[{"OA_type":"closed access","external_id":{"pmid":["35681046"]},"publication_status":"published","extern":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"09","publication_identifier":{"issn":["1755-4330"],"eissn":["1755-4349"]},"status":"public","year":"2022","publication":"Nature Chemistry","scopus_import":"1","pmid":1,"volume":14,"ddc":["540"],"doi":"10.1038/s41557-022-00947-8","intvolume":"        14","date_created":"2026-05-06T10:56:14Z","author":[{"last_name":"Stricker","id":"7aca2cfc-46cf-11f0-abd3-8c96b5186745","full_name":"Stricker, Friedrich J","first_name":"Friedrich J"},{"full_name":"Sanchez, David M.","first_name":"David M.","last_name":"Sanchez"},{"first_name":"Umberto","full_name":"Raucci, Umberto","last_name":"Raucci"},{"last_name":"Dolinski","full_name":"Dolinski, Neil D.","first_name":"Neil D."},{"first_name":"Manuel S.","full_name":"Zayas, Manuel S.","last_name":"Zayas"},{"last_name":"Meisner","first_name":"Jan","full_name":"Meisner, Jan"},{"first_name":"Craig. J.","full_name":"Hawker, Craig. J.","last_name":"Hawker"},{"first_name":"Todd. J.","full_name":"Martínez, Todd. J.","last_name":"Martínez"},{"first_name":"Javier","full_name":"Read de Alaniz, Javier","last_name":"Read de Alaniz"}],"title":"A multi-stage single photochrome system for controlled photoswitching responses","date_published":"2022-06-09T00:00:00Z","article_type":"original","date_updated":"2026-05-18T09:13:44Z","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Springer Nature","oa_version":"None","page":"942-948","month":"06","type":"journal_article","citation":{"mla":"Stricker, Friedrich J., et al. “A Multi-Stage Single Photochrome System for Controlled Photoswitching Responses.” <i>Nature Chemistry</i>, vol. 14, Springer Nature, 2022, pp. 942–48, doi:<a href=\"https://doi.org/10.1038/s41557-022-00947-8\">10.1038/s41557-022-00947-8</a>.","ieee":"F. J. Stricker <i>et al.</i>, “A multi-stage single photochrome system for controlled photoswitching responses,” <i>Nature Chemistry</i>, vol. 14. Springer Nature, pp. 942–948, 2022.","apa":"Stricker, F. J., Sanchez, D. M., Raucci, U., Dolinski, N. D., Zayas, M. S., Meisner, J., … Read de Alaniz, J. (2022). A multi-stage single photochrome system for controlled photoswitching responses. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41557-022-00947-8\">https://doi.org/10.1038/s41557-022-00947-8</a>","short":"F.J. Stricker, D.M. Sanchez, U. Raucci, N.D. Dolinski, M.S. Zayas, J. Meisner, C.J. Hawker, T.J. Martínez, J. Read de Alaniz, Nature Chemistry 14 (2022) 942–948.","ista":"Stricker FJ, Sanchez DM, Raucci U, Dolinski ND, Zayas MS, Meisner J, Hawker CJ, Martínez TJ, Read de Alaniz J. 2022. A multi-stage single photochrome system for controlled photoswitching responses. Nature Chemistry. 14, 942–948.","chicago":"Stricker, Friedrich J, David M. Sanchez, Umberto Raucci, Neil D. Dolinski, Manuel S. Zayas, Jan Meisner, Craig. J. Hawker, Todd. J. Martínez, and Javier Read de Alaniz. “A Multi-Stage Single Photochrome System for Controlled Photoswitching Responses.” <i>Nature Chemistry</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41557-022-00947-8\">https://doi.org/10.1038/s41557-022-00947-8</a>.","ama":"Stricker FJ, Sanchez DM, Raucci U, et al. A multi-stage single photochrome system for controlled photoswitching responses. <i>Nature Chemistry</i>. 2022;14:942-948. doi:<a href=\"https://doi.org/10.1038/s41557-022-00947-8\">10.1038/s41557-022-00947-8</a>"},"_id":"21819","abstract":[{"text":"The ability of molecular photoswitches to convert on/off responses into large macroscale property change is fundamental to light-responsive materials. However, moving beyond simple binary responses necessitates the introduction of new elements that control the chemistry of the photoswitching process at the molecular scale. To achieve this goal, we designed, synthesized and developed a single photochrome, based on a modified donor–acceptor Stenhouse adduct (DASA), capable of independently addressing multiple molecular states. The multi-stage photoswitch enables complex switching phenomena. To demonstrate this, we show spatial control of the transformation of a three-stage photoswitch by tuning the population of intermediates along the multi-step reaction pathway of the DASAs without interfering with either the first or final stage. This allows for a photonic three-stage logic gate where the secondary wavelength solely negates the input of the primary wavelength. These results provide a new strategy to move beyond traditional on/off binary photochromic systems and enable the design of future molecular logic systems.","lang":"eng"}]},{"author":[{"last_name":"Peterson","full_name":"Peterson, Julie A.","first_name":"Julie A."},{"first_name":"Friedrich J","full_name":"Stricker, Friedrich J","last_name":"Stricker","id":"7aca2cfc-46cf-11f0-abd3-8c96b5186745"},{"last_name":"Read de Alaniz","full_name":"Read de Alaniz, Javier","first_name":"Javier"}],"title":"Improving the kinetics and dark equilibrium of donor-acceptor Stenhouse adduct by triene backbone design","date_created":"2026-05-06T10:59:03Z","issue":"14","date_published":"2022-01-17T00:00:00Z","article_type":"original","year":"2022","publication":"Chemical Communications","scopus_import":"1","pmid":1,"volume":58,"ddc":["540"],"doi":"10.1039/d1cc06235b","intvolume":"        58","external_id":{"pmid":["35075464"]},"extern":"1","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","publication_identifier":{"eissn":["1364-548X"],"issn":["1359-7345"]},"day":"17","status":"public","main_file_link":[{"url":"https://doi.org/10.1039/D1CC06235B","open_access":"1"}],"OA_type":"green","oa":1,"page":"2303-2306","citation":{"chicago":"Peterson, Julie A., Friedrich J Stricker, and Javier Read de Alaniz. “Improving the Kinetics and Dark Equilibrium of Donor-Acceptor Stenhouse Adduct by Triene Backbone Design.” <i>Chemical Communications</i>. Royal Society of Chemistry, 2022. <a href=\"https://doi.org/10.1039/d1cc06235b\">https://doi.org/10.1039/d1cc06235b</a>.","ista":"Peterson JA, Stricker FJ, Read de Alaniz J. 2022. Improving the kinetics and dark equilibrium of donor-acceptor Stenhouse adduct by triene backbone design. Chemical Communications. 58(14), 2303–2306.","ama":"Peterson JA, Stricker FJ, Read de Alaniz J. Improving the kinetics and dark equilibrium of donor-acceptor Stenhouse adduct by triene backbone design. <i>Chemical Communications</i>. 2022;58(14):2303-2306. doi:<a href=\"https://doi.org/10.1039/d1cc06235b\">10.1039/d1cc06235b</a>","apa":"Peterson, J. A., Stricker, F. J., &#38; Read de Alaniz, J. (2022). Improving the kinetics and dark equilibrium of donor-acceptor Stenhouse adduct by triene backbone design. <i>Chemical Communications</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d1cc06235b\">https://doi.org/10.1039/d1cc06235b</a>","short":"J.A. Peterson, F.J. Stricker, J. Read de Alaniz, Chemical Communications 58 (2022) 2303–2306.","ieee":"J. A. Peterson, F. J. Stricker, and J. Read de Alaniz, “Improving the kinetics and dark equilibrium of donor-acceptor Stenhouse adduct by triene backbone design,” <i>Chemical Communications</i>, vol. 58, no. 14. Royal Society of Chemistry, pp. 2303–2306, 2022.","mla":"Peterson, Julie A., et al. “Improving the Kinetics and Dark Equilibrium of Donor-Acceptor Stenhouse Adduct by Triene Backbone Design.” <i>Chemical Communications</i>, vol. 58, no. 14, Royal Society of Chemistry, 2022, pp. 2303–06, doi:<a href=\"https://doi.org/10.1039/d1cc06235b\">10.1039/d1cc06235b</a>."},"month":"01","type":"journal_article","_id":"21823","abstract":[{"text":"DFT calculations were used to find an optimal substitution site on the triene backbone of a donor–acceptor Stenhouse adduct photoswitch to tune the equillibrium and switching kinetics of DASA without modifying the donor and acceptor groups. Using this approach we demonstrate a new means to tuning DASA based photoswitches by increasing the energy of the closed form relative to the open form. To highlight the potential of this approach a new DASA derivative bearing a methyl substituent on the 5-position of the triene was synthesized and the effect of this substitution was studied using 1H NMR spectroscopy, time-dependent UV-Vis and solvatochromic analysis. The new DASA derivative shows a higher dark equillibrium, favoring the open form, and drastically faster thermal recovery than the unsubstituted derivative with the same donor and acceptor.","lang":"eng"}],"date_updated":"2026-05-18T09:46:30Z","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Royal Society of Chemistry","oa_version":"Accepted Version"},{"related_material":{"record":[{"id":"14517","status":"public","relation":"used_in_publication"}]},"month":"06","citation":{"ama":"Zemlicka M, Redchenko E, Peruzzo M, et al. Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses. 2022. doi:<a href=\"https://doi.org/10.5281/ZENODO.8408897\">10.5281/ZENODO.8408897</a>","chicago":"Zemlicka, Martin, Elena Redchenko, Matilda Peruzzo, Farid Hassani, Andrea Trioni, Shabir Barzanjeh, and Johannes M Fink. “Compact Vacuum Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses.” Zenodo, 2022. <a href=\"https://doi.org/10.5281/ZENODO.8408897\">https://doi.org/10.5281/ZENODO.8408897</a>.","ista":"Zemlicka M, Redchenko E, Peruzzo M, Hassani F, Trioni A, Barzanjeh S, Fink JM. 2022. Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8408897\">10.5281/ZENODO.8408897</a>.","short":"M. Zemlicka, E. Redchenko, M. Peruzzo, F. Hassani, A. Trioni, S. Barzanjeh, J.M. Fink, (2022).","apa":"Zemlicka, M., Redchenko, E., Peruzzo, M., Hassani, F., Trioni, A., Barzanjeh, S., &#38; Fink, J. M. (2022). Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8408897\">https://doi.org/10.5281/ZENODO.8408897</a>","ieee":"M. Zemlicka <i>et al.</i>, “Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses.” Zenodo, 2022.","mla":"Zemlicka, Martin, et al. <i>Compact Vacuum Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses</i>. Zenodo, 2022, doi:<a href=\"https://doi.org/10.5281/ZENODO.8408897\">10.5281/ZENODO.8408897</a>."},"type":"research_data_reference","oa":1,"date_created":"2023-11-13T08:09:10Z","author":[{"last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","orcid":"0009-0005-0878-3032","first_name":"Martin","full_name":"Zemlicka, Martin"},{"id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","last_name":"Redchenko","full_name":"Redchenko, Elena","first_name":"Elena"},{"last_name":"Peruzzo","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628","first_name":"Matilda","full_name":"Peruzzo, Matilda"},{"last_name":"Hassani","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6937-5773","first_name":"Farid","full_name":"Hassani, Farid"},{"id":"42F71B44-F248-11E8-B48F-1D18A9856A87","last_name":"Trioni","first_name":"Andrea","full_name":"Trioni, Andrea"},{"full_name":"Barzanjeh, Shabir","first_name":"Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M","first_name":"Johannes M"}],"title":"Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses","abstract":[{"lang":"eng","text":"This dataset comprises all data shown in the figures of the submitted article \"Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses\" at arxiv.org/abs/2206.14104. Additional raw data are available from the corresponding author on reasonable request."