array.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2408.07829.","mla":"Mukhopadhyay, Soham, et al. “Dual Relaxation Oscillations in a Josephson Junction Array.” ArXiv, 2408.07829, doi:10.48550/arXiv.2408.07829.","ista":"Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. arXiv, 2408.07829.","ieee":"S. Mukhopadhyay, D. A. Lancheros Naranjo, J. L. Senior, and A. P. Higginbotham, “Dual relaxation oscillations in a Josephson junction array,” arXiv. .","ama":"Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. arXiv. doi:10.48550/arXiv.2408.07829"},"publication":"arXiv","corr_author":"1","arxiv":1,"ec_funded":1,"date_updated":"2026-05-27T22:30:27Z","title":"Dual relaxation oscillations in a Josephson junction array","publication_status":"draft","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"P33692","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","name":"Cavity electromechanics across a quantum phase transition"},{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"}],"date_published":"2024-08-14T00:00:00Z","external_id":{"arxiv":["2408.07829"]},"abstract":[{"text":"We report relaxation oscillations in a one-dimensional array of Josephson\r\njunctions. The oscillations are circuit-dual to those ordinarily observed in\r\nsingle junctions. The dual circuit quantitatively accounts for temporal\r\ndynamics of the array, including the dependence on biasing conditions.\r\nInjection locking the oscillations results in well-developed current plateaux.\r\nA thermal model explains the relaxation step of the oscillations.","lang":"eng"}]},{"quality_controlled":"1","abstract":[{"text":"GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing phasic release exhibits looser coupling distance than the tonic release. Furthermore, the tonic and phasic release are selectively affected by deletion of synaptoporin (SPO) and Ca\r\n 2+\r\n -dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. The cytosolic protein CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane protein SPO, and they were colocalized in the same terminals. We developed the “Flash and Freeze-fracture” method, and revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP increase. Thus, we identified structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals.","lang":"eng"}],"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)"},"external_id":{"pmid":["38346189"],"isi":["001208567300006"]},"isi":1,"date_published":"2024-02-20T00:00:00Z","APC_amount":"5887,8 EUR","publication_status":"published","project":[{"grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020"},{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"title":"GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles","date_updated":"2026-05-27T22:30:28Z","ec_funded":1,"corr_author":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication":"Proceedings of the National Academy of Sciences of the United States of America","pmid":1,"citation":{"apa":"Koppensteiner, P., Bhandari, P., Önal, C., Borges Merjane, C., Le Monnier, E., Roy, U., … Shigemoto, R. (2024). GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2301449121","chicago":"Koppensteiner, Peter, Pradeep Bhandari, Cihan Önal, Carolina Borges Merjane, Elodie Le Monnier, Utsa Roy, Yukihiro Nakamura, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2301449121.","short":"P. Koppensteiner, P. Bhandari, C. Önal, C. Borges Merjane, E. Le Monnier, U. Roy, Y. Nakamura, T. Sadakata, M. Sanbo, M. Hirabayashi, J. Rhee, N. Brose, P.M. Jonas, R. Shigemoto, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ieee":"P. Koppensteiner et al., “GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 8. National Academy of Sciences, 2024.","ama":"Koppensteiner P, Bhandari P, Önal C, et al. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(8). doi:10.1073/pnas.2301449121","ista":"Koppensteiner P, Bhandari P, Önal C, Borges Merjane C, Le Monnier E, Roy U, Nakamura Y, Sadakata T, Sanbo M, Hirabayashi M, Rhee J, Brose N, Jonas PM, Shigemoto R. 2024. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences of the United States of America. 121(8), e2301449121.","mla":"Koppensteiner, Peter, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 8, e2301449121, National Academy of Sciences, 2024, doi:10.1073/pnas.2301449121."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"publisher","acknowledgement":"We thank Erwin Neher and Ipe Ninan for critical comments on the manuscript. This project has received funding from the European Research Council (ERC) and European Commission, under the European Union’s Horizon 2020 research and innovation program (ERC grant agreement no. 694539 to R.S. and the Marie Skłodowska-Curie grant agreement no. 665385 to C.Ö.). This study was supported by the Cooperative Study Program of Center for Animal Resources and Collaborative Study of NINS. We thank Kohgaku Eguchi for statistical analysis, Yu Kasugai for additional EM imaging, Robert Beattie for the design of the slice recovery chamber for Flash and Freeze experiments, Todor Asenov from the ISTA machine shop for custom part preparations for high-pressure freezing, the ISTA preclinical facility for animal caretaking, and the ISTA EM facilities for technical support.","type":"journal_article","file":[{"content_type":"application/pdf","relation":"main_file","checksum":"b25b2a057c266ff317a48b0d54d6fc8a","file_id":"15110","file_size":13648221,"date_updated":"2024-03-12T13:42:42Z","success":1,"access_level":"open_access","creator":"dernst","date_created":"2024-03-12T13:42:42Z","file_name":"2024_PNAS_Koppensteiner.pdf"}],"volume":121,"date_created":"2024-03-05T09:23:55Z","related_material":{"record":[{"id":"13173","relation":"research_data","status":"public"},{"status":"public","relation":"dissertation_contains","id":"19271"}],"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/neuronal-insights-flash-and-freeze-fracture/"}]},"author":[{"first_name":"Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter","last_name":"Koppensteiner"},{"full_name":"Bhandari, Pradeep","last_name":"Bhandari","orcid":"0000-0003-0863-4481","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","first_name":"Pradeep"},{"first_name":"Hüseyin C","id":"4659D740-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2771-2011","full_name":"Önal, Hüseyin C","last_name":"Önal"},{"orcid":"0000-0003-0005-401X","last_name":"Borges Merjane","full_name":"Borges Merjane, Carolina","first_name":"Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Le Monnier, Elodie","last_name":"Le Monnier","id":"3B59276A-F248-11E8-B48F-1D18A9856A87","first_name":"Elodie"},{"last_name":"Roy","full_name":"Roy, Utsa","first_name":"Utsa","id":"4d26cf11-5355-11ee-ae5a-eb05e255b9b2"},{"full_name":"Nakamura, Yukihiro","last_name":"Nakamura","first_name":"Yukihiro"},{"last_name":"Sadakata","full_name":"Sadakata, Tetsushi","first_name":"Tetsushi"},{"first_name":"Makoto","full_name":"Sanbo, Makoto","last_name":"Sanbo"},{"full_name":"Hirabayashi, Masumi","last_name":"Hirabayashi","first_name":"Masumi"},{"last_name":"Rhee","full_name":"Rhee, JeongSeop","first_name":"JeongSeop"},{"first_name":"Nils","full_name":"Brose, Nils","last_name":"Brose"},{"orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"}],"intvolume":" 121","doi":"10.1073/pnas.2301449121","scopus_import":"1","article_number":"e2301449121","file_date_updated":"2024-03-12T13:42:42Z","_id":"15084","ddc":["570"],"status":"public","oa_version":"Published Version","month":"02","oa":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","year":"2024","language":[{"iso":"eng"}],"OA_type":"hybrid","department":[{"_id":"RySh"},{"_id":"PeJo"}],"article_processing_charge":"Yes (in subscription journal)","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"has_accepted_license":"1","issue":"8","day":"20","article_type":"original","publisher":"National Academy of Sciences"},{"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"article_processing_charge":"No","has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"}],"day":"11","publisher":"Institute of Science and Technology Austria","keyword":["Sex chromosomes","evolution","selection","sheltering"],"page":"181","year":"2024","language":[{"iso":"eng"}],"_id":"18531","file_date_updated":"2025-05-11T22:30:04Z","ddc":["576"],"status":"public","oa_version":"Published