[{"article_type":"original","abstract":[{"lang":"eng","text":"Many insects carry an ancient X chromosome - the Drosophila Muller element F - that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 MY. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure, to that of several dipteran species as well as more distantly-related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the two homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects."}],"project":[{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810"},{"_id":"ebb230e0-77a9-11ec-83b8-87a37e0241d3","name":"Mechanisms and Evolution of Reproductive Plasticity","grant_number":"ESP39 49461"}],"quality_controlled":"1","external_id":{"pmid":["37988296"],"isi":["001122489000003"]},"day":"01","oa_version":"Published Version","volume":40,"isi":1,"article_number":"msad245","title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","department":[{"_id":"BeVi"}],"month":"12","date_updated":"2026-04-22T22:31:07Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"doi":"10.1093/molbev/msad245","article_processing_charge":"Yes","publisher":"Oxford University Press","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"publication_status":"published","citation":{"ista":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 40(12), msad245.","mla":"Lasne, Clementine, et al. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” <i>Molecular Biology and Evolution</i>, vol. 40, no. 12, msad245, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/molbev/msad245\">10.1093/molbev/msad245</a>.","ieee":"C. Lasne, M. N. Elkrewi, M. A. Toups, L. A. Layana Franco, A. Macon, and B. Vicoso, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome,” <i>Molecular Biology and Evolution</i>, vol. 40, no. 12. Oxford University Press, 2023.","apa":"Lasne, C., Elkrewi, M. N., Toups, M. A., Layana Franco, L. A., Macon, A., &#38; Vicoso, B. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msad245\">https://doi.org/10.1093/molbev/msad245</a>","short":"C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso, Molecular Biology and Evolution 40 (2023).","chicago":"Lasne, Clementine, Marwan N Elkrewi, Melissa A Toups, Lorena Alexandra Layana Franco, Ariana Macon, and Beatriz Vicoso. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/molbev/msad245\">https://doi.org/10.1093/molbev/msad245</a>.","ama":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. <i>Molecular Biology and Evolution</i>. 2023;40(12). doi:<a href=\"https://doi.org/10.1093/molbev/msad245\">10.1093/molbev/msad245</a>"},"year":"2023","date_published":"2023-12-01T00:00:00Z","pmid":1,"intvolume":"        40","ddc":["570"],"file":[{"relation":"main_file","file_size":8623505,"success":1,"access_level":"open_access","checksum":"47c1c72fb499f26ea52d216b242208c8","date_created":"2024-01-02T11:39:38Z","file_id":"14727","creator":"dernst","content_type":"application/pdf","date_updated":"2024-01-02T11:39:38Z","file_name":"2023_MolecularBioEvo_Lasne.pdf"}],"language":[{"iso":"eng"}],"publication":"Molecular Biology and Evolution","acknowledged_ssus":[{"_id":"ScienComp"}],"has_accepted_license":"1","keyword":["Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"status":"public","date_created":"2023-11-27T16:14:37Z","scopus_import":"1","type":"journal_article","acknowledgement":"We thank the Vicoso lab for their assistance with specimen collection, and Tim Connallon for valuable comments and suggestions on earlier versions of the manuscript. Computational resources and support were provided by the Scientific Computing unit at the ISTA. This research was supported by grants from the Austrian Science Foundation to C.L.\r\n(FWF ESP 39), and to B.V. (FWF SFB F88-10).","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"full_name":"Lasne, Clementine","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","last_name":"Lasne","orcid":"0000-0002-1197-8616","first_name":"Clementine"},{"last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N","first_name":"Marwan N","orcid":"0000-0002-5328-7231"},{"last_name":"Toups","full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","orcid":"0000-0002-9752-7380"},{"first_name":"Lorena Alexandra","orcid":"0000-0002-1253-6297","full_name":"Layana Franco, Lorena Alexandra","id":"02814589-eb8f-11eb-b029-a70074f3f18f","last_name":"Layana Franco"},{"first_name":"Ariana","last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306"}],"issue":"12","corr_author":"1","file_date_updated":"2024-01-02T11:39:38Z","_id":"14613","related_material":{"link":[{"url":"https://ista.ac.at/en/news/on-the-hunt/","description":"News on ISTA webpage","relation":"press_release"}],"record":[{"relation":"research_data","id":"14614","status":"public"},{"status":"public","id":"19386","relation":"dissertation_contains"}]},"oa":1},{"has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"Nature Communications","APC_amount":"6228 EUR","status":"public","date_created":"2023-07-09T22:01:11Z","scopus_import":"1","intvolume":"        14","pmid":1,"file":[{"file_size":1349134,"relation":"main_file","success":1,"access_level":"open_access","checksum":"ec7ccd2c08f90d59cab302fd0d7776a4","date_created":"2023-07-10T10:10:54Z","file_id":"13206","creator":"alisjak","content_type":"application/pdf","date_updated":"2023-07-10T10:10:54Z","file_name":"2023_NatureComms_Qiu.pdf"}],"ddc":["000"],"OA_place":"publisher","_id":"13200","DOAJ_listed":"1","arxiv":1,"related_material":{"record":[{"id":"18871","status":"public","relation":"dissertation_contains"}]},"oa":1,"type":"journal_article","acknowledgement":"This work was supported by the European Research Council under grant agreement no. 758053 (ERC StG QUNNECT), the European Union’s Horizon 2020 research and innovation program under grant agreement no. 899354 (FETopen SuperQuLAN), and the Austrian Science Fund (FWF) through BeyondC (F7105). L.Q. acknowledges generous support from the ISTFELLOW programme. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 754411. G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria.","author":[{"orcid":"0000-0003-4345-4267","first_name":"Liu","full_name":"Qiu, Liu","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","last_name":"Qiu"},{"first_name":"Rishabh","orcid":"0000-0001-6264-2162","last_name":"Sahu","full_name":"Sahu, Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87"},{"first_name":"William J","orcid":"0000-0001-9868-2166","last_name":"Hease","full_name":"Hease, William J","id":"29705398-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-1397-7876","first_name":"Georg M","last_name":"Arnold","id":"3770C838-F248-11E8-B48F-1D18A9856A87","full_name":"Arnold, Georg M"},{"first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","last_name":"Fink"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-07-10T10:10:54Z","corr_author":"1","project":[{"grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020","name":"Quantum Local Area Networks with Superconducting Qubits","grant_number":"899354"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","grant_number":"F07105"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies","_id":"2671EB66-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund"}],"external_id":{"pmid":["37355691"],"arxiv":["2210.12443"],"isi":["001018100800002"]},"quality_controlled":"1","volume":14,"oa_version":"Published Version","day":"24","ec_funded":1,"OA_type":"gold","abstract":[{"lang":"eng","text":"Recent quantum technologies have established precise quantum control of various microscopic systems using electromagnetic waves. Interfaces based on cryogenic cavity electro-optic systems are particularly promising, due to the direct interaction between microwave and optical fields in the quantum regime. Quantum optical control of superconducting microwave circuits has been precluded so far due to the weak electro-optical coupling as well as quasi-particles induced by the pump laser. Here we report the coherent control of a superconducting microwave cavity using laser pulses in a multimode electro-optical device at millikelvin temperature with near-unity cooperativity. Both the stationary and instantaneous responses of the microwave and optical modes comply with the coherent electro-optical interaction, and reveal only minuscule amount of excess back-action with an unanticipated time delay. Our demonstration enables wide ranges of applications beyond quantum transductions, from squeezing and quantum non-demolition measurements of microwave fields, to entanglement generation and hybrid quantum networks."}],"article_type":"original","publication_status":"published","doi":"10.1038/s41467-023-39493-3","article_processing_charge":"Yes","publication_identifier":{"eissn":["2041-1723"]},"publisher":"Nature Research","citation":{"mla":"Qiu, Liu, et al. “Coherent Optical Control of a Superconducting Microwave Cavity via Electro-Optical Dynamical Back-Action.” <i>Nature Communications</i>, vol. 14, 3784, Nature Research, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-39493-3\">10.1038/s41467-023-39493-3</a>.","ieee":"L. Qiu, R. Sahu, W. J. Hease, G. M. Arnold, and J. M. Fink, “Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action,” <i>Nature Communications</i>, vol. 14. Nature Research, 2023.","ista":"Qiu L, Sahu R, Hease WJ, Arnold GM, Fink JM. 2023. Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. Nature Communications. 14, 3784.","chicago":"Qiu, Liu, Rishabh Sahu, William J Hease, Georg M Arnold, and Johannes M Fink. “Coherent Optical Control of a Superconducting Microwave Cavity via Electro-Optical Dynamical Back-Action.” <i>Nature Communications</i>. Nature Research, 2023. <a href=\"https://doi.org/10.1038/s41467-023-39493-3\">https://doi.org/10.1038/s41467-023-39493-3</a>.","ama":"Qiu L, Sahu R, Hease WJ, Arnold GM, Fink JM. Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-39493-3\">10.1038/s41467-023-39493-3</a>","apa":"Qiu, L., Sahu, R., Hease, W. J., Arnold, G. M., &#38; Fink, J. M. (2023). Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. <i>Nature Communications</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41467-023-39493-3\">https://doi.org/10.1038/s41467-023-39493-3</a>","short":"L. Qiu, R. Sahu, W.J. Hease, G.M. Arnold, J.M. Fink, Nature Communications 14 (2023)."},"date_published":"2023-06-24T00:00:00Z","year":"2023","title":"Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action","article_number":"3784","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"department":[{"_id":"JoFi"}],"month":"06","date_updated":"2026-04-22T22:31:08Z"},{"language":[{"iso":"eng"}],"publication":"arXiv","status":"public","date_created":"2025-01-29T11:11:34Z","type":"preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Georg M","orcid":"0000-0003-1397-7876","full_name":"Arnold, Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","last_name":"Arnold"},{"id":"1fcd8497-dba3-11ea-a45e-c6fbd715f7c7","full_name":"Werner, Thomas","last_name":"Werner","first_name":"Thomas","orcid":"0009-0001-2346-5236"},{"full_name":"Sahu, Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","last_name":"Sahu","orcid":"0000-0001-6264-2162","first_name":"Rishabh"},{"last_name":"Kapoor","id":"84b9700b-15b2-11ec-abd3-831089e67615","full_name":"Kapoor, Lucky","orcid":"0000-0001-8319-2148","first_name":"Lucky"},{"orcid":"0000-0003-4345-4267","first_name":"Liu","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","full_name":"Qiu, Liu","last_name":"Qiu"},{"orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"We thank F. Hassani and M. Zemlicka for assistance\r\nwith qubit design and high power readout respectively,\r\nand P. Winkel and I. Pop at KIT for providing the JPA.\r\nThis work was supported by the European Research\r\nCouncil under grant agreement no. 758053 (ERC StG\r\nQUNNECT) and no. 101089099 (ERC CoG cQEO), the\r\nEuropean Union’s Horizon 2020 research and innovation\r\nprogram under grant agreement no. 899354 (FETopen\r\nSuperQuLAN) and the Austrian Science Fund (FWF)\r\nthrough BeyondC (grant no. F7105). L.Q. acknowledges\r\ngenerous support from the ISTFELLOW programme\r\nand G.A. is the recipient of a DOC fellowship of the\r\nAustrian Academy of Sciences at IST Austria.","corr_author":"1","arxiv":1,"OA_place":"repository","_id":"18953","oa":1,"related_material":{"record":[{"relation":"later_version","status":"public","id":"19073"},{"status":"public","id":"18871","relation":"dissertation_contains"}]},"abstract":[{"text":"The rapid development of superconducting quantum hardware is expected to run into significant I/O restrictions due to the need for large-scale error correction in a cryogenic environment. Classical data centers rely on fiber-optic interconnects to remove similar networking bottlenecks and to allow for reconfigurable, software-defined infrastructures. In the same spirit, ultra-cold electro-optic links have been proposed and used to generate qubit control signals, or to replace cryogenic readout electronics. So far, the latter suffered from either low efficiency, low bandwidth and the need for additional microwave drives, or breaking of Cooper pairs and qubit states. In this work we realize electro-optic microwave photonics at millikelvin temperatures to implement a radio-over-fiber qubit readout that does not require any active or passive cryogenic microwave equipment. We demonstrate all-optical single-shot-readout by means of the Jaynes-Cummings nonlinearity in a circulator-free readout scheme. Importantly, we do not observe any direct radiation impact on the qubit state as verified with high-fidelity quantum-non-demolition measurements despite the absence of shielding elements. This compatibility between superconducting circuits and telecom wavelength light is not only a prerequisite to establish modular quantum networks, it is also relevant for multiplexed readout of superconducting photon detectors and classical superconducting logic. Moreover, this experiment showcases the potential of electro-optic radiometry in harsh environments - an electronics-free sensing principle that extends into the THz regime with applications in radio astronomy, planetary missions and earth observation.