}],"date_published":"2022-06-28T00:00:00Z","_id":"14520","year":"2022","ddc":["530"],"doi":"10.5281/ZENODO.8408897","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JoFi"}],"has_accepted_license":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.8408897"}],"status":"public","day":"28","date_updated":"2026-06-03T07:16:02Z","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"corr_author":"1","oa_version":"Published Version","publisher":"Zenodo"},{"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"date_updated":"2026-06-12T12:43:34Z","language":[{"iso":"eng"}],"publisher":"Springer Nature","quality_controlled":"1","oa_version":"Published Version","corr_author":"1","oa":1,"citation":{"ista":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 84(8), 74.","chicago":"Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s11538-022-01029-z\">https://doi.org/10.1007/s11538-022-01029-z</a>.","ama":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. <i>Bulletin of Mathematical Biology</i>. 2022;84(8). doi:<a href=\"https://doi.org/10.1007/s11538-022-01029-z\">10.1007/s11538-022-01029-z</a>","apa":"Saona Urmeneta, R. J., Kondrashov, F., &#38; Khudiakova, K. (2022). Relation between the number of peaks and the number of reciprocal sign epistatic interactions. <i>Bulletin of Mathematical Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11538-022-01029-z\">https://doi.org/10.1007/s11538-022-01029-z</a>","short":"R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (2022).","mla":"Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical Biology</i>, vol. 84, no. 8, 74, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s11538-022-01029-z\">10.1007/s11538-022-01029-z</a>.","ieee":"R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between the number of peaks and the number of reciprocal sign epistatic interactions,” <i>Bulletin of Mathematical Biology</i>, vol. 84, no. 8. Springer Nature, 2022."},"type":"journal_article","related_material":{"record":[{"relation":"dissertation_contains","id":"21918","status":"public"}],"link":[{"url":"https://doi.org/10.1007/s11538-022-01118-z","relation":"erratum"}]},"month":"06","keyword":["Computational Theory and Mathematics","General Agricultural and Biological Sciences","Pharmacology","General Environmental Science","General Biochemistry","Genetics and Molecular Biology","General Mathematics","Immunology","General Neuroscience"],"_id":"11447","abstract":[{"text":"Empirical essays of fitness landscapes suggest that they may be rugged, that is having multiple fitness peaks. Such fitness landscapes, those that have multiple peaks, necessarily have special local structures, called reciprocal sign epistasis (Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the quantitative relationship between the number of fitness peaks and the number of reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis is a necessary but not sufficient condition for the existence of multiple peaks. Applying discrete Morse theory, which to our knowledge has never been used in this context, we extend this result by giving the minimal number of reciprocal sign epistatic interactions required to create a given number of peaks.","lang":"eng"}],"publication_status":"published","external_id":{"pmid":["35713756"],"isi":["000812509800001"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"article_processing_charge":"Yes (via OA deal)","day":"17","publication_identifier":{"eissn":["1522-9602"],"issn":["0092-8240"]},"status":"public","has_accepted_license":"1","isi":1,"file_date_updated":"2022-06-20T07:51:32Z","date_created":"2022-06-17T16:16:15Z","author":[{"full_name":"Saona Urmeneta, Raimundo J","first_name":"Raimundo J","orcid":"0000-0001-5103-038X","last_name":"Saona Urmeneta","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425"},{"first_name":"Fyodor","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","orcid":"0000-0001-8243-4694"},{"first_name":"Kseniia","full_name":"Khudiakova, Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","last_name":"Khudiakova","orcid":"0000-0002-6246-1465"}],"article_number":"74","title":"Relation between the number of peaks and the number of reciprocal sign epistatic interactions","ec_funded":1,"issue":"8","file":[{"date_updated":"2022-06-20T07:51:32Z","relation":"main_file","access_level":"open_access","file_id":"11455","success":1,"content_type":"application/pdf","checksum":"05a1fe7d10914a00c2bca9b447993a65","file_name":"2022_BulletinMathBiology_Saona.pdf","creator":"dernst","date_created":"2022-06-20T07:51:32Z","file_size":463025}],"date_published":"2022-06-17T00:00:00Z","project":[{"call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425"},{"name":"Evolutionary analysis of gene regulation","_id":"34e076d6-11ca-11ed-8bc3-aec76c41a181","grant_number":"I05127"}],"article_type":"original","pmid":1,"scopus_import":"1","year":"2022","publication":"Bulletin of Mathematical Biology","volume":84,"acknowledgement":"We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful discussions. Open access funding provided by Austrian Science Fund (FWF). Partially supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund (I5127-B) grants to FAK.","doi":"10.1007/s11538-022-01029-z","ddc":["510","570"],"intvolume":"        84"},{"citation":{"mla":"Friml, Jiří. “Fourteen Stations of Auxin.” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 14, no. 5, a039859, Cold Spring Harbor Laboratory Press, 2022, doi:<a href=\"https://doi.org/10.1101/cshperspect.a039859\">10.1101/cshperspect.a039859</a>.","ieee":"J. Friml, “Fourteen stations of auxin,” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 14, no. 5. Cold Spring Harbor Laboratory Press, 2022.","short":"J. Friml, Cold Spring Harbor Perspectives in Biology 14 (2022).","apa":"Friml, J. (2022). Fourteen stations of auxin. <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/cshperspect.a039859\">https://doi.org/10.1101/cshperspect.a039859</a>","chicago":"Friml, Jiří. “Fourteen Stations of Auxin.” <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press, 2022. <a href=\"https://doi.org/10.1101/cshperspect.a039859\">https://doi.org/10.1101/cshperspect.a039859</a>.","ista":"Friml J. 2022. Fourteen stations of auxin. Cold Spring Harbor Perspectives in Biology. 14(5), a039859.","ama":"Friml J. Fourteen stations of auxin. <i>Cold Spring Harbor Perspectives in Biology</i>. 2022;14(5). doi:<a href=\"https://doi.org/10.1101/cshperspect.a039859\">10.1101/cshperspect.a039859</a>"},"month":"05","type":"journal_article","oa":1,"abstract":[{"lang":"eng","text":"Auxin has always been at the forefront of research in plant physiology and development. Since the earliest contemplations by Julius von Sachs and Charles Darwin, more than a century-long struggle has been waged to understand its function. This largely reflects the failures, successes, and inevitable progress in the entire field of plant signaling and development. Here I present 14 stations on our long and sometimes mystical journey to understand auxin. These highlights were selected to give a flavor of the field and to show the scope and limits of our current knowledge. A special focus is put on features that make auxin unique among phytohormones, such as its dynamic, directional transport network, which integrates external and internal signals, including self-organizing feedback. Accented are persistent mysteries and controversies. The unexpected discoveries related to rapid auxin responses and growth regulation recently disturbed our contentment regarding understanding of the auxin signaling mechanism. These new revelations, along with advances in technology, usher us into a new, exciting era in auxin research. "}],"_id":"10016","language":[{"iso":"eng"}],"date_updated":"2026-06-18T08:35:48Z","oa_version":"Published Version","corr_author":"1","publisher":"Cold Spring Harbor Laboratory Press","quality_controlled":"1","issue":"5","article_number":"a039859","author":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","full_name":"Friml, Jiří"}],"date_created":"2021-09-14T11:36:53Z","title":"Fourteen stations of auxin","article_type":"review","date_published":"2022-05-27T00:00:00Z","volume":14,"pmid":1,"scopus_import":"1","publication":"Cold Spring Harbor Perspectives in Biology","year":"2022","intvolume":"        14","acknowledgement":"The author thanks the whole community of researchers consciously or unconsciously working on questions related to auxin, whose hard work and enthusiasm contributed to development of this exciting story. Particular thanks go to many\r\nbrilliant present and past members of the Friml group and our numerous excellent collaborators, without whom my own personal journey would not be possible. The way of the cross with its 14 stations is a popular devotion among Roman Catholics and inspires them to make a spiritual pilgrimage through contemplation of Christ on his last day. Its aspects of gradual progress, struggle, passion, and revelation served as an inspiration for the formal depiction of our journey to understanding auxin as described in this review. It is in no way intended to reflect the personal beliefs of the author and readers. I am grateful to Nick Barton, Eva Benková, Lenka Caisová, Matyáš Fendrych, Lukáš Fiedler, Monika Frátriková, Jarmila Frimlová, Michelle Gallei, Jakub Hajný, Lukas Hoermayer, Alexandra Mally, Ondrˇej Novák, Jan Petrášek, Aleš Pěnčík, Steffen Vanneste, Tongda Xu, and Zhenbiao Yang for their valuable comments. Special thanks go to Michelle Gallei for her invaluable assistance with the figures.","doi":"10.1101/cshperspect.a039859","ddc":["580"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"}],"article_processing_charge":"No","publication_status":"published","external_id":{"isi":["000806563000003"],"pmid":["34400554"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/cshperspect.a039859 "}],"status":"public","isi":1,"day":"27","publication_identifier":{"issn":["1943-0264"]}},{"issue":"2","title":"Rectifiable curves in proximally smooth sets","date_created":"2021-10-24T22:01:35Z","author":[{"full_name":"Ivanov, Grigory","first_name":"Grigory","orcid":"0000-0002-5021-3982","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","last_name":"Ivanov"},{"first_name":"Mariana S.","full_name":"Lopushanski, Mariana S.","last_name":"Lopushanski"}],"article_type":"original","date_published":"2022-06-01T00:00:00Z","volume":30,"year":"2022","publication":"Set-Valued and Variational Analysis","scopus_import":"1","intvolume":"        30","ddc":["500"],"acknowledgement":"Theorem 2 was obtained at Steklov Mathematical Institute RAS and supported by Russian Science Foundation, grant N 19-11-00087.","doi":"10.1007/s11228-021-00612-1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"UlWa"}],"external_id":{"isi":["000705774800001"],"arxiv":["2012.10691"]},"publication_status":"published","isi":1,"status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2012.10691"}],"publication_identifier":{"eissn":["1877-0541"],"issn":["0927-6947"]},"day":"01","citation":{"ieee":"G. Ivanov and M. S. Lopushanski, “Rectifiable curves in proximally smooth sets,” <i>Set-Valued and Variational Analysis</i>, vol. 30, no. 2. Springer Nature, pp. 657–675, 2022.","mla":"Ivanov, Grigory, and Mariana S. Lopushanski. “Rectifiable Curves in Proximally Smooth Sets.” <i>Set-Valued and Variational Analysis</i>, vol. 30, no. 2, Springer Nature, 2022, pp. 657–75, doi:<a href=\"https://doi.org/10.1007/s11228-021-00612-1\">10.1007/s11228-021-00612-1</a>.","apa":"Ivanov, G., &#38; Lopushanski, M. S. (2022). Rectifiable curves in proximally smooth sets. <i>Set-Valued and Variational Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11228-021-00612-1\">https://doi.org/10.1007/s11228-021-00612-1</a>","short":"G. Ivanov, M.S. Lopushanski, Set-Valued and Variational Analysis 30 (2022) 657–675.","ista":"Ivanov G, Lopushanski MS. 2022. Rectifiable curves in proximally smooth sets. Set-Valued and Variational Analysis. 