Version","month":"11","oa":1,"date_created":"2024-11-11T08:40:45Z","related_material":{"record":[{"status":"public","id":"12521","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"18549"}]},"author":[{"first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac"}],"doi":"10.15479/at:ista:18531","OA_place":"publisher","supervisor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","checksum":"3e48b163c22114ef5d5371f758668289","embargo_to":"open_access","file_size":26870629,"file_id":"18551","date_updated":"2025-05-11T22:30:04Z","title":"Early stages of sex chromosome evolution","access_level":"closed","creator":"amrnjava","date_created":"2024-11-13T12:15:28Z","file_name":"AMrnjavac_thesis_library.docx"},{"date_created":"2024-11-13T12:15:54Z","file_name":"AMrnjavac_thesis_library.pdf","date_updated":"2025-05-11T22:30:04Z","title":"Early stages of sex chromosome evolution","access_level":"open_access","creator":"amrnjava","file_size":4228766,"embargo":"2025-05-11","file_id":"18552","content_type":"application/pdf","relation":"main_file","checksum":"3ead60c1b678e7dcf018043aef3b5db2"}],"citation":{"short":"A. Mrnjavac, Early Stages of Sex Chromosome Evolution, Institute of Science and Technology Austria, 2024.","apa":"Mrnjavac, A. (2024). Early stages of sex chromosome evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18531","chicago":"Mrnjavac, Andrea. “Early Stages of Sex Chromosome Evolution.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18531.","ista":"Mrnjavac A. 2024. Early stages of sex chromosome evolution. Institute of Science and Technology Austria.","mla":"Mrnjavac, Andrea. Early Stages of Sex Chromosome Evolution. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18531.","ama":"Mrnjavac A. Early stages of sex chromosome evolution. 2024. doi:10.15479/at:ista:18531","ieee":"A. Mrnjavac, “Early stages of sex chromosome evolution,” Institute of Science and Technology Austria, 2024."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","corr_author":"1","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","OA_embargo":"6","abstract":[{"text":"Sex chromosomes and autosomes exhibit very different evolutionary dynamics.\r\nThe Y chromosome usually degenerates, leaving many X-linked loci hemizygous in\r\nmales. Since recessive X-linked mutations are always exposed to selection in males,\r\nselection is more efficient on the X chromosome than on autosomes on recessive\r\nmutations, leading to faster adaptation on the X chromosome than other genomic\r\nregions, if beneficial mutations are on average recessive (known as the Faster-X\r\neffect). In the presence of the functional, but non-recombining gametolog on the Y (as\r\nis often the case in young non-recombining regions), recessive mutations are\r\nsheltered from selection on the X chromosome. We model this scenario and show that\r\nthe efficiency of selection is reduced on diploid X loci due to sheltering by the Y\r\nchromosome. Reduced efficiency of selection leads to slower adaptation and\r\nincreased accumulation of deleterious mutations (Slower-X effect). We extended this\r\nmodel to explore the effect of sex-specific selection on degeneration of sex\r\nchromosomes, showing theoretically that male-limited genes degenerate on the X\r\nchromosome and female-biased genes degenerate on the Y chromosome. This\r\nprediction depends on the effective population size and the mutation rate, explaining\r\nthe variety of sex chromosome degeneration patterns observed in nature.\r\nTo test for direct evidence of a Slower-X (or Slower-Z) effect, we analyzed the\r\nZW sex chromosomes of the flatworm Schistosoma japonicum, which have a very\r\nyoung non-recombining region with non-degenerated W. Diploid Z-linked genes have\r\nhigher ratios of non-synonymous to synonymous polymorphisms than autosomal\r\ngenes, supporting reduced efficiency of selection on the diploid Z region. These results\r\nprovide evidence of sheltering by the W chromosome, a mechanism that could\r\ncontribute to Z (X) chromosome degeneration, and illustrate contrasting evolutionary\r\npatterns in old and young sex chromosome regions. In addition, genes with sexspecific patterns of expression show opposite patterns of selection in the young\r\n(diploid) and old (hemizygous) Z, showing the complex manner in which sex-specific selection shapes the evolutionary patterns of sex chromosomes. ","lang":"eng"}],"date_published":"2024-11-11T00:00:00Z","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)"},"title":"Early stages of sex chromosome evolution","publication_status":"published","date_updated":"2026-04-07T13:22:45Z"},{"doi":"10.15479/at:ista:18661","author":[{"id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","first_name":"Miguel","full_name":"Santana de Freitas Amaral, Miguel","last_name":"Santana de Freitas Amaral"}],"date_created":"2024-12-16T10:53:39Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"18670"}]},"oa":1,"month":"12","oa_version":"Published Version","status":"public","file_date_updated":"2025-06-18T22:30:03Z","_id":"18661","ddc":["572","530"],"language":[{"iso":"eng"}],"year":"2024","license":"https://creativecommons.org/licenses/by-sa/4.0/","page":"57","publisher":"Institute of Science and Technology Austria","day":"17","has_accepted_license":"1","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"AnSa"}],"date_updated":"2026-04-07T13:22:29Z","title":"Archaeal membranes : In silico modelling and design","publication_status":"published","date_published":"2024-12-17T00:00:00Z","tmp":{"short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png"},"abstract":[{"lang":"eng","text":"Across the tree of life, distinct designs of cellular membranes have evolved that are both stable\r\nand flexible. In bacteria and eukaryotes this trade-off is accomplished by single-headed lipids\r\nthat self-assemble into flexible bilayer membranes. By contrast, archaea in many cases possess\r\nboth bilayer and double-headed, monolayer spanning bolalipids. This composition is believed\r\nto enable extremophile archaea to survive harsh environments. Here, through the creation of a\r\nminimal computational model for bolalipid membranes, we discover trade-offs when forming\r\nmembranes using lipids of a single type. Similar to living archaea, we can tune the stiffness of\r\nbolalipid molecules. We find that membranes made out of flexible bolalipid molecules resemble\r\nbilayer membranes as they can adopt U-shaped conformations to enable higher curvatures.\r\nConversely, rigid bolalipid molecules, like those found in archaea at higher temperatures,\r\npreferentially take on a straight conformation to self-assemble into liquid membranes that are\r\nstable, stiff, prone to pore formation, and which tear during membrane reshaping. Strikingly,\r\nhowever, our analysis reveals that it is possible to achieve the best of both worlds – membranes\r\nthat are fluid, stable at high temperatures and flexible enough to be reshaped without leaking –\r\nthrough the inclusion of a small fraction of bilayer lipids into a bolalipid membrane. Additionally,\r\nthe curvature-dependent softening of bolalipid membranes made of lipids with tension-sensitive\r\nconformation can also enable high rigidity at low curvatures while softening at high curvatures,\r\nmaking the membrane effectively a plastic material. Taken together, our study compares the\r\ndifferent membrane designs across the tree of life and indicates how combining lipids can be\r\nused to resolve trade-offs when generating membranes for (bio)technological applications.\r\n"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-046-6"]},"corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"short":"M. Santana de Freitas Amaral, Archaeal Membranes : In Silico Modelling and Design, Institute of Science and Technology Austria, 2024.","apa":"Santana de Freitas Amaral, M. (2024). Archaeal membranes : In silico modelling and design. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18661","chicago":"Santana de Freitas Amaral, Miguel. “Archaeal Membranes : In Silico Modelling and Design.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18661.","mla":"Santana de Freitas Amaral, Miguel. Archaeal Membranes : In Silico Modelling and Design. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18661.","ista":"Santana de Freitas Amaral M. 2024. Archaeal membranes : In silico modelling and design. Institute of Science and Technology Austria.","ieee":"M. Santana de Freitas Amaral, “Archaeal membranes : In silico modelling and design,” Institute of Science and Technology Austria, 2024.","ama":"Santana de Freitas Amaral M. Archaeal membranes : In silico modelling and design. 