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2310.16817"}],"project":[{"grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"101089099","_id":"bdadfa0d-d553-11ed-ba76-fb85edbd456a","name":"Cavity Quantum Electro Optics: Microwave photonics with nonclassical states"},{"grant_number":"899354","call_identifier":"H2020","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","name":"Quantum Local Area Networks with Superconducting Qubits"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"},{"grant_number":"F07105","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"external_id":{"arxiv":["2310.16817"]},"ec_funded":1,"oa_version":"Preprint","day":"25","title":"All-optical single-shot readout of a superconducting qubit","department":[{"_id":"JoFi"}],"month":"10","date_updated":"2026-04-22T22:31:07Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"doi":"10.48550/ARXIV.2310.16817","article_processing_charge":"No","publication_status":"draft","citation":{"mla":"Arnold, Georg M., et al. “All-Optical Single-Shot Readout of a Superconducting Qubit.” <i>ArXiv</i>, doi:<a href=\"https://doi.org/10.48550/ARXIV.2310.16817\">10.48550/ARXIV.2310.16817</a>.","ieee":"G. M. Arnold, T. Werner, R. Sahu, L. Kapoor, L. Qiu, and J. M. Fink, “All-optical single-shot readout of a superconducting qubit,” <i>arXiv</i>. .","ista":"Arnold GM, Werner T, Sahu R, Kapoor L, Qiu L, Fink JM. All-optical single-shot readout of a superconducting qubit. arXiv, <a href=\"https://doi.org/10.48550/ARXIV.2310.16817\">10.48550/ARXIV.2310.16817</a>.","chicago":"Arnold, Georg M, Thomas Werner, Rishabh Sahu, Lucky Kapoor, Liu Qiu, and Johannes M Fink. “All-Optical Single-Shot Readout of a Superconducting Qubit.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/ARXIV.2310.16817\">https://doi.org/10.48550/ARXIV.2310.16817</a>.","ama":"Arnold GM, Werner T, Sahu R, Kapoor L, Qiu L, Fink JM. All-optical single-shot readout of a superconducting qubit. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/ARXIV.2310.16817\">10.48550/ARXIV.2310.16817</a>","apa":"Arnold, G. M., Werner, T., Sahu, R., Kapoor, L., Qiu, L., &#38; Fink, J. M. (n.d.). All-optical single-shot readout of a superconducting qubit. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/ARXIV.2310.16817\">https://doi.org/10.48550/ARXIV.2310.16817</a>","short":"G.M. Arnold, T. Werner, R. Sahu, L. Kapoor, L. Qiu, J.M. Fink, ArXiv (n.d.)."},"year":"2023","date_published":"2023-10-25T00:00:00Z"},{"quality_controlled":"1","external_id":{"arxiv":["2205.03293"],"isi":["001001099700002"],"pmid":["37225689"]},"project":[{"call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053"},{"name":"Controllable Collective States of Superconducting Qubit Ensembles","_id":"26B354CA-B435-11E9-9278-68D0E5697425"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"},{"grant_number":"F07105","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"oa_version":"Published Version","day":"24","volume":14,"ec_funded":1,"abstract":[{"lang":"eng","text":"The ability to control the direction of scattered light is crucial to provide flexibility and scalability for a wide range of on-chip applications, such as integrated photonics, quantum information processing, and nonlinear optics. Tunable directionality can be achieved by applying external magnetic fields that modify optical selection rules, by using nonlinear effects, or interactions with vibrations. However, these approaches are less suitable to control microwave photon propagation inside integrated superconducting quantum devices. Here, we demonstrate on-demand tunable directional scattering based on two periodically modulated transmon qubits coupled to a transmission line at a fixed distance. By changing the relative phase between the modulation tones, we realize unidirectional forward or backward photon scattering. Such an in-situ switchable mirror represents a versatile tool for intra- and inter-chip microwave photonic processors. In the future, a lattice of qubits can be used to realize topological circuits that exhibit strong nonreciprocity or chirality."}],"article_type":"original","publication_status":"published","publisher":"Springer Nature","article_processing_charge":"No","publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-023-38761-6","year":"2023","date_published":"2023-05-24T00:00:00Z","citation":{"ista":"Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. 2023. Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. 14, 2998.","ieee":"E. Redchenko, A. V. Poshakinskiy, R. Sett, M. Zemlicka, A. N. Poddubny, and J. M. Fink, “Tunable directional photon scattering from a pair of superconducting qubits,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","mla":"Redchenko, Elena, et al. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” <i>Nature Communications</i>, vol. 14, 2998, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-38761-6\">10.1038/s41467-023-38761-6</a>.","short":"E. Redchenko, A.V. Poshakinskiy, R. Sett, M. Zemlicka, A.N. Poddubny, J.M. Fink, Nature Communications 14 (2023).","apa":"Redchenko, E., Poshakinskiy, A. V., Sett, R., Zemlicka, M., Poddubny, A. N., &#38; Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-38761-6\">https://doi.org/10.1038/s41467-023-38761-6</a>","ama":"Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-38761-6\">10.1038/s41467-023-38761-6</a>","chicago":"Redchenko, Elena, Alexander V. Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander N. Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-38761-6\">https://doi.org/10.1038/s41467-023-38761-6</a>."},"title":"Tunable directional photon scattering from a pair of superconducting qubits","isi":1,"article_number":"2998","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_updated":"2026-04-22T22:31:08Z","department":[{"_id":"JoFi"}],"month":"05","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"has_accepted_license":"1","publication":"Nature Communications","language":[{"iso":"eng"}],"date_created":"2023-06-04T22:01:02Z","status":"public","scopus_import":"1","intvolume":"        14","pmid":1,"file":[{"file_id":"13123","creator":"dernst","content_type":"application/pdf","file_name":"2023_NaturePhysics_Redchenko.pdf","date_updated":"2023-06-06T07:31:20Z","file_size":1654389,"relation":"main_file","success":1,"access_level":"open_access","checksum":"a857df40f0882859c48a1ff1e2001ec2","date_created":"2023-06-06T07:31:20Z"}],"ddc":["530"],"_id":"13117","arxiv":1,"oa":1,"related_material":{"record":[{"relation":"research_data","id":"13124","status":"public"},{"status":"public","id":"19533","relation":"dissertation_contains"}]},"acknowledgement":"The authors thank W.D. Oliver for discussions, L. Drmic and P. Zielinski for software development, and the MIBA workshop and the IST nanofabrication facility for technical support. This work was supported by the Austrian Science Fund (FWF) through BeyondC (F7105) and IST Austria. E.R. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. and M.Z. acknowledge support from the European Research Council under grant agreement No 758053 (ERC StG QUNNECT) and a NOMIS foundation research grant. The work of A.N.P. and A.V.P. has been supported by the Russian Science Foundation under the grant No 20-12-00194.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","last_name":"Redchenko","first_name":"Elena"},{"first_name":"Alexander V.","last_name":"Poshakinskiy","full_name":"Poshakinskiy, Alexander V."},{"orcid":"0000-0001-7641-8348","first_name":"Riya","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","full_name":"Sett, Riya","last_name":"Sett"},{"last_name":"Zemlicka","full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","orcid":"0009-0005-0878-3032","first_name":"Martin"},{"last_name":"Poddubny","full_name":"Poddubny, Alexander N.","first_name":"Alexander N."},{"orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M"}],"type":"journal_article","file_date_updated":"2023-06-06T07:31:20Z","corr_author":"1"},{"has_accepted_license":"1","publication":"ACM Transactions on Graphics","PlanS_conform":"1","language":[{"iso":"eng"}],"status":"public","date_created":"2022-06-10T06:41:47Z","scopus_import":"1","intvolume":"        41","file":[{"date_updated":"2022-06-28T08:32:58Z","file_name":"2022_ACM_acceptedversion_Piovarci.pdf","content_type":"application/pdf","creator":"dernst","file_id":"11467","date_created":"2022-06-28T08:32:58Z","checksum":"27f6fe41c6ff84d50445cc9b0176d45b","success":1,"access_level":"open_access","relation":"main_file","file_size":33994829}],"ddc":["000"],"_id":"11442","OA_place":"publisher","arxiv":1,"oa":1,"related_material":{"link":[{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/machine-learning-3d-printing-fluids/","relation":"press_release"}]},"author":[{"first_name":"Michael","orcid":"0000-0002-5062-4474","full_name":"Piovarci, Michael","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","last_name":"Piovarci"},{"full_name":"Foshey, Michael","last_name":"Foshey","first_name":"Michael"},{"first_name":"Jie","full_name":"Xu, Jie","last_name":"Xu"},{"first_name":"Timothy","full_name":"Erps, Timothy","last_name":"Erps"},{"first_name":"Vahid","last_name":"Babaei","full_name":"Babaei, Vahid"},{"last_name":"Didyk","full_name":"Didyk, Piotr","first_name":"Piotr"},{"first_name":"Szymon","full_name":"Rusinkiewicz, Szymon","last_name":"Rusinkiewicz"},{"last_name":"Matusik","full_name":"Matusik, Wojciech","first_name":"Wojciech"},{"last_name":"Bickel","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd"}],"acknowledgement":"This work is graciously supported by the following grant agencies: FWF Lise Meitner (Grant M 3319), SNSF (Grant 200502), ERC Starting Grant (MATERIALIZABLE-715767), NSF (Grant IIS-181507).\r\n","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","file_date_updated":"2022-06-28T08:32:58Z","corr_author":"1","issue":"4","external_id":{"arxiv":["2201.11819"],"isi":["000830989200091"]},"quality_controlled":"1","project":[{"name":"Perception-Aware Appearance Fabrication","_id":"eb901961-77a9-11ec-83b8-f5c883a62027","grant_number":"M03319"},{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}],"day":"01","oa_version":"Submitted Version","volume":41,"ec_funded":1,"OA_type":"hybrid","abstract":[{"text":"Enabling additive manufacturing to employ a wide range of novel, functional materials can be a major boost to this technology. However, making such materials printable requires painstaking trial-and-error by an expert operator,\r\nas they typically tend to exhibit peculiar rheological or hysteresis properties. Even in the case of successfully finding the process parameters, there is no guarantee of print-to-print consistency due to material differences between batches. These challenges make closed-loop feedback an attractive option where the process parameters are adjusted on-the-fly. There are several challenges for designing an efficient controller: the deposition parameters are complex and highly coupled, artifacts occur after long time horizons, simulating the deposition is computationally costly, and learning on hardware is intractable. In this work, we demonstrate the feasibility of learning a closed-loop control policy for additive manufacturing using reinforcement learning. We show that approximate, but efficient, numerical simulation is\r\nsufficient as long as it allows learning the behavioral patterns of deposition that translate to real-world experiences. In combination with reinforcement learning, our model can be used to discover control policies that outperform\r\nbaseline controllers. Furthermore, the recovered policies have a minimal sim-to-real gap. We showcase this by applying our control policy in-vivo on a single-layer, direct ink writing printer. ","lang":"eng"}],"article_type":"original","publication_status":"published","article_processing_charge":"No","publisher":"Association for Computing Machinery","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"doi":"10.1145/3528223.3530144","date_published":"2022-06-01T00:00:00Z","year":"2022","citation":{"mla":"Piovarci, Michael, et al. “Closed-Loop Control of Direct Ink Writing via Reinforcement Learning.” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4, 112, Association for Computing Machinery, 2022, doi:<a href=\"https://doi.org/10.1145/3528223.3530144\">10.1145/3528223.3530144</a>.","ieee":"M. Piovarci <i>et al.