30(2), 657–675.","chicago":"Ivanov, Grigory, and Mariana S. Lopushanski. “Rectifiable Curves in Proximally Smooth Sets.” <i>Set-Valued and Variational Analysis</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s11228-021-00612-1\">https://doi.org/10.1007/s11228-021-00612-1</a>.","ama":"Ivanov G, Lopushanski MS. Rectifiable curves in proximally smooth sets. <i>Set-Valued and Variational Analysis</i>. 2022;30(2):657-675. doi:<a href=\"https://doi.org/10.1007/s11228-021-00612-1\">10.1007/s11228-021-00612-1</a>"},"month":"06","type":"journal_article","oa":1,"page":"657-675","abstract":[{"lang":"eng","text":"In this article we study some geometric properties of proximally smooth sets. First, we introduce a modification of the metric projection and prove its existence. Then we provide an algorithm for constructing a rectifiable curve between two sufficiently close points of a proximally smooth set in a uniformly convex and uniformly smooth Banach space, with the moduli of smoothness and convexity of power type. Our algorithm returns a reasonably short curve between two sufficiently close points of a proximally smooth set, is iterative and uses our modification of the metric projection. We estimate the length of the constructed curve and its deviation from the segment with the same endpoints. These estimates coincide up to a constant factor with those for the geodesics in a proximally smooth set in a Hilbert space."}],"_id":"10181","arxiv":1,"date_updated":"2026-06-18T08:36:30Z","language":[{"iso":"eng"}],"oa_version":"Published Version","quality_controlled":"1","publisher":"Springer Nature"},{"acknowledged_ssus":[{"_id":"EM-Fac"}],"oa_version":"Published Version","quality_controlled":"1","publisher":"American Society for Microbiology","language":[{"iso":"eng"}],"date_updated":"2026-06-18T08:44:25Z","abstract":[{"lang":"eng","text":"With more than 80 members worldwide, the Orthobunyavirus genus in the Peribunyaviridae family is a large genus of enveloped RNA viruses, many of which are emerging pathogens in humans and livestock. How orthobunyaviruses (OBVs) penetrate and infect mammalian host cells remains poorly characterized. Here, we investigated the entry mechanisms of the OBV Germiston (GERV). Viral particles were visualized by cryo-electron microscopy and appeared roughly spherical with an average diameter of 98 nm. Labeling of the virus with fluorescent dyes did not adversely affect its infectivity and allowed the monitoring of single particles in fixed and live cells. Using this approach, we found that endocytic internalization of bound viruses was asynchronous and occurred within 30-40 min. The virus entered Rab5a+ early endosomes and, subsequently, late endosomal vacuoles containing Rab7a but not LAMP-1. Infectious entry did not require proteolytic cleavage, and endosomal acidification was sufficient and necessary for viral fusion. Acid-activated penetration began 15-25 min after initiation of virus internalization and relied on maturation of early endosomes to late endosomes. The optimal pH for viral membrane fusion was slightly below 6.0, and penetration was hampered when the potassium influx was abolished. Overall, our study provides real-time visualization of GERV entry into host cells and demonstrates the importance of late endosomal maturation in facilitating OBV penetration."}],"_id":"10639","keyword":["virology","insect science","immunology","microbiology"],"citation":{"ista":"Windhaber S, Xin Q, Uckeley ZM, Koch J, Obr M, Garnier C, Luengo-Guyonnot C, Duboeuf M, Schur FK, Lozach P-Y. 2022. The Orthobunyavirus Germiston enters host cells from late endosomes. Journal of Virology. 96(5), e02146-21.","chicago":"Windhaber, Stefan, Qilin Xin, Zina M. Uckeley, Jana Koch, Martin Obr, Céline Garnier, Catherine Luengo-Guyonnot, Maëva Duboeuf, Florian KM Schur, and Pierre-Yves Lozach. “The Orthobunyavirus Germiston Enters Host Cells from Late Endosomes.” <i>Journal of Virology</i>. American Society for Microbiology, 2022. <a href=\"https://doi.org/10.1128/jvi.02146-21\">https://doi.org/10.1128/jvi.02146-21</a>.","ama":"Windhaber S, Xin Q, Uckeley ZM, et al. The Orthobunyavirus Germiston enters host cells from late endosomes. <i>Journal of Virology</i>. 2022;96(5). doi:<a href=\"https://doi.org/10.1128/jvi.02146-21\">10.1128/jvi.02146-21</a>","apa":"Windhaber, S., Xin, Q., Uckeley, Z. M., Koch, J., Obr, M., Garnier, C., … Lozach, P.-Y. (2022). The Orthobunyavirus Germiston enters host cells from late endosomes. <i>Journal of Virology</i>. American Society for Microbiology. <a href=\"https://doi.org/10.1128/jvi.02146-21\">https://doi.org/10.1128/jvi.02146-21</a>","short":"S. Windhaber, Q. Xin, Z.M. Uckeley, J. Koch, M. Obr, C. Garnier, C. Luengo-Guyonnot, M. Duboeuf, F.K. Schur, P.-Y. Lozach, Journal of Virology 96 (2022).","mla":"Windhaber, Stefan, et al. “The Orthobunyavirus Germiston Enters Host Cells from Late Endosomes.” <i>Journal of Virology</i>, vol. 96, no. 5, e02146-21, American Society for Microbiology, 2022, doi:<a href=\"https://doi.org/10.1128/jvi.02146-21\">10.1128/jvi.02146-21</a>.","ieee":"S. Windhaber <i>et al.</i>, “The Orthobunyavirus Germiston enters host cells from late endosomes,” <i>Journal of Virology</i>, vol. 96, no. 5. American Society for Microbiology, 2022."},"month":"03","type":"journal_article","oa":1,"status":"public","isi":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8906410"}],"publication_identifier":{"issn":["0022-538X"],"eissn":["1098-5514"]},"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","department":[{"_id":"FlSc"}],"external_id":{"isi":["000779305000033"],"pmid":["35019710"]},"publication_status":"published","article_type":"original","project":[{"grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structural conservation and diversity in retroviral capsid"}],"date_published":"2022-03-01T00:00:00Z","issue":"5","title":"The Orthobunyavirus Germiston enters host cells from late endosomes","author":[{"last_name":"Windhaber","first_name":"Stefan","full_name":"Windhaber, Stefan"},{"full_name":"Xin, Qilin","first_name":"Qilin","last_name":"Xin"},{"last_name":"Uckeley","full_name":"Uckeley, Zina M.","first_name":"Zina M."},{"last_name":"Koch","full_name":"Koch, Jana","first_name":"Jana"},{"full_name":"Obr, Martin","first_name":"Martin","orcid":"0000-0003-1756-6564","last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Garnier, Céline","first_name":"Céline","last_name":"Garnier"},{"first_name":"Catherine","full_name":"Luengo-Guyonnot, Catherine","last_name":"Luengo-Guyonnot"},{"last_name":"Duboeuf","full_name":"Duboeuf, Maëva","first_name":"Maëva"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","orcid":"0000-0003-4790-8078","first_name":"Florian KM","full_name":"Schur, Florian KM"},{"first_name":"Pierre-Yves","full_name":"Lozach, Pierre-Yves","last_name":"Lozach"}],"article_number":"e02146-21","date_created":"2022-01-18T10:04:18Z","intvolume":"        96","ddc":["570"],"acknowledgement":"This work  was  supported  by  INRAE  starter  funds, Project IDEXLYON  (University  of  Lyon) within  the  Programme  Investissements  d’Avenir  (ANR-16-IDEX-0005),  and  FINOVIAO14 (Fondation  pour  l’Université  de  Lyon),  all  to  P.Y.L.  This  work  was  also  supported  by CellNetworks  Research  Group  funds  and  Deutsche  Forschungsgemeinschaft  (DFG)  funding (grant  numbers  LO-2338/1-1  and  LO-2338/3-1)  awarded  to  P.Y.L., Austrian  Science  Fund (FWF)  grant  P31445  to  F.K.M.S., a  Chinese  Scholarship  Council (CSC;no.  201904910701) fellowship  to   Q.X.,  and  a  ministére  de  l’enseignement  supérieur,  de  la  recherche  et  de l’innovation (MESRI) doctoral thesis grant to M.D.","doi":"10.1128/jvi.02146-21","volume":96,"publication":"Journal of Virology","year":"2022","pmid":1,"scopus_import":"1"},{"day":"21","publication_identifier":{"issn":["0032-0781"],"eissn":["1471-9053"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/pcp/pcab149"}],"status":"public","isi":1,"publication_status":"published","external_id":{"isi":["000877899400009"],"pmid":["34791413"]},"department":[{"_id":"JiFr"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The authors thank Ralf Stracke (Bielefeld University, Bielefeld, Germany) for providing the myb mutants and their colleagues Bert De Rybel for the tmo5t;mo5l1 double mutant, Boris Parizot for tips on the RNA-seq analysis, Veronique Storme for statistical help on both the RNA-seq and lateral root density, and Martine De Cock for help in preparing the manuscript.","doi":"10.1093/pcp/pcab149","ddc":["580"],"intvolume":"        63","scopus_import":"1","pmid":1,"publication":"Plant & Cell Physiology","year":"2022","volume":63,"date_published":"2022-01-21T00:00:00Z","article_type":"original","author":[{"first_name":"Sylwia","full_name":"Struk, Sylwia","last_name":"Struk"},{"last_name":"Braem","full_name":"Braem, Lukas","first_name":"Lukas"},{"last_name":"Matthys","first_name":"Cedrick","full_name":"Matthys, Cedrick"},{"first_name":"Alan","full_name":"Walton, Alan","last_name":"Walton"},{"full_name":"Vangheluwe, Nick","first_name":"Nick","last_name":"Vangheluwe"},{"full_name":"Van Praet, Stan","first_name":"Stan","last_name":"Van Praet"},{"last_name":"Jiang","first_name":"Lingxiang","full_name":"Jiang, Lingxiang"},{"id":"3028BD74-F248-11E8-B48F-1D18A9856A87","last_name":"Baster","full_name":"Baster, Pawel","first_name":"Pawel"},{"first_name":"Carolien","full_name":"De Cuyper, Carolien","last_name":"De Cuyper"},{"last_name":"Boyer","first_name":"Francois-Didier","full_name":"Boyer, Francois-Didier"},{"last_name":"Stes","full_name":"Stes, Elisabeth","first_name":"Elisabeth"},{"first_name":"Tom","full_name":"Beeckman, Tom","last_name":"Beeckman"},{"full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gevaert","first_name":"Kris","full_name":"Gevaert, Kris"},{"last_name":"Goormachtig","full_name":"Goormachtig, Sofie","first_name":"Sofie"}],"title":"Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density","date_created":"2021-12-28T11:44:18Z","issue":"1","publisher":"Oxford University Press","quality_controlled":"1","oa_version":"Published Version","date_updated":"2026-06-18T08:43:19Z","language":[{"iso":"eng"}],"keyword":["flavonols","MAX2","rac-Gr24","RNA-seq","root development","transcriptional regulation"],"_id":"10583","abstract":[{"text":"The synthetic strigolactone (SL) analog, rac-GR24, has been instrumental in studying the role of SLs as well as karrikins because it activates the receptors DWARF14 (D14) and KARRIKIN INSENSITIVE 2 (KAI2) of their signaling pathways, respectively. Treatment with rac-GR24 modifies the root architecture at different levels, such as decreasing the lateral root density (LRD), while promoting root hair elongation or flavonol accumulation. Previously, we have shown that the flavonol biosynthesis is transcriptionally activated in the root by rac-GR24 treatment, but, thus far, the molecular players involved in that response have remained unknown. To get an in-depth insight into the changes that occur after the compound is perceived by the roots, we compared the root transcriptomes of the wild type and the more axillary growth2 (max2) mutant, affected in both SL and karrikin signaling pathways, with and without rac-GR24 treatment. Quantitative reverse transcription (qRT)-PCR, reporter line analysis and mutant phenotyping indicated that the flavonol response and the root hair elongation are controlled by the ELONGATED HYPOCOTYL 5 (HY5) and MYB12 transcription factors, but HY5, in contrast to MYB12, affects the LRD as well. Furthermore, we identified the transcription factors TARGET OF MONOPTEROS 5 (TMO5) and TMO5 LIKE1 as negative and the Mediator complex as positive regulators of the rac-GR24 effect on LRD. Altogether, hereby, we get closer toward understanding the molecular mechanisms that underlay the rac-GR24 responses in the root.","lang":"eng"}],"page":"104-119","oa":1,"month":"01","citation":{"short":"S. Struk, L. Braem, C. Matthys, A. Walton, N. Vangheluwe, S. Van Praet, L. Jiang, P. Baster, C. De Cuyper, F.