[{"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"4668-4698","dataavailabilitystatement":"All the raw data in this work has been deposited to Biostudies with the accession number: S-BIAD1023. One can access the data through the link below: https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1023?key=426953ee-3da4-4cf4-a496-e607ce240aff.  The source data of this paper are collected in the following database record: biostudies:S-SCDT-10_1038-S44318-024-00207-0.","oa":1,"file_date_updated":"2025-01-13T08:43:20Z","article_processing_charge":"Yes","has_accepted_license":"1","OA_place":"publisher","supplementarymaterial":"yes","ddc":["570"],"type":"journal_article","OA_type":"gold","status":"public","isi":1,"fulldoi":"https://doi.org/10.1038/s44318-024-00207-0","publication_status":"published","title":"Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering","file":[{"file_id":"18827","file_size":10080854,"creator":"dernst","checksum":"04f4df1a561083f2846676442fc4eb3c","relation":"main_file","date_updated":"2025-01-13T08:43:20Z","success":1,"content_type":"application/pdf","date_created":"2025-01-13T08:43:20Z","access_level":"open_access","file_name":"2024_Embo_Kettel.pdf"}],"acknowledgement":"We thank late Thomas Peterbauer at the Max Perutz Labs Biooptics Light Microscopy Facility for his help and support. We are grateful to Kitti Csalyi and Thomas Sauer at Max Perutz Labs Biooptics FACS facility for their help. We thank Grzegorz Scibisz and Sertan Atilla for their support with the expression and purification of mCherry-IRE1α LD-10His. We are grateful to Aleksandra S Anisimova with her help in the generation of stable cell lines and the statistical analyses of the data. We thank Venja Vieweger for her help with the characterization of the WLLI and D123P IRE1 mutants in cells. We are thankful to Monika Kubickova for the help with the AUC experiments. We acknowledge CF BIC of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2023042)) and European Regional Development Fund-Project, UP CIISB“ (No. CZ.02.1.01/0.0/0.0/18_046/0015974). We thank the members of the Karagöz lab for the critical reading and editing of the manuscript. We are thankful to our colleagues Diego Acosta-Alvear, Vladislav Belyy, Jirka Peschek, Yasin Dagdas, Javier Martinez, Sascha Martens and Alwin Köhler for their invaluable input on the manuscript. We are grateful to Life Science Editors, especially Katrina Woolcock for her useful edits and comments on the manuscript. We acknowledge funding from Austrian Science Fund (FWF-SFB F79 and FWF-W 1261) to GEK. PK acknowledges the support of the Max Perutz PhD fellowship. GAV is funded by Stand-Alone grants (P30231-B, P30415-B, P36572), Special Research Grant (SFB grant F79), and Doctoral School grant (DK grant W1261) from the Austrian Science Fund (FWF). ES and RC acknowledge support and funding by the Frankfurt Institute of Advanced Studies, the LOEWE Center for Multiscale Modelling in Life Sciences of the state of Hesse, the Collaborative Research Center 1507 “Membrane-associated Protein Assemblies, Machineries, and Supercomplexes” (Project ID 450648163), and the International Max Planck Research School on Cellular Biophysics (to RC), the Center for Scientific Computing of the Goethe University and the Jülich Supercomputing Centre for computational resources and support.","department":[{"_id":"MaLo"},{"_id":"JiFr"}],"_id":"18073","publisher":"Embo Press","month":"10","oa_version":"Published Version","external_id":{"isi":["001306286100002"],"pmid":["39232130"]},"intvolume":"        43","publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"article_type":"original","researchdata_availability":"yes","volume":43,"quality_controlled":"1","pmid":1,"issue":"20","citation":{"chicago":"Kettel, Paulina, Laura Marosits, Elena Spinetti, Michael Rechberger, Caterina Giannini, Philipp Radler, Isabell Niedermoser, et al. “Disordered Regions in the IRE1α ER Lumenal Domain Mediate Its Stress-Induced Clustering.” <i>EMBO Journal</i>. Embo Press, 2024. <a href=\"https://doi.org/10.1038/s44318-024-00207-0\">https://doi.org/10.1038/s44318-024-00207-0</a>.","mla":"Kettel, Paulina, et al. “Disordered Regions in the IRE1α ER Lumenal Domain Mediate Its Stress-Induced Clustering.” <i>EMBO Journal</i>, vol. 43, no. 20, Embo Press, 2024, pp. 4668–98, doi:<a href=\"https://doi.org/10.1038/s44318-024-00207-0\">10.1038/s44318-024-00207-0</a>.","ieee":"P. Kettel <i>et al.</i>, “Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering,” <i>EMBO Journal</i>, vol. 43, no. 20. Embo Press, pp. 4668–4698, 2024.","short":"P. Kettel, L. Marosits, E. Spinetti, M. Rechberger, C. Giannini, P. Radler, I. Niedermoser, I. Fischer, G.A. Versteeg, M. Loose, R. Covino, G.E. Karagöz, EMBO Journal 43 (2024) 4668–4698.","ama":"Kettel P, Marosits L, Spinetti E, et al. Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering. <i>EMBO Journal</i>. 2024;43(20):4668-4698. doi:<a href=\"https://doi.org/10.1038/s44318-024-00207-0\">10.1038/s44318-024-00207-0</a>","ista":"Kettel P, Marosits L, Spinetti E, Rechberger M, Giannini C, Radler P, Niedermoser I, Fischer I, Versteeg GA, Loose M, Covino R, Karagöz GE. 2024. Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering. EMBO Journal. 43(20), 4668–4698.","apa":"Kettel, P., Marosits, L., Spinetti, E., Rechberger, M., Giannini, C., Radler, P., … Karagöz, G. E. (2024). Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering. <i>EMBO Journal</i>. Embo Press. <a href=\"https://doi.org/10.1038/s44318-024-00207-0\">https://doi.org/10.1038/s44318-024-00207-0</a>"},"year":"2024","date_created":"2024-09-15T22:01:42Z","publication":"EMBO Journal","author":[{"full_name":"Kettel, Paulina","first_name":"Paulina","last_name":"Kettel"},{"full_name":"Marosits, Laura","first_name":"Laura","last_name":"Marosits"},{"first_name":"Elena","last_name":"Spinetti","full_name":"Spinetti, Elena"},{"first_name":"Michael","last_name":"Rechberger","full_name":"Rechberger, Michael"},{"id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","first_name":"Caterina","last_name":"Giannini","full_name":"Giannini, Caterina"},{"last_name":"Radler","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp"},{"full_name":"Niedermoser, Isabell","first_name":"Isabell","last_name":"Niedermoser"},{"last_name":"Fischer","first_name":"Irmgard","full_name":"Fischer, Irmgard"},{"full_name":"Versteeg, Gijs A.","first_name":"Gijs A.","last_name":"Versteeg"},{"orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","last_name":"Loose","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Covino","first_name":"Roberto","full_name":"Covino, Roberto"},{"first_name":"G. Elif","last_name":"Karagöz","full_name":"Karagöz, G. Elif"}],"date_updated":"2026-10-16T10:37:47Z","das_tickbox":"1","abstract":[{"text":"Conserved signaling cascades monitor protein-folding homeostasis to ensure proper cellular function. One of the evolutionary conserved key players is IRE1, which maintains endoplasmic reticulum (ER) homeostasis through the unfolded protein response (UPR). Upon accumulation of misfolded proteins in the ER, IRE1 forms clusters on the ER membrane to initiate UPR signaling. What regulates IRE1 cluster formation is not fully understood. Here, we show that the ER lumenal domain (LD) of human IRE1α forms biomolecular condensates in vitro. IRE1α LD condensates were stabilized both by binding to unfolded polypeptides as well as by tethering to model membranes, suggesting their role in assembling IRE1α into signaling-competent stable clusters. Molecular dynamics simulations indicated that weak multivalent interactions drive IRE1α LD clustering. Mutagenesis experiments identified disordered regions in IRE1α LD to control its clustering in vitro and in cells. Importantly, dysregulated clustering of IRE1α mutants led to defects in IRE1α signaling. Our results revealed that disordered regions in IRE1α LD control its clustering and suggest their role as a common strategy in regulating protein assembly on membranes.","lang":"eng"}],"scopus_import":"1","day":"15","date_published":"2024-10-15T00:00:00Z","doi":"10.1038/s44318-024-00207-0"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"has_accepted_license":"1","file_date_updated":"2024-07-16T12:07:20Z","article_processing_charge":"Yes","oa":1,"corr_author":"1","keyword":["Cell Biology","General Medicine","Histology","Pathology and Forensic Medicine"],"supplementarymaterial":"no","type":"journal_article","ddc":["570"],"status":"public","fulldoi":"https://doi.org/10.1016/j.ejcb.2023.151380","isi":1,"file":[{"file_size":9995304,"file_id":"17265","creator":"dernst","checksum":"5d170abbc87585205c010657e4552360","date_updated":"2024-07-16T12:07:20Z","success":1,"relation":"main_file","content_type":"application/pdf","date_created":"2024-07-16T12:07:20Z","access_level":"open_access","file_name":"2024_EJCB_Radler.pdf"}],"project":[{"name":"In vitro reconstitution of bacterial cell division","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607"}],"title":"A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches","publication_status":"published","_id":"14834","department":[{"_id":"MaLo"}],"acknowledgement":"We acknowledge members of the Loose laboratory at ISTA for helpful discussions—in particular M. Kojic for his insightful comments. This work was supported by the Austrian Science Fund (FWF P34607) to M.L.","external_id":{"pmid":["38218128"],"isi":["001166216800001"]},"month":"03","oa_version":"Published Version","publisher":"Elsevier","volume":103,"researchdata_availability":"no","article_type":"review","publication_identifier":{"issn":["0171-9335"]},"intvolume":"       103","issue":"1","pmid":1,"article_number":"151380","quality_controlled":"1","publication":"European Journal of Cell Biology","year":"2024","date_created":"2024-01-18T08:16:43Z","citation":{"apa":"Radler, P., &#38; Loose, M. (2024). A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. <i>European Journal of Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ejcb.2023.151380\">https://doi.org/10.1016/j.ejcb.2023.151380</a>","ista":"Radler P, Loose M. 2024. A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. European Journal of Cell Biology. 103(1), 151380.","ama":"Radler P, Loose M. A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. <i>European Journal of Cell Biology</i>. 2024;103(1). doi:<a href=\"https://doi.org/10.1016/j.ejcb.2023.151380\">10.1016/j.ejcb.2023.151380</a>","mla":"Radler, Philipp, and Martin Loose. “A Dynamic Duo: Understanding the Roles of FtsZ and FtsA for Escherichia Coli Cell Division through in Vitro Approaches.” <i>European Journal of Cell Biology</i>, vol. 103, no. 1, 151380, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.ejcb.2023.151380\">10.1016/j.ejcb.2023.151380</a>.","short":"P. Radler, M. Loose, European Journal of Cell Biology 103 (2024).","ieee":"P. Radler and M. Loose, “A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches,” <i>European Journal of Cell Biology</i>, vol. 103, no. 1. Elsevier, 2024.","chicago":"Radler, Philipp, and Martin Loose. “A Dynamic Duo: Understanding the Roles of FtsZ and FtsA for Escherichia Coli Cell Division through in Vitro Approaches.” <i>European Journal of Cell Biology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.ejcb.2023.151380\">https://doi.org/10.1016/j.ejcb.2023.151380</a>."