</i>, “Closed-loop control of direct ink writing via reinforcement learning,” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4. Association for Computing Machinery, 2022.","ista":"Piovarci M, Foshey M, Xu J, Erps T, Babaei V, Didyk P, Rusinkiewicz S, Matusik W, Bickel B. 2022. Closed-loop control of direct ink writing via reinforcement learning. ACM Transactions on Graphics. 41(4), 112.","chicago":"Piovarci, Michael, Michael Foshey, Jie Xu, Timothy Erps, Vahid Babaei, Piotr Didyk, Szymon Rusinkiewicz, Wojciech Matusik, and Bernd Bickel. “Closed-Loop Control of Direct Ink Writing via Reinforcement Learning.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3528223.3530144\">https://doi.org/10.1145/3528223.3530144</a>.","ama":"Piovarci M, Foshey M, Xu J, et al. Closed-loop control of direct ink writing via reinforcement learning. <i>ACM Transactions on Graphics</i>. 2022;41(4). doi:<a href=\"https://doi.org/10.1145/3528223.3530144\">10.1145/3528223.3530144</a>","apa":"Piovarci, M., Foshey, M., Xu, J., Erps, T., Babaei, V., Didyk, P., … Bickel, B. (2022). Closed-loop control of direct ink writing via reinforcement learning. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3528223.3530144\">https://doi.org/10.1145/3528223.3530144</a>","short":"M. Piovarci, M. Foshey, J. Xu, T. Erps, V. Babaei, P. Didyk, S. Rusinkiewicz, W. Matusik, B. Bickel, ACM Transactions on Graphics 41 (2022)."},"title":"Closed-loop control of direct ink writing via reinforcement learning","isi":1,"article_number":"112","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_updated":"2025-09-10T09:36:45Z","month":"06","department":[{"_id":"BeBi"}]},{"oa":1,"_id":"11443","arxiv":1,"corr_author":"1","issue":"6","author":[{"orcid":"0000-0002-4003-7567","first_name":"Matthew Alan","last_name":"Kwan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan"},{"full_name":"Sauermann, Lisa","last_name":"Sauermann","first_name":"Lisa"},{"last_name":"Zhao","full_name":"Zhao, Yufei","first_name":"Yufei"}],"acknowledgement":"The research of the first author was supported by SNSF Project 178493 and NSF Award DMS-1953990. The research of the second author supported by NSF Award DMS-1953772.\r\nThe research of the third author was supported by NSF Award DMS-1764176, NSF CAREER Award DMS-2044606, a Sloan Research Fellowship, and the MIT Solomon Buchsbaum Fund. ","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","date_created":"2022-06-12T22:01:45Z","scopus_import":"1","status":"public","publication":"Transactions of the American Mathematical Society","language":[{"iso":"eng"}],"page":"4209-4250","intvolume":"       375","year":"2022","date_published":"2022-06-01T00:00:00Z","citation":{"ieee":"M. A. Kwan, L. Sauermann, and Y. Zhao, “Extension complexity of low-dimensional polytopes,” <i>Transactions of the American Mathematical Society</i>, vol. 375, no. 6. American Mathematical Society, pp. 4209–4250, 2022.","mla":"Kwan, Matthew Alan, et al. “Extension Complexity of Low-Dimensional Polytopes.” <i>Transactions of the American Mathematical Society</i>, vol. 375, no. 6, American Mathematical Society, 2022, pp. 4209–50, doi:<a href=\"https://doi.org/10.1090/tran/8614\">10.1090/tran/8614</a>.","ista":"Kwan MA, Sauermann L, Zhao Y. 2022. Extension complexity of low-dimensional polytopes. Transactions of the American Mathematical Society. 375(6), 4209–4250.","ama":"Kwan MA, Sauermann L, Zhao Y. Extension complexity of low-dimensional polytopes. <i>Transactions of the American Mathematical Society</i>. 2022;375(6):4209-4250. doi:<a href=\"https://doi.org/10.1090/tran/8614\">10.1090/tran/8614</a>","chicago":"Kwan, Matthew Alan, Lisa Sauermann, and Yufei Zhao. “Extension Complexity of Low-Dimensional Polytopes.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2022. <a href=\"https://doi.org/10.1090/tran/8614\">https://doi.org/10.1090/tran/8614</a>.","short":"M.A. Kwan, L. Sauermann, Y. Zhao, Transactions of the American Mathematical Society 375 (2022) 4209–4250.","apa":"Kwan, M. A., Sauermann, L., &#38; Zhao, Y. (2022). Extension complexity of low-dimensional polytopes. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/8614\">https://doi.org/10.1090/tran/8614</a>"},"publication_status":"published","publisher":"American Mathematical Society","publication_identifier":{"issn":["0002-9947"],"eissn":["1088-6850"]},"article_processing_charge":"No","doi":"10.1090/tran/8614","date_updated":"2024-10-09T21:02:31Z","month":"06","department":[{"_id":"MaKw"}],"title":"Extension complexity of low-dimensional polytopes","isi":1,"volume":375,"oa_version":"Preprint","day":"01","external_id":{"arxiv":["2006.08836"],"isi":["000798461500001"]},"quality_controlled":"1","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2006.08836","open_access":"1"}],"abstract":[{"text":"Sometimes, it is possible to represent a complicated polytope as a projection of a much simpler polytope. To quantify this phenomenon, the extension complexity of a polytope P is defined to be the minimum number of facets of a (possibly higher-dimensional) polytope from which P can be obtained as a (linear) projection. This notion is motivated by its relevance to combinatorial optimisation, and has been studied intensively for various specific polytopes associated with important optimisation problems. In this paper we study extension complexity as a parameter of general polytopes, more specifically considering various families of low-dimensional polytopes. First, we prove that for a fixed dimension d, the extension complexity of a random d-dimensional polytope (obtained as the convex hull of random points in a ball or on a sphere) is typically on the order of the square root of its number of vertices. Second, we prove that any cyclic n-vertex polygon (whose vertices lie on a circle) has extension complexity at most 24√n. This bound is tight up to the constant factor 24. Finally, we show that there exists an no(1)-dimensional polytope with at most n vertices and extension complexity n1−o(1). Our theorems are proved with a range of different techniques, which we hope will be of further interest.","lang":"eng"}],"article_type":"original"},{"citation":{"ama":"Chlebak CA, Reid PH. From the prefect’s desk: Gerard van Swieten’s library correspondence. <i>Library and Information History</i>. 2022;38(1):23-41. doi:<a href=\"https://doi.org/10.3366/lih.2022.0097\">10.3366/lih.2022.0097</a>","chicago":"Chlebak, Clara A, and Peter H. Reid. “From the Prefect’s Desk: Gerard van Swieten’s Library Correspondence.” <i>Library and Information History</i>. Edinburgh University Press, 2022. <a href=\"https://doi.org/10.3366/lih.2022.0097\">https://doi.org/10.3366/lih.2022.0097</a>.","short":"C.A. Chlebak, P.H. Reid, Library and Information History 38 (2022) 23–41.","apa":"Chlebak, C. A., &#38; Reid, P. H. (2022). From the prefect’s desk: Gerard van Swieten’s library correspondence. <i>Library and Information History</i>. Edinburgh University Press. <a href=\"https://doi.org/10.3366/lih.2022.0097\">https://doi.org/10.3366/lih.2022.0097</a>","ieee":"C. A. Chlebak and P. H. Reid, “From the prefect’s desk: Gerard van Swieten’s library correspondence,” <i>Library and Information History</i>, vol. 38, no. 1. Edinburgh University Press, pp. 23–41, 2022.","mla":"Chlebak, Clara A., and Peter H. Reid. “From the Prefect’s Desk: Gerard van Swieten’s Library Correspondence.” <i>Library and Information History</i>, vol. 38, no. 1, Edinburgh University Press, 2022, pp. 23–41, doi:<a href=\"https://doi.org/10.3366/lih.2022.0097\">10.3366/lih.2022.0097</a>.","ista":"Chlebak CA, Reid PH. 2022. From the prefect’s desk: Gerard van Swieten’s library correspondence. Library and Information History. 38(1), 23–41."},"date_published":"2022-04-01T00:00:00Z","year":"2022","doi":"10.3366/lih.2022.0097","publisher":"Edinburgh University Press","publication_identifier":{"issn":["1758-3489"],"eissn":["1758-3497"]},"article_processing_charge":"No","publication_status":"published","month":"04","department":[{"_id":"E-Lib"}],"date_updated":"2024-10-09T21:02:31Z","title":"From the prefect’s desk: Gerard van Swieten’s library correspondence","volume":38,"day":"01","oa_version":"Submitted Version","quality_controlled":"1","article_type":"original","main_file_link":[{"open_access":"1","url":"https://rgu-repository.worktribe.com/output/1635939"}],"abstract":[{"text":"This article investigates library-related documents written by Gerard van Swieten (1700–72) during his tenure as Library Prefect in the Imperial Library of Vienna (1745–72). Van Swieten’s time as Library Prefect is considered through a textual analysis. Handwritten letters were deconstructed in terms of their appearance, layout, and tone in order to mine them for meaning. Furthermore, the contents were examined for library matters such as censorship, catalogues, and collection development. The Imperial Court Library held a prominent role as a repository for rare and valuable works, later becoming the National Library of Austria.\r\nGerard van Swieten’s work as a librarian tends to be overlooked, perhaps because he is better known as the private physician of Maria Theresia, as well as a medical reformer. Nevertheless, he was a hard-working chief librarian deeply involved in all aspects of librarianship. Van Swieten endorsed modern scientific works, which were otherwise banned officially by the censorship commission, for the use of scholars in the library, expanded the collection by acquiring books through his network of scholars and publishers, and reissued library catalogues. He also provided for the comfort of users in the library reading room, at a time when such considerations were unusual. In conclusion, a proposal is made that van Swieten viewed his role as librarian with some importance and pride.","lang":"eng"}],"oa":1,"_id":"11444","issue":"1","corr_author":"1","type":"journal_article","author":[{"orcid":"0000-0002-3385-3865","first_name":"Clara A","last_name":"Chlebak","full_name":"Chlebak, Clara A","id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"last_name":"Reid","full_name":"Reid, Peter H.","first_name":"Peter H."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","scopus_import":"1","date_created":"2022-06-12T22:01:45Z","language":[{"iso":"eng"}],"publication":"Library and Information History","page":"23-41","intvolume":"        38"},{"day":"15","oa_version":"Published Version","volume":13,"ec_funded":1,"quality_controlled":"1","external_id":{"pmid":["35452605"],"isi":["000814124400002"]},"project":[{"grant_number":"725780","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"grant_number":"LS13-002","_id":"25D92700-B435-11E9-9278-68D0E5697425","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain"}],"main_file_link":[{"url":"https://doi.org/10.1016/j.cels.2022.03.006","open_access":"1"}],"abstract":[{"text":"Mutations are acquired frequently, such that each cell's genome inscribes its history of cell divisions. Common genomic alterations involve loss of heterozygosity (LOH). LOH accumulates throughout the genome, offering large encoding capacity for inferring cell lineage. Using only single-cell RNA sequencing (scRNA-seq) of mouse brain cells, we found that LOH events spanning multiple genes are revealed as tracts of monoallelically expressed, constitutionally heterozygous single-nucleotide variants (SNVs). We simultaneously inferred cell lineage and marked developmental time points based on X chromosome inactivation and the total number of LOH events while identifying cell types from gene expression patterns. Our results are consistent with progenitor cells giving rise to multiple cortical cell types through stereotyped expansion and distinct waves of neurogenesis. This type of retrospective analysis could be incorporated into scRNA-seq pipelines and, compared with experimental approaches for determining lineage in model organisms, is applicable where genetic engineering is prohibited, such as humans.","lang":"eng"}],"article_type":"original","year":"2022","date_published":"2022-06-15T00:00:00Z","citation":{"ama":"Anderson DJ, Pauler F, Mckenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development. <i>Cell Systems</i>. 2022;13(6):438-453.e5. doi:<a href=\"https://doi.org/10.1016/j.cels.2022.03.006\">10.1016/j.cels.2022.03.006</a>","chicago":"Anderson, Donovan J., Florian Pauler, Aaron Mckenna, Jay Shendure, Simon Hippenmeyer, and Marshall S. Horwitz. “Simultaneous Brain Cell Type and Lineage Determined by ScRNA-Seq Reveals Stereotyped Cortical Development.” <i>Cell Systems</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.cels.2022.03.006\">https://doi.org/10.1016/j.cels.2022.03.006</a>.","short":"D.J. Anderson, F. Pauler, A. Mckenna, J. Shendure, S. Hippenmeyer, M.S. Horwitz, Cell Systems 13 (2022) 438–453.e5.","apa":"Anderson, D. J., Pauler, F., Mckenna, A., Shendure, J., Hippenmeyer, S., &#38; Horwitz, M. S. (2022). Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development. <i>Cell Systems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cels.2022.03.006\">https://doi.org/10.1016/j.cels.2022.03.006</a>","ieee":"D. J. Anderson, F. Pauler, A. Mckenna, J. Shendure, S. Hippenmeyer, and M. S. Horwitz, “Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development,” <i>Cell Systems</i>, vol. 13, no. 6. Elsevier, p. 438–453.e5, 2022.","mla":"Anderson, Donovan J., et al. “Simultaneous Brain Cell Type and Lineage Determined by ScRNA-Seq Reveals Stereotyped Cortical Development.” <i>Cell Systems</i>, vol. 13, no. 6, Elsevier, 2022, p. 438–453.e5, doi:<a href=\"https://doi.org/10.1016/j.cels.2022.03.006\">10.1016/j.cels.2022.03.006</a>.","ista":"Anderson DJ, Pauler F, Mckenna A, Shendure J, Hippenmeyer S, Horwitz MS. 2022. Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development. Cell Systems. 13(6), 438–453.e5."},"publication_status":"published","publisher":"Elsevier","article_processing_charge":"No","publication_identifier":{"eissn":["2405-4720"],"issn":["2405-4712"]},"doi":"10.1016/j.cels.2022.03.006","date_updated":"2025-04-14T07:43:05Z","department":[{"_id":"SiHi"}],"month":"06","title":"Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development","isi":1,"date_created":"2022-06-19T22:01:57Z","status":"public","scopus_import":"1","publication":"Cell Systems","language":[{"iso":"eng"}],"pmid":1,"intvolume":"        13","page":"438-453.e5","oa":1,"_id":"11449","issue":"6","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"D.J.A. thanks Wayne K. Potts, Alan R. Rogers, Kristen Hawkes, Ryk Ward, and Jon Seger for inspiring a young undergraduate to apply evolutionary theory to intraorganism development. Supported by the Paul G. Allen Frontiers Group (University of Washington); NIH R00HG010152 (Dartmouth); and NÖ Forschung und Bildung n[f+b] life science call grant (C13-002) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program 725780 LinPro to S.H.","author":[{"full_name":"Anderson, Donovan J.","last_name":"Anderson","first_name":"Donovan J."},{"last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","first_name":"Florian"},{"full_name":"Mckenna, Aaron","last_name":"Mckenna","first_name":"Aaron"},{"full_name":"Shendure, Jay","last_name":"Shendure","first_name":"Jay"},{"orcid":"0000-0003-2279-1061","first_name":"Simon","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer"},{"last_name":"Horwitz","full_name":"Horwitz, Marshall S.","first_name":"Marshall S."}],"type":"journal_article"},{"publication":"Angewandte Chemie - International Edition","language":[{"iso":"eng"}],"has_accepted_license":"1","date_created":"2022-06-19T22:01:58Z","status":"public","scopus_import":"1","intvolume":"        61","pmid":1,"ddc":["540"],"file":[{"file_name":"2022_AngewandteChemieInternat_Parvizian.pdf","date_updated":"2022-07-29T09:29:20Z","content_type":"application/pdf","creator":"dernst","file_id":"11696","date_created":"2022-07-29T09:29:20Z","checksum":"2a3ee0bb59e044b808ebe85cd94ac899","success":1,"access_level":"open_access","relation":"main_file","file_size":1303202}],"_id":"11451","oa":1,"related_material":{"record":[{"status":"public","id":"11695","relation":"research_data"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"J.D.R. and M.P. acknowledge the SNF Eccellenza funding scheme (project number: 194172). We acknowledge DESY (Hamburg, Germany), a member of the Helmholtz Association HGF, for the provision of experimental facilities. Parts of this research were carried out at beamline P21.1, PETRA III. We thank Dr. Soham Banerjee for acquiring the PDF data and helpful advice. A.R. acknowledges the support from the Analytical Chemistry Trust Fund for her CAMS-UK Fellowship. C.K. acknowledges the support from the Department of Chemistry, UCL. The authors acknowledge Dr Stephan Lany from NREL for providing the Cu3N DFT calculations. The authors thank Prof. Raymond Schaak and Dr. Robert William Lord for helpful advice and suggestions regarding the purification procedure. Open access funding provided by Universitat Basel.","author":[{"first_name":"Mahsa","last_name":"Parvizian","full_name":"Parvizian, Mahsa"},{"last_name":"Duràn Balsa","full_name":"Duràn Balsa, Alejandra","first_name":"Alejandra"},{"first_name":"Rohan","last_name":"Pokratath","full_name":"Pokratath, Rohan"},{"last_name":"Kalha","full_name":"Kalha, Curran","first_name":"Curran"},{"orcid":"0000-0002-6962-8598","first_name":"Seungho","last_name":"Lee","id":"BB243B88-D767-11E9-B658-BC13E6697425","full_name":"Lee, Seungho"},{"first_name":"Dietger","full_name":"Van Den Eynden, Dietger","last_name":"Van Den Eynden"},{"first_name":"Maria","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez"},{"first_name":"Anna","last_name":"Regoutz","full_name":"Regoutz, Anna"},{"last_name":"De Roo","full_name":"De Roo, Jonathan","first_name":"Jonathan"}],"type":"journal_article","issue":"31","file_date_updated":"2022-07-29T09:29:20Z","quality_controlled":"1","external_id":{"isi":["000811084000001"],"pmid":["35612297"]},"oa_version":"Published Version","volume":61,"day":"01","article_type":"original","abstract":[{"text":"The precursor conversion chemistry and surface chemistry of Cu3N and Cu3PdN nanocrystals are unknown or contested. Here, we first obtain phase-pure, colloidally stable nanocubes. Second, we elucidate the pathway by which copper(II) nitrate and oleylamine form Cu3N. We find that oleylamine is both a reductant and a nitrogen source. Oleylamine is oxidized by nitrate to a primary aldimine, which reacts further with excess oleylamine to a secondary aldimine, eliminating ammonia. Ammonia reacts with CuI to form Cu3N. Third, we investigated the surface chemistry and find a mixed ligand shell of aliphatic amines and carboxylates (formed in situ). While the carboxylates appear tightly bound, the amines are easily desorbed from the surface. Finally, we show that doping with palladium decreases the band gap and the material becomes semi-metallic. These results bring insight into the chemistry of metal nitrides and might help the development of other metal nitride nanocrystals.","lang":"eng"}],"publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"publisher":"Wiley","article_processing_charge":"No","doi":"10.1002/anie.202207013","publication_status":"published","date_published":"2022-08-01T00:00:00Z","year":"2022","citation":{"ista":"Parvizian M, Duràn Balsa A, Pokratath R, Kalha C, Lee S, Van Den Eynden D, Ibáñez M, Regoutz A, De Roo J. 2022. The chemistry of Cu₃N and Cu₃PdN nanocrystals. Angewandte Chemie - International Edition. 61(31), e202207013.","ieee":"M. Parvizian <i>et al.</i>, “The chemistry of Cu₃N and Cu₃PdN nanocrystals,” <i>Angewandte Chemie - International Edition</i>, vol. 61, no. 31. Wiley, 2022.","mla":"Parvizian, Mahsa, et al. “The Chemistry of Cu₃N and Cu₃PdN Nanocrystals.” <i>Angewandte Chemie - International Edition</i>, vol. 61, no. 31, e202207013, Wiley, 2022, doi:<a href=\"https://doi.org/10.1002/anie.202207013\">10.1002/anie.202207013</a>.","short":"M. Parvizian, A. Duràn Balsa, R. Pokratath, C. Kalha, S. Lee, D. Van Den Eynden, M. Ibáñez, A. Regoutz, J. De Roo, Angewandte Chemie - International Edition 61 (2022).","apa":"Parvizian, M., Duràn Balsa, A., Pokratath, R., Kalha, C., Lee, S., Van Den Eynden, D., … De Roo, J. (2022). The chemistry of Cu₃N and Cu₃PdN nanocrystals. <i>Angewandte Chemie - International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202207013\">https://doi.org/10.1002/anie.202207013</a>","ama":"Parvizian M, Duràn Balsa A, Pokratath R, et al. The chemistry of Cu₃N and Cu₃PdN nanocrystals. <i>Angewandte Chemie - International Edition</i>. 2022;61(31). doi:<a href=\"https://doi.org/10.1002/anie.202207013\">10.1002/anie.202207013</a>","chicago":"Parvizian, Mahsa, Alejandra Duràn Balsa, Rohan Pokratath, Curran Kalha, Seungho Lee, Dietger Van Den Eynden, Maria Ibáñez, Anna Regoutz, and Jonathan De Roo. “The Chemistry of Cu₃N and Cu₃PdN Nanocrystals.” <i>Angewandte Chemie - International Edition</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/anie.202207013\">https://doi.org/10.1002/anie.202207013</a>."},"isi":1,"article_number":"e202207013","title":"The chemistry of Cu₃N and Cu₃PdN nanocrystals","date_updated":"2023-08-03T07:19:12Z","department":[{"_id":"MaIb"}],"month":"08","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"publication_status":"published","article_processing_charge":"No","publisher":"Springer Nature","publication_identifier":{"isbn":["9781071623206"],"eissn":["1940-6045"],"issn":["0893-2336"],"eisbn":["9781071623213"]},"doi":"10.1007/978-1-0716-2321-3_15","date_published":"2022-06-04T00:00:00Z","year":"2022","citation":{"ieee":"M. Artan and M. de Bono, “Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling,” in <i>Behavioral Neurogenetics</i>, vol. 181, D. Yamamoto, Ed. New York: Springer Nature, 2022, pp. 277–294.","mla":"Artan, Murat, and Mario de Bono. “Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling.” <i>Behavioral Neurogenetics</i>, edited by Daisuke Yamamoto, vol. 181, Springer Nature, 2022, pp. 277–94, doi:<a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">10.1007/978-1-0716-2321-3_15</a>.","ista":"Artan M, de Bono M. 2022.Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling. In: Behavioral Neurogenetics. Neuromethods, vol. 181, 277–294.","ama":"Artan M, de Bono M. Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling. In: Yamamoto D, ed. <i>Behavioral Neurogenetics</i>. Vol 181. NM. New York: Springer Nature; 2022:277-294. doi:<a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">10.1007/978-1-0716-2321-3_15</a>","chicago":"Artan, Murat, and Mario de Bono. “Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling.” In <i>Behavioral Neurogenetics</i>, edited by Daisuke Yamamoto, 181:277–94. NM. New York: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">https://doi.org/10.1007/978-1-0716-2321-3_15</a>.","short":"M. Artan, M. de Bono, in:, D. Yamamoto (Ed.), Behavioral Neurogenetics, Springer Nature, New York, 2022, pp. 277–294.","apa":"Artan, M., &#38; de Bono, M. (2022). Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling. In D. Yamamoto (Ed.), <i>Behavioral Neurogenetics</i> (Vol. 181, pp. 277–294). New York: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">https://doi.org/10.1007/978-1-0716-2321-3_15</a>"},"title":"Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling","date_updated":"2025-04-14T07:43:58Z","month":"06","department":[{"_id":"MaDe"}],"quality_controlled":"1","project":[{"name":"Molecular mechanisms of neural circuit function","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","grant_number":"209504/A/17/Z"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"}],"alternative_title":["Neuromethods"],"day":"04","volume":181,"oa_version":"None","ec_funded":1,"abstract":[{"text":"The proteomes of specialized structures, and the interactomes of proteins of interest, provide entry points to elucidate the functions of molecular machines. Here, we review a proximity-labeling strategy that uses the improved E. coli biotin ligase TurboID to characterize C. elegans protein complexes. Although the focus is on C. elegans neurons, the method is applicable regardless of cell type. We describe detailed extraction procedures that solubilize the bulk of C. elegans proteins and highlight the importance of tagging endogenous genes, to ensure physiological expression levels. We review issues associated with non-specific background noise and the importance of appropriate controls. As proof of principle, we review our analysis of the interactome of a presynaptic active zone protein, ELKS-1. Our aim is to provide a detailed protocol for TurboID-based proximity labeling in C. elegans and to highlight its potential and its limitations to characterize protein complexes and subcellular compartments in this animal.","lang":"eng"}],"_id":"11456","place":"New York","editor":[{"first_name":"Daisuke","full_name":"Yamamoto, Daisuke","last_name":"Yamamoto"}],"acknowledgement":"We thank de Bono lab members for the helpful comments on the manuscript. The biotin-auxotrophic E. coli strain MG1655bioB:kan was a generous gift from J. Cronan (University of Illinois) and was kindly sent to us by Jessica Feldman and Ariana Sanchez (Stanford University). dg398 pEntryslot2_mNeongreen::3XFLAG::stop and dg397 pEntryslot3_mNeongreen::3XFLAG::stop::unc-54 3’UTR entry vector were kindly sent by Dr. Dominique Glauser (University of Fribourg). This work was supported by an Advanced ERC Grant (269058 ACMO) and a Wellcome Investigator Award (209504/Z/17/Z) to MdB and an ISTplus Fellowship to MA (Marie Sklodowska-Curie agreement No 754411).