-D. Boyer, E. Stes, T. Beeckman, J. Friml, K. Gevaert, S. Goormachtig, Plant &#38; Cell Physiology 63 (2022) 104–119.","apa":"Struk, S., Braem, L., Matthys, C., Walton, A., Vangheluwe, N., Van Praet, S., … Goormachtig, S. (2022). Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density. <i>Plant &#38; Cell Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/pcp/pcab149\">https://doi.org/10.1093/pcp/pcab149</a>","ista":"Struk S, Braem L, Matthys C, Walton A, Vangheluwe N, Van Praet S, Jiang L, Baster P, De Cuyper C, Boyer F-D, Stes E, Beeckman T, Friml J, Gevaert K, Goormachtig S. 2022. Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density. Plant &#38; Cell Physiology. 63(1), 104–119.","chicago":"Struk, Sylwia, Lukas Braem, Cedrick Matthys, Alan Walton, Nick Vangheluwe, Stan Van Praet, Lingxiang Jiang, et al. “Transcriptional Analysis in the Arabidopsis Roots Reveals New Regulators That Link Rac-GR24 Treatment with Changes in Flavonol Accumulation, Root Hair Elongation and Lateral Root Density.” <i>Plant &#38; Cell Physiology</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/pcp/pcab149\">https://doi.org/10.1093/pcp/pcab149</a>.","ama":"Struk S, Braem L, Matthys C, et al. Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density. <i>Plant &#38; Cell Physiology</i>. 2022;63(1):104-119. doi:<a href=\"https://doi.org/10.1093/pcp/pcab149\">10.1093/pcp/pcab149</a>","mla":"Struk, Sylwia, et al. “Transcriptional Analysis in the Arabidopsis Roots Reveals New Regulators That Link Rac-GR24 Treatment with Changes in Flavonol Accumulation, Root Hair Elongation and Lateral Root Density.” <i>Plant &#38; Cell Physiology</i>, vol. 63, no. 1, Oxford University Press, 2022, pp. 104–19, doi:<a href=\"https://doi.org/10.1093/pcp/pcab149\">10.1093/pcp/pcab149</a>.","ieee":"S. Struk <i>et al.</i>, “Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density,” <i>Plant &#38; Cell Physiology</i>, vol. 63, no. 1. Oxford University Press, pp. 104–119, 2022."},"type":"journal_article"},{"intvolume":"        54","doi":"10.1146/annurev-fluid-022421-011319","acknowledgement":"C.M. gratefully acknowledges funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, grant agreement 805041). She also thanks Grand Équipement National de Calcul Intensif (GENCI), France, for providing access to their computing platforms at Très Grand Centre de Calcul (TGCC). J.O.H. gratefully acknowledges funding from the Villum Foundation (grant 13168), the ERC under the Horizon 2020 research and innovation program (grant 771859), and the Novo Nordisk Foundation's Interdisciplinary Synergy Program (grant NNF19OC0057374). G.C. gratefully acknowledges the support of the transregional collaborative research center (SFB/TRR 165) “Waves to Weather” (http://www.wavestoweather.de) funded by the German Research Foundation (DFG). D.Y. is supported by a Packard Fellowship in Science and Engineering, the France–Berkeley Fund, Laboratory Directed Research and Development (LDRD) funding from the Lawrence Berkeley National Laboratory, and the US Department of Energy, Office of Science, Office of Biological and Environmental Research, Climate and Environmental Sciences Division, Regional and Global Climate Modeling Program under award DE-AC02-05CH11231.","ddc":["550"],"volume":54,"scopus_import":"1","publication":"Annual Review of Fluid Mechanics","year":"2022","project":[{"_id":"629205d8-2b32-11ec-9570-e1356ff73576","grant_number":"805041","call_identifier":"H2020","name":"Organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate"}],"article_type":"original","date_published":"2022-01-01T00:00:00Z","title":"Spontaneous aggregation of convective storms","author":[{"full_name":"Muller, Caroline J","first_name":"Caroline J","orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller"},{"last_name":"Yang","first_name":"Da","full_name":"Yang, Da"},{"last_name":"Craig","full_name":"Craig, George","first_name":"George"},{"first_name":"Timothy","full_name":"Cronin, Timothy","last_name":"Cronin"},{"last_name":"Fildier","full_name":"Fildier, Benjamin","first_name":"Benjamin"},{"last_name":"Haerter","first_name":"Jan O.","full_name":"Haerter, Jan O."},{"first_name":"Cathy","full_name":"Hohenegger, Cathy","last_name":"Hohenegger"},{"last_name":"Mapes","full_name":"Mapes, Brian","first_name":"Brian"},{"first_name":"David","full_name":"Randall, David","last_name":"Randall"},{"last_name":"Shamekh","first_name":"Sara","full_name":"Shamekh, Sara"},{"full_name":"Sherwood, Steven C.","first_name":"Steven C.","last_name":"Sherwood"}],"date_created":"2022-01-23T23:01:29Z","ec_funded":1,"isi":1,"main_file_link":[{"url":"https://doi.org/10.1146/annurev-fluid-022421-011319","open_access":"1"}],"status":"public","day":"01","publication_identifier":{"eissn":["1545-4479"],"issn":["0066-4189"]},"department":[{"_id":"CaMu"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publication_status":"published","external_id":{"isi":["000794152800006"]},"abstract":[{"lang":"eng","text":"Idealized simulations of the tropical atmosphere have predicted that clouds can spontaneously clump together in space, despite perfectly homogeneous settings. This phenomenon has been called self-aggregation, and it results in a state where a moist cloudy region with intense deep convective storms is surrounded by extremely dry subsiding air devoid of deep clouds. We review here the main findings from theoretical work and idealized models of this phenomenon, highlighting the physical processes believed to play a key role in convective self-aggregation. We also review the growing literature on the importance and implications of this phenomenon for the tropical atmosphere, notably, for the hydrological cycle and for precipitation extremes, in our current and in a warming climate."}],"_id":"10656","citation":{"mla":"Muller, Caroline J., et al. “Spontaneous Aggregation of Convective Storms.” <i>Annual Review of Fluid Mechanics</i>, vol. 54, Annual Reviews, 2022, pp. 133–57, doi:<a href=\"https://doi.org/10.1146/annurev-fluid-022421-011319\">10.1146/annurev-fluid-022421-011319</a>.","ieee":"C. J. Muller <i>et al.</i>, “Spontaneous aggregation of convective storms,” <i>Annual Review of Fluid Mechanics</i>, vol. 54. Annual Reviews, pp. 133–157, 2022.","short":"C.J. Muller, D. Yang, G. Craig, T. Cronin, B. Fildier, J.O. Haerter, C. Hohenegger, B. Mapes, D. Randall, S. Shamekh, S.C. Sherwood, Annual Review of Fluid Mechanics 54 (2022) 133–157.","apa":"Muller, C. J., Yang, D., Craig, G., Cronin, T., Fildier, B., Haerter, J. O., … Sherwood, S. C. (2022). Spontaneous aggregation of convective storms. <i>Annual Review of Fluid Mechanics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-fluid-022421-011319\">https://doi.org/10.1146/annurev-fluid-022421-011319</a>","ama":"Muller CJ, Yang D, Craig G, et al. Spontaneous aggregation of convective storms. <i>Annual Review of Fluid Mechanics</i>. 2022;54:133-157. doi:<a href=\"https://doi.org/10.1146/annurev-fluid-022421-011319\">10.1146/annurev-fluid-022421-011319</a>","chicago":"Muller, Caroline J, Da Yang, George Craig, Timothy Cronin, Benjamin Fildier, Jan O. Haerter, Cathy Hohenegger, et al. “Spontaneous Aggregation of Convective Storms.” <i>Annual Review of Fluid Mechanics</i>. Annual Reviews, 2022. <a href=\"https://doi.org/10.1146/annurev-fluid-022421-011319\">https://doi.org/10.1146/annurev-fluid-022421-011319</a>.","ista":"Muller CJ, Yang D, Craig G, Cronin T, Fildier B, Haerter JO, Hohenegger C, Mapes B, Randall D, Shamekh S, Sherwood SC. 2022. Spontaneous aggregation of convective storms. Annual Review of Fluid Mechanics. 54, 133–157."},"month":"01","type":"journal_article","page":"133-157","oa":1,"oa_version":"Published Version","corr_author":"1","publisher":"Annual Reviews","quality_controlled":"1","language":[{"iso":"eng"}],"date_updated":"2026-06-18T08:46:40Z"},{"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"}],"external_id":{"pmid":["35018726"],"isi":["000761281200011"]},"publication_status":"published","isi":1,"status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jipb.13225"}],"publication_identifier":{"eissn":["1744-7909"],"issn":["1672-9072"]},"day":"01","volume":64,"year":"2022","publication":"Journal of Integrative Plant Biology","scopus_import":"1","pmid":1,"intvolume":"        64","ddc":["580"],"acknowledgement":"This research was financially supported by the National Natural Science Foundation of China and the Israel Science Foundation (NSFC-ISF; 32061143005), National Natural Science Foundation of China (32000225), Natural Science Foundation of Shandong Province (ZR2020QC036), and China Postdoctoral Science Foundation (2020M682165).\r\n","doi":"10.1111/jipb.13225","issue":"2","date_created":"2022-02-03T09:52:59Z","author":[{"last_name":"Yu","full_name":"Yu, Z","first_name":"Z"},{"first_name":"F","full_name":"Zhang, F","last_name":"Zhang"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří"},{"last_name":"Ding","full_name":"Ding, Z","first_name":"Z"}],"title":"Auxin signaling: Research advances over the past 30 years","article_type":"review","date_published":"2022-02-01T00:00:00Z","date_updated":"2026-06-18T08:47:21Z","language":[{"iso":"eng"}],"corr_author":"1","oa_version":"Published Version","quality_controlled":"1","publisher":"Wiley","month":"02","citation":{"ieee":"Z. Yu, F. Zhang, J. Friml, and Z. Ding, “Auxin signaling: Research advances over the past 30 years,” <i>Journal of Integrative Plant Biology</i>, vol. 64, no. 2. Wiley, pp. 371–392, 2022.","mla":"Yu, Z., et al. “Auxin Signaling: Research Advances over the Past 30 Years.” <i>Journal of Integrative Plant Biology</i>, vol. 64, no. 2, Wiley, 2022, pp. 371–92, doi:<a href=\"https://doi.org/10.1111/jipb.13225\">10.1111/jipb.13225</a>.","ama":"Yu Z, Zhang F, Friml J, Ding Z. Auxin signaling: Research advances over the past 30 years. <i>Journal of Integrative Plant Biology</i>. 2022;64(2):371-392. doi:<a href=\"https://doi.org/10.1111/jipb.13225\">10.1111/jipb.13225</a>","chicago":"Yu, Z, F Zhang, Jiří Friml, and Z Ding. “Auxin Signaling: Research Advances over the Past 30 Years.” <i>Journal of Integrative Plant Biology</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/jipb.13225\">https://doi.org/10.1111/jipb.13225</a>.","ista":"Yu Z, Zhang F, Friml J, Ding Z. 2022. Auxin signaling: Research advances over the past 30 years. Journal of Integrative Plant Biology. 