2024. doi:10.15479/at:ista:18661"},"file":[{"file_name":"2024_msfa_thesis.zip","date_created":"2024-12-18T12:27:01Z","access_level":"closed","creator":"mamaral","date_updated":"2025-06-18T22:30:03Z","file_size":19161387,"file_id":"18671","embargo_to":"open_access","checksum":"eca06497a29078558395455c890a32d9","relation":"source_file","content_type":"application/zip"},{"date_updated":"2025-06-18T22:30:03Z","access_level":"open_access","creator":"mamaral","date_created":"2024-12-18T12:26:30Z","file_name":"2024_msfa_thesis.pdf","content_type":"application/pdf","relation":"main_file","checksum":"2dc30ea46c5daf48d07e4cccb3c3de00","embargo":"2025-06-18","file_id":"18672","file_size":16530084}],"alternative_title":["ISTA Thesis"],"supervisor":[{"orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"type":"dissertation","OA_place":"publisher"},{"publication":"bioRxiv","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"M. Santana de Freitas Amaral, F. F. Frey, X. Jiang, B. Baum, and A. Šarić, “Stability vs flexibility: Reshaping archaeal membranes in silico,” bioRxiv. .","ama":"Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability vs flexibility: Reshaping archaeal membranes in silico. bioRxiv. doi:10.1101/2024.10.18.619072","ista":"Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability vs flexibility: Reshaping archaeal membranes in silico. bioRxiv, 10.1101/2024.10.18.619072.","mla":"Santana de Freitas Amaral, Miguel, et al. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.” BioRxiv, doi:10.1101/2024.10.18.619072.","chicago":"Santana de Freitas Amaral, Miguel, Felix F Frey, Xiuyun Jiang, Buzz Baum, and Anđela Šarić. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.” BioRxiv, n.d. https://doi.org/10.1101/2024.10.18.619072.","apa":"Santana de Freitas Amaral, M., Frey, F. F., Jiang, X., Baum, B., & Šarić, A. (n.d.). Stability vs flexibility: Reshaping archaeal membranes in silico. bioRxiv. https://doi.org/10.1101/2024.10.18.619072","short":"M. Santana de Freitas Amaral, F.F. Frey, X. Jiang, B. Baum, A. Šarić, BioRxiv (n.d.)."},"language":[{"iso":"eng"}],"year":"2024","type":"preprint","acknowledgement":"MA, BB, and AŠ acknowledge funding by the\r\nVolkswagen Foundation Grant Az 96727. FF\r\nacknowledges fnancial support by the NOMIS\r\nfoundation. AŠ acknowledges funding by ERC\r\nStarting Grant “NEPA” 802960. We thank\r\nClaudia Flandoli for help with illustrations.","article_processing_charge":"No","OA_place":"repository","department":[{"_id":"AnSa"}],"day":"27","main_file_link":[{"url":"https://doi.org/10.1101/2024.10.18.619072","open_access":"1"}],"abstract":[{"text":"Across the tree of life, distinct designs of cellular membranes have evolved. In bacteria and eukaryotes single-headed lipids self-assemble into flexible bilayer membranes. By contrast, archaea often possess double-headed, monolayer spanning bolalipids, mixed with bilayer lipids, enabling them to survive in harsh environments. Here, using a minimal computational model for bolalipid membranes, we discover trade-offs when forming membranes. We find that membranes made out of flexible bolalipids resemble bilayer membranes as bolalipids exhibit conformational switch into U-shaped conformations to enable higher curvatures. Conversely, stiffer bolalipids, resembling those in extremophile archaea, take on straight conformations and form liquid membranes that are stiff, and prone to pore formation during membrane reshaping. Strikingly, we show how to achieve fluid bolalipid membranes that are both stable and flexible – by including small amounts of bilayer lipids, as archaea do. Our study explains how different organisms resolve trade-offs when generating membranes of desired material properties.","lang":"eng"}],"author":[{"last_name":"Santana de Freitas Amaral","full_name":"Santana de Freitas Amaral, Miguel","first_name":"Miguel","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501"},{"first_name":"Felix F","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","orcid":"0000-0001-8501-6017","last_name":"Frey","full_name":"Frey, Felix F"},{"full_name":"Jiang, Xiuyun","last_name":"Jiang","first_name":"Xiuyun"},{"first_name":"Buzz","last_name":"Baum","full_name":"Baum, Buzz"},{"full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"18661","status":"public"}]},"date_created":"2024-12-18T10:07:45Z","date_updated":"2026-05-27T22:30:30Z","doi":"10.1101/2024.10.18.619072","publication_status":"draft","project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","grant_number":"802960"}],"title":"Stability vs flexibility: Reshaping archaeal membranes in silico","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)"},"date_published":"2024-11-27T00:00:00Z","status":"public","oa_version":"Preprint","ec_funded":1,"_id":"18670","oa":1,"corr_author":"1","month":"11"},{"date_updated":"2026-05-27T22:30:29Z","doi":"10.1101/2024.07.02.601697","title":"Evidence of a Slower-Z effect in Schistosoma japonicum","publication_status":"draft","date_published":"2024-07-04T00:00:00Z","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)"},"abstract":[{"lang":"eng","text":"Sex-linked and autosomal loci experience different selective pressures and\r\nevolutionary dynamics. X (or Z) chromosomes are often hemizygous, as Y (or W)\r\nchromosomes often degenerate. Such hemizygous regions can be under greater\r\nefficacy of selection, as recessive mutations are immediately exposed to selection in\r\nthe heterogametic sex (the so-called Faster-X or Faster-Z effect). However, in young\r\nnon-recombining regions, Y/W chromosomes often have many functional genes, and\r\nmany X/Z-linked loci are therefore diploid. The sheltering of recessive mutations on\r\nthe X/Z by the Y/W homolog is expected to drive a Slower-X (Slower-Z) effect for\r\ndiploid X/Z loci, i.e. a reduction in the efficacy of selection. While the Faster-X effect\r\nhas been studied extensively, much less is known empirically about the evolutionary\r\ndynamics of diploid X or Z chromosomes. Here, we took advantage of published\r\npopulation genomic data in the female-heterogametic human parasite Schistosoma\r\njaponicum to characterize the gene content and diversity levels of the diploid and\r\nhemizygous regions of the Z chromosome. We used different metrics of selective\r\npressures acting on genes to test for differences in the efficacy of selection in\r\nhemizygous and diploid Z regions, relative to autosomes. We found consistent\r\npatterns suggesting reduced Ne, and reduced efficacy of purifying selection, on both\r\nhemizygous and diploid Z regions. Moreover, relaxed selection was particularly\r\npronounced for female-biased genes on the diploid Z, as predicted by Slower-Z\r\ntheory.\r\n"}],"main_file_link":[{"url":"https://doi.org/10.1101/2024.07.02.601697","open_access":"1"}],"author":[{"full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac","first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"date_created":"2024-11-13T09:12:08Z","related_material":{"record":[{"id":"19370","relation":"later_version","status":"public"},{"id":"18531","relation":"dissertation_contains","status":"public"}]},"oa":1,"corr_author":"1","month":"07","oa_version":"Preprint","status":"public","_id":"18549","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Mrnjavac A, Vicoso B. Evidence of a Slower-Z effect in Schistosoma japonicum. bioRxiv, 10.1101/2024.07.02.601697.","mla":"Mrnjavac, Andrea, and Beatriz Vicoso. “Evidence of a Slower-Z Effect in Schistosoma Japonicum.” BioRxiv, doi:10.1101/2024.07.02.601697.","ama":"Mrnjavac A, Vicoso B. Evidence of a Slower-Z effect in Schistosoma japonicum. bioRxiv. doi:10.1101/2024.07.02.601697","ieee":"A. Mrnjavac and B. Vicoso, “Evidence of a Slower-Z effect in Schistosoma japonicum,” bioRxiv. .","short":"A. Mrnjavac, B. Vicoso, BioRxiv (n.d.).","chicago":"Mrnjavac, Andrea, and Beatriz Vicoso. “Evidence of a Slower-Z Effect in Schistosoma Japonicum.” BioRxiv, n.d. https://doi.org/10.1101/2024.07.02.601697.","apa":"Mrnjavac, A., & Vicoso, B. (n.d.). Evidence of a Slower-Z effect in Schistosoma japonicum. bioRxiv. https://doi.org/10.1101/2024.07.02.601697"},"language":[{"iso":"eng"}],"year":"2024","publication":"bioRxiv","day":"04","type":"preprint","OA_place":"repository","article_processing_charge":"No","department":[{"_id":"BeVi"}]},{"citation":{"ista":"Puglia D. 2024. Everyday electromechanics: Capacitive strong coupling to mechanical motion. Institute of Science and Technology Austria.","mla":"Puglia, Denise. Everyday Electromechanics: Capacitive Strong Coupling to Mechanical Motion. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18104.","ieee":"D. Puglia, “Everyday electromechanics: Capacitive strong coupling to mechanical motion,” Institute of Science and Technology Austria, 2024.","ama":"Puglia D. Everyday electromechanics: Capacitive strong coupling to mechanical motion. 2024. doi:10.15479/at:ista:18104","short":"D. Puglia, Everyday Electromechanics: Capacitive Strong Coupling to Mechanical Motion, Institute of Science and Technology Austria, 2024.","chicago":"Puglia, Denise. “Everyday Electromechanics: Capacitive Strong Coupling to Mechanical Motion.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18104.","apa":"Puglia, D. (2024). Everyday electromechanics: Capacitive strong coupling to mechanical motion. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18104"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","supervisor":[{"last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"checksum":"7969263451b2356bfa0924725aa9de10","relation":"main_file","content_type":"application/pdf","embargo":"2025-05-20","file_id":"18105","file_size":10778238,"creator":"cchlebak","access_level":"open_access","date_updated":"2025-05-20T22:30:05Z","file_name":"PhD_DPuglia_Final.pdf","date_created":"2024-09-20T12:07:48Z"},{"checksum":"98dfe7675775e30efffa03f7ff7c091b","relation":"source_file","content_type":"application/x-zip-compressed","file_size":385419748,"file_id":"18106","embargo_to":"open_access","creator":"cchlebak","access_level":"closed","date_updated":"2025-05-20T22:30:05Z","file_name":"PhD_DPuglia_Thesis.zip","date_created":"2024-09-20T12:13:09Z"}],"degree_awarded":"PhD","abstract":[{"text":"We introduce a new all-electric platform, that strong couples light to mechanical motion\r\nby ensuring that the external environmental coupling dominates over internal mechanical\r\ndissipation. The system only has three everyday components: AC, DC, and a fip-chip, in which\r\na metallized silicon nitride membrane is fipped on top of the device under test. This everyday\r\nelectromechanical device can be operated at low or room temperature and has 10000× lower\r\ninsertion loss than a comparable commercial quartz crystal, achieves a position imprecision\r\nmatching state-of-the-art optical interferometer, and enables remote cooling of mechanical\r\nmotion. The spatial properties of higher order mechanical modes are a promising feature for\r\nreconstructing unknown charge distributions.\r\n","lang":"eng"}],"date_published":"2024-09-20T00:00:00Z","tmp":{"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)","image":"/images/cc_by_nc.png"},"title":"Everyday electromechanics: Capacitive strong coupling to mechanical motion","publication_status":"published","project":[{"grant_number":"P33692","name":"Cavity electromechanics across a quantum phase transition","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931"},{"_id":"62843413-2b32-11ec-9570-c4ec6eabfae7","name":"Surface Charge and Tunneling Multi-Mode Imaging","grant_number":"26088"}],"date_updated":"2026-04-07T13:22:10Z","corr_author":"1","publication_identifier":{"issn":["2663-337X"]},"page":"63","license":"https://creativecommons.org/licenses/by-nc/4.0/","year":"2024","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"AnHi"}],"article_processing_charge":"No","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"has_accepted_license":"1","day":"20","publisher":"Institute of Science and Technology Austria","date_created":"2024-09-20T12:13:30Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"18143","status":"public"}]},"author":[{"id":"4D495994-AE37-11E9-AC72-31CAE5697425","first_name":"Denise","full_name":"Puglia, Denise","last_name":"Puglia","orcid":"0000-0003-1144-2763"}],"doi":"10.15479/at:ista:18104","ddc":["530"],"_id":"18104","file_date_updated":"2025-05-20T22:30:05Z","status":"public","oa_version":"Published Version","month":"09","oa":1},{"author":[{"last_name":"Puglia","full_name":"Puglia, Denise","orcid":"0000-0003-1144-2763","id":"4D495994-AE37-11E9-AC72-31CAE5697425","first_name":"Denise"},{"full_name":"Odessey, Rachel H","last_name":"Odessey","id":"9a7a5123-8972-11ed-ae7b-dd1f2af457bd","first_name":"Rachel H"},{"first_name":"Peter S.","full_name":"Burns, Peter S.","last_name":"Burns"},{"first_name":"Niklas","last_name":"Luhmann","full_name":"Luhmann, Niklas"},{"last_name":"Schmid","full_name":"Schmid, Silvan","first_name":"Silvan"},{"first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","last_name":"Higginbotham"}],"abstract":[{"text":"Strong optomechanical coupling -- a regime where mechanical motion is damped\r\nby environmental radiation -- has traditionally required demanding experimental\r\ningredients such as superconducting resonators, high-quality optical cavities,\r\nor large magnetic fields. Here we demonstrate a room temperature, cavity-free,\r\nall-electric device reaching this regime at radio frequencies, enabled by a\r\nmechanically compliant parallel-plate capacitor with a nanoscale plate\r\nseparation and an aspect ratio exceeding 1,000. The device has four orders of\r\nmagnitude lower insertion loss than a comparable commercial quartz crystal, and\r\nachieves a position imprecision rivaling an optical interferometer. With the\r\nhelp of a back-action isolation scheme, we observe radiative cooling of\r\nmechanical motion by a remote cryogenic load. This work provides a\r\ntechnologically accessible route to high-precision sensing, transduction, and\r\nsignal processing.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2407.15314","open_access":"1"}],"related_material":{"record":[{"id":"19026","relation":"later_version","status":"public"},{"status":"public","id":"18104","relation":"dissertation_contains"}]},"date_created":"2024-09-26T06:58:27Z","doi":"10.48550/arXiv.2407.15314","title":"Room temperature, cavity-free capacitive strong coupling to mechanical motion","publication_status":"draft","project":[{"grant_number":"26088","_id":"62843413-2b32-11ec-9570-c4ec6eabfae7","name":"Surface Charge and Tunneling Multi-Mode Imaging"},{"grant_number":"P33692","name":"Cavity electromechanics across a quantum phase transition","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931"}],"date_updated":"2026-05-27T22:30:31Z","date_published":"2024-08-24T00:00:00Z","external_id":{"arxiv":["2407.15314"]},"_id":"18143","arxiv":1,"status":"public","oa_version":"Preprint","article_number":"2407.15314","corr_author":"1","oa":1,"month":"08","publication":"arXiv","citation":{"short":"D. Puglia, R.H. Odessey, P.S. Burns, N. Luhmann, S. Schmid, A.P. Higginbotham, ArXiv (n.d.).","apa":"Puglia, D., Odessey, R. H., Burns, P. S., Luhmann, N., Schmid, S., & Higginbotham, A. P. (n.d.). Room temperature, cavity-free capacitive strong coupling to mechanical motion. arXiv. https://doi.org/10.48550/arXiv.2407.15314","chicago":"Puglia, Denise, Rachel H Odessey, Peter S. Burns, Niklas Luhmann, Silvan Schmid, and Andrew P Higginbotham. “Room Temperature, Cavity-Free Capacitive Strong Coupling to Mechanical Motion.