},"date_updated":"2026-10-16T10:15:15Z","author":[{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","last_name":"Radler","full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 "},{"orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"das_tickbox":"0","doi":"10.1016/j.ejcb.2023.151380","date_published":"2024-03-01T00:00:00Z","day":"01","scopus_import":"1","abstract":[{"text":"Bacteria divide by binary fission. The protein machine responsible for this process is the divisome, a transient assembly of more than 30 proteins in and on the surface of the cytoplasmic membrane. Together, they constrict the cell envelope and remodel the peptidoglycan layer to eventually split the cell into two. For Escherichia coli, most molecular players involved in this process have probably been identified, but obtaining the quantitative information needed for a mechanistic understanding can often not be achieved from experiments in vivo alone. Since the discovery of the Z-ring more than 30 years ago, in vitro reconstitution experiments have been crucial to shed light on molecular processes normally hidden in the complex environment of the living cell. In this review, we summarize how rebuilding the divisome from purified components – or at least parts of it - have been instrumental to obtain the detailed mechanistic understanding of the bacterial cell division machinery that we have today.","lang":"eng"}]},{"corr_author":"1","OA_place":"repository","supplementarymaterial":"no","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"413-443","article_processing_charge":"No","related_material":{"record":[{"id":"22664","status":"public","relation":"dissertation_contains"}]},"oa":1,"fulldoi":"https://doi.org/10.1007/978-3-031-78011-0_14","isi":1,"publication_status":"published","title":"The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging","type":"conference","OA_type":"green","status":"public","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031780103"],"eissn":["1611-3349"]},"researchdata_availability":"no","volume":15364,"intvolume":"     15364","quality_controlled":"1","department":[{"_id":"MaKw"},{"_id":"KrPi"}],"alternative_title":["LNCS"],"_id":"18702","external_id":{"isi":["001545628900014"]},"conference":{"location":"Milan, Italy","name":"TCC: Theory of Cryptography","end_date":"2024-12-06","start_date":"2024-12-02"},"publisher":"Springer Nature","month":"12","oa_version":"Preprint","das_tickbox":"0","day":"02","date_published":"2024-12-02T00:00:00Z","doi":"10.1007/978-3-031-78011-0_14","scopus_import":"1","abstract":[{"text":"In this work we prove lower bounds on the (communication) cost of maintaining a shared key among a dynamic group of users. Being “dynamic” means one can add and remove users from the group. This captures important protocols like multicast encryption (ME) and continuous group-key agreement (CGKA), which is the primitive underlying many group messaging applications. We prove our bounds in a combinatorial setting where the state of the protocol progresses in rounds. The state of the protocol in each round is captured by a set system, with each of its elements specifying a set of users who share a secret key. We show this combinatorial model implies bounds in symbolic models for ME and CGKA that capture, as building blocks, PRGs, PRFs, dual PRFs, secret sharing, and symmetric encryption in the setting of ME, and PRGs, PRFs, dual PRFs, secret sharing, public-key encryption, and key-updatable public-key encryption in the setting of CGKA. The models are related to the ones used by Micciancio and Panjwani (Eurocrypt’04) and Bienstock et al. (TCC’20) to analyze ME and CGKA, respectively. We prove – using the Bollobás’ Set Pairs Inequality – that the cost (number of uploaded ciphertexts) for replacing a set of d users in a group of size n is Ω(dln(n/d)). Our lower bound is asymptotically tight and both improves on a bound of Ω(d) by Bienstock et al. (TCC’20), and generalizes a result by Micciancio and Panjwani (Eurocrypt’04), who proved a lower bound of Ω(log(n)) for d=1. ","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2024/1097"}],"publication":"22nd International Conference on Theory of Cryptography","citation":{"ieee":"M. Anastos <i>et al.</i>, “The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging,” in <i>22nd International Conference on Theory of Cryptography</i>, Milan, Italy, 2024, vol. 15364, pp. 413–443.","short":"M. Anastos, B. Auerbach, M.A. Baig, M. Cueto Noval, M.A. Kwan, G. Pascual Perez, K.Z. Pietrzak, in:, 22nd International Conference on Theory of Cryptography, Springer Nature, 2024, pp. 413–443.","mla":"Anastos, Michael, et al. “The Cost of Maintaining Keys in Dynamic Groups with Applications to Multicast Encryption and Group Messaging.” <i>22nd International Conference on Theory of Cryptography</i>, vol. 15364, Springer Nature, 2024, pp. 413–43, doi:<a href=\"https://doi.org/10.1007/978-3-031-78011-0_14\">10.1007/978-3-031-78011-0_14</a>.","chicago":"Anastos, Michael, Benedikt Auerbach, Mirza Ahad Baig, Miguel Cueto Noval, Matthew Alan Kwan, Guillermo Pascual Perez, and Krzysztof Z Pietrzak. “The Cost of Maintaining Keys in Dynamic Groups with Applications to Multicast Encryption and Group Messaging.” In <i>22nd International Conference on Theory of Cryptography</i>, 15364:413–43. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-78011-0_14\">https://doi.org/10.1007/978-3-031-78011-0_14</a>.","apa":"Anastos, M., Auerbach, B., Baig, M. A., Cueto Noval, M., Kwan, M. A., Pascual Perez, G., &#38; Pietrzak, K. Z. (2024). The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging. In <i>22nd International Conference on Theory of Cryptography</i> (Vol. 15364, pp. 413–443). Milan, Italy: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-78011-0_14\">https://doi.org/10.1007/978-3-031-78011-0_14</a>","ista":"Anastos M, Auerbach B, Baig MA, Cueto Noval M, Kwan MA, Pascual Perez G, Pietrzak KZ. 2024. The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging. 22nd International Conference on Theory of Cryptography. TCC: Theory of Cryptography, LNCS, vol. 15364, 413–443.","ama":"Anastos M, Auerbach B, Baig MA, et al. The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging. In: <i>22nd International Conference on Theory of Cryptography</i>. Vol 15364. Springer Nature; 2024:413-443. doi:<a href=\"https://doi.org/10.1007/978-3-031-78011-0_14\">10.1007/978-3-031-78011-0_14</a>"},"year":"2024","date_created":"2024-12-22T23:01:47Z","date_updated":"2026-10-16T10:14:41Z","author":[{"last_name":"Anastos","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","first_name":"Michael","full_name":"Anastos, Michael"},{"full_name":"Auerbach, Benedikt","orcid":"0000-0002-7553-6606","first_name":"Benedikt","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","last_name":"Auerbach"},{"id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","first_name":"Mirza Ahad","last_name":"Baig","full_name":"Baig, Mirza Ahad"},{"last_name":"Cueto Noval","id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc","first_name":"Miguel","orcid":"0000-0002-2505-4246","full_name":"Cueto Noval, Miguel"},{"last_name":"Kwan","first_name":"Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","orcid":"0000-0002-4003-7567","full_name":"Kwan, Matthew Alan"},{"last_name":"Pascual Perez","first_name":"Guillermo","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8630-415X","full_name":"Pascual Perez, Guillermo"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654"}]},{"issue":"3","quality_controlled":"1","volume":75,"researchdata_availability":"no","publication_identifier":{"eissn":["1464-3847"],"issn":["0033-5606"]},"article_type":"original","intvolume":"        75","external_id":{"arxiv":["2309.09788"],"isi":["001249741500001"]},"month":"06","oa_version":"Published Version","publisher":"Oxford University Press","_id":"17475","department":[{"_id":"MaKw"},{"_id":"VaKa"}],"acknowledgement":"Matthew Kwan was supported by ERC Starting Grant ‘RANDSTRUCT’ No. 101076777.","doi":"10.1093/qmath/haae030","day":"19","date_published":"2024-06-19T00:00:00Z","abstract":[{"lang":"eng","text":"As a discrete analogue of Kac’s celebrated question on ‘hearing the shape of a drum’ and towards a practical\r\ngraph isomorphism test, it is of interest to understand which graphs are determined up to isomorphism by\r\ntheir spectrum (of their adjacency matrix). A striking conjecture in this area, due to van Dam and Haemers,\r\nis that ‘almost all graphs are determined by their spectrum’, meaning that the fraction of unlabelled n-vertex\r\ngraphs which are determined by their spectrum converges to 1 as n → ∞.\r\nIn this paper, we make a step towards this conjecture, showing that there are exponentially many n-vertex\r\ngraphs which are determined by their spectrum. This improves on previous bounds (of shape e\r\nc\r\n√\r\nn\r\n). We also\r\npropose a number of further directions of research.\r\n"}],"scopus_import":"1","das_tickbox":"0","date_updated":"2026-10-16T10:14:59Z","author":[{"full_name":"Koval, Illya","id":"2eed1f3b-896a-11ed-bdf8-93c7c4bf159e","first_name":"Illya","last_name":"Koval"},{"full_name":"Kwan, Matthew Alan","orcid":"0000-0002-4003-7567","first_name":"Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","last_name":"Kwan"}],"publication":"Quarterly Journal of Mathematics","year":"2024","date_created":"2024-09-01T22:01:07Z","citation":{"ama":"Koval I, Kwan MA. Exponentially many graphs are determined by their spectrum. <i>Quarterly Journal of Mathematics</i>. 2024;75(3):869-899. doi:<a href=\"https://doi.org/10.1093/qmath/haae030\">10.1093/qmath/haae030</a>","ista":"Koval I, Kwan MA. 2024. Exponentially many graphs are determined by their spectrum. Quarterly Journal of Mathematics. 75(3), 869–899.","apa":"Koval, I., &#38; Kwan, M. A. (2024). Exponentially many graphs are determined by their spectrum. <i>Quarterly Journal of Mathematics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/qmath/haae030\">https://doi.org/10.1093/qmath/haae030</a>","chicago":"Koval, Illya, and Matthew Alan Kwan. “Exponentially Many Graphs Are Determined by Their Spectrum.” <i>Quarterly Journal of Mathematics</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/qmath/haae030\">https://doi.org/10.1093/qmath/haae030</a>.","mla":"Koval, Illya, and Matthew Alan Kwan. “Exponentially Many Graphs Are Determined by Their Spectrum.” <i>Quarterly Journal of Mathematics</i>, vol. 75, no. 3, Oxford University Press, 2024, pp. 869–99, doi:<a href=\"https://doi.org/10.1093/qmath/haae030\">10.1093/qmath/haae030</a>.","short":"I. Koval, M.A. Kwan, Quarterly Journal of Mathematics 75 (2024) 869–899.","ieee":"I. Koval and M. A. Kwan, “Exponentially many graphs are determined by their spectrum,” <i>Quarterly Journal of Mathematics</i>, vol. 75, no. 3. Oxford University Press, pp. 869–899, 2024."},"supplementarymaterial":"no","corr_author":"1","file_date_updated":"2024-09-06T12:23:57Z","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","oa":1,"page":"869-899","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"project":[{"name":"Randomness and structure in combinatorics","grant_number":"101076777","_id":"bd95085b-d553-11ed-ba76-e55d3349be45"}],"title":"Exponentially many graphs are determined by their spectrum","file":[{"creator":"cchlebak","checksum":"abf200d37ad69e6f2c0750a30296ad97","file_id":"17851","file_size":946411,"content_type":"application/pdf","date_created":"2024-09-06T12:23:57Z","file_name":"2024_QuJofMath_Koval.pdf","access_level":"open_access","success":1,"date_updated":"2024-09-06T12:23:57Z","relation":"main_file"}],"publication_status":"published","fulldoi":"https://doi.org/10.1093/qmath/haae030","arxiv":1,"isi":1,"status":"public","type":"journal_article","ddc":["500"]},{"publication":"Nature Microbiology","date_created":"2024-03-17T23:00:58Z","year":"2024","citation":{"mla":"Nußbaum, Phillip, et al. “Proteins Containing Photosynthetic Reaction Centre Domains Modulate FtsZ-Based Archaeal Cell Division.” <i>Nature Microbiology</i>, vol. 9, no. 3, Springer Nature, 2024, pp. 698–711, doi:<a href=\"https://doi.org/10.1038/s41564-024-01600-5\">10.1038/s41564-024-01600-5</a>.","ieee":"P. Nußbaum <i>et al.</i>, “Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division,” <i>Nature Microbiology</i>, vol. 9, no. 3. Springer Nature, pp. 698–711, 2024.","short":"P. Nußbaum, D. Kureisaite-Ciziene, D. Bellini, C. Van Der Does, M. Kojic, N. Taib, A. Yeates, M. Tourte, S. Gribaldo, M. Loose, J. Löwe, S.V. Albers, Nature Microbiology 9 (2024) 698–711.","chicago":"Nußbaum, Phillip, Danguole Kureisaite-Ciziene, Dom Bellini, Chris Van Der Does, Marko Kojic, Najwa Taib, Anna Yeates, et al. “Proteins Containing Photosynthetic Reaction Centre Domains Modulate FtsZ-Based Archaeal Cell Division.” <i>Nature Microbiology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41564-024-01600-5\">https://doi.org/10.1038/s41564-024-01600-5</a>.","apa":"Nußbaum, P., Kureisaite-Ciziene, D., Bellini, D., Van Der Does, C., Kojic, M., Taib, N., … Albers, S. V. (2024). Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. <i>Nature Microbiology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41564-024-01600-5\">https://doi.org/10.1038/s41564-024-01600-5</a>","ama":"Nußbaum P, Kureisaite-Ciziene D, Bellini D, et al. Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. <i>Nature Microbiology</i>. 2024;9(3):698-711. doi:<a href=\"https://doi.org/10.1038/s41564-024-01600-5\">10.1038/s41564-024-01600-5</a>","ista":"Nußbaum P, Kureisaite-Ciziene D, Bellini D, Van Der Does C, Kojic M, Taib N, Yeates A, Tourte M, Gribaldo S, Loose M, Löwe J, Albers SV. 2024. Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. Nature Microbiology. 9(3), 698–711."},"date_updated":"2026-10-16T10:35:48Z","author":[{"full_name":"Nußbaum, Phillip","first_name":"Phillip","last_name":"Nußbaum"},{"first_name":"Danguole","last_name":"Kureisaite-Ciziene","full_name":"Kureisaite-Ciziene, Danguole"},{"first_name":"Dom","last_name":"Bellini","full_name":"Bellini, Dom"},{"last_name":"Van Der Does","first_name":"Chris","full_name":"Van Der Does, Chris"},{"orcid":"0000-0001-7244-8128","full_name":"Kojic, Marko","last_name":"Kojic","first_name":"Marko","id":"73e7ecd4-dc85-11ea-9058-88a16394b160"},{"last_name":"Taib","first_name":"Najwa","full_name":"Taib, Najwa"},{"full_name":"Yeates, Anna","first_name":"Anna","last_name":"Yeates"},{"first_name":"Maxime","last_name":"Tourte","full_name":"Tourte, Maxime"},{"last_name":"Gribaldo","first_name":"Simonetta","full_name":"Gribaldo, Simonetta"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose"},{"last_name":"Löwe","first_name":"Jan","full_name":"Löwe, Jan"},{"first_name":"Sonja Verena","last_name":"Albers","full_name":"Albers, Sonja Verena"}],"das_tickbox":"1","acknowledged_ssus":[{"_id":"LifeSc"}],"doi":"10.1038/s41564-024-01600-5","date_published":"2024-03-04T00:00:00Z","day":"04","scopus_import":"1","abstract":[{"lang":"eng","text":"Cell division in all domains of life requires the orchestration of many proteins, but in Archaea most of the machinery remains poorly characterized. Here we investigate the FtsZ-based cell division mechanism in Haloferax volcanii and find proteins containing photosynthetic reaction centre (PRC) barrel domains that play an essential role in archaeal cell division. We rename these proteins cell division protein B 1 (CdpB1) and CdpB2. Depletions and deletions in their respective genes cause severe cell division defects, generating drastically enlarged cells. Fluorescence microscopy of tagged FtsZ1, FtsZ2 and SepF in CdpB1 and CdpB2 mutant strains revealed an unusually disordered divisome that is not organized into a distinct ring-like structure. Biochemical analysis shows that SepF forms a tripartite complex with CdpB1/2 and crystal structures suggest that these two proteins might form filaments, possibly aligning SepF and the FtsZ2 ring during cell division. Overall our results indicate that PRC-domain proteins play essential roles in FtsZ-based cell division in Archaea."}],"_id":"15118","department":[{"_id":"MaLo"}],"acknowledgement":"We thank X. Ye (ISTA) for providing the His–SUMO expression plasmid pSVA13429. pCDB302 was a gift from C. Bahl (Addgene plasmid number 113673; http://n2t.net/addgene:113673; RRID Addgene_113673). We thank B. Ahsan, G. Sharov, G. Cannone and S. Chen from the Medical Research Council (MRC) LMB Electron Microscopy Facility for help and support. We thank Scientific Computing at the MRC LMB for their support. We thank L. Trübestein and N. Krasnici of the protein service unit of the ISTA Lab Support Facility for help with the SEC coupled with multi-angle light scattering experiments. We thank D. Grohmann and R. Reichelt from the Archaea Centre at the University of Regensburg for providing the P. furiosus cell material. P.N. and S.-V.A. were supported by a Momentum grant from the Volkswagen (VW) Foundation (grant number 94933). D.K.-C. and D.B. were supported by the VW Stiftung ‘Life?’ programme (to J.L.; grant number Az 96727) and by the MRC, as part of UK Research and Innovation (UKRI), MRC file reference number U105184326 (to J.L.). N.T. and S.G. acknowledge support from the French Government’s Investissement d’Avenir program, Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (grant number ANR-10-LABX-62-IBEID), and the computational and storage services (Maestro cluster) provided by the IT department at Institut Pasteur. M.K. and M.L. were supported by the Austrian Science Fund (FWF) Stand-Alone P34607. For the purpose of open access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any author accepted manuscript version arising.","external_id":{"pmid":["38443575"],"isi":["001183270800021"]},"oa_version":"None","month":"03","publisher":"Springer Nature","volume":9,"researchdata_availability":"yes","article_type":"original","publication_identifier":{"eissn":["2058-5276"]},"intvolume":"         9","pmid":1,"issue":"3","quality_controlled":"1","type":"journal_article","status":"public","fulldoi":"https://doi.org/10.1038/s41564-024-01600-5","isi":1,"title":"Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division","project":[{"name":"In vitro reconstitution of bacterial cell division","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607"}],"publication_status":"published","dataavailabilitystatement":"The data that support the findings of this study are available in the Source Data. Source data are provided with this paper. Coordinates have been submitted to the Protein Data Bank (PDB) with accession code 8QZO.","page":"698-711","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"article_processing_charge":"No","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"20741"}]},"supplementarymaterial":"yes"},{"intvolume":"       137","article_type":"original","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"volume":137,"researchdata_availability":"no","quality_controlled":"1","article_number":"jcs.261720","issue":"8","pmid":1,"acknowledgement":"Nataliia Gnyliukh was partially funded by the European Union’s Horizon 2020 research and\r\ninnovation program (2018-2020) under the Marie Sklodowska-Curie Grant (agreement no.\r\n665385). Taif University Researchers Supporting Project: TURSP-HC2022/02. and Austrian\r\nScience Fund (FWF): I 6123-B.We thank Prof. Eileen Lafer and Liping Wang for their suggestions regarding the optimisation of protein expression and purification. We thank Prof. Sebastian Y. Bednarek for the useful comments and constructive criticism of the project. We thank Maciek Adamowski for providing genetic material. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Electron microscopy (EMF), Lab Support Facility (LSF) (particularly Dorota Jaworska) and the Bioimaging Facility (BIF).","department":[{"_id":"MaLo"},{"_id":"JiFr"},{"_id":"CaBe"}],"_id":"15330","publisher":"The Company of Biologists","month":"04","oa_version":"Published Version","external_id":{"pmid":["38506228"],"isi":["001266917100005"]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"das_tickbox":"0","abstract":[{"text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scission machinery in plants, but the precise roles of these proteins in this process are not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the sh3p123 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME.","lang":"eng"}],"scopus_import":"1","day":"01","date_published":"2024-04-01T00:00:00Z","doi":"10.1242/jcs.261720","citation":{"ista":"Gnyliukh N, Johnson AJ, Nagel M, Monzer A, Babic D, Hlavata A, Alotaibi S, Isono E, Loose M, Friml J. 2024. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana. Journal of Cell Science. 137(8), jcs. 261720.","ama":"Gnyliukh N, Johnson AJ, Nagel M, et al. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana. <i>Journal of Cell Science</i>. 2024;137(8). doi:<a href=\"https://doi.org/10.1242/jcs.261720\">10.1242/jcs.261720</a>","apa":"Gnyliukh, N., Johnson, A. J., Nagel, M., Monzer, A., Babic, D., Hlavata, A., … Friml, J. (2024). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.261720\">https://doi.org/10.1242/jcs.261720</a>","chicago":"Gnyliukh, Nataliia, Alexander J Johnson, MK Nagel, Aline Monzer, David Babic, Annamaria Hlavata, SS Alotaibi, E Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Arabidopsis Thaliana.” <i>Journal of Cell Science</i>. The Company of Biologists, 2024. <a href=\"https://doi.org/10.1242/jcs.261720\">https://doi.org/10.1242/jcs.261720</a>.","short":"N. Gnyliukh, A.J. Johnson, M. Nagel, A. Monzer, D. Babic, A. Hlavata, S. Alotaibi, E. Isono, M. Loose, J. Friml, Journal of Cell Science 137 (2024).","ieee":"N. Gnyliukh <i>et al.</i>, “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana,” <i>Journal of Cell Science</i>, vol. 137, no. 8. The Company of Biologists, 2024.","mla":"Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Arabidopsis Thaliana.” <i>Journal of Cell Science</i>, vol. 137, no. 8, jcs. 261720, The Company of Biologists, 2024, doi:<a href=\"https://doi.org/10.1242/jcs.261720\">10.1242/jcs.261720</a>."},"year":"2024","date_created":"2024-04-19T09:54:59Z","publication":"Journal of Cell Science","author":[{"orcid":"0000-0002-2198-0509","full_name":"Gnyliukh, Nataliia","last_name":"Gnyliukh","first_name":"Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Johnson","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J"},{"full_name":"Nagel, MK","first_name":"MK","last_name":"Nagel"},{"full_name":"Monzer, Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","first_name":"Aline","last_name":"Monzer"},{"full_name":"Babic, David","id":"db566d23-f6e0-11ea-865d-e6f270e968e7","first_name":"David","last_name":"Babic"},{"id":"36062FEC-F248-11E8-B48F-1D18A9856A87","first_name":"Annamaria","last_name":"Hlavata","full_name":"Hlavata, Annamaria"},{"first_name":"SS","last_name":"Alotaibi","full_name":"Alotaibi, SS"},{"full_name":"Isono, E","first_name":"E","last_name":"Isono"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"date_updated":"2026-10-16T10:38:13Z","corr_author":"1","OA_place":"publisher","supplementarymaterial":"yes","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","related_material":{"record":[{"id":"14591","status":"public","relation":"earlier_version"}]},"oa":1,"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2025-01-09T08:41:16Z","isi":1,"fulldoi":"https://doi.org/10.1242/jcs.261720","publication_status":"published","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"grant_number":"I06123","_id":"bd76d395-d553-11ed-ba76-f678c14f9033","name":"Peptide receptors for auxin canalization in Arabidopsis"}],"file":[{"creator":"dernst","checksum":"6dc023f0cc7052ad3cf0a42589d2e30f","file_id":"18792","file_size":25845948,"date_created":"2025-01-09T08:41:16Z","content_type":"application/pdf","file_name":"2024_JourCellScience_Gnyliukh.pdf","access_level":"open_access","date_updated":"2025-01-09T08:41:16Z","success":1,"relation":"main_file"}],"title":"Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana","ddc":["570"],"ec_funded":1,"type":"journal_article","OA_type":"hybrid","status":"public"},{"das_tickbox":"0","scopus_import":"1","abstract":[{"text":"We propose a novel approach to concentration for non-independent random variables. The main idea is to “pretend” that the random variables are independent and pay a multiplicative price measuring how far they are from actually being independent. This price is encapsulated in the Hellinger integral between the joint and the product of the marginals, which is then upper bounded leveraging tensorisation properties. Our bounds represent a natural generalisation of concentration inequalities in the presence of dependence: we recover exactly the classical bounds (McDiarmid’s inequality) when the random variables are independent. Furthermore, in a “large deviations” regime, we obtain the same decay in the probability as for the independent case, even when the random variables display non-trivial dependencies. To show this, we consider a number of applications of interest. First, we provide a bound for Markov chains with finite state space. Then, we consider the Simple Symmetric Random Walk, which is a non-contracting Markov chain, and a non-Markovian setting in which the stochastic process depends on its entire past. To conclude, we propose an application to Markov Chain Monte Carlo methods, where our approach leads to an improved lower bound on the minimum burn-in period required to reach a certain accuracy. In all of these settings, we provide a regime of parameters in which our bound fares better than what the state of the art can provide.","lang":"eng"}],"doi":"10.1109/TIT.2024.3367767","day":"01","date_published":"2024-06-01T00:00:00Z","date_created":"2024-03-24T23:01:00Z","year":"2024","citation":{"ama":"Esposito AR, Mondelli M. Concentration without independence via information measures. <i>IEEE Transactions on Information Theory</i>. 2024;70(6):3823-3839. doi:<a href=\"https://doi.org/10.1109/TIT.2024.3367767\">10.1109/TIT.2024.3367767</a>","ista":"Esposito AR, Mondelli M. 2024. Concentration without independence via information measures. IEEE Transactions on Information Theory. 