64(2), 371–392.","short":"Z. Yu, F. Zhang, J. Friml, Z. Ding, Journal of Integrative Plant Biology 64 (2022) 371–392.","apa":"Yu, Z., Zhang, F., Friml, J., &#38; Ding, Z. (2022). Auxin signaling: Research advances over the past 30 years. <i>Journal of Integrative Plant Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jipb.13225\">https://doi.org/10.1111/jipb.13225</a>"},"type":"journal_article","oa":1,"page":"371-392","abstract":[{"lang":"eng","text":"Auxin, one of the first identified and most widely studied phytohormones, has been and will remain a hot topic in plant biology. After more than a century of passionate exploration, the mysteries of its synthesis, transport, signaling, and metabolism have largely been unlocked. Due to the rapid development of new technologies, new methods, and new genetic materials, the study of auxin has entered the fast lane over the past 30 years. Here, we highlight advances in understanding auxin signaling, including auxin perception, rapid auxin responses, TRANSPORT INHIBITOR RESPONSE 1 and AUXIN SIGNALING F-boxes (TIR1/AFBs)-mediated transcriptional and non-transcriptional branches, and the epigenetic regulation of auxin signaling. We also focus on feedback inhibition mechanisms that prevent the over-amplification of auxin signals. In addition, we cover the TRANSMEMBRANE KINASEs (TMKs)-mediated non-canonical signaling, which converges with TIR1/AFBs-mediated transcriptional regulation to coordinate plant growth and development. The identification of additional auxin signaling components and their regulation will continue to open new avenues of research in this field, leading to an increasingly deeper, more comprehensive understanding of how auxin signals are interpreted at the cellular level to regulate plant growth and development."}],"_id":"10719"},{"date_updated":"2026-06-18T08:47:45Z","language":[{"iso":"eng"}],"publisher":"Elsevier","quality_controlled":"1","oa_version":"Published Version","corr_author":"1","page":"361-362","oa":1,"citation":{"ieee":"B. J. Confavreux and T. P. Vogels, “A familiar thought: Machines that replace us?,” <i>Neuron</i>, vol. 110, no. 3. Elsevier, pp. 361–362, 2022.","mla":"Confavreux, Basile J., and Tim P. Vogels. “A Familiar Thought: Machines That Replace Us?” <i>Neuron</i>, vol. 110, no. 3, Elsevier, 2022, pp. 361–62, doi:<a href=\"https://doi.org/10.1016/j.neuron.2022.01.014\">10.1016/j.neuron.2022.01.014</a>.","chicago":"Confavreux, Basile J, and Tim P Vogels. “A Familiar Thought: Machines That Replace Us?” <i>Neuron</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.neuron.2022.01.014\">https://doi.org/10.1016/j.neuron.2022.01.014</a>.","ista":"Confavreux BJ, Vogels TP. 2022. A familiar thought: Machines that replace us? Neuron. 110(3), 361–362.","ama":"Confavreux BJ, Vogels TP. A familiar thought: Machines that replace us? <i>Neuron</i>. 2022;110(3):361-362. doi:<a href=\"https://doi.org/10.1016/j.neuron.2022.01.014\">10.1016/j.neuron.2022.01.014</a>","apa":"Confavreux, B. J., &#38; Vogels, T. P. (2022). A familiar thought: Machines that replace us? <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2022.01.014\">https://doi.org/10.1016/j.neuron.2022.01.014</a>","short":"B.J. Confavreux, T.P. Vogels, Neuron 110 (2022) 361–362."},"type":"journal_article","month":"02","_id":"10753","abstract":[{"text":"This is a comment on \"Meta-learning synaptic plasticity and memory addressing for continual familiarity detection.\" Neuron. 2022 Feb 2;110(3):544-557.e8.","lang":"eng"}],"publication_status":"published","external_id":{"isi":["000751819100005"],"pmid":["35114107"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"TiVo"}],"article_processing_charge":"No","publication_identifier":{"eissn":["1097-4199"]},"day":"02","main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2022.01.014","open_access":"1"}],"isi":1,"status":"public","date_created":"2022-02-13T23:01:34Z","author":[{"last_name":"Confavreux","id":"C7610134-B532-11EA-BD9F-F5753DDC885E","full_name":"Confavreux, Basile J","first_name":"Basile J"},{"last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","first_name":"Tim P","full_name":"Vogels, Tim P"}],"title":"A familiar thought: Machines that replace us?","issue":"3","date_published":"2022-02-02T00:00:00Z","article_type":"letter_note","pmid":1,"scopus_import":"1","publication":"Neuron","year":"2022","volume":110,"doi":"10.1016/j.neuron.2022.01.014","ddc":["570"],"intvolume":"       110"},{"pmid":1,"scopus_import":"1","year":"2022","publication":"Microscopy","volume":71,"acknowledgement":"European Research Council Advanced Grant (694539 to R.S.).","doi":"10.1093/jmicro/dfab048","ddc":["570"],"intvolume":"        71","date_created":"2022-03-20T23:01:39Z","title":"Electron microscopic visualization of single molecules by tag-mediated metal particle labeling","author":[{"first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444"}],"ec_funded":1,"issue":"Supplement_1","date_published":"2022-03-01T00:00:00Z","project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539","call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour"}],"article_type":"original","publication_status":"published","external_id":{"pmid":["35275179"],"isi":["000768384100011"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"RySh"}],"day":"01","publication_identifier":{"eissn":["2050-5701"],"issn":["2050-5698"]},"main_file_link":[{"url":"https://doi.org/10.1093/jmicro/dfab048","open_access":"1"}],"status":"public","isi":1,"page":"i72-i80","oa":1,"month":"03","citation":{"ieee":"R. Shigemoto, “Electron microscopic visualization of single molecules by tag-mediated metal particle labeling,” <i>Microscopy</i>, vol. 71, no. Supplement_1. Oxford University Press, pp. i72–i80, 2022.","mla":"Shigemoto, Ryuichi. “Electron Microscopic Visualization of Single Molecules by Tag-Mediated Metal Particle Labeling.” <i>Microscopy</i>, vol. 71, no. Supplement_1, Oxford University Press, 2022, pp. i72–80, doi:<a href=\"https://doi.org/10.1093/jmicro/dfab048\">10.1093/jmicro/dfab048</a>.","ama":"Shigemoto R. Electron microscopic visualization of single molecules by tag-mediated metal particle labeling. <i>Microscopy</i>. 2022;71(Supplement_1):i72-i80. doi:<a href=\"https://doi.org/10.1093/jmicro/dfab048\">10.1093/jmicro/dfab048</a>","chicago":"Shigemoto, Ryuichi. “Electron Microscopic Visualization of Single Molecules by Tag-Mediated Metal Particle Labeling.” <i>Microscopy</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/jmicro/dfab048\">https://doi.org/10.1093/jmicro/dfab048</a>.","ista":"Shigemoto R. 2022. Electron microscopic visualization of single molecules by tag-mediated metal particle labeling. Microscopy. 71(Supplement_1), i72–i80.","apa":"Shigemoto, R. (2022). Electron microscopic visualization of single molecules by tag-mediated metal particle labeling. <i>Microscopy</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jmicro/dfab048\">https://doi.org/10.1093/jmicro/dfab048</a>","short":"R. Shigemoto, Microscopy 71 (2022) i72–i80."},"type":"journal_article","_id":"10889","abstract":[{"lang":"eng","text":"Genetically encoded tags have introduced extensive lines of application from purification of tagged proteins to their visualization at the single molecular, cellular, histological and whole-body levels. Combined with other rapidly developing technologies such as clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, proteomics, super-resolution microscopy and proximity labeling, a large variety of genetically encoded tags have been developed in the last two decades. In this review, I focus on the current status of tag development for electron microscopic (EM) visualization of proteins with metal particle labeling. Compared with conventional immunoelectron microscopy using gold particles, tag-mediated metal particle labeling has several advantages that could potentially improve the sensitivity, spatial and temporal resolution, and applicability to a wide range of proteins of interest (POIs). It may enable researchers to detect single molecules in situ, allowing the quantitative measurement of absolute numbers and exact localization patterns of POI in the ultrastructural context. Thus, genetically encoded tags for EM could revolutionize the field as green fluorescence protein did for light microscopy, although we still have many challenges to overcome before reaching this goal."}],"language":[{"iso":"eng"}],"date_updated":"2026-06-18T10:44:57Z","publisher":"Oxford University Press","quality_controlled":"1","oa_version":"Published Version","corr_author":"1"},{"article_type":"original","date_published":"2022-02-19T00:00:00Z","issue":"5","title":"MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications","author":[{"first_name":"Murat","full_name":"Artan, Murat","last_name":"Artan","id":"C407B586-6052-11E9-B3AE-7006E6697425","orcid":"0000-0001-8945-6992"},{"full_name":"Sohn, Jooyeon","first_name":"Jooyeon","last_name":"Sohn"},{"first_name":"Cheolju","full_name":"Lee, Cheolju","last_name":"Lee"},{"first_name":"Seung Yeol","full_name":"Park, Seung Yeol","last_name":"Park"},{"last_name":"Lee","full_name":"Lee, Seung Jae V.","first_name":"Seung Jae V."}],"date_created":"2022-03-13T23:01:47Z","intvolume":"        18","acknowledgement":"This work is funded by National Research Foundation of Korea (NRF) grants NRF-2019R1A3B2067745 from the Korean Government (Ministry of Science and Information and Communications Technology (S-J.V.L.). NRF-2017R1A5A1015366 (S.Y.P, S-J.V.L). Korea Institute of Science and Technology (KIST) intramural grant (C.L).","doi":"10.1080/15548627.2022.2039523","ddc":["570"],"volume":18,"scopus_import":"1","pmid":1,"year":"2022","publication":"Autophagy","isi":1,"main_file_link":[{"url":"https://doi.org/10.1080/15548627.2022.2039523","open_access":"1"}],"status":"public","publication_identifier":{"eissn":["1554-8635"],"issn":["1554-8627"]},"day":"19","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MaDe"}],"publication_status":"published","external_id":{"pmid":["35188063"],"isi":["000758859600001"]},"abstract":[{"lang":"eng","text":"The Golgi apparatus regulates the process of modification and subcellular localization of macromolecules, including proteins and lipids. Aberrant protein sorting caused by defects in the Golgi leads to various diseases in mammals. However, the role of the Golgi apparatus in organismal longevity remained largely unknown. By employing a quantitative proteomic approach, we demonstrated that MON-2, an evolutionarily conserved Arf-GEF protein implicated in Golgi-to-endosome trafficking, promotes longevity via upregulating macroautophagy/autophagy in C. elegans. Our data using cultured mammalian cells indicate that MON2 translocates from the Golgi to the endosome under starvation conditions, subsequently increasing autophagic flux by binding LGG-1/GABARAPL2. Thus, Golgi-to-endosome trafficking appears to be an evolutionarily conserved process for the upregulation of autophagy, which contributes to organismal longevity."}],"_id":"10846","month":"02","type":"journal_article","citation":{"apa":"Artan, M., Sohn, J., Lee, C., Park, S. Y., &#38; Lee, S. J. V. (2022). MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications. <i>Autophagy</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/15548627.2022.2039523\">https://doi.org/10.1080/15548627.2022.2039523</a>","short":"M. Artan, J. Sohn, C. Lee, S.Y. Park, S.J.V. Lee, Autophagy 18 (2022) 1208–1210.","ama":"Artan M, Sohn J, Lee C, Park SY, Lee SJV. MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications. <i>Autophagy</i>. 2022;18(5):1208-1210. doi:<a href=\"https://doi.org/10.1080/15548627.2022.2039523\">10.1080/15548627.2022.2039523</a>","ista":"Artan M, Sohn J, Lee C, Park SY, Lee SJV. 2022. MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications. Autophagy. 18(5), 1208–1210.","chicago":"Artan, Murat, Jooyeon Sohn, Cheolju Lee, Seung Yeol Park, and Seung Jae V. Lee. “MON-2, a Golgi Protein, Promotes Longevity by Upregulating Autophagy through Mediating Inter-Organelle Communications.” <i>Autophagy</i>. Taylor &#38; Francis, 2022. <a href=\"https://doi.org/10.1080/15548627.2022.2039523\">https://doi.org/10.1080/15548627.2022.2039523</a>.","mla":"Artan, Murat, et al. “MON-2, a Golgi Protein, Promotes Longevity by Upregulating Autophagy through Mediating Inter-Organelle Communications.” <i>Autophagy</i>, vol. 18, no. 5, Taylor &#38; Francis, 2022, pp. 1208–10, doi:<a href=\"https://doi.org/10.1080/15548627.2022.2039523\">10.1080/15548627.2022.2039523</a>.","ieee":"M. Artan, J. Sohn, C. Lee, S. Y. Park, and S. J. V. Lee, “MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications,” <i>Autophagy</i>, vol. 18, no. 5. Taylor &#38; Francis, pp. 1208–1210, 2022."