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2407.15314.","ista":"Puglia D, Odessey RH, Burns PS, Luhmann N, Schmid S, Higginbotham AP. Room temperature, cavity-free capacitive strong coupling to mechanical motion. arXiv, 2407.15314.","mla":"Puglia, Denise, et al. “Room Temperature, Cavity-Free Capacitive Strong Coupling to Mechanical Motion.” ArXiv, 2407.15314, doi:10.48550/arXiv.2407.15314.","ieee":"D. Puglia, R. H. Odessey, P. S. Burns, N. Luhmann, S. Schmid, and A. P. Higginbotham, “Room temperature, cavity-free capacitive strong coupling to mechanical motion,” arXiv. .","ama":"Puglia D, Odessey RH, Burns PS, Luhmann N, Schmid S, Higginbotham AP. Room temperature, cavity-free capacitive strong coupling to mechanical motion. arXiv. doi:10.48550/arXiv.2407.15314"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2024","language":[{"iso":"eng"}],"OA_place":"repository","article_processing_charge":"No","type":"preprint","department":[{"_id":"AnHi"}],"day":"24"},{"department":[{"_id":"GradSch"},{"_id":"MaRo"}],"has_accepted_license":"1","article_processing_charge":"No","day":"11","publisher":"Institute of Science and Technology Austria","page":"138","language":[{"iso":"eng"}],"year":"2024","oa_version":"Published Version","status":"public","ddc":["576"],"_id":"18642","file_date_updated":"2025-06-12T22:30:02Z","month":"12","oa":1,"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"18648"},{"status":"public","id":"8707","relation":"part_of_dissertation"}]},"date_created":"2024-12-10T13:49:15Z","author":[{"first_name":"Nick N","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6617-9742","last_name":"Machnik","full_name":"Machnik, Nick N"}],"doi":"10.15479/at:ista:18642","type":"dissertation","acknowledgement":"I would like to thank the Swiss National Science Foundation for funding parts of this work\r\nthrough the Eccellenza Grant \"Improving estimation and prediction of common complex\r\ndisease risk\" with grant number PCEGP3_181181.","supervisor":[{"orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","last_name":"Robinson","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"}],"OA_place":"publisher","alternative_title":["ISTA Thesis"],"file":[{"date_created":"2024-12-11T11:59:54Z","file_name":"NickMachnikThesisFinal_pdfa_conv.pdf","date_updated":"2025-06-12T22:30:02Z","creator":"nmachnik","access_level":"open_access","embargo":"2025-06-12","file_size":12845009,"file_id":"18649","content_type":"application/pdf","relation":"main_file","checksum":"d45e4d170f9a70a1f69b44b99bd058e4"},{"file_name":"thesis.zip","date_created":"2024-12-11T11:59:34Z","date_updated":"2025-06-12T22:30:02Z","access_level":"closed","creator":"nmachnik","embargo_to":"open_access","file_size":14189810,"file_id":"18650","relation":"source_file","content_type":"application/zip","checksum":"f88c9acc62002395ec4dcbdb5eea8b82"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"short":"N.N. Machnik, Algorithms for Causal Learning and Comparative Analysis for Genomic Data, Institute of Science and Technology Austria, 2024.","apa":"Machnik, N. N. (2024). Algorithms for causal learning and comparative analysis for genomic data. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18642","chicago":"Machnik, Nick N. “Algorithms for Causal Learning and Comparative Analysis for Genomic Data.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18642.","mla":"Machnik, Nick N. Algorithms for Causal Learning and Comparative Analysis for Genomic Data. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18642.","ista":"Machnik NN. 2024. Algorithms for causal learning and comparative analysis for genomic data. Institute of Science and Technology Austria.","ama":"Machnik NN. Algorithms for causal learning and comparative analysis for genomic data. 2024. doi:10.15479/at:ista:18642","ieee":"N. N. Machnik, “Algorithms for causal learning and comparative analysis for genomic data,” Institute of Science and Technology Austria, 2024."},"publication_identifier":{"issn":["2663-337X"]},"corr_author":"1","degree_awarded":"PhD","abstract":[{"lang":"eng","text":"This thesis consists of two pieces of work in the broader feld of computational biology,\r\nboth of which are methods for the analysis of large scale biological data, implemented in\r\nefcient software.\r\nChapter 2 introduces a statistical software for causal discovery and inference from observed\r\ngenetic marker and phenotypic trait data. We explore in simulation how well the method\r\ncan fne-map genetic efects, fnd the correct causal structure among tens of traits and\r\nmillions of genetic markers, and infer the causal efect size for the discovered causal\r\nrelations. We then apply the method to 8 million markers and 17 traits from the UK\r\nBiobank and show that many relationships found with other methods are likely due to\r\nthe efects of hidden confounders.\r\nChapter 3 describes how this method can be applied to longitudinal data. I show how one\r\ncan incorporate the background knowledge present in the known order of measurements to\r\nimprove the accuracy of the causal discovery process, and explore the method’s ability to\r\nidentify age specifc genetic efects, and how the error rates of this recovery are infuenced\r\nby missing data due to diferent censoring mechanisms.\r\nChapter 4 introduces a statistical software for the comparison of chromatin contact maps\r\nbased on the structural similarity index. We explore the robustness of the method to\r\nnoise and size diferences of the compared maps, show how it can measure evolutionary\r\nconservation of topological features by providing a similarity ranking of syntenic regions,\r\nand fnally how it can detect alterations in 3D genome structure due to genetic mutations\r\nin samples of medical relevance.\r\n"}],"date_published":"2024-12-11T00:00:00Z","date_updated":"2026-04-07T13:23:06Z","publication_status":"published","project":[{"grant_number":"PCEGP3_181181","name":"Improving estimation and prediction of common complex disease risk","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A"}],"title":"Algorithms for causal learning and comparative analysis for genomic data"},{"year":"2024","language":[{"iso":"eng"}],"OA_type":"free access","department":[{"_id":"MaRo"}],"article_processing_charge":"No","acknowledged_ssus":[{"_id":"ScienComp"}],"day":"10","date_created":"2024-12-11T10:42:59Z","related_material":{"record":[{"status":"public","id":"18642","relation":"dissertation_contains"}]},"author":[{"first_name":"Nick N","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6617-9742","full_name":"Machnik, Nick N","last_name":"Machnik"},{"id":"b9f6d5ef-7774-11eb-a47f-df2c75c02ee7","first_name":"Seyed Mahdi","full_name":"Mahmoudi, Seyed Mahdi","last_name":"Mahmoudi"},{"first_name":"Malgorzata","full_name":"Borczyk, Malgorzata","last_name":"Borczyk"},{"id":"30d4014e-7753-11eb-b44b-db6d61112e73","first_name":"Ilse","last_name":"Krätschmer","full_name":"Krätschmer, Ilse","orcid":"0000-0002-5636-9259"},{"full_name":"Bauer, Markus J.","last_name":"Bauer","first_name":"Markus J."},{"orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","last_name":"Robinson","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"}],"main_file_link":[{"url":"https://doi.org/10.1101/2023.12.06.570392","open_access":"1"}],"doi":"10.1101/2023.12.06.570392","_id":"18648","status":"public","oa_version":"Preprint","month":"08","oa":1,"publication":"bioRxiv","citation":{"short":"N.N. Machnik, S.M. Mahmoudi, M. Borczyk, I. Krätschmer, M.J. Bauer, M.R. Robinson, BioRxiv (2024).","chicago":"Machnik, Nick N, Seyed Mahdi Mahmoudi, Malgorzata Borczyk, Ilse Krätschmer, Markus J. Bauer, and Matthew Richard Robinson. “Causal Inference for Multiple Risk Factors and Diseases from Genomics Data.” BioRxiv, 2024. https://doi.org/10.1101/2023.12.06.570392.","apa":"Machnik, N. N., Mahmoudi, S. M., Borczyk, M., Krätschmer, I., Bauer, M. J., & Robinson, M. R. (2024). Causal inference for multiple risk factors and diseases from genomics data. bioRxiv. https://doi.org/10.1101/2023.12.06.570392","ista":"Machnik NN, Mahmoudi SM, Borczyk M, Krätschmer I, Bauer MJ, Robinson MR. 2024. Causal inference for multiple risk factors and diseases from genomics data. bioRxiv, 10.1101/2023.12.06.570392.","mla":"Machnik, Nick N., et al. “Causal Inference for Multiple Risk Factors and Diseases from Genomics Data.” BioRxiv, 2024, doi:10.1101/2023.12.06.570392.","ieee":"N. N. Machnik, S. M. Mahmoudi, M. Borczyk, I. Krätschmer, M. J. Bauer, and M. R. Robinson, “Causal inference for multiple risk factors and diseases from genomics data,” bioRxiv. 2024.","ama":"Machnik NN, Mahmoudi SM, Borczyk M, Krätschmer I, Bauer MJ, Robinson MR. Causal inference for multiple risk factors and diseases from genomics data. bioRxiv. 2024. doi:10.1101/2023.12.06.570392"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","OA_place":"repository","acknowledgement":"We thank Zoltan Kutalik and members of the Robinson group \r\nat ISTA for their comments, which improved this manuscript. This work was funded \r\nby a research collaboration agreement between Boehringer Ingelheim and the research \r\ngroup of MRR at the Institute of Science and Technology Austria. Additional funding \r\nwas also provided by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by \r\ncore funding from the Institute of Science and Technology Austria. We would like \r\nto acknowledge the participants and investigators of the UK Biobank study. High- \r\nperformance computing was supported by the Scientific Service Units (SSU) of IST \r\nAustria through resources provided by Scientific Computing (SciComp). ","type":"preprint","abstract":[{"lang":"eng","text":"Statistical causal learning in genomics relies on the instrumental variable method of\r\nMendelian Randomization (MR). Currently, an overwhelming number of MR studies\r\npurport to show causal relationships among a wide range of risk factors and outcomes.