70(6), 3823–3839.","apa":"Esposito, A. R., &#38; Mondelli, M. (2024). Concentration without independence via information measures. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/TIT.2024.3367767\">https://doi.org/10.1109/TIT.2024.3367767</a>","chicago":"Esposito, Amedeo Roberto, and Marco Mondelli. “Concentration without Independence via Information Measures.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2024. <a href=\"https://doi.org/10.1109/TIT.2024.3367767\">https://doi.org/10.1109/TIT.2024.3367767</a>.","ieee":"A. R. Esposito and M. Mondelli, “Concentration without independence via information measures,” <i>IEEE Transactions on Information Theory</i>, vol. 70, no. 6. IEEE, pp. 3823–3839, 2024.","short":"A.R. Esposito, M. Mondelli, IEEE Transactions on Information Theory 70 (2024) 3823–3839.","mla":"Esposito, Amedeo Roberto, and Marco Mondelli. “Concentration without Independence via Information Measures.” <i>IEEE Transactions on Information Theory</i>, vol. 70, no. 6, IEEE, 2024, pp. 3823–39, doi:<a href=\"https://doi.org/10.1109/TIT.2024.3367767\">10.1109/TIT.2024.3367767</a>."},"publication":"IEEE Transactions on Information Theory","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2303.07245"}],"author":[{"id":"9583e921-e1ad-11ec-9862-cef099626dc9","first_name":"Amedeo Roberto","last_name":"Esposito","full_name":"Esposito, Amedeo Roberto"},{"first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020"}],"date_updated":"2026-10-16T10:39:43Z","intvolume":"        70","volume":70,"researchdata_availability":"no","article_type":"original","publication_identifier":{"issn":["0018-9448"],"eissn":["1557-9654"]},"quality_controlled":"1","issue":"6","_id":"15172","department":[{"_id":"MaMo"}],"oa_version":"Preprint","month":"06","publisher":"IEEE","external_id":{"isi":["001230181100001"],"arxiv":["2303.07245"]},"isi":1,"fulldoi":"https://doi.org/10.1109/TIT.2024.3367767","arxiv":1,"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"title":"Concentration without independence via information measures","publication_status":"published","type":"journal_article","status":"public","corr_author":"1","supplementarymaterial":"yes","page":"3823-3839","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"oa":1,"related_material":{"record":[{"id":"14922","status":"public","relation":"earlier_version"}]},"article_processing_charge":"No"},{"supplementarymaterial":"no","corr_author":"1","oa":1,"article_processing_charge":"No","language":[{"iso":"eng"}],"page":"3178-3183","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","title":"Properties of the strong data processing constant for Rényi divergence","isi":1,"arxiv":1,"fulldoi":"https://doi.org/10.1109/ISIT57864.2024.10619367","status":"public","type":"conference","quality_controlled":"1","publication_identifier":{"isbn":["9798350382846"],"issn":["2157-8095"]},"researchdata_availability":"no","publisher":"IEEE","month":"08","oa_version":"Preprint","external_id":{"arxiv":["2403.10656"],"isi":["001304426903055"]},"conference":{"end_date":"2024-07-12","name":"ISIT: International Symposium on Information Theory","start_date":"2024-07-07","location":"Athens, Greece"},"acknowledgement":"The work in this paper was supported in part by the Swiss National Science Foundation under Grant 200364.\r\n","department":[{"_id":"MaMo"}],"_id":"17893","abstract":[{"lang":"eng","text":"Strong data processing inequalities (SDPI) are an important object of study in Information Theory and have been well studied for f -divergences. Universal upper and lower bounds have been provided along with several applications, connecting them to impossibility (converse) results, concentration of measure, hypercontractivity, and so on. In this paper, we study Renyi divergence and the corresponding SDPI constant whose behavior seems to deviate from that of ordinary <1>-divergences. In particular, one can find examples showing that the universal upper bound relating its SDPI constant to the one of Total Variation does not hold in general. In this work, we prove, however, that the universal lower bound involving the SDPI constant of the Chi-square divergence does indeed hold. Furthermore, we also provide a characterization of the distribution that achieves the supremum when is equal to 2 and consequently compute the SDPI constant for Renyi divergence of the general binary channel."}],"scopus_import":"1","day":"19","date_published":"2024-08-19T00:00:00Z","doi":"10.1109/ISIT57864.2024.10619367","das_tickbox":"0","author":[{"first_name":"Lifu","last_name":"Jin","full_name":"Jin, Lifu"},{"full_name":"Esposito, Amedeo Roberto","first_name":"Amedeo Roberto","id":"9583e921-e1ad-11ec-9862-cef099626dc9","last_name":"Esposito"},{"full_name":"Gastpar, Michael","last_name":"Gastpar","first_name":"Michael"}],"date_updated":"2026-10-16T10:38:29Z","citation":{"apa":"Jin, L., Esposito, A. R., &#38; Gastpar, M. (2024). Properties of the strong data processing constant for Rényi divergence. In <i>Proceedings of the 2024 IEEE International Symposium on Information Theory</i> (pp. 3178–3183). Athens, Greece: IEEE. <a href=\"https://doi.org/10.1109/ISIT57864.2024.10619367\">https://doi.org/10.1109/ISIT57864.2024.10619367</a>","ista":"Jin L, Esposito AR, Gastpar M. 2024. Properties of the strong data processing constant for Rényi divergence. Proceedings of the 2024 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory, 3178–3183.","ama":"Jin L, Esposito AR, Gastpar M. Properties of the strong data processing constant for Rényi divergence. In: <i>Proceedings of the 2024 IEEE International Symposium on Information Theory</i>. IEEE; 2024:3178-3183. doi:<a href=\"https://doi.org/10.1109/ISIT57864.2024.10619367\">10.1109/ISIT57864.2024.10619367</a>","mla":"Jin, Lifu, et al. “Properties of the Strong Data Processing Constant for Rényi Divergence.” <i>Proceedings of the 2024 IEEE International Symposium on Information Theory</i>, IEEE, 2024, pp. 3178–83, doi:<a href=\"https://doi.org/10.1109/ISIT57864.2024.10619367\">10.1109/ISIT57864.2024.10619367</a>.","ieee":"L. Jin, A. R. Esposito, and M. Gastpar, “Properties of the strong data processing constant for Rényi divergence,” in <i>Proceedings of the 2024 IEEE International Symposium on Information Theory</i>, Athens, Greece, 2024, pp. 3178–3183.","short":"L. Jin, A.R. Esposito, M. Gastpar, in:, Proceedings of the 2024 IEEE International Symposium on Information Theory, IEEE, 2024, pp. 3178–3183.","chicago":"Jin, Lifu, Amedeo Roberto Esposito, and Michael Gastpar. “Properties of the Strong Data Processing Constant for Rényi Divergence.” In <i>Proceedings of the 2024 IEEE International Symposium on Information Theory</i>, 3178–83. IEEE, 2024. <a href=\"https://doi.org/10.1109/ISIT57864.2024.10619367\">https://doi.org/10.1109/ISIT57864.2024.10619367</a>."},"year":"2024","date_created":"2024-09-08T22:01:12Z","publication":"Proceedings of the 2024 IEEE International Symposium on Information Theory","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2403.10656 "}]},{"article_processing_charge":"No","oa":1,"page":"1008-1039","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"supplementarymaterial":"yes","corr_author":"1","status":"public","type":"journal_article","title":"Multiple packing: Lower bounds via error exponents","publication_status":"published","fulldoi":"https://doi.org/10.1109/TIT.2023.3334032","arxiv":1,"isi":1,"external_id":{"arxiv":["2211.04408"],"isi":["001166812100008"]},"month":"02","oa_version":"Preprint","publisher":"IEEE","_id":"14665","department":[{"_id":"MaMo"}],"acknowledgement":"The work of Yihan Zhang was supported by the European Union’s Horizon 2020 Research and Innovation Programme under Grant 682203-ERC-[Inf-Speed-Tradeoff]. The work of Shashank Vatedka was supported in part by the Core Research Grant from the Science and\r\nEngineering Research Board, India, under Grant CRG/2022/004464; and in\r\npart by the Department of Science and Technology (DST), India, under Grant\r\nDST/INT/RUS/RSF/P-41/2020 (TPN No. 65025).","issue":"2","quality_controlled":"1","volume":70,"researchdata_availability":"no","article_type":"original","publication_identifier":{"issn":["0018-9448"],"eissn":["1557-9654"]},"intvolume":"        70","date_updated":"2026-10-16T10:39:20Z","author":[{"full_name":"Zhang, Yihan","orcid":"0000-0002-6465-6258","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","first_name":"Yihan","last_name":"Zhang"},{"last_name":"Vatedka","first_name":"Shashank","full_name":"Vatedka, Shashank"}],"publication":"IEEE Transactions on Information Theory","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.04408"}],"year":"2024","date_created":"2023-12-10T23:01:00Z","citation":{"apa":"Zhang, Y., &#38; Vatedka, S. (2024). Multiple packing: Lower bounds via error exponents. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/TIT.2023.3334032\">https://doi.org/10.1109/TIT.2023.3334032</a>","ama":"Zhang Y, Vatedka S. Multiple packing: Lower bounds via error exponents. <i>IEEE Transactions on Information Theory</i>. 2024;70(2):1008-1039. doi:<a href=\"https://doi.org/10.1109/TIT.2023.3334032\">10.1109/TIT.2023.3334032</a>","ista":"Zhang Y, Vatedka S. 2024. Multiple packing: Lower bounds via error exponents. IEEE Transactions on Information Theory. 70(2), 1008–1039.","ieee":"Y. Zhang and S. Vatedka, “Multiple packing: Lower bounds via error exponents,” <i>IEEE Transactions on Information Theory</i>, vol. 70, no. 2. IEEE, pp. 1008–1039, 2024.","short":"Y. Zhang, S. Vatedka, IEEE Transactions on Information Theory 70 (2024) 1008–1039.","mla":"Zhang, Yihan, and Shashank Vatedka. “Multiple Packing: Lower Bounds via Error Exponents.” <i>IEEE Transactions on Information Theory</i>, vol. 70, no. 2, IEEE, 2024, pp. 1008–39, doi:<a href=\"https://doi.org/10.1109/TIT.2023.3334032\">10.1109/TIT.2023.3334032</a>.","chicago":"Zhang, Yihan, and Shashank Vatedka. “Multiple Packing: Lower Bounds via Error Exponents.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2024. <a href=\"https://doi.org/10.1109/TIT.2023.3334032\">https://doi.org/10.1109/TIT.2023.3334032</a>."},"doi":"10.1109/TIT.2023.3334032","date_published":"2024-02-01T00:00:00Z","day":"01","scopus_import":"1","abstract":[{"text":"We derive lower bounds on the maximal rates for multiple packings in high-dimensional Euclidean spaces. For any N > 0 and L ∈ Z ≥2 , a multiple packing is a set C of points in R n such that any point in R n lies in the intersection of at most L - 1 balls of radius √ nN around points in C . This is a natural generalization of the sphere packing problem. We study the multiple packing problem for both bounded point sets whose points have norm at most √ nP for some constant P > 0, and unbounded point sets whose points are allowed to be anywhere in R n . Given a well-known connection with coding theory, multiple packings can be viewed as the Euclidean analog of list-decodable codes, which are well-studied over finite fields. We derive the best known lower bounds on the optimal multiple packing density. This is accomplished by establishing an inequality which relates the list-decoding error exponent for additive white Gaussian noise channels, a quantity of average-case nature, to the list-decoding radius, a quantity of worst-case nature. We also derive novel bounds on the list-decoding error exponent for infinite constellations and closed-form expressions for the list-decoding error exponents for the power-constrained AWGN channel, which may be of independent interest beyond multiple packing.","lang":"eng"}],"das_tickbox":"0"},{"supplementarymaterial":"no","language":[{"iso":"eng"}],"page":"1586-1591","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","isi":1,"fulldoi":"https://doi.org/10.1109/ISIT57864.2024.10619362","publication_status":"published","title":"Computationally efficient codes for strongly Dobrushin-Stambler nonsymmetrizable oblivious AVCs","type":"conference","status":"public","publication_identifier":{"isbn":["9798350382846"],"issn":["2157-8095"]},"researchdata_availability":"no","quality_controlled":"1","acknowledgement":"The work of M. Langberg and A. D. Sarwate was supported in part by the US NSF under awards CCF-1909451 and CCF1909468. B. K. Dey was supported in part by the Bharti Centre\r\nfor Communication in IIT Bombay. ","department":[{"_id":"MaMo"}],"_id":"17895","publisher":"IEEE","month":"08","oa_version":"None","external_id":{"isi":["001304426901091"]},"conference":{"location":"Athens, Greece","start_date":"2024-07-07","end_date":"2024-07-12","name":"ISIT: International Symposium on Information Theory"},"das_tickbox":"0","abstract":[{"lang":"eng","text":"We propose a concatenated code construction for a class of discrete-alphabet oblivious arbitrarily varying channels (AVCs) with cost constraints. The code has time and space complexity polynomial in the blocklength n . It uses a Reed-Solomon outer code, logarithmic blocklength random inner codes, and stochastic encoding by permuting the codeword before transmission. When the channel satisfies a condition called strong DS-nonsymmetrizability (a modified version of nonsymmetrizability originally due to Dobrushin and Stambler), we show that the code achieves a rate that for a variety of oblivious AVCs (such as classically studied error/erasure channels) match the known capacities."