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Artan","id":"C407B586-6052-11E9-B3AE-7006E6697425","full_name":"Artan, Murat","orcid":"0000-0001-8945-6992","first_name":"Murat"},{"first_name":"Mario","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono"}],"type":"book_chapter","corr_author":"1","publication":"Behavioral Neurogenetics","language":[{"iso":"eng"}],"date_created":"2022-06-20T08:10:34Z","status":"public","scopus_import":"1","page":"277-294","intvolume":"       181","series_title":"NM"},{"page":"442-457","ddc":["000"],"file":[{"date_created":"2022-06-27T07:38:21Z","checksum":"7eb915a2ca5b5ce4729321f33b2e16e1","access_level":"open_access","success":1,"relation":"main_file","file_size":318697,"file_name":"2022_PLDI_Zikelic.pdf","date_updated":"2022-06-27T07:38:21Z","content_type":"application/pdf","creator":"dernst","file_id":"11466"}],"language":[{"iso":"eng"}],"publication":"Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation","has_accepted_license":"1","scopus_import":"1","date_created":"2022-06-21T09:26:15Z","status":"public","type":"conference","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"We thank Shaun Willows, Thomas Lugnet, and the Living Room Application Vending team for suggesting threshold\r\nbounds as a developer-friendly way to interact with a differential cost analyzer, and we thank Jim Christy, Daniel\r\nSchoepe, and the Prime Video Automated Reasoning team for their support and helpful suggestions throughout the\r\nproject. We also thank Michael Emmi for feedback on an earlier version of this paper. And finally, we thank the anonymous reviewers for their useful feedback and Aws Albarghouthi for shepherding the final version of the paper. Ðorđe Žikelić was also partially supported by ERC CoG 863818 (FoRM-SMArt).","author":[{"last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde","first_name":"Dorde","orcid":"0000-0002-4681-1699"},{"first_name":"Bor-Yuh Evan","last_name":"Chang","full_name":"Chang, Bor-Yuh Evan"},{"last_name":"Bolignano","full_name":"Bolignano, Pauline","first_name":"Pauline"},{"full_name":"Raimondi, Franco","last_name":"Raimondi","first_name":"Franco"}],"corr_author":"1","file_date_updated":"2022-06-27T07:38:21Z","arxiv":1,"_id":"11459","oa":1,"conference":{"name":"PLDI: Programming Language Design and Implementation","end_date":"2022-06-17","start_date":"2022-06-13","location":"San Diego, CA, United States"},"abstract":[{"text":"We present a novel approach to differential cost analysis that, given a program revision, attempts to statically bound the difference in resource usage, or cost, between the two program versions. Differential cost analysis is particularly interesting because of the many compelling applications for it, such as detecting resource-use regressions at code-review time or proving the absence of certain side-channel vulnerabilities. One prior approach to differential cost analysis is to apply relational reasoning that conceptually constructs a product program on which one can over-approximate the difference in costs between the two program versions. However, a significant challenge in any relational approach is effectively aligning the program versions to get precise results. In this paper, our key insight is that we can avoid the need for and the limitations of program alignment if, instead, we bound the difference of two cost-bound summaries rather than directly bounding the concrete cost difference. In particular, our method computes a threshold value for the maximal difference in cost between two program versions simultaneously using two kinds of cost-bound summaries---a potential function that evaluates to an upper bound for the cost incurred in the first program and an anti-potential function that evaluates to a lower bound for the cost incurred in the second. Our method has a number of desirable properties: it can be fully automated, it allows optimizing the threshold value on relative cost, it is suitable for programs that are not syntactically similar, and it supports non-determinism. We have evaluated an implementation of our approach on a number of program pairs collected from the literature, and we find that our method computes tight threshold values on relative cost in most examples.","lang":"eng"}],"project":[{"grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"quality_controlled":"1","external_id":{"arxiv":["2204.00870"],"isi":["000850435600030"]},"ec_funded":1,"oa_version":"Published Version","day":"09","isi":1,"title":"Differential cost analysis with simultaneous potentials and anti-potentials","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"month":"06","date_updated":"2025-04-14T07:52:47Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"doi":"10.1145/3519939.3523435","article_processing_charge":"No","publisher":"Association for Computing Machinery","publication_identifier":{"isbn":["9781450392655"]},"publication_status":"published","citation":{"mla":"Zikelic, Dorde, et al. “Differential Cost Analysis with Simultaneous Potentials and Anti-Potentials.” <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2022, pp. 442–57, doi:<a href=\"https://doi.org/10.1145/3519939.3523435\">10.1145/3519939.3523435</a>.","ieee":"D. Zikelic, B.-Y. E. Chang, P. Bolignano, and F. Raimondi, “Differential cost analysis with simultaneous potentials and anti-potentials,” in <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, San Diego, CA, United States, 2022, pp. 442–457.","ista":"Zikelic D, Chang B-YE, Bolignano P, Raimondi F. 2022. Differential cost analysis with simultaneous potentials and anti-potentials. Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 442–457.","chicago":"Zikelic, Dorde, Bor-Yuh Evan Chang, Pauline Bolignano, and Franco Raimondi. “Differential Cost Analysis with Simultaneous Potentials and Anti-Potentials.” In <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, 442–57. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3519939.3523435\">https://doi.org/10.1145/3519939.3523435</a>.","ama":"Zikelic D, Chang B-YE, Bolignano P, Raimondi F. Differential cost analysis with simultaneous potentials and anti-potentials. In: <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2022:442-457. doi:<a href=\"https://doi.org/10.1145/3519939.3523435\">10.1145/3519939.3523435</a>","apa":"Zikelic, D., Chang, B.-Y. E., Bolignano, P., &#38; Raimondi, F. (2022). Differential cost analysis with simultaneous potentials and anti-potentials. In <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i> (pp. 442–457). San Diego, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3519939.3523435\">https://doi.org/10.1145/3519939.3523435</a>","short":"D. Zikelic, B.-Y.E. Chang, P. Bolignano, F. Raimondi, in:, Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2022, pp. 442–457."},"date_published":"2022-06-09T00:00:00Z","year":"2022"},{"publication_status":"published","doi":"10.1186/s13229-022-00508-3","publisher":"Springer Nature","article_processing_charge":"No","publication_identifier":{"issn":["2040-2392"]},"citation":{"ama":"Schaaf ZA, Tat L, Cannizzaro N, et al. WDFY3 mutation alters laminar position and morphology of cortical neurons. <i>Molecular Autism</i>. 2022;13. doi:<a href=\"https://doi.org/10.1186/s13229-022-00508-3\">10.1186/s13229-022-00508-3</a>","chicago":"Schaaf, Zachary A., Lyvin Tat, Noemi Cannizzaro, Ralph Green, Thomas Rülicke, Simon Hippenmeyer, and Konstantinos S. Zarbalis. “WDFY3 Mutation Alters Laminar Position and Morphology of Cortical Neurons.” <i>Molecular Autism</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1186/s13229-022-00508-3\">https://doi.org/10.1186/s13229-022-00508-3</a>.","short":"Z.A. Schaaf, L. Tat, N. Cannizzaro, R. Green, T. Rülicke, S. Hippenmeyer, K.S. Zarbalis, Molecular Autism 13 (2022).","apa":"Schaaf, Z. A., Tat, L., Cannizzaro, N., Green, R., Rülicke, T., Hippenmeyer, S., &#38; Zarbalis, K. S. (2022). WDFY3 mutation alters laminar position and morphology of cortical neurons. <i>Molecular Autism</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13229-022-00508-3\">https://doi.org/10.1186/s13229-022-00508-3</a>","ieee":"Z. A. Schaaf <i>et al.</i>, “WDFY3 mutation alters laminar position and morphology of cortical neurons,” <i>Molecular Autism</i>, vol. 13. Springer Nature, 2022.","mla":"Schaaf, Zachary A., et al. “WDFY3 Mutation Alters Laminar Position and Morphology of Cortical Neurons.” <i>Molecular Autism</i>, vol. 13, 27, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1186/s13229-022-00508-3\">10.1186/s13229-022-00508-3</a>.","ista":"Schaaf ZA, Tat L, Cannizzaro N, Green R, Rülicke T, Hippenmeyer S, Zarbalis KS. 2022. WDFY3 mutation alters laminar position and morphology of cortical neurons. Molecular Autism. 13, 27."},"date_published":"2022-06-22T00:00:00Z","year":"2022","title":"WDFY3 mutation alters laminar position and morphology of cortical neurons","article_number":"27","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"month":"06","department":[{"_id":"SiHi"}],"date_updated":"2025-06-11T13:34:57Z","quality_controlled":"1","external_id":{"pmid":["35733184"],"isi":["000814641400001"]},"day":"22","volume":13,"oa_version":"Published Version","abstract":[{"text":"Background: Proper cerebral cortical development depends on the tightly orchestrated migration of newly born neurons from the inner ventricular and subventricular zones to the outer cortical plate. Any disturbance in this process during prenatal stages may lead to neuronal migration disorders (NMDs), which can vary in extent from focal to global. Furthermore, NMDs show a substantial comorbidity with other neurodevelopmental disorders, notably autism spectrum disorders (ASDs). Our previous work demonstrated focal neuronal migration defects in mice carrying loss-of-function alleles of the recognized autism risk gene WDFY3. However, the cellular origins of these defects in Wdfy3 mutant mice remain elusive and uncovering it will provide critical insight into WDFY3-dependent disease pathology.\r\nMethods: Here, in an effort to untangle the origins of NMDs in Wdfy3lacZ mice, we employed mosaic analysis with double markers (MADM). MADM technology enabled us to genetically distinctly track and phenotypically analyze mutant and wild-type cells concomitantly in vivo using immunofluorescent techniques.\r\nResults: We revealed a cell autonomous requirement of WDFY3 for accurate laminar positioning of cortical projection neurons and elimination of mispositioned cells during early postnatal life. In addition, we identified significant deviations in dendritic arborization, as well as synaptic density and morphology between wild type, heterozygous, and homozygous Wdfy3 mutant neurons in Wdfy3-MADM reporter mice at postnatal stages.\r\nLimitations: While Wdfy3 mutant mice have provided valuable insight into prenatal aspects of ASD pathology that remain inaccessible to investigation in humans, like most animal models, they do not a perfectly replicate all aspects of human ASD biology. The lack of human data makes it indeterminate whether morphological deviations described here apply to ASD patients or some of the other neurodevelopmental conditions associated with WDFY3 mutation.\r\nConclusions: Our genetic approach revealed several cell autonomous requirements of WDFY3 in neuronal development that could underlie the pathogenic mechanisms of WDFY3-related neurodevelopmental conditions. The results are also consistent with findings in other ASD animal models and patients and suggest an important role for WDFY3 in regulating neuronal function and interconnectivity in postnatal life.","lang":"eng"}],"article_type":"original","_id":"11460","oa":1,"related_material":{"link":[{"url":"https://doi.org/10.1186/s13229-023-00539-4","relation":"erratum"}]},"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Zachary A.","last_name":"Schaaf","full_name":"Schaaf, Zachary A."},{"full_name":"Tat, Lyvin","last_name":"Tat","first_name":"Lyvin"},{"first_name":"Noemi","last_name":"Cannizzaro","full_name":"Cannizzaro, Noemi"},{"first_name":"Ralph","last_name":"Green","full_name":"Green, Ralph"},{"first_name":"Thomas","last_name":"Rülicke","full_name":"Rülicke, Thomas"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon"},{"first_name":"Konstantinos S.","last_name":"Zarbalis","full_name":"Zarbalis, Konstantinos S."}],"acknowledgement":"This study was funded by NIMH R21MH115347 to KSZ. KSZ is further supported by Shriners Hospitals for Children.\r\nWe would like to thank Angelo Harlan de Crescenzo for early contributions to this project.","file_date_updated":"2022-06-24T08:22:59Z","has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"Molecular Autism","date_created":"2022-06-23T14:28:55Z","status":"public","keyword":["Psychiatry and Mental health","Developmental Biology","Developmental Neuroscience","Molecular Biology"],"scopus_import":"1","pmid":1,"intvolume":"        13","file":[{"checksum":"525d2618e855139089bbfc3e3d49d1b2","date_created":"2022-06-24T08:22:59Z","relation":"main_file","file_size":7552298,"success":1,"access_level":"open_access","content_type":"application/pdf","date_updated":"2022-06-24T08:22:59Z","file_name":"2022_MolecularAutism_Schaaf.pdf","file_id":"11461","creator":"dernst"}],"ddc":["570"]},{"volume":106,"oa_version":"None","day":"01","external_id":{"pmid":["35723693"],"isi":["000813677500001"]},"quality_controlled":"1","abstract":[{"text":"Nanobodies (VHH) from camelid antibody libraries hold great promise as therapeutic agents and components of immunoassay systems. Synthetic antibody libraries that could be designed and generated once and for various applications could yield binders to virtually any targets, even for non-immunogenic or toxic ones, in a short term. One of the most difficult tasks is to obtain antibodies with a high affinity and specificity to polyglycosylated proteins. It requires antibody libraries with extremely high functional diversity and the use of sophisticated selection techniques. Here we report a development of a novel sandwich immunoassay involving a combination of the synthetic library-derived VHH-Fc fusion protein as a capture antibody and the immune single-chain fragment variable (scFv) as a tracer for the detection of pregnancy-associated glycoprotein (PAG) of cattle (Bos taurus). We succeeded in the generation of a number of specific scFv antibodies against PAG from the mouse immune library. Subsequent selection using the immobilized scFv-Fc capture antibody allowed to isolate 1.9 nM VHH binder from the diverse synthetic library without any overlapping with the capture antibody binding site. The prototype sandwich ELISA based on the synthetic VHH and the immune scFv was established. This is the first successful example of the combination of synthetic and immune antibody libraries in a single sandwich immunoassay. Thus, our approach could be used for the express isolation of antibody pairs and the development of sandwich immunoassays for challenging antigens.","lang":"eng"}],"article_type":"original","citation":{"apa":"Dormeshkin, D., Shapira, M., Karputs, A., Kavaleuski, A., Kuzminski, I., Stepanova, E., &#38; Gilep, A. (2022). Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. <i>Applied Microbiology and Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00253-022-12022-w\">https://doi.org/10.1007/s00253-022-12022-w</a>","short":"D. Dormeshkin, M. Shapira, A. Karputs, A. Kavaleuski, I. Kuzminski, E. Stepanova, A. Gilep, Applied Microbiology and Biotechnology 106 (2022) 5093–5103.","chicago":"Dormeshkin, Dmitri, Michail Shapira, Alena Karputs, Anton Kavaleuski, Ivan Kuzminski, Elena Stepanova, and Andrei Gilep. “Combining of Synthetic VHH and Immune ScFv Libraries for Pregnancy-Associated Glycoproteins ELISA Development.” <i>Applied Microbiology and Biotechnology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00253-022-12022-w\">https://doi.org/10.1007/s00253-022-12022-w</a>.","ama":"Dormeshkin D, Shapira M, Karputs A, et al. Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. <i>Applied Microbiology and Biotechnology</i>. 2022;106:5093-5103. doi:<a href=\"https://doi.org/10.1007/s00253-022-12022-w\">10.1007/s00253-022-12022-w</a>","ista":"Dormeshkin D, Shapira M, Karputs A, Kavaleuski A, Kuzminski I, Stepanova E, Gilep A. 2022. Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. Applied Microbiology and Biotechnology. 106, 5093–5103.","mla":"Dormeshkin, Dmitri, et al. “Combining of Synthetic VHH and Immune ScFv Libraries for Pregnancy-Associated Glycoproteins ELISA Development.” <i>Applied Microbiology and Biotechnology</i>, vol. 106, Springer Nature, 2022, pp. 5093–103, doi:<a href=\"https://doi.org/10.1007/s00253-022-12022-w\">10.1007/s00253-022-12022-w</a>.","ieee":"D. Dormeshkin <i>et al.</i>, “Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development,” <i>Applied Microbiology and Biotechnology</i>, vol. 106. Springer Nature, pp. 5093–5103, 2022."},"date_published":"2022-08-01T00:00:00Z","year":"2022","publication_status":"published","doi":"10.1007/s00253-022-12022-w","publication_identifier":{"eissn":["1432-0614"],"issn":["0175-7598"]},"article_processing_charge":"No","publisher":"Springer Nature","month":"08","department":[{"_id":"GradSch"},{"_id":"LeSa"}],"date_updated":"2023-10-10T07:15:02Z","title":"Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development","isi":1,"date_created":"2022-06-26T22:01:34Z","scopus_import":"1","status":"public","language":[{"iso":"eng"}],"publication":"Applied Microbiology and Biotechnology","pmid":1,"page":"5093-5103","intvolume":"       106","_id":"11462","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This study was financially supported by the State Committee on Science and Technology. We would like to thank Elena Tumar and Elena Kisileva at the Institute of Bioorganic Chemistry of NASB for their kind assistance with mouse immunizations.","author":[{"first_name":"Dmitri","full_name":"Dormeshkin, Dmitri","last_name":"Dormeshkin"},{"full_name":"Shapira, Michail","last_name":"Shapira","first_name":"Michail"},{"full_name":"Karputs, Alena","last_name":"Karputs","first_name":"Alena"},{"id":"62304f89-eb97-11eb-a6c2-8903dd183976","full_name":"Kavaleuski, Anton","last_name":"Kavaleuski","first_name":"Anton","orcid":"0000-0003-2091-526X"},{"last_name":"Kuzminski","full_name":"Kuzminski, Ivan","first_name":"Ivan"},{"first_name":"Elena","full_name":"Stepanova, Elena","last_name":"Stepanova"},{"first_name":"Andrei","full_name":"Gilep, Andrei","last_name":"Gilep"}]},{"has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"International Journal of Molecular Sciences","date_created":"2022-07-05T15:14:34Z","status":"public","scopus_import":"1","pmid":1,"intvolume":"        23","page":"6352","file":[{"checksum":"e997a57a928ec9d51fad8ce824a05935","date_created":"2022-07-06T07:36:59Z","file_size":2324542,"relation":"main_file","access_level":"open_access","success":1,"content_type":"application/pdf","date_updated":"2022-07-06T07:36:59Z","file_name":"2022_IntJMolSci_Bilanovicova.pdf","file_id":"11492","creator":"cchlebak"}],"ddc":["570"],"_id":"11489","oa":1,"type":"journal_article","acknowledgement":"We thank Charo del Genio from Coventry University and Richard Napier from the University of Warwick for helpful discussion concerning protein modeling and inspiration concerning CD spectroscopy, respectively. We thank Jan Hejatko for sharing the published AHP2 construct. We also thank Josef Houser from the core facility BIC CEITEC for valuable assistance, discussions, and ideas relating to CD. We acknowledge the: Core Facility CELLIM of CEITEC supported by the Czech-BioImaging large RI project (LM2018129 funded by MEYS CR), part of the Euro-BioImaging (www.eurobioimaging.eu accessed on 1 January 2016) ALM and medical imaging Node (Brno, CZ), CF Biomolecular Interactions and Crystallization of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127) and European Regional Development Fund-Project “UP CIISB“ (No. CZ.02.1.01/0.0/0.0/18_046/0015974) for their support with obtaining scientific data presented in this paper; Plant Sciences Core Facility of CEITEC Masaryk University for technical support. Open Access Funding by the Austrian Science Fund (FWF).","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Bilanovičová","full_name":"Bilanovičová, V","first_name":"V"},{"full_name":"Rýdza, N","last_name":"Rýdza","first_name":"N"},{"first_name":"L","full_name":"Koczka, L","last_name":"Koczka"},{"first_name":"M","full_name":"Hess, M","last_name":"Hess"},{"first_name":"E","full_name":"Feraru, E","last_name":"Feraru"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"full_name":"Nodzyński, T","last_name":"Nodzyński","first_name":"T"}],"file_date_updated":"2022-07-06T07:36:59Z","issue":"11","corr_author":"1","project":[{"grant_number":"P29988","name":"RNA-directed DNA methylation in plant development","_id":"262EF96E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"external_id":{"pmid":["35683031"],"isi":["000808733300001"]},"quality_controlled":"1","day":"06","volume":23,"oa_version":"Published Version","abstract":[{"text":"Much of plant development depends on cell-to-cell redistribution of the plant hormone auxin, which is facilitated by the plasma membrane (PM) localized PIN FORMED (PIN) proteins. Auxin export activity, developmental roles, subcellular trafficking, and polarity of PINs have been well studied, but their structure remains elusive besides a rough outline that they contain two groups of 5 alpha-helices connected by a large hydrophilic loop (HL). Here, we focus on the PIN1 HL as we could produce it in sufficient quantities for biochemical investigations to provide insights into its secondary structure. Circular dichroism (CD) studies revealed its nature as an intrinsically disordered protein (IDP), manifested by the increase of structure content upon thermal melting. Consistent with IDPs serving as interaction platforms, PIN1 loops homodimerize. PIN1 HL cytoplasmic overexpression in Arabidopsis disrupts early endocytic trafficking of PIN1 and PIN2 and causes defects in the cotyledon vasculature formation. In summary, we demonstrate that PIN1 HL has an intrinsically disordered nature, which must be considered to gain further structural insights. Some secondary structures may form transiently during pairing with known and yet-to-be-discovered interactors.","lang":"eng"}],"article_type":"original","publication_status":"published","doi":"10.3390/ijms23116352","publisher":"MDPI","article_processing_charge":"Yes","publication_identifier":{"issn":["1422-0067"]},"citation":{"ista":"Bilanovičová V, Rýdza N, Koczka L, Hess M, Feraru E, Friml J, Nodzyński T. 2022. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. International Journal of Molecular Sciences. 23(11), 6352.","mla":"Bilanovičová, V., et al. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” <i>International Journal of Molecular Sciences</i>, vol. 23, no. 11, MDPI, 2022, p. 6352, doi:<a href=\"https://doi.org/10.3390/ijms23116352\">10.3390/ijms23116352</a>.","ieee":"V. Bilanovičová <i>et al.</i>, “The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein,” <i>International Journal of Molecular Sciences</i>, vol. 23, no. 11. MDPI, p. 6352, 2022.","apa":"Bilanovičová, V., Rýdza, N., Koczka, L., Hess, M., Feraru, E., Friml, J., &#38; Nodzyński, T. (2022). The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms23116352\">https://doi.org/10.3390/ijms23116352</a>","short":"V. Bilanovičová, N. Rýdza, L. Koczka, M. Hess, E. Feraru, J. Friml, T. Nodzyński, International Journal of Molecular Sciences 23 (2022) 6352.","chicago":"Bilanovičová, V, N Rýdza, L Koczka, M Hess, E Feraru, Jiří Friml, and T Nodzyński. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” <i>International Journal of Molecular Sciences</i>. MDPI, 2022. <a href=\"https://doi.org/10.3390/ijms23116352\">https://doi.org/10.3390/ijms23116352</a>.","ama":"Bilanovičová V, Rýdza N, Koczka L, et al. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. <i>International Journal of Molecular Sciences</i>. 2022;23(11):6352. doi:<a href=\"https://doi.org/10.3390/ijms23116352\">10.3390/ijms23116352</a>"},"year":"2022","date_published":"2022-06-06T00:00:00Z","title":"The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"department":[{"_id":"JiFr"}],"month":"06","date_updated":"2025-04-15T08:12:07Z"},{"status":"public","date_created":"2022-07-08T11:03:02Z","oa_version":"None","has_accepted_license":"1","file":[{"date_created":"2022-07-08T10:56:52Z","checksum":"71e8186583f3adbb6c69a88ac9e6e49b","access_level":"open_access","success":1,"relation":"main_file","file_size":135784571,"file_name":"Source Data.xlsx","date_updated":"2022-07-08T10:56:52Z","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_id":"11543","creator":"rschulz"}],"citation":{"apa":"Schulz, R. (2022). Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses). Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">https://doi.org/10.15479/AT:ISTA:11542</a>","short":"R. Schulz, (2022).","chicago":"Schulz, Rouven. “Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses).” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">https://doi.org/10.15479/AT:ISTA:11542</a>.","ama":"Schulz R. Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses). 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>","ista":"Schulz R. 2022. Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses), Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>.","mla":"Schulz, Rouven. <i>Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses)</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>.","ieee":"R. Schulz, “Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses).” Institute of Science and Technology Austria, 2022."},"date_published":"2022-01-01T00:00:00Z","year":"2022","oa":1,"related_material":{"record":[{"status":"public","id":"11995","relation":"used_in_publication"}],"link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.06.21.449162v1","relation":"contains"}]},"doi":"10.15479/AT:ISTA:11542","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","_id":"11542","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"contributor":[{"contributor_type":"contact_person","orcid":"0000-0001-8635-0877","first_name":"Sandra","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2025-04-15T07:27:21Z","corr_author":"1","file_date_updated":"2022-07-08T10:56:52Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data","author":[{"first_name":"Rouven","orcid":"0000-0001-5297-733X","last_name":"Schulz","full_name":"Schulz, Rouven","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses)"},{"publisher":"Elsevier","publication_identifier":{"issn":["0021-8693"]},"article_processing_charge":"Yes (via OA deal)","doi":"10.1016/j.jalgebra.2022.06.017","publication_status":"published","date_published":"2022-11-01T00:00:00Z","year":"2022","citation":{"ieee":"A. Brown and A. Romanov, “Contravariant pairings between standard Whittaker modules and Verma modules,” <i>Journal of Algebra</i>, vol. 609, no. 11. Elsevier, pp. 145–179, 2022.","mla":"Brown, Adam, and Anna Romanov. “Contravariant Pairings between Standard Whittaker Modules and Verma Modules.” <i>Journal of Algebra</i>, vol. 609, no. 11, Elsevier, 2022, pp. 145–79, doi:<a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">10.1016/j.jalgebra.2022.06.017</a>.","ista":"Brown A, Romanov A. 2022. Contravariant pairings between standard Whittaker modules and Verma modules. Journal of Algebra. 