\r\nHere, we show that selecting instrument variables from genome-wide association study\r\nestimates leads to high false discovery rates for many MR approaches, which can be\r\ngreatly reduced by employing a graphical inference approach which: (i) explicitly tests\r\ninstrumental variable assumptions; (ii) distinguishes direct from indirect factors in very\r\nhigh-dimensional data; (iii) discriminates pleiotropic from trait-specific markers, controlling for LD genome-wide; (iv) accommodates rare variants and binary outcomes in a\r\nprincipled way; and (v) identifies potential unobserved latent confounding. For 17 traits\r\nand 8.4M variants recorded for 458,747 individuals in the UK Biobank, we show that\r\nstandard MR analysis gives an abundance of findings that disappear under stringent\r\nassumption checks, with many relationships reflecting potential unmeasured confounding. This implies that mixtures of temporal precedence and potential for reverse-causality\r\nprohibit understanding the underlying nature of phenotypic and genetic correlations in\r\nbiobank data. We propose that well-curated longitudinal records are likely needed and\r\nthat our approach provides a first-step toward robust principled screening for potential\r\ncausal links.\r\n"}],"date_published":"2024-08-10T00:00:00Z","tmp":{"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)","image":"/images/cc_by_nc.png"},"title":"Causal inference for multiple risk factors and diseases from genomics data","publication_status":"published","project":[{"grant_number":"PCEGP3_181181","name":"Improving estimation and prediction of common complex disease risk","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A"},{"grant_number":"590359","_id":"bd936e6f-d553-11ed-ba76-a82299f63e8c","name":"Advanced statistical modelling to facilitate more accurate characterisation of disease phenotypes, improved genetic mapping, and effective therapeutic hypothesis generation"}],"date_updated":"2026-05-27T22:30:33Z","corr_author":"1"},{"OA_embargo":"12","abstract":[{"lang":"eng","text":"Biological vision is unlike a camera; rather than transmitting light information faithfully, early\r\nvisual circuits process the visual scene to convey only the relevant information in an efficient\r\nmanner. Consequentially, the nature of this visual processing then depends on what is the\r\nrelevant information in a scene and on the notion of efficiency. In this work, I study how visual\r\nprocessing is modulated by two different variations in the visual scene. First, I discovered that\r\nin the mouse (Mus musculus) retina, Retinal Ganglion Cells in the upper and lower visual\r\nfield have differences in the center surround structure of their receptive fields. Comparison\r\nwith models of efficient coding show that this adaptation likely evolved to cope with the\r\nbrightness gradient from the sky to the ground that is pervasive in natural scenes. In the\r\nsecond project, I study how the downstream neurons in the Superior Colliculus dynamically\r\nchange their temporal selectivity depending on the ambient luminance and behavioral state.\r\nAs the scene gets darker or when the animal is is less aroused, the neuronal responses get\r\nlaggier, while still maintaining their relative timing with respect to the population. Overall, this\r\nwork emphasises the need to understand visual processing in the context of specific demands\r\nof the animal in its the environment. The adaptive changes in the visual system, from the\r\nretinal ganglion cells to the superior colliculus, highlight the intricate ways in which biological\r\nvision optimizes the processing of visual information.\r\n"}],"degree_awarded":"PhD","project":[{"name":"Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses","_id":"bdaf81a8-d553-11ed-ba76-c95961984540","grant_number":"101086580"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"},{"_id":"2634E9D2-B435-11E9-9278-68D0E5697425","name":"Circuits of Visual Attention","call_identifier":"H2020","grant_number":"756502"}],"publication_status":"published","title":"Visual adaptations to natural statistics","date_updated":"2026-04-07T13:24:48Z","tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"date_published":"2024-11-22T00:00:00Z","ec_funded":1,"corr_author":"1","publication_identifier":{"isbn":["978-3-99078-050-3"],"issn":["2663-337X"]},"citation":{"mla":"Gupta, Divyansh. Visual Adaptations to Natural Statistics. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18574.","ista":"Gupta D. 2024. Visual adaptations to natural statistics. Institute of Science and Technology Austria.","ama":"Gupta D. Visual adaptations to natural statistics. 2024. doi:10.15479/at:ista:18574","ieee":"D. Gupta, “Visual adaptations to natural statistics,” Institute of Science and Technology Austria, 2024.","short":"D. Gupta, Visual Adaptations to Natural Statistics, Institute of Science and Technology Austria, 2024.","chicago":"Gupta, Divyansh. “Visual Adaptations to Natural Statistics.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18574.","apa":"Gupta, D. (2024). Visual adaptations to natural statistics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18574"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","type":"dissertation","acknowledgement":"This work would have been impossible without the Scientific Service Units of IST Austria. The resources and expertise provided by Scientific Computing (especially Alois Schlögl), the MIBA Machine Shop (especially Todor Asenov), the Preclinical Facility (especially Freyja Langer), the Library, the Lab Support Facility and the Imaging and Optics Facility were the essential bedrock I could build upon. I would also like to thank IT support at ISTA for powering through remote work and a cyberattack.\r\nI am grateful for having been funded initially by the European Union Horizon 2020 Marie Skłodowska-Curie grant 665385 and later by Prof. Maximilian Joesch's the European Research Council Starting (756502) and Consolidator (101086580) Grants.","supervisor":[{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A","full_name":"Jösch, Maximilian A","last_name":"Jösch","orcid":"0000-0002-3937-1330"}],"file":[{"content_type":"application/zip","relation":"source_file","checksum":"ebb000d361c36b22ed6e639a931c6b7c","embargo_to":"open_access","file_id":"18589","file_size":75512262,"date_updated":"2025-11-11T23:30:02Z","creator":"dgupta","access_level":"closed","date_created":"2024-11-25T14:44:03Z","file_name":"PhD Thesis - Divyansh Gupta.zip"},{"content_type":"application/pdf","relation":"main_file","checksum":"1282401eb71598bc311058b0fcefc6a1","file_id":"18591","embargo":"2025-11-11","file_size":6412619,"date_updated":"2025-11-11T23:30:02Z","access_level":"open_access","creator":"dgupta","date_created":"2024-11-26T11:43:19Z","file_name":"PDFA_PhD_Thesis___Divyansh_Gupta-26_11_24.pdf"}],"alternative_title":["ISTA Thesis"],"author":[{"first_name":"Divyansh","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7400-6665","last_name":"Gupta","full_name":"Gupta, Divyansh"}],"related_material":{"record":[{"id":"12349","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"research_data","id":"12370"}]},"date_created":"2024-11-20T21:30:44Z","doi":"10.15479/at:ista:18574","_id":"18574","file_date_updated":"2025-11-11T23:30:02Z","ddc":["573"],"status":"public","oa_version":"Published Version","oa":1,"month":"11","page":"86","year":"2024","language":[{"iso":"eng"}],"article_processing_charge":"No","has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"publisher":"Institute of Science and Technology Austria","day":"22"},{"citation":{"apa":"Agudelo Duenas, N. (2024). Visualizing the neuronal transcriptional landscape with tissue context. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18471","chicago":"Agudelo Duenas, Nathalie. “Visualizing the Neuronal Transcriptional Landscape with Tissue Context.