}],"scopus_import":"1","day":"19","date_published":"2024-08-19T00:00:00Z","doi":"10.1109/ISIT57864.2024.10619362","citation":{"chicago":"Dey, B. K., S. Jaggi, M. Langberg, A. D. Sarwate, and Yihan Zhang. “Computationally Efficient Codes for Strongly Dobrushin-Stambler Nonsymmetrizable Oblivious AVCs.” In <i>Proceedings of the 2024 IEEE International Symposium on Information Theory </i>, 1586–91. IEEE, 2024. <a href=\"https://doi.org/10.1109/ISIT57864.2024.10619362\">https://doi.org/10.1109/ISIT57864.2024.10619362</a>.","mla":"Dey, B. K., et al. “Computationally Efficient Codes for Strongly Dobrushin-Stambler Nonsymmetrizable Oblivious AVCs.” <i>Proceedings of the 2024 IEEE International Symposium on Information Theory </i>, IEEE, 2024, pp. 1586–91, doi:<a href=\"https://doi.org/10.1109/ISIT57864.2024.10619362\">10.1109/ISIT57864.2024.10619362</a>.","ieee":"B. K. Dey, S. Jaggi, M. Langberg, A. D. Sarwate, and Y. Zhang, “Computationally efficient codes for strongly Dobrushin-Stambler nonsymmetrizable oblivious AVCs,” in <i>Proceedings of the 2024 IEEE International Symposium on Information Theory </i>, Athens, Greece, 2024, pp. 1586–1591.","short":"B.K. Dey, S. Jaggi, M. Langberg, A.D. Sarwate, Y. Zhang, in:, Proceedings of the 2024 IEEE International Symposium on Information Theory , IEEE, 2024, pp. 1586–1591.","ama":"Dey BK, Jaggi S, Langberg M, Sarwate AD, Zhang Y. Computationally efficient codes for strongly Dobrushin-Stambler nonsymmetrizable oblivious AVCs. In: <i>Proceedings of the 2024 IEEE International Symposium on Information Theory </i>. IEEE; 2024:1586-1591. doi:<a href=\"https://doi.org/10.1109/ISIT57864.2024.10619362\">10.1109/ISIT57864.2024.10619362</a>","ista":"Dey BK, Jaggi S, Langberg M, Sarwate AD, Zhang Y. 2024. Computationally efficient codes for strongly Dobrushin-Stambler nonsymmetrizable oblivious AVCs. Proceedings of the 2024 IEEE International Symposium on Information Theory . ISIT: International Symposium on Information Theory, 1586–1591.","apa":"Dey, B. K., Jaggi, S., Langberg, M., Sarwate, A. D., &#38; Zhang, Y. (2024). Computationally efficient codes for strongly Dobrushin-Stambler nonsymmetrizable oblivious AVCs. In <i>Proceedings of the 2024 IEEE International Symposium on Information Theory </i> (pp. 1586–1591). Athens, Greece: IEEE. <a href=\"https://doi.org/10.1109/ISIT57864.2024.10619362\">https://doi.org/10.1109/ISIT57864.2024.10619362</a>"},"date_created":"2024-09-08T22:01:12Z","year":"2024","publication":"Proceedings of the 2024 IEEE International Symposium on Information Theory ","author":[{"full_name":"Dey, B. K.","first_name":"B. K.","last_name":"Dey"},{"first_name":"S.","last_name":"Jaggi","full_name":"Jaggi, S."},{"full_name":"Langberg, M.","last_name":"Langberg","first_name":"M."},{"full_name":"Sarwate, A. D.","first_name":"A. D.","last_name":"Sarwate"},{"first_name":"Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","last_name":"Zhang","full_name":"Zhang, Yihan","orcid":"0000-0002-6465-6258"}],"date_updated":"2026-10-16T10:39:03Z"},{"article_processing_charge":"No","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"2110-2115","supplementarymaterial":"no","corr_author":"1","status":"public","type":"conference","publication_status":"published","title":"Variational characterizations of Sibson's α-mutual information","fulldoi":"https://doi.org/10.1109/ISIT57864.2024.10619378","isi":1,"external_id":{"isi":["001304426902023"]},"conference":{"start_date":"2024-07-07","name":"ISIT: International Symposium on Information Theory","end_date":"2024-07-12","location":"Athens, Greece"},"publisher":"IEEE","month":"08","oa_version":"None","department":[{"_id":"MaMo"}],"_id":"17894","acknowledgement":"The work in this paper was supported in part by the Swiss National Science Foundation under Grant 200364.","quality_controlled":"1","publication_identifier":{"issn":["2157-8095"],"isbn":["9798350382846"]},"researchdata_availability":"no","date_updated":"2026-10-16T10:38:46Z","author":[{"first_name":"Amedeo Roberto","id":"9583e921-e1ad-11ec-9862-cef099626dc9","last_name":"Esposito","full_name":"Esposito, Amedeo Roberto"},{"full_name":"Gastpar, Michael","last_name":"Gastpar","first_name":"Michael"},{"full_name":"Issa, Ibrahim","last_name":"Issa","first_name":"Ibrahim"}],"publication":"Proceedings of the 2024 IEEE International Symposium on Information Theory ","citation":{"chicago":"Esposito, Amedeo Roberto, Michael Gastpar, and Ibrahim Issa. “Variational Characterizations of Sibson’s α-Mutual Information.” In <i>Proceedings of the 2024 IEEE International Symposium on Information Theory </i>, 2110–15. IEEE, 2024. <a href=\"https://doi.org/10.1109/ISIT57864.2024.10619378\">https://doi.org/10.1109/ISIT57864.2024.10619378</a>.","mla":"Esposito, Amedeo Roberto, et al. “Variational Characterizations of Sibson’s α-Mutual Information.” <i>Proceedings of the 2024 IEEE International Symposium on Information Theory </i>, IEEE, 2024, pp. 2110–15, doi:<a href=\"https://doi.org/10.1109/ISIT57864.2024.10619378\">10.1109/ISIT57864.2024.10619378</a>.","short":"A.R. Esposito, M. Gastpar, I. Issa, in:, Proceedings of the 2024 IEEE International Symposium on Information Theory , IEEE, 2024, pp. 2110–2115.","ieee":"A. R. Esposito, M. Gastpar, and I. Issa, “Variational characterizations of Sibson’s α-mutual information,” in <i>Proceedings of the 2024 IEEE International Symposium on Information Theory </i>, Athens, Greece, 2024, pp. 2110–2115.","ista":"Esposito AR, Gastpar M, Issa I. 2024. Variational characterizations of Sibson’s α-mutual information. Proceedings of the 2024 IEEE International Symposium on Information Theory . ISIT: International Symposium on Information Theory, 2110–2115.","ama":"Esposito AR, Gastpar M, Issa I. Variational characterizations of Sibson’s α-mutual information. In: <i>Proceedings of the 2024 IEEE International Symposium on Information Theory </i>. IEEE; 2024:2110-2115. doi:<a href=\"https://doi.org/10.1109/ISIT57864.2024.10619378\">10.1109/ISIT57864.2024.10619378</a>","apa":"Esposito, A. R., Gastpar, M., &#38; Issa, I. (2024). Variational characterizations of Sibson’s α-mutual information. In <i>Proceedings of the 2024 IEEE International Symposium on Information Theory </i> (pp. 2110–2115). Athens, Greece: IEEE. <a href=\"https://doi.org/10.1109/ISIT57864.2024.10619378\">https://doi.org/10.1109/ISIT57864.2024.10619378</a>"},"year":"2024","date_created":"2024-09-08T22:01:12Z","date_published":"2024-08-19T00:00:00Z","day":"19","doi":"10.1109/ISIT57864.2024.10619378","scopus_import":"1","abstract":[{"lang":"eng","text":"Sibson's α -mutual information has received renewed attention recently in several contexts: concentration of measure under dependence, statistical learning, hypothesis testing, and estimation theory. In this work, we introduce several variational representations of Sibson's α -mutual information: 1) as a supremum over joint distributions of (a combination of) KL divergences; and 2) as a supremum over functions of opportune expected values. Leveraging them, we produce a variety of novel and known results, including a generalization of transportation-cost inequalities and Fano's inequality."}],"das_tickbox":"0"},{"ddc":["570"],"type":"journal_article","status":"public","isi":1,"fulldoi":"https://doi.org/10.1007/s11692-023-09624-1","file":[{"file_id":"17311","file_size":1705974,"checksum":"416ab4dac751c443b9de51fb58278ff2","creator":"dernst","relation":"main_file","success":1,"date_updated":"2024-07-22T11:53:43Z","access_level":"open_access","file_name":"2024_EvolutionaryBio_Tsuboi.pdf","date_created":"2024-07-22T11:53:43Z","content_type":"application/pdf"}],"title":"Antler allometry, the Irish elk and Gould revisited","publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"149-165","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"dataavailabilitystatement":"All data used in this paper are available from the authors on request.","oa":1,"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2024-07-22T11:53:43Z","supplementarymaterial":"yes","year":"2024","date_created":"2024-02-04T23:00:53Z","citation":{"mla":"Tsuboi, Masahito, et al. “Antler Allometry, the Irish Elk and Gould Revisited.” <i>Evolutionary Biology</i>, vol. 51, Springer Nature, 2024, pp. 149–65, doi:<a href=\"https://doi.org/10.1007/s11692-023-09624-1\">10.1007/s11692-023-09624-1</a>.","ieee":"M. Tsuboi <i>et al.</i>, “Antler allometry, the Irish elk and Gould revisited,” <i>Evolutionary Biology</i>, vol. 51. Springer Nature, pp. 149–165, 2024.","short":"M. Tsuboi, B.T. Kopperud, M. Matschiner, M. Grabowski, C. Syrowatka, C. Pélabon, T.F. Hansen, Evolutionary Biology 51 (2024) 149–165.","chicago":"Tsuboi, Masahito, Bjørn Tore Kopperud, Michael Matschiner, Mark Grabowski, Chrsitine Syrowatka, Christophe Pélabon, and Thomas F. Hansen. “Antler Allometry, the Irish Elk and Gould Revisited.” <i>Evolutionary Biology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s11692-023-09624-1\">https://doi.org/10.1007/s11692-023-09624-1</a>.","apa":"Tsuboi, M., Kopperud, B. T., Matschiner, M., Grabowski, M., Syrowatka, C., Pélabon, C., &#38; Hansen, T. F. (2024). Antler allometry, the Irish elk and Gould revisited. <i>Evolutionary Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11692-023-09624-1\">https://doi.org/10.1007/s11692-023-09624-1</a>","ista":"Tsuboi M, Kopperud BT, Matschiner M, Grabowski M, Syrowatka C, Pélabon C, Hansen TF. 2024. Antler allometry, the Irish elk and Gould revisited. Evolutionary Biology. 51, 149–165.","ama":"Tsuboi M, Kopperud BT, Matschiner M, et al. Antler allometry, the Irish elk and Gould revisited. <i>Evolutionary Biology</i>. 2024;51:149-165. doi:<a href=\"https://doi.org/10.1007/s11692-023-09624-1\">10.1007/s11692-023-09624-1</a>"},"publication":"Evolutionary Biology","author":[{"full_name":"Tsuboi, Masahito","first_name":"Masahito","last_name":"Tsuboi"},{"full_name":"Kopperud, Bjørn Tore","first_name":"Bjørn Tore","last_name":"Kopperud"},{"full_name":"Matschiner, Michael","last_name":"Matschiner","first_name":"Michael"},{"full_name":"Grabowski, Mark","first_name":"Mark","last_name":"Grabowski"},{"last_name":"Syrowatka","first_name":"Chrsitine","id":"205ffb76-7fe7-11eb-aa17-958bd11b99ad","full_name":"Syrowatka, Chrsitine"},{"first_name":"Christophe","last_name":"Pélabon","full_name":"Pélabon, Christophe"},{"full_name":"Hansen, Thomas F.","first_name":"Thomas F.","last_name":"Hansen"}],"date_updated":"2026-10-16T10:43:26Z","das_tickbox":"1","scopus_import":"1","abstract":[{"lang":"eng","text":"The huge antlers of the extinct Irish elk have invited evolutionary speculation since Darwin. In the 1970s, Stephen Jay Gould presented the first extensive data on antler size in the Irish elk and combined these with comparative data from other deer to test the hypothesis that the gigantic antlers were the outcome of a positive allometry that constrained large-bodied deer to have proportionally even larger antlers. He concluded that the Irish elk had antlers as predicted for its size and interpreted this within his emerging framework of developmental constraints as an explanatory factor in evolution. Here we reanalyze antler allometry based on new morphometric data for 57 taxa of the family Cervidae. We also present a new phylogeny for the Cervidae, which we use for comparative analyses. In contrast to Gould, we find that the antlers of Irish elk were larger than predicted from the allometry within the true deer, Cervini, as analyzed by Gould, but follow the allometry across Cervidae as a whole. After dissecting the discrepancy, we reject the allometric-constraint hypothesis because, contrary to Gould, we find no similarity between static and evolutionary allometries, and because we document extensive non-allometric evolution of antler size across the Cervidae."