609(11), 145–179.","ama":"Brown A, Romanov A. Contravariant pairings between standard Whittaker modules and Verma modules. <i>Journal of Algebra</i>. 2022;609(11):145-179. doi:<a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">10.1016/j.jalgebra.2022.06.017</a>","chicago":"Brown, Adam, and Anna Romanov. “Contravariant Pairings between Standard Whittaker Modules and Verma Modules.” <i>Journal of Algebra</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">https://doi.org/10.1016/j.jalgebra.2022.06.017</a>.","short":"A. Brown, A. Romanov, Journal of Algebra 609 (2022) 145–179.","apa":"Brown, A., &#38; Romanov, A. (2022). Contravariant pairings between standard Whittaker modules and Verma modules. <i>Journal of Algebra</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">https://doi.org/10.1016/j.jalgebra.2022.06.017</a>"},"isi":1,"title":"Contravariant pairings between standard Whittaker modules and Verma modules","date_updated":"2025-04-14T07:43:58Z","department":[{"_id":"HeEd"}],"month":"11","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"quality_controlled":"1","external_id":{"isi":["000861841100004"]},"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"ec_funded":1,"day":"01","oa_version":"Published Version","volume":609,"article_type":"original","abstract":[{"lang":"eng","text":"We classify contravariant pairings between standard Whittaker modules and Verma modules over a complex semisimple Lie algebra. These contravariant pairings are useful in extending several classical techniques for category O to the Miličić–Soergel category N . We introduce a class of costandard modules which generalize dual Verma modules, and describe canonical maps from standard to costandard modules in terms of contravariant pairings.\r\nWe show that costandard modules have unique irreducible submodules and share the same composition factors as the corresponding standard Whittaker modules. We show that costandard modules give an algebraic characterization of the global sections of costandard twisted Harish-Chandra sheaves on the associated flag variety, which are defined using holonomic duality of D-modules. We prove that with these costandard modules, blocks of category\r\nN have the structure of highest weight categories and we establish a BGG reciprocity theorem for N ."}],"_id":"11545","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"We thank Catharina Stroppel and Jens Niklas Eberhardt for interesting discussions. The first author acknowledges the support of the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. The second author is supported by the National Science Foundation Award No. 1803059 and the Australian Research Council grant DP170101579.","author":[{"first_name":"Adam","id":"70B7FDF6-608D-11E9-9333-8535E6697425","full_name":"Brown, Adam","last_name":"Brown"},{"first_name":"Anna","full_name":"Romanov, Anna","last_name":"Romanov"}],"type":"journal_article","corr_author":"1","issue":"11","file_date_updated":"2023-02-02T07:32:48Z","publication":"Journal of Algebra","language":[{"iso":"eng"}],"has_accepted_license":"1","keyword":["Algebra and Number Theory"],"date_created":"2022-07-08T11:40:07Z","status":"public","scopus_import":"1","page":"145-179","intvolume":"       609","ddc":["510"],"file":[{"creator":"dernst","file_id":"12473","file_name":"2022_JournalAlgebra_Brown.pdf","date_updated":"2023-02-02T07:32:48Z","content_type":"application/pdf","access_level":"open_access","success":1,"file_size":582962,"relation":"main_file","date_created":"2023-02-02T07:32:48Z","checksum":"82abaee3d7837f703e499a9ecbb25b7c"}]},{"scopus_import":"1","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"status":"public","date_created":"2022-07-08T11:41:56Z","has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","file":[{"success":1,"access_level":"open_access","file_size":920304,"relation":"main_file","date_created":"2023-02-02T08:20:29Z","checksum":"49f69428f3dcf5ce3ff281f7d199e9df","file_id":"12479","creator":"dernst","file_name":"2022_PhilosophicalTransactionsB_Westram.pdf","date_updated":"2023-02-02T08:20:29Z","content_type":"application/pdf"}],"ddc":["570"],"intvolume":"       377","pmid":1,"oa":1,"_id":"11546","file_date_updated":"2023-02-02T08:20:29Z","issue":"1856","corr_author":"1","type":"journal_article","author":[{"last_name":"Westram","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","orcid":"0000-0003-1050-4969"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"first_name":"Roger","full_name":"Butlin, Roger","last_name":"Butlin"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"acknowledgement":"We thank the editor and two anonymous reviewers for their helpful and interesting comments on this manuscript.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":377,"day":"01","oa_version":"Published Version","project":[{"grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation"}],"external_id":{"pmid":["35694747"],"isi":["000812317300005"]},"quality_controlled":"1","abstract":[{"lang":"eng","text":"Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. However, little is known about whether inversions also contribute disproportionately to parallel evolution. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions."}],"article_type":"original","citation":{"ista":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. 2022. Inversions and parallel evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1856), 20210203.","ieee":"A. M. Westram, R. Faria, K. Johannesson, R. Butlin, and N. H. Barton, “Inversions and parallel evolution,” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856. Royal Society of London, 2022.","mla":"Westram, Anja M., et al. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856, 20210203, Royal Society of London, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>.","short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, N.H. Barton, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","apa":"Westram, A. M., Faria, R., Johannesson, K., Butlin, R., &#38; Barton, N. H. (2022). Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>","ama":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. 2022;377(1856). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>","chicago":"Westram, Anja M, Rui Faria, Kerstin Johannesson, Roger Butlin, and Nicholas H Barton. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>."},"date_published":"2022-08-01T00:00:00Z","year":"2022","publication_status":"published","doi":"10.1098/rstb.2021.0203","publisher":"Royal Society of London","publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"article_processing_charge":"Yes (via OA deal)","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"month":"08","date_updated":"2025-06-12T06:10:18Z","title":"Inversions and parallel evolution","article_number":"20210203","isi":1},{"ec_funded":1,"oa_version":"Published Version","day":"01","volume":8,"project":[{"grant_number":"885707","_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020","name":"Spectral rigidity and integrability for billiards and geodesic flows"}],"quality_controlled":"1","article_type":"original","abstract":[{"text":"In holomorphic dynamics, complex box mappings arise as first return maps to wellchosen domains. They are a generalization of polynomial-like mapping, where the domain of the return map can have infinitely many components. They turned out to be extremely useful in tackling diverse problems. The purpose of this paper is:\r\n• To illustrate some pathologies that can occur when a complex box mapping is not induced by a globally defined map and when its domain has infinitely many components, and to give conditions to avoid these issues.\r\n• To show that once one has a box mapping for a rational map, these conditions can be assumed to hold in a very natural setting. Thus, we call such complex box mappings dynamically natural. Having such box mappings is the first step in tackling many problems in one-dimensional dynamics.\r\n• Many results in holomorphic dynamics rely on an interplay between combinatorial and analytic techniques. In this setting, some of these tools are:\r\n  • the Enhanced Nest (a nest of puzzle pieces around critical points) from Kozlovski, Shen, van Strien (AnnMath 165:749–841, 2007), referred to below as KSS;\r\n  • the Covering Lemma (which controls the moduli of pullbacks of annuli) from Kahn and Lyubich (Ann Math 169(2):561–593, 2009);\r\n   • the QC-Criterion and the Spreading Principle from KSS.\r\nThe purpose of this paper is to make these tools more accessible so that they can be used as a ‘black box’, so one does not have to redo the proofs in new settings.\r\n• To give an intuitive, but also rather detailed, outline of the proof from KSS and Kozlovski and van Strien (Proc Lond Math Soc (3) 99:275–296, 2009) of the following results for non-renormalizable dynamically natural complex box mappings:\r\n   • puzzle pieces shrink to points,\r\n   • (under some assumptions) topologically conjugate non-renormalizable polynomials and box mappings are quasiconformally conjugate.\r\n• We prove the fundamental ergodic properties for dynamically natural box mappings. This leads to some necessary conditions for when such a box mapping supports a measurable invariant line field on its filled Julia set. These mappings\r\nare the analogues of Lattès maps in this setting.\r\n• We prove a version of Mañé’s Theorem for complex box mappings concerning expansion along orbits of points that avoid a neighborhood of the set of critical points.","lang":"eng"}],"OA_type":"hybrid","citation":{"short":"T. Clark, K. Drach, O. Kozlovski, S.V. Strien, Arnold Mathematical Journal 8 (2022) 319–410.","apa":"Clark, T., Drach, K., Kozlovski, O., &#38; Strien, S. V. (2022). The dynamics of complex box mappings. <i>Arnold Mathematical Journal</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s40598-022-00200-7\">https://doi.org/10.1007/s40598-022-00200-7</a>","ama":"Clark T, Drach K, Kozlovski O, Strien SV. The dynamics of complex box mappings. <i>Arnold Mathematical Journal</i>. 2022;8(2):319-410. doi:<a href=\"https://doi.org/10.1007/s40598-022-00200-7\">10.1007/s40598-022-00200-7</a>","chicago":"Clark, Trevor, Kostiantyn Drach, Oleg Kozlovski, and Sebastian Van Strien. “The Dynamics of Complex Box Mappings.” <i>Arnold Mathematical Journal</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s40598-022-00200-7\">https://doi.org/10.1007/s40598-022-00200-7</a>.","ista":"Clark T, Drach K, Kozlovski O, Strien SV. 2022. The dynamics of complex box mappings. Arnold Mathematical Journal. 8(2), 319–410.","ieee":"T. Clark, K. Drach, O. Kozlovski, and S. V. Strien, “The dynamics of complex box mappings,” <i>Arnold Mathematical Journal</i>, vol. 8, no. 2. Springer Nature, pp. 319–410, 2022.","mla":"Clark, Trevor, et al. “The Dynamics of Complex Box Mappings.” <i>Arnold Mathematical Journal</i>, vol. 8, no. 2, Springer Nature, 2022, pp. 319–410, doi:<a href=\"https://doi.org/10.1007/s40598-022-00200-7\">10.1007/s40598-022-00200-7</a>."},"date_published":"2022-06-01T00:00:00Z","year":"2022","doi":"10.1007/s40598-022-00200-7","publisher":"Springer Nature","article_processing_charge":"No","publication_identifier":{"issn":["2199-6792"],"eissn":["2199-6806"]},"publication_status":"published","department":[{"_id":"VaKa"}],"month":"06","date_updated":"2025-07-10T11:50:12Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"title":"The dynamics of complex box mappings","scopus_import":"1","date_created":"2022-07-10T22:01:53Z","status":"public","language":[{"iso":"eng"}],"publication":"Arnold Mathematical Journal","has_accepted_license":"1","ddc":["500"],"file":[{"file_id":"11559","creator":"kschuh","content_type":"application/pdf","date_updated":"2022-07-12T10:04:55Z","file_name":"2022_ArnoldMathematicalJournal_Clark.pdf","relation":"main_file","file_size":2509915,"access_level":"open_access","success":1,"checksum":"16e7c659dee9073c6c8aeb87316ef201","date_created":"2022-07-12T10:04:55Z"}],"page":"319-410","intvolume":"         8","oa":1,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1007/s40598-022-00209-y"},{"relation":"erratum","url":"https://doi.org/10.1007/s40598-022-00218-x"}]},"OA_place":"publisher","_id":"11553","issue":"2","file_date_updated":"2022-07-12T10:04:55Z","type":"journal_article","author":[{"last_name":"Clark","full_name":"Clark, Trevor","first_name":"Trevor"},{"full_name":"Drach, Kostiantyn","id":"fe8209e2-906f-11eb-847d-950f8fc09115","last_name":"Drach","first_name":"Kostiantyn","orcid":"0000-0002-9156-8616"},{"first_name":"Oleg","last_name":"Kozlovski","full_name":"Kozlovski, Oleg"},{"first_name":"Sebastian Van","full_name":"Strien, Sebastian Van","last_name":"Strien"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We would also like to thank Dzmitry Dudko and Dierk Schleicher for many stimulating discussions and encouragement during our work on this project, and Weixiao Shen, Mikhail Hlushchanka and the referee for helpful comments. We are grateful to Leon Staresinic who carefully read the revised version of the manuscript and provided many helpful suggestions."