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18471.","short":"N. Agudelo Duenas, Visualizing the Neuronal Transcriptional Landscape with Tissue Context, Institute of Science and Technology Austria, 2024.","ama":"Agudelo Duenas N. Visualizing the neuronal transcriptional landscape with tissue context. 2024. doi:10.15479/at:ista:18471","ieee":"N. Agudelo Duenas, “Visualizing the neuronal transcriptional landscape with tissue context,” Institute of Science and Technology Austria, 2024.","ista":"Agudelo Duenas N. 2024. Visualizing the neuronal transcriptional landscape with tissue context. Institute of Science and Technology Austria.","mla":"Agudelo Duenas, Nathalie. Visualizing the Neuronal Transcriptional Landscape with Tissue Context. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18471."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","type":"dissertation","supervisor":[{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl"}],"alternative_title":["ISTA Thesis"],"file":[{"file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.docx","date_created":"2024-10-26T22:29:06Z","access_level":"closed","creator":"nagudelo","date_updated":"2025-05-05T22:30:04Z","file_id":"18475","file_size":183077763,"embargo_to":"open_access","checksum":"6d7c7725d040d8debc070dcb35ac965d","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"checksum":"52f9c0bf2bdafa3baf827b73814a53ff","relation":"main_file","content_type":"application/pdf","file_id":"18476","embargo":"2025-05-05","file_size":47027710,"access_level":"open_access","creator":"nagudelo","date_updated":"2025-05-05T22:30:04Z","file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.pdf","date_created":"2024-10-26T23:13:33Z"}],"degree_awarded":"PhD","abstract":[{"lang":"eng","text":"Spatial omics technologies are enriching our understanding of complex biological samples, by\r\nallowing us to study their molecular composition while preserving the spatial relationships\r\nbetween molecules in their native context. As the field continues to advance, there are\r\ntechnical challenges that need to be addressed in order to take full advantage of the spatial\r\ncapabilities of these methods. In this work, I present two technical developments that I\r\nestablished for multiplexed error robust FISH (MERFISH) throughout my PhD: (1) pushing the\r\nspatial resolution limits to the nanoscale, and (2) adding rich tissue context to the mouse brain\r\ntranscriptome. To achieve nanoscale resolution with MERFISH in cultured cells, I combined it\r\nwith stimulated emission depletion (STED) and expansion microscopy (ExM) to achieve a\r\nspatial resolution as low as ~20 nm, and explored the compatibility of MERFISH with singlemolecule localization microscopy (SMLM) techniques. To visualize targeted mRNAs in mouse\r\nbrain tissue, I applied the comprehensive analysis of tissues across scales (CATS) toolbox, which\r\nprovides an unbiased morphological readout by labeling the extracellular domain. I\r\nsuccessfully established this method, which we call CATS-MERFISH-ExM, to work with thick\r\nmouse brain slices, being able to extract transcriptomics information with 3D tissue context.\r\nCATS-MERFISH-ExM enabled us to identify cell types and further visualize the subcellular\r\ndistribution of transcripts in mouse brain tissue, shedding light on the neuropil-specific\r\ntranscriptome. This method provides integrated information on cellular structure and\r\ntranscriptomes in situ, and could potentially be applied with other modalities, opening new\r\navenues for scientific discovery. "}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2024-10-28T00:00:00Z","publication_status":"published","title":"Visualizing the neuronal transcriptional landscape with tissue context","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"},{"call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232"}],"date_updated":"2026-04-14T08:34:37Z","ec_funded":1,"corr_author":"1","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-044-2"]},"page":"97","year":"2024","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"JoDa"}],"article_processing_charge":"No","has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"day":"28","publisher":"Institute of Science and Technology Austria","date_created":"2024-10-26T20:02:42Z","author":[{"full_name":"Agudelo Duenas, Nathalie","last_name":"Agudelo Duenas","first_name":"Nathalie","id":"40E7F008-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/at:ista:18471","ddc":["570"],"_id":"18471","file_date_updated":"2025-05-05T22:30:04Z","status":"public","oa_version":"Published Version","month":"10","oa":1},{"page":"1940-1953.e10","language":[{"iso":"eng"}],"year":"2024","OA_type":"hybrid","department":[{"_id":"AnKi"}],"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","issue":"15","day":"01","publisher":"Elsevier","article_type":"original","date_created":"2024-06-16T22:01:07Z","related_material":{"record":[{"status":"public","id":"19763","relation":"dissertation_contains"}]},"volume":59,"author":[{"first_name":"Teresa","last_name":"Krammer","full_name":"Krammer, Teresa"},{"first_name":"Hannah T.","last_name":"Stuart","full_name":"Stuart, Hannah T."},{"full_name":"Gromberg, Elena","last_name":"Gromberg","first_name":"Elena"},{"first_name":"Keisuke","last_name":"Ishihara","full_name":"Ishihara, Keisuke"},{"first_name":"Dillon","full_name":"Cislo, Dillon","last_name":"Cislo"},{"first_name":"Manuela","full_name":"Melchionda, Manuela","last_name":"Melchionda"},{"first_name":"Fernando","last_name":"Becerril Perez","full_name":"Becerril Perez, Fernando"},{"last_name":"Wang","full_name":"Wang, Jingkui","first_name":"Jingkui"},{"full_name":"Costantini, Elena","last_name":"Costantini","first_name":"Elena"},{"id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","first_name":"Stefanie","last_name":"Rus","full_name":"Rus, Stefanie","orcid":"0000-0001-8703-1093"},{"first_name":"Laura","last_name":"Arbanas","full_name":"Arbanas, Laura"},{"first_name":"Alexandra","full_name":"Hörmann, Alexandra","last_name":"Hörmann"},{"first_name":"Ralph A.","last_name":"Neumüller","full_name":"Neumüller, Ralph A."},{"full_name":"Elvassore, Nicola","last_name":"Elvassore","first_name":"Nicola"},{"full_name":"Siggia, Eric","last_name":"Siggia","first_name":"Eric"},{"first_name":"James","last_name":"Briscoe","full_name":"Briscoe, James"},{"full_name":"Kicheva, Anna","last_name":"Kicheva","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"},{"full_name":"Tanaka, Elly M.","last_name":"Tanaka","first_name":"Elly M."}],"intvolume":" 59","scopus_import":"1","doi":"10.1016/j.devcel.2024.04.021","status":"public","oa_version":"Published Version","file_date_updated":"2025-01-13T10:59:12Z","_id":"17148","ddc":["570"],"month":"08","oa":1,"publication":"Developmental Cell","pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"apa":"Krammer, T., Stuart, H. T., Gromberg, E., Ishihara, K., Cislo, D., Melchionda, M., … Tanaka, E. M. (2024). Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2024.04.021","chicago":"Krammer, Teresa, Hannah T. Stuart, Elena Gromberg, Keisuke Ishihara, Dillon Cislo, Manuela Melchionda, Fernando Becerril Perez, et al. “Mouse Neural Tube Organoids Self-Organize Floorplate through BMP-Mediated Cluster Competition.” Developmental Cell. Elsevier, 2024. https://doi.org/10.1016/j.devcel.2024.04.021.","short":"T. Krammer, H.T. Stuart, E. Gromberg, K. Ishihara, D. Cislo, M. Melchionda, F. Becerril Perez, J. Wang, E. Costantini, S. Rus, L. Arbanas, A. Hörmann, R.A. Neumüller, N. Elvassore, E. Siggia, J. Briscoe, A. Kicheva, E.M. Tanaka, Developmental Cell 59 (2024) 1940–1953.e10.","ieee":"T. Krammer et al., “Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition,” Developmental Cell, vol. 59, no. 15. Elsevier, p. 1940–1953.e10, 2024.","ama":"Krammer T, Stuart HT, Gromberg E, et al. Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. Developmental Cell. 2024;59(15):1940-1953.e10. doi:10.1016/j.devcel.2024.04.021","ista":"Krammer T, Stuart HT, Gromberg E, Ishihara K, Cislo D, Melchionda M, Becerril Perez F, Wang J, Costantini E, Rus S, Arbanas L, Hörmann A, Neumüller RA, Elvassore N, Siggia E, Briscoe J, Kicheva A, Tanaka EM. 2024. Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. Developmental Cell. 59(15), 1940–1953.e10.","mla":"Krammer, Teresa, et al. “Mouse Neural Tube Organoids Self-Organize Floorplate through BMP-Mediated Cluster Competition.” Developmental Cell, vol. 59, no. 15, Elsevier, 2024, p. 1940–1953.e10, doi:10.1016/j.devcel.2024.04.021."