}],"doi":"10.1007/s11692-023-09624-1","day":"01","date_published":"2024-03-01T00:00:00Z","acknowledgement":"Open access funding provided by University of Oslo (incl Oslo University Hospital).\r\nWe thank Adrian Lister, Louis Tomsett, Roberto Portela Miguez and Roula Pappa (NHMUK), Brian O'Toole and Eileen Westwig (AMNH), Daniela Kalthoff (NHRM), Alexander Bibl and Zachos Frank (NHMW), Darrin Lunde and John Ososky (NMNH), Matthew Parkes and Nigel Monaghan (NMI), Elizabetta Cioppi and Luca Bellucci (IGF), and Yoshihiro Tanaka and Hiroyuki Taruno (OMNH), who helped us in obtaining the museum data, and a special thanks to Jørgen Sikkeland (NTNU NHM) for assistance in obtaining the ontogenetic data for the red deer. We thank Olja Toljagic and Kjetil L. Voje for discussions, Ayumu Tsuboi for assistance with data collection, and Jean-Michel Gaillard and the anonymous reviewers for comments on the manuscript. We thank the Centre of Advanced Study (CAS) at the Norwegian Academy of Sciences and Letters for hosting us during the academic year of 2019/2020 when much of the analysis and writing were done. MT was funded by JSPS Research Fellowship for Young Scientists (201603238).","_id":"14932","department":[{"_id":"MaRo"}],"month":"03","oa_version":"Published Version","publisher":"Springer Nature","external_id":{"isi":["001151285200001"]},"intvolume":"        51","volume":51,"researchdata_availability":"upon request","publication_identifier":{"issn":["0071-3260"],"eissn":["1934-2845"]},"article_type":"original","quality_controlled":"1"},{"status":"public","type":"conference","OA_type":"green","publication_status":"published","title":"Inference of genetic effects via approximate message passing","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"},{"_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","grant_number":"PCEGP3_181181","name":"Improving estimation and prediction of common complex disease risk"}],"fulldoi":"https://doi.org/10.1109/ICASSP48485.2024.10447198","isi":1,"article_processing_charge":"No","oa":1,"language":[{"iso":"eng"}],"page":"13151-13155","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","supplementarymaterial":"no","corr_author":"1","OA_place":"repository","date_updated":"2026-10-16T10:42:55Z","author":[{"first_name":"Al","id":"0b77531d-dbcd-11ea-9d1d-a8eee0bf3830","last_name":"Depope","full_name":"Depope, Al"},{"orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco"},{"orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","last_name":"Robinson","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"}],"publication":"2024 IEEE International Conference on Acoustics, Speech, and Signal Processing","main_file_link":[{"url":"https://openreview.net/forum?id=aQYCDxfZV0","open_access":"1"}],"citation":{"apa":"Depope, A., Mondelli, M., &#38; Robinson, M. R. (2024). Inference of genetic effects via approximate message passing. In <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i> (pp. 13151–13155). Seoul, Korea: IEEE. <a href=\"https://doi.org/10.1109/ICASSP48485.2024.10447198\">https://doi.org/10.1109/ICASSP48485.2024.10447198</a>","ista":"Depope A, Mondelli M, Robinson MR. 2024. Inference of genetic effects via approximate message passing. 2024 IEEE International Conference on Acoustics, Speech, and Signal Processing. ICASSP: International Conference on Acoustics, Speech and Signal Processing, 13151–13155.","ama":"Depope A, Mondelli M, Robinson MR. Inference of genetic effects via approximate message passing. In: <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i>. IEEE; 2024:13151-13155. doi:<a href=\"https://doi.org/10.1109/ICASSP48485.2024.10447198\">10.1109/ICASSP48485.2024.10447198</a>","mla":"Depope, Al, et al. “Inference of Genetic Effects via Approximate Message Passing.” <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i>, IEEE, 2024, pp. 13151–55, doi:<a href=\"https://doi.org/10.1109/ICASSP48485.2024.10447198\">10.1109/ICASSP48485.2024.10447198</a>.","short":"A. Depope, M. Mondelli, M.R. Robinson, in:, 2024 IEEE International Conference on Acoustics, Speech, and Signal Processing, IEEE, 2024, pp. 13151–13155.","ieee":"A. Depope, M. Mondelli, and M. R. Robinson, “Inference of genetic effects via approximate message passing,” in <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i>, Seoul, Korea, 2024, pp. 13151–13155.","chicago":"Depope, Al, Marco Mondelli, and Matthew Richard Robinson. “Inference of Genetic Effects via Approximate Message Passing.” In <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i>, 13151–55. IEEE, 2024. <a href=\"https://doi.org/10.1109/ICASSP48485.2024.10447198\">https://doi.org/10.1109/ICASSP48485.2024.10447198</a>."},"year":"2024","date_created":"2024-06-16T22:01:07Z","date_published":"2024-04-19T00:00:00Z","day":"19","doi":"10.1109/ICASSP48485.2024.10447198","abstract":[{"lang":"eng","text":"Efficient utilization of large-scale biobank data is crucial for inferring the genetic basis of disease and predicting health outcomes from the DNA. Yet we lack efficient, accurate methods that scale to data where electronic health records are linked to whole genome sequence information. To address this issue, our paper develops a new algorithmic paradigm based on Approximate Message Passing (AMP), which is specifically tailored for genomic prediction and association testing. Our method yields comparable out-of-sample prediction accuracy to the state of the art on UK Biobank traits, whilst dramatically improving computational complexity, with a 8x-speed up in the run time. In addition, AMP theory provides a joint association testing framework, which outperforms the currently used REGENIE method, in roughly a third of the compute time. This first, truly large-scale application of the AMP framework lays the foundations for a far wider range of statistical analyses for hundreds of millions of variables measured on millions of people."}],"scopus_import":"1","das_tickbox":"0","acknowledged_ssus":[{"_id":"ScienComp"}],"external_id":{"isi":["001396233806078"]},"conference":{"location":"Seoul, Korea","start_date":"2024-04-14","end_date":"2024-04-19","name":"ICASSP: International Conference on Acoustics, Speech and Signal Processing"},"publisher":"IEEE","oa_version":"Submitted Version","month":"04","department":[{"_id":"MaMo"},{"_id":"MaRo"}],"_id":"17147","acknowledgement":"This work was supported by a Lopez-Loreta Prize to MM, an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and core funding from ISTA. The authors thank Philip Schniter, Matthew Stephens and Pragya Sur for valuable suggestions on an early version of the work. The authors acknowledge the participants and investigators of the UK Biobank study. High-performance\r\ncomputing was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","quality_controlled":"1","publication_identifier":{"isbn":["9798350344851"],"issn":["1520-6149"]},"researchdata_availability":"no"},{"date_updated":"2026-10-16T10:42:17Z","author":[{"id":"ca726dda-de17-11ea-bc14-f9da834f63aa","first_name":"Simone","last_name":"Bombari","full_name":"Bombari, Simone"},{"first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2402.02969","open_access":"1"}],"publication":"41st International Conference on Machine Learning","citation":{"ista":"Bombari S, Mondelli M. 2024. Towards understanding the word sensitivity of attention layers: A study via random features. 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 4300–4328.","ama":"Bombari S, Mondelli M. Towards understanding the word sensitivity of attention layers: A study via random features. In: <i>41st International Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:4300-4328.","apa":"Bombari, S., &#38; Mondelli, M. (2024). Towards understanding the word sensitivity of attention layers: A study via random features. In <i>41st International Conference on Machine Learning</i> (Vol. 235, pp. 4300–4328). Vienna, Austria: ML Research Press.","chicago":"Bombari, Simone, and Marco Mondelli. “Towards Understanding the Word Sensitivity of Attention Layers: A Study via Random Features.” In <i>41st International Conference on Machine Learning</i>, 235:4300–4328. ML Research Press, 2024.","ieee":"S. Bombari and M. Mondelli, “Towards understanding the word sensitivity of attention layers: A study via random features,” in <i>41st International Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 4300–4328.","short":"S. Bombari, M. Mondelli, in:, 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 4300–4328.","mla":"Bombari, Simone, and Marco Mondelli. “Towards Understanding the Word Sensitivity of Attention Layers: A Study via Random Features.” <i>41st International Conference on Machine Learning</i>, vol. 235, ML Research Press, 2024, pp. 4300–28."},"year":"2024","date_created":"2025-01-30T07:35:49Z","day":"30","date_published":"2024-07-30T00:00:00Z","scopus_import":"1","abstract":[{"lang":"eng","text":"Understanding the reasons behind the exceptional success of transformers requires a better analysis of why attention layers are suitable for NLP tasks. In particular, such tasks require predictive models to capture contextual meaning which often depends on one or few words, even if the sentence is long. Our work studies this key property, dubbed word sensitivity (WS), in the prototypical setting of random features. We show that attention layers enjoy high WS, namely, there exists a vector in the space of embeddings that largely perturbs the random attention features map. The argument critically exploits the role of the softmax in the attention layer, highlighting its benefit compared to other activations (e.g., ReLU). In contrast, the WS of standard random features is of order 1/n−−√, n being the number of words in the textual sample, and thus it decays with the length of the context. We then translate these results on the word sensitivity into generalization bounds: due to their low WS, random features provably cannot learn to distinguish between two sentences that differ only in a single word; in contrast, due to their high WS, random attention features have higher generalization capabilities. We validate our theoretical results with experimental evidence over the BERT-Base word embeddings of the imdb review dataset."}],"das_tickbox":"0","external_id":{"arxiv":["2402.02969"]},"conference":{"location":"Vienna, Austria","start_date":"2024-07-21","name":"ICML: International Conference on Machine Learning","end_date":"2024-07-27"},"publisher":"ML Research Press","month":"07","oa_version":"Preprint","alternative_title":["PMLR"],"department":[{"_id":"MaMo"}],"_id":"18973","acknowledgement":"The authors were partially supported by the 2019 LopezLoreta prize, and they would like to thank Mohammad Hossein Amani, Lorenzo Beretta, and Clement Rebuffel for helpful discussions.","quality_controlled":"1","publication_identifier":{"eissn":["2640-3498"]},"researchdata_availability":"no","volume":235,"intvolume":"       235","status":"public","type":"conference","OA_type":"green","publication_status":"published","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"title":"Towards understanding the word sensitivity of attention layers: A study via random features","arxiv":1,"article_processing_charge":"No","related_material":{"record":[{"id":"22857","status":"public","relation":"dissertation_contains"}]},"oa":1,"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"4300-4328","supplementarymaterial":"no","corr_author":"1","OA_place":"repository"},{"das_tickbox":"0","day":"30","date_published":"2024-07-30T00:00:00Z","abstract":[{"lang":"eng","text":"Deep learning models are known to overfit and memorize spurious features in the training dataset. While numerous empirical studies have aimed at understanding this phenomenon, a rigorous theoretical framework to quantify it is still missing. In this paper, we consider spurious features that are uncorrelated with the learning task, and we provide a precise characterization of how they are memorized via two separate terms: (i) the stability of the model with respect to individual training samples, and (ii) the feature alignment between the spurious pattern and the full sample. While the first term is well established in learning theory and it is connected to the generalization error in classical work, the second one is, to the best of our knowledge, novel. Our key technical result gives a precise characterization of the feature alignment for the two prototypical settings of random features (RF) and neural tangent kernel (NTK) regression. We prove that the memorization of spurious features weakens as the generalization capability increases and, through the analysis of the feature alignment, we unveil the role of the model and of its activation function. Numerical experiments show the predictive power of our theory on standard datasets (MNIST, CIFAR-10)."