},{"year":"2022","date_published":"2022-10-15T00:00:00Z","citation":{"chicago":"Kalinov, Aleksei, A.I. Osinskiy, S.A. Matveev, W. Otieno, and N.V. Brilliantov. “Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.” <i>Journal of Computational Physics</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">https://doi.org/10.1016/j.jcp.2022.111439</a>.","ama":"Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. <i>Journal of Computational Physics</i>. 2022;467. doi:<a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">10.1016/j.jcp.2022.111439</a>","apa":"Kalinov, A., Osinskiy, A. I., Matveev, S. A., Otieno, W., &#38; Brilliantov, N. V. (2022). Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. <i>Journal of Computational Physics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">https://doi.org/10.1016/j.jcp.2022.111439</a>","short":"A. Kalinov, A.I. Osinskiy, S.A. Matveev, W. Otieno, N.V. Brilliantov, Journal of Computational Physics 467 (2022).","mla":"Kalinov, Aleksei, et al. “Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.” <i>Journal of Computational Physics</i>, vol. 467, 111439, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">10.1016/j.jcp.2022.111439</a>.","ieee":"A. Kalinov, A. I. Osinskiy, S. A. Matveev, W. Otieno, and N. V. Brilliantov, “Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics,” <i>Journal of Computational Physics</i>, vol. 467. Elsevier, 2022.","ista":"Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. 2022. Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. Journal of Computational Physics. 467, 111439."},"publication_status":"published","publication_identifier":{"issn":["0021-9991"]},"publisher":"Elsevier","article_processing_charge":"No","doi":"10.1016/j.jcp.2022.111439","date_updated":"2024-10-21T06:01:47Z","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"month":"10","title":"Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics","isi":1,"article_number":"111439","oa_version":"Preprint","day":"15","volume":467,"quality_controlled":"1","external_id":{"arxiv":["2103.09481"],"isi":["000917225500013"]},"abstract":[{"lang":"eng","text":"We revisit two basic Direct Simulation Monte Carlo Methods to model aggregation kinetics and extend them for aggregation processes with collisional fragmentation (shattering). We test the performance and accuracy of the extended methods and compare their performance with efficient deterministic finite-difference method applied to the same model. We validate the stochastic methods on the test problems and apply them to verify the existence of oscillating regimes in the aggregation-fragmentation kinetics recently detected in deterministic simulations. We confirm the emergence of steady oscillations of densities in such systems and prove the stability of the\r\noscillations with respect to fluctuations and noise."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2103.09481"}],"article_type":"original","oa":1,"_id":"11556","arxiv":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"Zhores supercomputer of Skolkovo Institute of Science and Technology [68] has been used in the present research. S.A.M. was supported by Moscow Center for Fundamental and Applied Mathematics (the agreement with the Ministry of Education and Science of the Russian Federation No. 075-15-2019-1624). A.I.O. acknowledges RFBR project No. 20-31-90022. N.V.B. acknowledges the support of the Analytical Center (subsidy agreement 000000D730321P5Q0002, Grant No. 70-2021-00145 02.11.2021).","author":[{"id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","full_name":"Kalinov, Aleksei","last_name":"Kalinov","first_name":"Aleksei","orcid":"0000-0003-2189-3904"},{"first_name":"A.I.","last_name":"Osinskiy","full_name":"Osinskiy, A.I."},{"first_name":"S.A.","last_name":"Matveev","full_name":"Matveev, S.A."},{"first_name":"W.","last_name":"Otieno","full_name":"Otieno, W."},{"last_name":"Brilliantov","full_name":"Brilliantov, N.V.","first_name":"N.V."}],"type":"journal_article","status":"public","date_created":"2022-07-11T12:19:59Z","keyword":["Computer Science Applications","Physics and Astronomy (miscellaneous)","Applied Mathematics","Computational Mathematics","Modeling and Simulation","Numerical Analysis"],"scopus_import":"1","publication":"Journal of Computational Physics","language":[{"iso":"eng"}],"ddc":["518"],"intvolume":"       467"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"month":"07","department":[{"_id":"FyKo"}],"date_updated":"2025-06-11T13:37:00Z","title":"A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis","isi":1,"article_number":"149","citation":{"apa":"Zhang, R., Kuo, R., Coulter, M., Calixto, C. P. G., Entizne, J. C., Guo, W., … Brown, J. W. S. (2022). A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. <i>Genome Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13059-022-02711-0\">https://doi.org/10.1186/s13059-022-02711-0</a>","short":"R. Zhang, R. Kuo, M. Coulter, C.P.G. Calixto, J.C. Entizne, W. Guo, Y. Marquez, L. Milne, S. Riegler, A. Matsui, M. Tanaka, S. Harvey, Y. Gao, T. Wießner-Kroh, A. Paniagua, M. Crespi, K. Denby, A.B. Hur, E. Huq, M. Jantsch, A. Jarmolowski, T. Koester, S. Laubinger, Q.Q. Li, L. Gu, M. Seki, D. Staiger, R. Sunkar, Z. Szweykowska-Kulinska, S.L. Tu, A. Wachter, R. Waugh, L. Xiong, X.N. Zhang, A. Conesa, A.S.N. Reddy, A. Barta, M. Kalyna, J.W.S. Brown, Genome Biology 23 (2022).","chicago":"Zhang, Runxuan, Richard Kuo, Max Coulter, Cristiane P.G. Calixto, Juan Carlos Entizne, Wenbin Guo, Yamile Marquez, et al. “A High-Resolution Single-Molecule Sequencing-Based Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.” <i>Genome Biology</i>. BioMed Central, 2022. <a href=\"https://doi.org/10.1186/s13059-022-02711-0\">https://doi.org/10.1186/s13059-022-02711-0</a>.","ama":"Zhang R, Kuo R, Coulter M, et al. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. <i>Genome Biology</i>. 2022;23. doi:<a href=\"https://doi.org/10.1186/s13059-022-02711-0\">10.1186/s13059-022-02711-0</a>","ista":"Zhang R, Kuo R, Coulter M, Calixto CPG, Entizne JC, Guo W, Marquez Y, Milne L, Riegler S, Matsui A, Tanaka M, Harvey S, Gao Y, Wießner-Kroh T, Paniagua A, Crespi M, Denby K, Hur AB, Huq E, Jantsch M, Jarmolowski A, Koester T, Laubinger S, Li QQ, Gu L, Seki M, Staiger D, Sunkar R, Szweykowska-Kulinska Z, Tu SL, Wachter A, Waugh R, Xiong L, Zhang XN, Conesa A, Reddy ASN, Barta A, Kalyna M, Brown JWS. 2022. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biology. 23, 149.","mla":"Zhang, Runxuan, et al. “A High-Resolution Single-Molecule Sequencing-Based Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.” <i>Genome Biology</i>, vol. 23, 149, BioMed Central, 2022, doi:<a href=\"https://doi.org/10.1186/s13059-022-02711-0\">10.1186/s13059-022-02711-0</a>.","ieee":"R. Zhang <i>et al.</i>, “A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis,” <i>Genome Biology</i>, vol. 23. BioMed Central, 2022."},"date_published":"2022-07-07T00:00:00Z","year":"2022","publication_status":"published","doi":"10.1186/s13059-022-02711-0","article_processing_charge":"No","publisher":"BioMed Central","publication_identifier":{"eissn":["1474-760X"]},"abstract":[{"lang":"eng","text":"Background: Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis.\r\nResults: We present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 169,000 transcripts—twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We develop novel methods to determine splice junctions and transcription start and end sites accurately. Mismatch profiles around splice junctions provide a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identify high-confidence transcription start and end sites and remove fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides higher resolution of transcript expression profiling and identifies cold-induced differential transcription start and polyadenylation site usage.\r\nConclusions: AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single-molecule sequencing analysis from any species."}],"article_type":"original","volume":23,"oa_version":"Published Version","day":"07","external_id":{"isi":["000821915500002"],"pmid":["35799267"]},"quality_controlled":"1","file_date_updated":"2022-07-18T08:15:24Z","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was jointly supported by funding from the Biotechnology and Biological Sciences Research Council (BBSRC) BB/P009751/1 to JB; BB/R014582/1 to RW and RZ; BB/S020160/1 to RZ; BB/S004610/1 (16 ERA-CAPS BARN) to RW; the Scottish Government Rural and Environment Science and Analytical Services division (RESAS) [to RZ, RW, and JB]; the\r\nNational Science Foundation (MCB-2014408) and the National Institute of Health (NIH) (GM-114297) to E.H.; S. H. was supported by funding to K.D. from the University of York; the Austrian Science Fund (FWF) SFB F43 to AB and MJ and [P26333] to MK; The French Agence Nationale de la Recherche grant ANR-16-CE12-0032 to MC; the Japan Science and\r\nTechnology Agency (JST), the Core Research for Evolutionary Science and Technology (CREST; Grant Number JPMJCR13B4) to M.S.; the National Science Foundation (Grant No. DBI1949036 to A.b.H and A.S.N.R, and Grant No. MCB 2014542 to E.H. and A.S.N.R.); and the DOE Office of Science, Office of Biological and Environmental Research (Grant\r\nNo. DE-SC0010733) to A.S.N.R and A.b.H.; the Deutsche Forschungsgemeinschaft (DFG) STA653/14-1 and STA653/15-1 to DS; the National Science Foundation grant (IOS-154173) to Q.Q.L.; the German Research Foundation (DFG) WA2167/8-1 to AW and SFB1101/C03 to AW and TWK; the Research Grants Council (RGC) of Hong Kong (GRF 12103020) to LX. NSF grant IOS-1849708 and NSF EPSCoR grant 1826836 to RS; the Academia Sinica to S.-L. T.","author":[{"full_name":"Zhang, Runxuan","last_name":"Zhang","first_name":"Runxuan"},{"first_name":"Richard","full_name":"Kuo, Richard","last_name":"Kuo"},{"first_name":"Max","full_name":"Coulter, Max","last_name":"Coulter"},{"first_name":"Cristiane P.G.","full_name":"Calixto, Cristiane P.G.","last_name":"Calixto"},{"first_name":"Juan Carlos","last_name":"Entizne","full_name":"Entizne, Juan Carlos"},{"full_name":"Guo, Wenbin","last_name":"Guo","first_name":"Wenbin"},{"first_name":"Yamile","last_name":"Marquez","full_name":"Marquez, Yamile"},{"first_name":"Linda","full_name":"Milne, Linda","last_name":"Milne"},{"first_name":"Stefan","orcid":"0000-0003-3413-1343","last_name":"Riegler","id":"FF6018E0-D806-11E9-8E43-0B14E6697425","full_name":"Riegler, Stefan"},{"last_name":"Matsui","full_name":"Matsui, Akihiro","first_name":"Akihiro"},{"first_name":"Maho","last_name":"Tanaka","full_name":"Tanaka, Maho"},{"full_name":"Harvey, Sarah","last_name":"Harvey","first_name":"Sarah"},{"last_name":"Gao","full_name":"Gao, Yubang","first_name":"Yubang"},{"first_name":"Theresa","last_name":"Wießner-Kroh","full_name":"Wießner-Kroh, Theresa"},{"first_name":"Alejandro","last_name":"Paniagua","full_name":"Paniagua, Alejandro"},{"first_name":"Martin","last_name":"Crespi","full_name":"Crespi, Martin"},{"first_name":"Katherine","last_name":"Denby","full_name":"Denby, Katherine"},{"full_name":"Hur, Asa Ben","last_name":"Hur","first_name":"Asa Ben"},{"last_name":"Huq","full_name":"Huq, Enamul","first_name":"Enamul"},{"first_name":"Michael","last_name":"Jantsch","full_name":"Jantsch, Michael"},{"last_name":"Jarmolowski","full_name":"Jarmolowski, Artur","first_name":"Artur"},{"first_name":"Tino","last_name":"Koester","full_name":"Koester, Tino"},{"first_name":"Sascha","full_name":"Laubinger, Sascha","last_name":"Laubinger"},{"first_name":"Qingshun Quinn","last_name":"Li","full_name":"Li, Qingshun Quinn"},{"first_name":"Lianfeng","last_name":"Gu","full_name":"Gu, Lianfeng"},{"full_name":"Seki, Motoaki","last_name":"Seki","first_name":"Motoaki"},{"last_name":"Staiger","full_name":"Staiger, Dorothee","first_name":"Dorothee"},{"full_name":"Sunkar, Ramanjulu","last_name":"Sunkar","first_name":"Ramanjulu"},{"first_name":"Zofia","last_name":"Szweykowska-Kulinska","full_name":"Szweykowska-Kulinska, Zofia"},{"last_name":"Tu","full_name":"Tu, Shih Long","first_name":"Shih Long"},{"last_name":"Wachter","full_name":"Wachter, Andreas","first_name":"Andreas"},{"last_name":"Waugh","full_name":"Waugh, Robbie","first_name":"Robbie"},{"last_name":"Xiong","full_name":"Xiong, Liming","first_name":"Liming"},{"full_name":"Zhang, Xiao Ning","last_name":"Zhang","first_name":"Xiao Ning"},{"last_name":"Conesa","full_name":"Conesa, Ana","first_name":"Ana"},{"full_name":"Reddy, Anireddy S.N.","last_name":"Reddy","first_name":"Anireddy S.N."},{"last_name":"Barta","full_name":"Barta, Andrea","first_name":"Andrea"},{"first_name":"Maria","last_name":"Kalyna","full_name":"Kalyna, Maria"},{"first_name":"John W.S.","last_name":"Brown","full_name":"Brown, John W.S."}],"oa":1,"_id":"11587","file":[{"file_id":"11597","creator":"dernst","date_updated":"2022-07-18T08:15:24Z","file_name":"2022_GenomeBiology_Zhang.pdf","content_type":"application/pdf","success":1,"access_level":"open_access","relation":"main_file","file_size":3146207,"date_created":"2022-07-18T08:15:24Z","checksum":"2c30ef84151d257a6b835b4e069b70ac"}],"ddc":["570"],"intvolume":"        23","pmid":1,"status":"public","date_created":"2022-07-17T22:01:53Z","scopus_import":"1","has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"Genome Biology"}]