},"type":"journal_article","acknowledgement":"We thank P. Pasierbek, A.C. Moreno, T. Lendl, and K. Aumayr for microscopy support; G. Schmauss for FACS support; M. Novatchkova for assistance with Bioinformatic analyses; J. Ahel, A. Polikarpova, S. Horer, E. Cesare, and E. Norouzi for technical assistance; A. Meinhardt for supervision; DRESDEN-concept Genome Center, A. Vogt, A. Sommer, and the Vienna BioCenter NGS facility for RNA sequencing. We are grateful to M. Placzek and E. Martí for discussions about the floorplate; to S. Shvartsman for valuable input; to A. Aszodi, W. Masselink, and S. Raiders for advice on statistical analyses; to J. Cornwall Scoones, G. Martello, and Tanaka lab members for critical reading of the manuscript; E. Bassat and E. Chatzidaki for contributing schematics; and to K. Lust for support. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement ERC AdG 742046) to E.M.T. This research was funded in whole or in part by the Austrian Science Fund (FWF) (10.55776/F7803-B) (Stem Cell Modulation) to E.M.T. and A.K., Sir Henry Wellcome postdoctoral fellowship to H.T.S., ELBE fellowship to K.I., and National Science Foundation (US) Phy 2013131 to E.S. The A.K. lab is also supported by ISTA and the European Research Council under Horizon Europe grant 101044579, and S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. This work was supported in part by the Francis Crick Institute, which receives its core funding from Cancer Research UK (CC001051), the UK Medical Research Council (CC001051), and the Wellcome Trust (CC001051). For the purpose of open access, the authors have applied a CC BY public copyright license to any author accepted manuscript (AAM) version arising from this submission.","OA_place":"publisher","file":[{"date_updated":"2025-01-13T10:59:12Z","success":1,"access_level":"open_access","creator":"dernst","file_name":"2024_DevelopmentalCell_Krammer.pdf","date_created":"2025-01-13T10:59:12Z","relation":"main_file","content_type":"application/pdf","checksum":"fefdea9c02862b4bb74de49b65ce638a","file_id":"18841","file_size":6249076}],"quality_controlled":"1","abstract":[{"text":"During neural tube (NT) development, the notochord induces an organizer, the floorplate, which secretes Sonic Hedgehog (SHH) to pattern neural progenitors. Conversely, NT organoids (NTOs) from embryonic stem cells (ESCs) spontaneously form floorplates without the notochord, demonstrating that stem cells can self-organize without embryonic inducers. Here, we investigated floorplate self-organization in clonal mouse NTOs. Expression of the floorplate marker FOXA2 was initially spatially scattered before resolving into multiple clusters, which underwent competition and sorting, resulting in a stable “winning” floorplate. We identified that BMP signaling governed long-range cluster competition. FOXA2+ clusters expressed BMP4, suppressing FOXA2 in receiving cells while simultaneously expressing the BMP-inhibitor NOGGIN, promoting cluster persistence. Noggin mutation perturbed floorplate formation in NTOs and in the NT in vivo at mid/hindbrain regions, demonstrating how the floorplate can form autonomously without the notochord. Identifying the pathways governing organizer self-organization is critical for harnessing the developmental plasticity of stem cells in tissue engineering.","lang":"eng"}],"external_id":{"isi":["001289684800001"],"pmid":["38776925"]},"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)"},"isi":1,"date_published":"2024-08-01T00:00:00Z","date_updated":"2026-05-27T22:31:10Z","project":[{"grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa"},{"grant_number":"SC19-011","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube"}],"title":"Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition","publication_status":"published","publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]}},{"author":[{"orcid":"0000-0001-8703-1093","full_name":"Rus, Stefanie","last_name":"Rus","first_name":"Stefanie","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","last_name":"Merrin"},{"full_name":"Kulig, Monika Aleksandra","last_name":"Kulig","id":"3331f5ae-e896-11ec-af79-eeb79769bcb7","first_name":"Monika Aleksandra"},{"first_name":"Thomas","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","full_name":"Minchington, Thomas","last_name":"Minchington"},{"last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"}],"date_created":"2024-12-01T23:01:53Z","related_material":{"record":[{"status":"public","id":"19763","relation":"dissertation_contains"}]},"volume":5,"scopus_import":"1","doi":"10.1016/j.xpro.2024.103187","intvolume":" 5","oa_version":"Published Version","status":"public","ddc":["570"],"_id":"18601","file_date_updated":"2024-12-03T10:53:23Z","article_number":"103187","oa":1,"month":"12","OA_type":"gold","language":[{"iso":"eng"}],"year":"2024","has_accepted_license":"1","acknowledged_ssus":[{"_id":"NanoFab"}],"article_processing_charge":"Yes","department":[{"_id":"AnKi"},{"_id":"NanoFab"}],"article_type":"original","publisher":"Elsevier","day":"20","issue":"4","abstract":[{"lang":"eng","text":"Geometrically controlled stem cell differentiation promotes reproducible pattern formation. Here, we present a protocol to fabricate elastomeric stencils for patterned stem cell differentiation. We describe procedures for using photolithography to produce molds, followed by molding polydimethylsiloxane (PDMS) to obtain stencils with through holes. We then provide instructions for culturing cells on stencils and, finally, removing stencils to allow colony growth and cell migration. This approach yields reproducible two-dimensional organoids tailored for quantitative studies of growth and pattern formation.\r\nFor complete details on the use and execution of this protocol, please refer to Lehr et al.1"}],"quality_controlled":"1","DOAJ_listed":"1","date_updated":"2026-05-27T22:31:09Z","title":"Protocol for fabricating elastomeric stencils for patterned stem cell differentiation","publication_status":"published","project":[{"grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa"},{"grant_number":"SC19-011","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube"}],"APC_amount":"804 EUR","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2024-12-20T00:00:00Z","external_id":{"pmid":["39602310"]},"publication_identifier":{"eissn":["2666-1667"]},"corr_author":"1","publication":"STAR Protocols","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"S. Rus, J. Merrin, M. A. Kulig, T. Minchington, and A. Kicheva, “Protocol for fabricating elastomeric stencils for patterned stem cell differentiation,” STAR Protocols, vol. 5, no. 4. Elsevier, 2024.","ama":"Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. STAR Protocols. 2024;5(4). doi:10.1016/j.xpro.2024.103187","ista":"Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. 2024. Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. STAR Protocols. 5(4), 103187.","mla":"Rus, Stefanie, et al. “Protocol for Fabricating Elastomeric Stencils for Patterned Stem Cell Differentiation.” STAR Protocols, vol. 5, no. 4, 103187, Elsevier, 2024, doi:10.1016/j.xpro.2024.103187.","chicago":"Rus, Stefanie, Jack Merrin, Monika Aleksandra Kulig, Thomas Minchington, and Anna Kicheva. “Protocol for Fabricating Elastomeric Stencils for Patterned Stem Cell Differentiation.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2024.103187.","apa":"Rus, S., Merrin, J., Kulig, M. A., Minchington, T., & Kicheva, A. (2024). Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2024.103187","short":"S. Rus, J. Merrin, M.A. Kulig, T. Minchington, A. Kicheva, STAR Protocols 5 (2024)."},"pmid":1,"acknowledgement":"We thank the nanofabrication facility at ISTA for technical assistance. Work in the A.K. lab is supported by ISTA, the European Research Council under Horizon Europe (grant 101044579), and the Austrian Science Fund (FWF) (grant https://doi.org/10.55776/F78). S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011.","type":"journal_article","OA_place":"publisher","file":[{"file_size":4989169,"file_id":"18610","checksum":"0c61a6f9978608a103865905e06f4581","relation":"main_file","content_type":"application/pdf","file_name":"2024_STARProtoc_Lehr.pdf","date_created":"2024-12-03T10:53:23Z","access_level":"open_access","creator":"dernst","date_updated":"2024-12-03T10:53:23Z","success":1}]}]