}],"scopus_import":"1","publication":"41st International Conference on Machine Learning","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2305.12100","open_access":"1"}],"year":"2024","date_created":"2025-01-30T07:29:47Z","citation":{"apa":"Bombari, S., &#38; Mondelli, M. (2024). How spurious features are memorized: Precise analysis for random and NTK features. In <i>41st International Conference on Machine Learning</i> (Vol. 235, pp. 4267–4299). Vienna, Austria: ML Research Press.","ista":"Bombari S, Mondelli M. 2024. How spurious features are memorized: Precise analysis for random and NTK features. 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 4267–4299.","ama":"Bombari S, Mondelli M. How spurious features are memorized: Precise analysis for random and NTK features. In: <i>41st International Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:4267-4299.","ieee":"S. Bombari and M. Mondelli, “How spurious features are memorized: Precise analysis for random and NTK features,” in <i>41st International Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 4267–4299.","short":"S. Bombari, M. Mondelli, in:, 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 4267–4299.","mla":"Bombari, Simone, and Marco Mondelli. “How Spurious Features Are Memorized: Precise Analysis for Random and NTK Features.” <i>41st International Conference on Machine Learning</i>, vol. 235, ML Research Press, 2024, pp. 4267–99.","chicago":"Bombari, Simone, and Marco Mondelli. “How Spurious Features Are Memorized: Precise Analysis for Random and NTK Features.” In <i>41st International Conference on Machine Learning</i>, 235:4267–99. ML Research Press, 2024."},"date_updated":"2026-10-16T10:42:37Z","author":[{"full_name":"Bombari, Simone","id":"ca726dda-de17-11ea-bc14-f9da834f63aa","first_name":"Simone","last_name":"Bombari"},{"last_name":"Mondelli","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"}],"volume":235,"researchdata_availability":"no","publication_identifier":{"eissn":["2640-3498"]},"intvolume":"       235","quality_controlled":"1","_id":"18972","department":[{"_id":"MaMo"}],"alternative_title":["PMLR"],"acknowledgement":"The authors were partially supported by the 2019 LopezLoreta prize, and they would like to thank (in alphabetical order) Grigorios Chrysos, Simone Maria Giancola, Mahyar\r\nJafari Nodeh, Christoph Lampert, Marco Miani, GuanWen Qiu, and Peter Sukenık for helpful discussions.","conference":{"location":"Vienna, Austria","end_date":"2024-07-27","name":"ICML: International Conference on Machine Learning","start_date":"2024-07-21"},"external_id":{"arxiv":["2305.12100"]},"oa_version":"Preprint","month":"07","publisher":"ML Research Press","arxiv":1,"title":"How spurious features are memorized: Precise analysis for random and NTK features","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"publication_status":"published","OA_type":"green","type":"conference","status":"public","OA_place":"repository","corr_author":"1","supplementarymaterial":"yes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"4267-4299","language":[{"iso":"eng"}],"article_processing_charge":"No","oa":1,"related_material":{"record":[{"status":"public","id":"22857","relation":"dissertation_contains"}]}},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2210.07754"}],"publication":"IEEE Transactions on Information Theory","citation":{"apa":"Resch, N., Yuan, C., &#38; Zhang, Y. (2024). Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/TIT.2024.3430842\">https://doi.org/10.1109/TIT.2024.3430842</a>","ama":"Resch N, Yuan C, Zhang Y. Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. <i>IEEE Transactions on Information Theory</i>. 2024;70(9):6211-6238. doi:<a href=\"https://doi.org/10.1109/TIT.2024.3430842\">10.1109/TIT.2024.3430842</a>","ista":"Resch N, Yuan C, Zhang Y. 2024. Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. IEEE Transactions on Information Theory. 70(9), 6211–6238.","short":"N. Resch, C. Yuan, Y. Zhang, IEEE Transactions on Information Theory 70 (2024) 6211–6238.","ieee":"N. Resch, C. Yuan, and Y. Zhang, “Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery,” <i>IEEE Transactions on Information Theory</i>, vol. 70, no. 9. IEEE, pp. 6211–6238, 2024.","mla":"Resch, Nicolas, et al. “Zero-Rate Thresholds and New Capacity Bounds for List-Decoding and List-Recovery.” <i>IEEE Transactions on Information Theory</i>, vol. 70, no. 9, IEEE, 2024, pp. 6211–38, doi:<a href=\"https://doi.org/10.1109/TIT.2024.3430842\">10.1109/TIT.2024.3430842</a>.","chicago":"Resch, Nicolas, Chen Yuan, and Yihan Zhang. “Zero-Rate Thresholds and New Capacity Bounds for List-Decoding and List-Recovery.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2024. <a href=\"https://doi.org/10.1109/TIT.2024.3430842\">https://doi.org/10.1109/TIT.2024.3430842</a>."},"date_created":"2024-07-28T22:01:10Z","year":"2024","date_updated":"2026-10-16T10:41:59Z","author":[{"first_name":"Nicolas","last_name":"Resch","full_name":"Resch, Nicolas"},{"last_name":"Yuan","first_name":"Chen","full_name":"Yuan, Chen"},{"orcid":"0000-0002-6465-6258","full_name":"Zhang, Yihan","last_name":"Zhang","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","first_name":"Yihan"}],"das_tickbox":"0","day":"01","date_published":"2024-09-01T00:00:00Z","doi":"10.1109/TIT.2024.3430842","abstract":[{"lang":"eng","text":"In this work we consider the list-decodability and list-recoverability of arbitrary q -ary codes, for all integer values of q ⩾ 2. A code is called ( p , L ) q -list-decodable if every radius pn Hamming ball contains less than L codewords; ( p , ℓ, L ) q -recoverability is a generalization where we place radius pn Hamming balls on every point of a combinatorial rectangle with side length ℓ and again stipulate that there be less than L codewords. Our main contribution is to precisely calculate the maximum value of p for which there exist infinite families of positive rate ( p , ℓ, L ) q -list-recoverable codes, the quantity we call the zero-rate threshold . Denoting this value by p *, we in fact show that codes correcting a p * + ε fraction of errors must have size O ε (1), i.e., independent of n . Such a result is typically referred to as a “Plotkin bound.” To complement this, a standard random code with expurgation construction shows that there exist positive rate codes correcting a p * − ε fraction of errors. We also follow a classical proof template (typically attributed to Elias and Bassalygo) to derive from the zero-rate threshold other tradeoffs between rate and decoding radius for list-decoding and list-recovery. Technically, proving the Plotkin bound boils down to demon-strating the Schur convexity of a certain function defined on the q -simplex as well as the convexity of a univariate function derived from it. We remark that an earlier argument claimed similar results for q -ary list-decoding; however, we point out that this earlier proof is flawed."}],"scopus_import":"1","department":[{"_id":"MaMo"}],"_id":"17330","acknowledgement":"Part of this work was done while Nicolas Resch was affiliated with the Centrum Wiskunde & Informatica and supported in part by ERC H2020 grant No.74079 (ALGSTRONGCRYPTO). Chen Yuan is supported in part by the National Key Research and Development Projects under Grant 2022YFA1004900 and Grant 2021YFE0109900, the National Natural Science Foundation of China under Grant 12101403 and Grant 12031011.","external_id":{"arxiv":["2210.07754"],"isi":["001299623600019"]},"publisher":"IEEE","oa_version":"Preprint","month":"09","article_type":"original","publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"researchdata_availability":"no","volume":70,"intvolume":"        70","issue":"9","quality_controlled":"1","type":"journal_article","OA_type":"green","status":"public","arxiv":1,"fulldoi":"https://doi.org/10.1109/TIT.2024.3430842","isi":1,"publication_status":"published","title":"Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery","language":[{"iso":"eng"}],"page":"6211-6238","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","related_material":{"record":[{"status":"public","id":"14083","relation":"earlier_version"}]},"oa":1,"corr_author":"1","OA_place":"repository","supplementarymaterial":"no"},{"volume":21,"researchdata_availability":"unclear","publication_identifier":{"eissn":["1567-2328"],"issn":["1567-2190"]},"article_type":"original","intvolume":"        21","issue":"3-4","quality_controlled":"1","_id":"18652","department":[{"_id":"MaMo"}],"oa_version":"None","month":"12","publisher":"Now Publishers","doi":"10.1561/0100000112","date_published":"2024-12-03T00:00:00Z","day":"03","scopus_import":"1","abstract":[{"text":"Over the last 70 years, information theory and coding has enabled communication technologies that have had an astounding impact on our lives. This is possible due to the match between encoding/decoding strategies and corresponding channel models. Traditional studies of channels have taken one of two extremes: Shannon-theoretic models are inherently average-case in which channel noise is governed by a memoryless stochastic process, whereas coding-theoretic (referred to as “Hamming”) models take a worst-case, adversarial, view of the noise. However, for several existing and emerging communication systems the Shannon/average-case view may be too optimistic, whereas the Hamming/worstcase view may be too pessimistic. This monograph takes up the challenge of studying adversarial channel models that lie between the Shannon and Hamming extremes.","lang":"eng"}],"publication":"Foundations and Trends in Communications and Information Theory","year":"2024","date_created":"2024-12-15T23:01:50Z","citation":{"ista":"Dey BK, Jaggi S, Langberg M, Sarwate AD, Zhang Y. 2024. Codes for adversaries: Between worst-case and average-case jamming. Foundations and Trends in Communications and Information Theory. 21(3–4), 300–588.","ama":"Dey BK, Jaggi S, Langberg M, Sarwate AD, Zhang Y. Codes for adversaries: Between worst-case and average-case jamming. <i>Foundations and Trends in Communications and Information Theory</i>. 2024;21(3-4):300-588. doi:<a href=\"https://doi.org/10.1561/0100000112\">10.1561/0100000112</a>","apa":"Dey, B. K., Jaggi, S., Langberg, M., Sarwate, A. D., &#38; Zhang, Y. (2024). Codes for adversaries: Between worst-case and average-case jamming. <i>Foundations and Trends in Communications and Information Theory</i>. Now Publishers. <a href=\"https://doi.org/10.1561/0100000112\">https://doi.org/10.1561/0100000112</a>","chicago":"Dey, Bikash Kumar, Sidharth Jaggi, Michael Langberg, Anand D. Sarwate, and Yihan Zhang. “Codes for Adversaries: Between Worst-Case and Average-Case Jamming.” <i>Foundations and Trends in Communications and Information Theory</i>. Now Publishers, 2024. <a href=\"https://doi.org/10.1561/0100000112\">https://doi.org/10.1561/0100000112</a>.","mla":"Dey, Bikash Kumar, et al. “Codes for Adversaries: Between Worst-Case and Average-Case Jamming.” <i>Foundations and Trends in Communications and Information Theory</i>, vol. 21, no. 3–4, Now Publishers, 2024, pp. 300–588, doi:<a href=\"https://doi.org/10.1561/0100000112\">10.1561/0100000112</a>.","ieee":"B. K. Dey, S. Jaggi, M. Langberg, A. D. Sarwate, and Y. Zhang, “Codes for adversaries: Between worst-case and average-case jamming,” <i>Foundations and Trends in Communications and Information Theory</i>, vol. 21, no. 3–4. Now Publishers, pp. 300–588, 2024.","short":"B.K. Dey, S. Jaggi, M. Langberg, A.D. Sarwate, Y. Zhang, Foundations and Trends in Communications and Information Theory 21 (2024) 300–588."