},"page":"1208-1210","oa":1,"oa_version":"Published Version","publisher":"Taylor & Francis","quality_controlled":"1","date_updated":"2026-06-18T10:40:40Z","language":[{"iso":"eng"}]},{"ec_funded":1,"author":[{"first_name":"Sergey","full_name":"Knyazev, Sergey","last_name":"Knyazev"},{"full_name":"Chhugani, Karishma","first_name":"Karishma","last_name":"Chhugani"},{"last_name":"Sarwal","first_name":"Varuni","full_name":"Sarwal, Varuni"},{"full_name":"Ayyala, Ram","first_name":"Ram","last_name":"Ayyala"},{"last_name":"Singh","full_name":"Singh, Harman","first_name":"Harman"},{"full_name":"Karthikeyan, Smruthi","first_name":"Smruthi","last_name":"Karthikeyan"},{"last_name":"Deshpande","first_name":"Dhrithi","full_name":"Deshpande, Dhrithi"},{"last_name":"Baykal","first_name":"Pelin Icer","full_name":"Baykal, Pelin Icer"},{"full_name":"Comarova, Zoia","first_name":"Zoia","last_name":"Comarova"},{"full_name":"Lu, Angela","first_name":"Angela","last_name":"Lu"},{"first_name":"Yuri","full_name":"Porozov, Yuri","last_name":"Porozov"},{"first_name":"Tetyana I.","full_name":"Vasylyeva, Tetyana I.","last_name":"Vasylyeva"},{"last_name":"Wertheim","first_name":"Joel O.","full_name":"Wertheim, Joel O."},{"first_name":"Braden T.","full_name":"Tierney, Braden T.","last_name":"Tierney"},{"full_name":"Chiu, Charles Y.","first_name":"Charles Y.","last_name":"Chiu"},{"full_name":"Sun, Ren","first_name":"Ren","last_name":"Sun"},{"last_name":"Wu","first_name":"Aiping","full_name":"Wu, Aiping"},{"first_name":"Malak S.","full_name":"Abedalthagafi, Malak S.","last_name":"Abedalthagafi"},{"full_name":"Pak, Victoria M.","first_name":"Victoria M.","last_name":"Pak"},{"last_name":"Nagaraj","full_name":"Nagaraj, Shivashankar H.","first_name":"Shivashankar H."},{"last_name":"Smith","full_name":"Smith, Adam L.","first_name":"Adam L."},{"last_name":"Skums","full_name":"Skums, Pavel","first_name":"Pavel"},{"last_name":"Pasaniuc","full_name":"Pasaniuc, Bogdan","first_name":"Bogdan"},{"full_name":"Komissarov, Andrey","first_name":"Andrey","last_name":"Komissarov"},{"first_name":"Christopher E.","full_name":"Mason, Christopher E.","last_name":"Mason"},{"last_name":"Bortz","first_name":"Eric","full_name":"Bortz, Eric"},{"full_name":"Lemey, Philippe","first_name":"Philippe","last_name":"Lemey"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","first_name":"Fyodor"},{"full_name":"Beerenwinkel, Niko","first_name":"Niko","last_name":"Beerenwinkel"},{"last_name":"Lam","first_name":"Tommy Tsan Yuk","full_name":"Lam, Tommy Tsan Yuk"},{"last_name":"Wu","first_name":"Nicholas C.","full_name":"Wu, Nicholas C."},{"last_name":"Zelikovsky","first_name":"Alex","full_name":"Zelikovsky, Alex"},{"last_name":"Knight","full_name":"Knight, Rob","first_name":"Rob"},{"full_name":"Crandall, Keith A.","first_name":"Keith A.","last_name":"Crandall"},{"last_name":"Mangul","first_name":"Serghei","full_name":"Mangul, Serghei"}],"date_created":"2022-04-17T22:01:48Z","title":"Unlocking capacities of genomics for the COVID-19 response and future pandemics","issue":"4","date_published":"2022-04-08T00:00:00Z","article_type":"letter_note","project":[{"grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020"}],"publication":"Nature Methods","year":"2022","scopus_import":"1","pmid":1,"volume":19,"ddc":["570"],"acknowledgement":"Our paper is dedicated to all freedom-loving people around the world, and to the people of Ukraine who fight for our freedom. We thank William M. Switzer and Ellsworth M. Campbell from the Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA, for discussions and suggestions. We thank Jason Ladner from the Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, for providing suggestions and feedback. S.M. was partially supported by National Science Foundation grants 2041984. T.L. is supported by the NSFC Excellent Young Scientists Fund (Hong Kong and Macau; 31922087), Research Grants Council (RGC) Collaborative Research Fund (C7144-20GF), RGC Research Impact Fund (R7021-20), Innovation and Technology Commission’s InnoHK funding (D24H) and Health and Medical Research Fund (COVID190223). P.S. was supported by US National Institutes of Health (NIH) grant 1R01EB025022 and National Science Foundation (NSF) grant 2047828. M.A. acknowledges King Abdulaziz City for Science and Technology and the Saudi Human Genome Project for technical and financial support (https://shgp.kacst.edu.sa) N.W. was supported by US NIH grants R00 AI139445, DP2 AT011966 and R01 AI167910. A.S. acknowledge funding from NSF grant no. 2029025. A.Z. has been partially supported by NIH grants 1R01EB025022-01 and 1R21CA241044-01A1. S. Knyazev has been partly supported by Molecular Basis of Disease at Georgia State University and NIH awards R01 HG009120, R01 MH115676, R01 AI153827 and U01 HG011715. A.W. has been supported by the CAMS Innovation Fund for Medical Sciences (2021-I2M-1-061). R.K. was supported by NSF project 2038509, RAPID: Improving QIIME 2 and UniFrac for Viruses to Respond to COVID-19, CDC project 30055281 with Scripps led by Kristian Andersen, Genomic sequencing of SARS-CoV-2 to investigate local and cross-border emergence and spread. J.O.W. was supported by NIH–National Institute of Allergy and Infectious Diseases (NIAID) R01 AI135992 and receives funding from the CDC unrelated to this work. T.I.V. is supported by the Branco Weiss Fellowship. Y.P. was supported by the Ministry of Science and Higher Education of the Russian Federation within the framework of state support for the creation and development of World-Class Research Centers “Digital biodesign and personalized healthcare” N◦075-15-2020-926. E.B. was supported by a US National Institute of General Medical Sciences IDeA Alaska INBRE (P20GM103395) and NIAID CEIRR (75N93019R00028). C.E.M. thanks Testing for America (501c3), OpenCovidScreen Foundation, Igor Tulchinsky and the WorldQuant Foundation, Bill Ackman and Olivia Flatto and the Pershing Square Foundation, Ken Griffin and Citadel, the US National Institutes of Health (R01AI125416, R01AI151059, R21AI129851, U01DA053941), and the Alfred P. Sloan Foundation (G-2015-13964). C.Y.C. is supported by US CDC Epidemiology and Laboratory Capacity (ELC) for Infectious Diseases grant 6NU50CK000539 to the California Department of Public Health, the Innovative Genomics Institute (IGI) at the University of California, Berkeley, and University of California, San Francisco, NIH grant R33AI12945 and US CDC contract 75D30121C10991. A.K. was partly supported by RFBR grant 20-515-80017. P.L. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. ~725422 - ReservoirDOCS), the Wellcome Trust through project 206298/Z/17/Z (Artic Network) and NIH grants R01 AI153044 and U19 AI135995. K.C. acknowledges support from the US NSF award EEID-IOS-2109688. F.K.’s work was supported by an ERC Consolidator grant to F.K. (771209–CharFL).","doi":"10.1038/s41592-022-01444-z","intvolume":"        19","external_id":{"isi":["000781199600011"],"pmid":["35396471"]},"publication_status":"published","article_processing_charge":"No","department":[{"_id":"FyKo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"08","publication_identifier":{"eissn":["1548-7105"],"issn":["1548-7091"]},"isi":1,"status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41592-022-01444-z"}],"oa":1,"page":"374-380","month":"04","type":"journal_article","citation":{"short":"S. Knyazev, K. Chhugani, V. Sarwal, R. Ayyala, H. Singh, S. Karthikeyan, D. Deshpande, P.I. Baykal, Z. Comarova, A. Lu, Y. Porozov, T.I. Vasylyeva, J.O. Wertheim, B.T. Tierney, C.Y. Chiu, R. Sun, A. Wu, M.S. Abedalthagafi, V.M. Pak, S.H. Nagaraj, A.L. Smith, P. Skums, B. Pasaniuc, A. Komissarov, C.E. Mason, E. Bortz, P. Lemey, F. Kondrashov, N. Beerenwinkel, T.T.Y. Lam, N.C. Wu, A. Zelikovsky, R. Knight, K.A. Crandall, S. Mangul, Nature Methods 19 (2022) 374–380.","apa":"Knyazev, S., Chhugani, K., Sarwal, V., Ayyala, R., Singh, H., Karthikeyan, S., … Mangul, S. (2022). Unlocking capacities of genomics for the COVID-19 response and future pandemics. <i>Nature Methods</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41592-022-01444-z\">https://doi.org/10.1038/s41592-022-01444-z</a>","ama":"Knyazev S, Chhugani K, Sarwal V, et al. Unlocking capacities of genomics for the COVID-19 response and future pandemics. <i>Nature Methods</i>. 2022;19(4):374-380. doi:<a href=\"https://doi.org/10.1038/s41592-022-01444-z\">10.1038/s41592-022-01444-z</a>","chicago":"Knyazev, Sergey, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh, Smruthi Karthikeyan, Dhrithi Deshpande, et al. “Unlocking Capacities of Genomics for the COVID-19 Response and Future Pandemics.” <i>Nature Methods</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41592-022-01444-z\">https://doi.org/10.1038/s41592-022-01444-z</a>.","ista":"Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel N, Lam TTY, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. 2022. Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nature Methods. 19(4), 374–380.","ieee":"S. Knyazev <i>et al.</i>, “Unlocking capacities of genomics for the COVID-19 response and future pandemics,” <i>Nature Methods</i>, vol. 19, no. 4. Springer Nature, pp. 374–380, 2022.","mla":"Knyazev, Sergey, et al. “Unlocking Capacities of Genomics for the COVID-19 Response and Future Pandemics.” <i>Nature Methods</i>, vol. 19, no. 4, Springer Nature, 2022, pp. 374–80, doi:<a href=\"https://doi.org/10.1038/s41592-022-01444-z\">10.1038/s41592-022-01444-z</a>."},"_id":"11187","abstract":[{"text":"During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, facilitated the development of testing methods and allowed the timely tracking of novel SARS-CoV-2 variants. Yet the virtually unlimited potential for rapid generation and analysis of genomic data is also coupled with unique technical, scientific and organizational challenges. Here, we discuss the application of genomic and computational methods for efficient data-driven COVID-19 response, the advantages of the democratization of viral sequencing around the world and the challenges associated with viral genome data collection and processing.","lang":"eng"}],"date_updated":"2026-06-18T10:47:32Z","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Springer Nature","oa_version":"Published Version"},{"abstract":[{"text":"Direct numerical simulations (DNS) of turbulent channel flows up to  Reτ≈1000  are conducted to investigate the three-dimensional (consisting of streamwise wavenumber, spanwise wavenumber and frequency) spectrum of wall pressure fluctuations. To develop a predictive model of the wavenumber–frequency spectrum from the wavenumber spectrum, the time decorrelation mechanisms of wall pressure fluctuations are investigated. It is discovered that the energy-containing part of the wavenumber–frequency spectrum of wall pressure fluctuations can be well predicted using a similar random sweeping model for streamwise velocity fluctuations. To refine the investigation, we further decompose the spectrum of the total wall pressure fluctuations into the autospectra of rapid and slow pressure fluctuations, and the cross-spectrum between them. We focus on evaluating the assumption applied in many predictive models, that is, the magnitude of the cross-spectrum is negligibly small. The present DNS shows that neglecting the cross-spectrum causes a maximum error up to 4.7 dB in the subconvective region for all Reynolds numbers under test. Our analyses indicate that the approximation of neglecting the cross-spectrum needs to be applied carefully in the investigations of acoustics at low Mach numbers, in which the subconvective components of wall pressure fluctuations make important contributions to the radiated acoustic power.","lang":"eng"}],"_id":"10925","type":"journal_article","month":"04","citation":{"short":"B. Yang, Z. Yang, Journal of Fluid Mechanics 937 (2022).","apa":"Yang, B., &#38; Yang, Z. (2022). On the wavenumber-frequency spectrum of the wall pressure fluctuations in turbulent channel flow. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2022.137\">https://doi.org/10.1017/jfm.2022.137</a>","ama":"Yang B, Yang Z. On the wavenumber-frequency spectrum of the wall pressure fluctuations in turbulent channel flow. <i>Journal of Fluid Mechanics</i>. 2022;937. doi:<a href=\"https://doi.org/10.1017/jfm.2022.137\">10.1017/jfm.2022.137</a>","ista":"Yang B, Yang Z. 2022. On the wavenumber-frequency spectrum of the wall pressure fluctuations in turbulent channel flow. Journal of Fluid Mechanics. 937, A39.","chicago":"Yang, Bowen, and Zixuan Yang. “On the Wavenumber-Frequency Spectrum of the Wall Pressure Fluctuations in Turbulent Channel Flow.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2022. <a href=\"https://doi.org/10.1017/jfm.2022.137\">https://doi.org/10.1017/jfm.2022.137</a>.","ieee":"B. Yang and Z. Yang, “On the wavenumber-frequency spectrum of the wall pressure fluctuations in turbulent channel flow,” <i>Journal of Fluid Mechanics</i>, vol. 937. Cambridge University Press, 2022.","mla":"Yang, Bowen, and Zixuan Yang. “On the Wavenumber-Frequency Spectrum of the Wall Pressure Fluctuations in Turbulent Channel Flow.” <i>Journal of Fluid Mechanics</i>, vol. 937, A39, Cambridge University Press, 2022, doi:<a href=\"https://doi.org/10.1017/jfm.2022.137\">10.1017/jfm.2022.137</a>."},"oa":1,"arxiv":1,"oa_version":"Published Version","publisher":"Cambridge University Press","quality_controlled":"1","date_updated":"2026-06-18T10:46:00Z","language":[{"iso":"eng"}],"article_type":"original","date_published":"2022-04-25T00:00:00Z","article_number":"A39","date_created":"2022-03-27T22:01:45Z","title":"On the wavenumber-frequency spectrum of the wall pressure fluctuations in turbulent channel flow","author":[{"first_name":"Bowen","full_name":"Yang, Bowen","last_name":"Yang","id":"71b6ff4b-15b2-11ec-abd3-aef6b028cf7e","orcid":"0000-0002-4843-6853"},{"last_name":"Yang","first_name":"Zixuan","full_name":"Yang, Zixuan"}],"intvolume":"       937","doi":"10.1017/jfm.2022.137","acknowledgement":"This research is supported by the NSFC Basic Science Center Program for ‘Multiscale Problems in Nonlinear Mechanics’ (no. 11988102), National Key Project (GJXM92579) and the Strategic Priority Research Program (XDB22040104).","ddc":["530"],"volume":937,"scopus_import":"1","year":"2022","publication":"Journal of Fluid Mechanics","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/jfm.2022.137"}],"isi":1,"day":"25","publication_identifier":{"issn":["0022-1120"],"eissn":["1469-7645"]},"department":[{"_id":"GradSch"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publication_status":"published","external_id":{"arxiv":["2201.04702"],"isi":["000763547000001"]}},{"volume":28,"publication":"Chemistry - A European Journal","year":"2022","pmid":1,"scopus_import":"1","intvolume":"        28","ddc":["570"],"doi":"10.1002/chem.202200807","issue":"30","article_number":"e202200807","title":"Dynamic control of microbial movement by photoswitchable ATP antagonists","author":[{"last_name":"Thayyil","full_name":"Thayyil, Sampreeth","first_name":"Sampreeth"},{"last_name":"Nishigami","full_name":"Nishigami, Yukinori","first_name":"Yukinori"},{"full_name":"Islam, Muhammad J","first_name":"Muhammad J","id":"C94881D2-008F-11EA-8E08-2637E6697425","last_name":"Islam"},{"first_name":"P. K.","full_name":"Hashim, P. K.","last_name":"Hashim"},{"first_name":"Ken'Ya","full_name":"Furuta, Ken'Ya","last_name":"Furuta"},{"last_name":"Oiwa","full_name":"Oiwa, Kazuhiro","first_name":"Kazuhiro"},{"last_name":"Yu","full_name":"Yu, Jian","first_name":"Jian"},{"full_name":"Yao, Min","first_name":"Min","last_name":"Yao"},{"last_name":"Nakagaki","first_name":"Toshiyuki","full_name":"Nakagaki, Toshiyuki"},{"full_name":"Tamaoki, Nobuyuki","first_name":"Nobuyuki","last_name":"Tamaoki"}],"date_created":"2022-04-24T22:01:44Z","article_type":"original","date_published":"2022-05-25T00:00:00Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"RySh"}],"external_id":{"pmid":["35332959"],"isi":["000781658800001"]},"publication_status":"published","status":"public","main_file_link":[{"url":"https://doi.org/10.1002/chem.202200807","open_access":"1"}],"isi":1,"day":"25","publication_identifier":{"issn":["0947-6539"],"eissn":["1521-3765"]},"citation":{"short":"S. Thayyil, Y. Nishigami, M.J. Islam, P.K. Hashim, K. Furuta, K. Oiwa, J. Yu, M. Yao, T. Nakagaki, N. Tamaoki, Chemistry - A European Journal 28 (2022).","apa":"Thayyil, S., Nishigami, Y., Islam, M. J., Hashim, P. K., Furuta, K., Oiwa, K., … Tamaoki, N. (2022). Dynamic control of microbial movement by photoswitchable ATP antagonists. <i>Chemistry - A European Journal</i>. Wiley. <a href=\"https://doi.org/10.1002/chem.202200807\">https://doi.org/10.1002/chem.202200807</a>","ama":"Thayyil S, Nishigami Y, Islam MJ, et al. Dynamic control of microbial movement by photoswitchable ATP antagonists. <i>Chemistry - A European Journal</i>. 2022;28(30). doi:<a href=\"https://doi.org/10.1002/chem.202200807\">10.1002/chem.202200807</a>","chicago":"Thayyil, Sampreeth, Yukinori Nishigami, Muhammad J Islam, P. K. Hashim, Ken’Ya Furuta, Kazuhiro Oiwa, Jian Yu, Min Yao, Toshiyuki Nakagaki, and Nobuyuki Tamaoki. “Dynamic Control of Microbial Movement by Photoswitchable ATP Antagonists.” <i>Chemistry - A European Journal</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/chem.202200807\">https://doi.org/10.1002/chem.202200807</a>.","ista":"Thayyil S, Nishigami Y, Islam MJ, Hashim PK, Furuta K, Oiwa K, Yu J, Yao M, Nakagaki T, Tamaoki N. 2022. Dynamic control of microbial movement by photoswitchable ATP antagonists. Chemistry - A European Journal. 28(30), e202200807.","ieee":"S. Thayyil <i>et al.</i>, “Dynamic control of microbial movement by photoswitchable ATP antagonists,” <i>Chemistry - A European Journal</i>, vol. 28, no. 30. Wiley, 2022.","mla":"Thayyil, Sampreeth, et al. “Dynamic Control of Microbial Movement by Photoswitchable ATP Antagonists.” <i>Chemistry - A European Journal</i>, vol. 28, no. 30, e202200807, Wiley, 2022, doi:<a href=\"https://doi.org/10.1002/chem.202200807\">10.1002/chem.202200807</a>."},"month":"05","type":"journal_article","oa":1,"abstract":[{"lang":"eng","text":"Adenosine triphosphate (ATP) is the energy source for various biochemical processes and biomolecular motors in living things. Development of ATP antagonists and their stimuli-controlled actions offer a novel approach to regulate biological processes. Herein, we developed azobenzene-based photoswitchable ATP antagonists for controlling the activity of motor proteins; cytoplasmic and axonemal dyneins. The new ATP antagonists showed reversible photoswitching of cytoplasmic dynein activity in an in vitro dynein-microtubule system due to the trans and cis photoisomerization of their azobenzene segment. Importantly, our ATP antagonists reversibly regulated the axonemal dynein motor activity for the force generation in a demembranated model of Chlamydomonas reinhardtii. We found that the trans and cis isomers of ATP antagonists significantly differ in their affinity to the ATP binding site."}],"_id":"11333","language":[{"iso":"eng"}],"date_updated":"2026-06-18T10:49:46Z","oa_version":"Published Version","quality_controlled":"1","publisher":"Wiley"},{"date_published":"2022-06-15T00:00:00Z","article_type":"original","project":[{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","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"}],"ec_funded":1,"author":[{"last_name":"Anderson","full_name":"Anderson, Donovan J.","first_name":"Donovan J."},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","orcid":"0000-0002-7462-0048","first_name":"Florian","full_name":"Pauler, Florian"},{"full_name":"Mckenna, Aaron","first_name":"Aaron","last_name":"Mckenna"},{"last_name":"Shendure","first_name":"Jay","full_name":"Shendure, Jay"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Horwitz","first_name":"Marshall S.","full_name":"Horwitz, Marshall S."}],"title":"Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development","date_created":"2022-06-19T22:01:57Z","issue":"6","ddc":["570"],"doi":"10.1016/j.cels.2022.03.006","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.","intvolume":"        13","year":"2022","publication":"Cell Systems","scopus_import":"1","pmid":1,"volume":13,"publication_identifier":{"eissn":["2405-4720"],"issn":["2405-4712"]},"day":"15","status":"public","main_file_link":[{"url":"https://doi.org/10.1016/j.cels.2022.03.006","open_access":"1"}],"isi":1,"external_id":{"pmid":["35452605"],"isi":["000814124400002"]},"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","department":[{"_id":"SiHi"}],"_id":"11449","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"}],"oa":1,"page":"438-453.e5","month":"06","citation":{"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>","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>.","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.","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>."},"type":"journal_article","quality_controlled":"1","publisher":"Elsevier","oa_version":"Published Version","language":[{"iso":"eng"}],"date_updated":"2026-06-18T17:15:22Z"},{"ddc":["530"],"doi":"10.1063/5.0097339","acknowledgement":"We would like to thank all of the authors who contributed to\r\nthis Special Topic. We would also like to thank the editorial team at\r\nAPL including Jessica Trudeau, Emma Van Burns, Martin Weides,\r\nand Lesley Cohen.","intvolume":"       120","publication":"Applied Physics Letters","year":"2022","scopus_import":"1","volume":120,"date_published":"2022-05-12T00:00:00Z","article_type":"letter_note","article_number":"190401","author":[{"last_name":"Sigillito","first_name":"Anthony J.","full_name":"Sigillito, Anthony J."},{"last_name":"Covey","full_name":"Covey, Jacob P.","first_name":"Jacob P."},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","orcid":"0000-0001-8112-028X","first_name":"Johannes M","full_name":"Fink, Johannes M"},{"first_name":"Karl","full_name":"Petersson, Karl","last_name":"Petersson"},{"last_name":"Preble","full_name":"Preble, Stefan","first_name":"Stefan"}],"title":"Emerging qubit systems: Guest editorial","date_created":"2022-05-29T22:01:53Z","issue":"19","publication_identifier":{"issn":["0003-6951"]},"day":"12","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1063/5.0097339"}],"isi":1,"external_id":{"isi":["000796002100002"]},"publication_status":"published","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JoFi"}],"_id":"11417","abstract":[{"text":"Over the past few years, the field of quantum information science has seen tremendous progress toward realizing large-scale quantum computers. With demonstrations of quantum computers outperforming classical computers for a select range of problems,1–3 we have finally entered the noisy, intermediate-scale quantum (NISQ) computing era. While the quantum computers of today are technological marvels, they are not yet error corrected, and it is unclear whether any system will scale beyond a few hundred logical qubits without significant changes to architecture and control schemes. Today's quantum systems are analogous to the ENIAC (Electronic Numerical Integrator And Computer) and EDVAC (Electronic Discrete Variable Automatic Computer) systems of the 1940s, which ran on vacuum tubes. These machines were built on a solid, nominally scalable architecture and when they were developed, nobody could have predicted the development of the transistor and the impact of the resulting semiconductor industry. Simply put, the computers of today are nothing like the early computers of the 1940s. We believe that the qubits of future fault-tolerant quantum systems will look quite different from the qubits of the NISQ machines in operation today. This Special Topic issue is devoted to new and emerging quantum systems with a focus on enabling technologies that can eventually lead to the quantum analog to the transistor. We have solicited both research4–18 and perspective articles19–21 to discuss new and emerging qubit systems with a focus on novel materials, encodings, and architectures. We are proud to present a collection that touches on a wide range of technologies including superconductors,7–13,21 semiconductors,15–17,19 and individual atomic qubits.18\r\n","lang":"eng"}],"oa":1,"type":"journal_article","citation":{"ieee":"A. J. Sigillito, J. P. Covey, J. M. Fink, K. Petersson, and S. Preble, “Emerging qubit systems: Guest editorial,” <i>Applied Physics Letters</i>, vol. 120, no. 19. American Institute of Physics, 2022.","mla":"Sigillito, Anthony J., et al. “Emerging Qubit Systems: Guest Editorial.” <i>Applied Physics Letters</i>, vol. 120, no. 19, 190401, American Institute of Physics, 2022, doi:<a href=\"https://doi.org/10.1063/5.0097339\">10.1063/5.0097339</a>.","short":"A.J. Sigillito, J.P. Covey, J.M. Fink, K. Petersson, S. Preble, Applied Physics Letters 120 (2022).","apa":"Sigillito, A. J., Covey, J. P., Fink, J. M., Petersson, K., &#38; Preble, S. (2022). Emerging qubit systems: Guest editorial. <i>Applied Physics Letters</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/5.0097339\">https://doi.org/10.1063/5.0097339</a>","ama":"Sigillito AJ, Covey JP, Fink JM, Petersson K, Preble S. Emerging qubit systems: Guest editorial. <i>Applied Physics Letters</i>. 2022;120(19). doi:<a href=\"https://doi.org/10.1063/5.0097339\">10.1063/5.0097339</a>","ista":"Sigillito AJ, Covey JP, Fink JM, Petersson K, Preble S. 2022. Emerging qubit systems: Guest editorial. Applied Physics Letters. 120(19), 190401.","chicago":"Sigillito, Anthony J., Jacob P. Covey, Johannes M Fink, Karl Petersson, and Stefan Preble. “Emerging Qubit Systems: Guest Editorial.” <i>Applied Physics Letters</i>. American Institute of Physics, 2022. <a href=\"https://doi.org/10.1063/5.0097339\">https://doi.org/10.1063/5.0097339</a>."},"month":"05","quality_controlled":"1","publisher":"American Institute of Physics","oa_version":"Published Version","language":[{"iso":"eng"}],"date_updated":"2026-06-18T17:14:33Z"},{"pmid":1,"scopus_import":"1","year":"2022","publication":"Science Bulletin","volume":67,"acknowledgement":"This work was supported by the National Science Fund for Distinguished Young Scholars (51925101), National Key Research and Development Program of China (2018YFA0702100), 111 Project (B17002), and Lise Meitner Project (M2889-N).","doi":"10.1016/j.scib.2022.04.007","ddc":["530"],"intvolume":"        67","date_created":"2022-05-08T22:01:44Z","author":[{"orcid":"0000-0002-9515-4277","last_name":"Chang","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","full_name":"Chang, Cheng","first_name":"Cheng"},{"last_name":"Qin","first_name":"Bingchao","full_name":"Qin, Bingchao"},{"first_name":"Lizhong","full_name":"Su, Lizhong","last_name":"Su"},{"last_name":"Zhao","full_name":"Zhao, Li Dong","first_name":"Li Dong"}],"title":"Distinct electron and hole transports in SnSe crystals","issue":"11","date_published":"2022-06-15T00:00:00Z","project":[{"grant_number":"M02889","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","name":"Bottom-up Engineering for Thermoelectric Applications"}],"article_type":"letter_note","publication_status":"published","external_id":{"isi":["000835291100006"],"pmid":["36545972"]},"department":[{"_id":"MaIb"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"15","publication_identifier":{"issn":["2095-9273"],"eissn":["2095-9281"]},"status":"public","isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.scib.2022.04.007"}],"page":"1105-1107","oa":1,"month":"06","citation":{"mla":"Chang, Cheng, et al. “Distinct Electron and Hole Transports in SnSe Crystals.” <i>Science Bulletin</i>, vol. 67, no. 11, Elsevier, 2022, pp. 1105–07, doi:<a href=\"https://doi.org/10.1016/j.scib.2022.04.007\">10.1016/j.scib.2022.04.007</a>.","ieee":"C. Chang, B. Qin, L. Su, and L. D. Zhao, “Distinct electron and hole transports in SnSe crystals,” <i>Science Bulletin</i>, vol. 67, no. 11. Elsevier, pp. 1105–1107, 2022.","ama":"Chang C, Qin B, Su L, Zhao LD. Distinct electron and hole transports in SnSe crystals. <i>Science Bulletin</i>. 2022;67(11):1105-1107. doi:<a href=\"https://doi.org/10.1016/j.scib.2022.04.007\">10.1016/j.scib.2022.04.007</a>","ista":"Chang C, Qin B, Su L, Zhao LD. 2022. Distinct electron and hole transports in SnSe crystals. Science Bulletin. 67(11), 1105–1107.","chicago":"Chang, Cheng, Bingchao Qin, Lizhong Su, and Li Dong Zhao. “Distinct Electron and Hole Transports in SnSe Crystals.” <i>Science Bulletin</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.scib.2022.04.007\">https://doi.org/10.1016/j.scib.2022.04.007</a>.","short":"C. Chang, B. Qin, L. Su, L.D. Zhao, Science Bulletin 67 (2022) 1105–1107.","apa":"Chang, C., Qin, B., Su, L., &#38; Zhao, L. D. (2022). Distinct electron and hole transports in SnSe crystals. <i>Science Bulletin</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.scib.2022.04.007\">https://doi.org/10.1016/j.scib.2022.04.007</a>"},"type":"journal_article","_id":"11356","language":[{"iso":"eng"}],"date_updated":"2026-06-18T10:50:26Z","publisher":"Elsevier","quality_controlled":"1","oa_version":"Published Version"},{"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Published Version","publisher":"Association for Computing Machinery","quality_controlled":"1","language":[{"iso":"eng"}],"date_updated":"2026-06-18T17:20:41Z","abstract":[{"text":"This paper introduces a methodology for inverse-modeling of yarn-level mechanics of cloth, based on the mechanical response of fabrics in the real world. We compiled a database from physical tests of several different knitted fabrics used in the textile industry. These data span different types of complex knit patterns, yarn compositions, and fabric finishes, and the results demonstrate diverse physical properties like stiffness, nonlinearity, and anisotropy.\r\n\r\nWe then develop a system for approximating these mechanical responses with yarn-level cloth simulation. To do so, we introduce an efficient pipeline for converting between fabric-level data and yarn-level simulation, including a novel swatch-level approximation for speeding up computation, and some small-but-necessary extensions to yarn-level models used in computer graphics. The dataset used for this paper can be found at http://mslab.es/projects/YarnLevelFabrics.","lang":"eng"}],"_id":"11736","related_material":{"link":[{"url":"https://ista.ac.at/en/news/digital-yarn-real-socks/","description":"News on the ISTA website","relation":"press_release"}],"record":[{"id":"12358","status":"public","relation":"dissertation_contains"}]},"citation":{"apa":"Sperl, G., Sánchez-Banderas, R. M., Li, M., Wojtan, C., &#38; Otaduy, M. A. (2022). Estimation of yarn-level simulation models for production fabrics. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3528223.3530167\">https://doi.org/10.1145/3528223.3530167</a>","short":"G. Sperl, R.M. Sánchez-Banderas, M. Li, C. Wojtan, M.A. Otaduy, ACM Transactions on Graphics 41 (2022).","chicago":"Sperl, Georg, Rosa M. Sánchez-Banderas, Manwen Li, Chris Wojtan, and Miguel A. Otaduy. “Estimation of Yarn-Level Simulation Models for Production Fabrics.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3528223.3530167\">https://doi.org/10.1145/3528223.3530167</a>.","ista":"Sperl G, Sánchez-Banderas RM, Li M, Wojtan C, Otaduy MA. 2022. Estimation of yarn-level simulation models for production fabrics. ACM Transactions on Graphics. 41(4), 65.","ama":"Sperl G, Sánchez-Banderas RM, Li M, Wojtan C, Otaduy MA. Estimation of yarn-level simulation models for production fabrics. <i>ACM Transactions on Graphics</i>. 2022;41(4). doi:<a href=\"https://doi.org/10.1145/3528223.3530167\">10.1145/3528223.3530167</a>","mla":"Sperl, Georg, et al. “Estimation of Yarn-Level Simulation Models for Production Fabrics.” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4, 65, Association for Computing Machinery, 2022, doi:<a href=\"https://doi.org/10.1145/3528223.3530167\">10.1145/3528223.3530167</a>.","ieee":"G. Sperl, R. M. Sánchez-Banderas, M. Li, C. Wojtan, and M. A. Otaduy, “Estimation of yarn-level simulation models for production fabrics,” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4. Association for Computing Machinery, 2022."},"type":"journal_article","month":"07","oa":1,"isi":1,"status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3528223.3530167"}],"day":"22","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","department":[{"_id":"ChWo"}],"publication_status":"published","external_id":{"isi":["000830989200114"]},"article_type":"original","date_published":"2022-07-22T00:00:00Z","issue":"4","article_number":"65","date_created":"2022-08-07T22:01:58Z","author":[{"id":"4DD40360-F248-11E8-B48F-1D18A9856A87","last_name":"Sperl","full_name":"Sperl, Georg","first_name":"Georg"},{"full_name":"Sánchez-Banderas, Rosa M.","first_name":"Rosa M.","last_name":"Sánchez-Banderas"},{"full_name":"Li, Manwen","first_name":"Manwen","last_name":"Li"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","orcid":"0000-0001-6646-5546","first_name":"Christopher J","full_name":"Wojtan, Christopher J"},{"first_name":"Miguel A.","full_name":"Otaduy, Miguel A.","last_name":"Otaduy"}],"title":"Estimation of yarn-level simulation models for production fabrics","intvolume":"        41","doi":"10.1145/3528223.3530167","acknowledgement":"We wish to thank the anonymous reviewers for their helpful comments. To develop this project, we were helped by many people both at Under Armour (Clay Dean, Randall Harward, Kyle Blakely, Craig Simile, Michael Seiz, Brooke Malone, Brittainy McFarland, Emilie Phan, Lindsey Kern, Courtney Oswald, Haley Barkley, Bob Chin, Adam Bayer, Connie Kwok, Marielle Newman, Nick Pence, Allison Hicks, Allison White, Candace Rubenstein, Jeremy Stangland, Fred Fagergren, Michael Mazzoleni, Nathaniel Berry, Manuel Frank) and SEDDI (Gabriel Cirio, Alejandro Rodríguez, Sofía Dominguez, Alicia Nicas, Elena Garcés, Daniel Rodríguez, David Pascual, Manuel Godoy, Sergio Suja, Sergio Ruiz, Roberto Condori, Alberto Martín, Graham Sullivan). We also thank the members of the Visual Computing Group at IST Austria and the Multimodal Simulation Lab at URJC for their feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing, and it was funded in part by the European Research Council (ERC Consolidator Grant 772738 TouchDesign).","ddc":["000"],"volume":41,"scopus_import":"1","year":"2022","publication":"ACM Transactions on Graphics"}]