},"date_updated":"2026-10-16T10:40:55Z","author":[{"full_name":"Dey, Bikash Kumar","last_name":"Dey","first_name":"Bikash Kumar"},{"first_name":"Sidharth","last_name":"Jaggi","full_name":"Jaggi, Sidharth"},{"full_name":"Langberg, Michael","first_name":"Michael","last_name":"Langberg"},{"full_name":"Sarwate, Anand D.","first_name":"Anand D.","last_name":"Sarwate"},{"orcid":"0000-0002-6465-6258","full_name":"Zhang, Yihan","last_name":"Zhang","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","first_name":"Yihan"}],"corr_author":"1","supplementarymaterial":"unclear","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"300-588","language":[{"iso":"eng"}],"article_processing_charge":"No","fulldoi":"https://doi.org/10.1561/0100000112","title":"Codes for adversaries: Between worst-case and average-case jamming","publication_status":"published","OA_type":"closed access","type":"journal_article","status":"public"},{"oa":1,"has_accepted_license":"1","file_date_updated":"2024-10-30T08:59:09Z","article_processing_charge":"Yes","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","supplementarymaterial":"yes","corr_author":"1","OA_place":"publisher","status":"public","ec_funded":1,"ddc":["530"],"type":"journal_article","APC_amount":"3711,01 EUR","OA_type":"gold","publication_status":"published","project":[{"call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"file":[{"file_size":1151431,"file_id":"18489","checksum":"2e057ba021744d0a74602517935326b3","creator":"dernst","success":1,"relation":"main_file","date_updated":"2024-10-30T08:59:09Z","access_level":"open_access","file_name":"2024_PRXQuantum_Ljubotina.pdf","content_type":"application/pdf","date_created":"2024-10-30T08:59:09Z"}],"title":"Tangent space generators of matrix product states and exact floquet quantum scars","isi":1,"arxiv":1,"fulldoi":"https://doi.org/10.1103/prxquantum.5.040311","publisher":"American Physical Society","oa_version":"Published Version","month":"10","external_id":{"isi":["001346198800001"],"arxiv":["2403.12325"]},"acknowledgement":"We thank L. Piroli, S. Garratt, and A. Molnár for insightful discussions. This research was funded in part by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreements No. 850899 and No. 863476), the Austrian Science Fund (FWF) (Grant DOIs 10.55776/COE1, 10.55776/P36305, and 10.55776/F71), and the European Union (NextGenerationEU). This work was performed in part at the Aspen Center for Physics, which is supported by National Science Foundation Grant PHY-2210452. This research was supported in part by NSF Grant PHY-2309135 to the Kavli Institute for Theoretical Physics (KITP).","department":[{"_id":"MaSe"}],"_id":"18488","quality_controlled":"1","article_number":"040311","issue":"4","intvolume":"         5","article_type":"original","publication_identifier":{"eissn":["2691-3399"]},"volume":5,"researchdata_availability":"no","author":[{"orcid":"0000-0003-0038-7068","full_name":"Ljubotina, Marko","last_name":"Ljubotina","first_name":"Marko","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E"},{"full_name":"Petrova, Elena","last_name":"Petrova","first_name":"Elena","id":"0ac84990-897b-11ed-a09c-f5abb56a4ede"},{"full_name":"Schuch, Norbert","first_name":"Norbert","last_name":"Schuch"},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","last_name":"Serbyn"}],"date_updated":"2026-10-16T12:13:31Z","citation":{"chicago":"Ljubotina, Marko, Elena Petrova, Norbert Schuch, and Maksym Serbyn. “Tangent Space Generators of Matrix Product States and Exact Floquet Quantum Scars.” <i>PRX Quantum</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/prxquantum.5.040311\">https://doi.org/10.1103/prxquantum.5.040311</a>.","ieee":"M. Ljubotina, E. Petrova, N. Schuch, and M. Serbyn, “Tangent space generators of matrix product states and exact floquet quantum scars,” <i>PRX Quantum</i>, vol. 5, no. 4. American Physical Society, 2024.","short":"M. Ljubotina, E. Petrova, N. Schuch, M. Serbyn, PRX Quantum 5 (2024).","mla":"Ljubotina, Marko, et al. “Tangent Space Generators of Matrix Product States and Exact Floquet Quantum Scars.” <i>PRX Quantum</i>, vol. 5, no. 4, 040311, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/prxquantum.5.040311\">10.1103/prxquantum.5.040311</a>.","ista":"Ljubotina M, Petrova E, Schuch N, Serbyn M. 2024. Tangent space generators of matrix product states and exact floquet quantum scars. PRX Quantum. 5(4), 040311.","ama":"Ljubotina M, Petrova E, Schuch N, Serbyn M. Tangent space generators of matrix product states and exact floquet quantum scars. <i>PRX Quantum</i>. 2024;5(4). doi:<a href=\"https://doi.org/10.1103/prxquantum.5.040311\">10.1103/prxquantum.5.040311</a>","apa":"Ljubotina, M., Petrova, E., Schuch, N., &#38; Serbyn, M. (2024). Tangent space generators of matrix product states and exact floquet quantum scars. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxquantum.5.040311\">https://doi.org/10.1103/prxquantum.5.040311</a>"},"date_created":"2024-10-29T16:04:05Z","year":"2024","publication":"PRX Quantum","scopus_import":"1","abstract":[{"lang":"eng","text":"The advancement of quantum simulators motivates the development of a theoretical framework to assist with efficient state preparation in quantum many-body systems. Generally, preparing a target entangled state via unitary evolution with time-dependent couplings is a challenging task and very little is known about the existence of solutions and their properties. In this work we develop a constructive approach for preparing matrix product states (MPS) via continuous unitary evolution. We provide an explicit construction of the operator that exactly implements the evolution of a given MPS along a specified direction in its tangent space. This operator can be written as a sum of local terms of finite range, yet it is in general non-Hermitian. Relying on the explicit construction of the non-Hermitian generator of the dynamics, we demonstrate the existence of a Hermitian sequence of operators that implements the desired MPS evolution with an error that decreases exponentially with the operator range. The construction is benchmarked on an explicit periodic trajectory in a translationally invariant MPS manifold. We demonstrate that the Floquet unitary generating the dynamics over one period of the trajectory features an approximate MPS-like eigenstate embedded among a sea of thermalizing eigenstates. These results show that our construction is not only useful for state preparation and control of many-body systems, but also provides a generic route towards Floquet scars—periodically driven models with quasilocal generators of dynamics that have exact MPS eigenstates in their spectrum."}],"DOAJ_listed":"1","date_published":"2024-10-23T00:00:00Z","day":"23","doi":"10.1103/prxquantum.5.040311","das_tickbox":"0"},{"acknowledgement":"The authors thank Denis Bernard, Jérôme Dubail, Hosho Katsura, Kareljan Schoutens, and Alberto Zorzato for stimulating discussions. This work has been supported by: Slovenian Research Agency (ARIS) under Grants No. N1-0219 (T.P., L.Z.), No. N1-0334 (T.P., L.Z.), No. N1-0243 (E.I.), and under Research Program P1-0402 (E.I., T.P., L.Z.). European Research Council (ERC) under Consolidator Grant No. 771536—NEMO (L.Z.), Advanced Grant No.\r\n101096208—QUEST (T.P., L.Z.), and Starting Grant No. 850899—NEQuM (M.L.). Simons Foundation under Simons Junior Fellowship Grant No. 1141511 (Ž.K.). M.L. acknowledges the hospitality of the Aspen Center for Physics, which is supported by National Science Foundation Grant No. PHY-2210452. Numerical simulations were performed using the ITensor library [117]. ","_id":"18176","department":[{"_id":"MaSe"}],"month":"09","oa_version":"Published Version","publisher":"American Physical Society","external_id":{"arxiv":["2406.01571"],"isi":["001327172800001"]},"intvolume":"         5","volume":5,"researchdata_availability":"no","article_type":"original","publication_identifier":{"eissn":["2691-3399"]},"quality_controlled":"1","issue":"3","article_number":"030356","date_created":"2024-10-06T22:01:12Z","year":"2024","citation":{"apa":"Zadnik, L., Ljubotina, M., Krajnik, Ž., Ilievski, E., &#38; Prosen, T. (2024). Quantum many-body spin ratchets. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PRXQuantum.5.030356\">https://doi.org/10.1103/PRXQuantum.5.030356</a>","ama":"Zadnik L, Ljubotina M, Krajnik Ž, Ilievski E, Prosen T. Quantum many-body spin ratchets. <i>PRX Quantum</i>. 2024;5(3). doi:<a href=\"https://doi.org/10.1103/PRXQuantum.5.030356\">10.1103/PRXQuantum.5.030356</a>","ista":"Zadnik L, Ljubotina M, Krajnik Ž, Ilievski E, Prosen T. 2024. Quantum many-body spin ratchets. PRX Quantum. 5(3), 030356.","mla":"Zadnik, Lenart, et al. “Quantum Many-Body Spin Ratchets.” <i>PRX Quantum</i>, vol. 5, no. 3, 030356, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PRXQuantum.5.030356\">10.1103/PRXQuantum.5.030356</a>.","short":"L. Zadnik, M. Ljubotina, Ž. Krajnik, E. Ilievski, T. Prosen, PRX Quantum 5 (2024).","ieee":"L. Zadnik, M. Ljubotina, Ž. Krajnik, E. Ilievski, and T. Prosen, “Quantum many-body spin ratchets,” <i>PRX Quantum</i>, vol. 5, no. 3. American Physical Society, 2024.","chicago":"Zadnik, Lenart, Marko Ljubotina, Žiga Krajnik, Enej Ilievski, and Tomaž Prosen. “Quantum Many-Body Spin Ratchets.” <i>PRX Quantum</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PRXQuantum.5.030356\">https://doi.org/10.1103/PRXQuantum.5.030356</a>."},"publication":"PRX Quantum","author":[{"first_name":"Lenart","last_name":"Zadnik","full_name":"Zadnik, Lenart"},{"full_name":"Ljubotina, Marko","orcid":"0000-0003-0038-7068","first_name":"Marko","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","last_name":"Ljubotina"},{"full_name":"Krajnik, Žiga","last_name":"Krajnik","first_name":"Žiga"},{"full_name":"Ilievski, Enej","last_name":"Ilievski","first_name":"Enej"},{"last_name":"Prosen","first_name":"Tomaž","full_name":"Prosen, Tomaž"}],"date_updated":"2026-10-16T12:13:08Z","das_tickbox":"0","abstract":[{"lang":"eng","text":"Introducing a class of SU(2) invariant quantum unitary circuits generating chiral transport, we examine the role of broken space-reflection and time-reversal symmetries on spin-transport properties. Upon adjusting parameters of local unitary gates, the dynamics can be either chaotic or integrable. The latter corresponds to a generalization of the space-time discretized (Trotterized) higher-spin quantum Heisenberg chain. We demonstrate that breaking of space-reflection symmetry results in a drift in the dynamical spin susceptibility. Remarkably, we find a universal drift velocity given by a simple formula, which, at zero average magnetization, depends only on the values of SU(2) Casimir invariants associated with local spins. In the integrable case, the drift velocity formula is confirmed analytically based on the exact solution of thermodynamic Bethe ansatz equations. Finally, by inspecting the large fluctuations of the time-integrated current between two halves of the system in stationary maximum-entropy states, we demonstrate violation of the Gallavotti-Cohen symmetry, implying that such states cannot be regarded as equilibrium ones. We show that the scaled cumulant generating function of the time-integrated current instead obeys a generalized fluctuation relation."}],"scopus_import":"1","doi":"10.1103/PRXQuantum.5.030356","DOAJ_listed":"1","date_published":"2024-09-25T00:00:00Z","day":"25","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"has_accepted_license":"1","file_date_updated":"2024-10-07T11:04:12Z","article_processing_charge":"Yes","OA_place":"publisher","supplementarymaterial":"yes","ddc":["530"],"ec_funded":1,"OA_type":"gold","type":"journal_article","status":"public","isi":1,"fulldoi":"https://doi.org/10.1103/PRXQuantum.5.030356","arxiv":1,"title":"Quantum many-body spin ratchets","project":[{"call_identifier":"H2020","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"file":[{"checksum":"bc230631255d3bcf8bcbbc8fdbfefcf2","creator":"dernst","file_id":"18183","file_size":1061648,"file_name":"2024_PRXQuantum_Zadnik.pdf","access_level":"open_access","content_type":"application/pdf","date_created":"2024-10-07T11:04:12Z","success":1,"relation":"main_file","date_updated":"2024-10-07T11:04:12Z"}],"publication_status":"published"},{"das_tickbox":"0","doi":"10.1103/PhysRevResearch.6.013223","date_published":"2024-03-01T00:00:00Z","day":"01","DOAJ_listed":"1","abstract":[{"lang":"eng","text":"Quantum computers are increasing in size and quality but are still very noisy. Error mitigation extends the size of the quantum circuits that noisy devices can meaningfully execute. However, state-of-the-art error mitigation methods are hard to implement and the limited qubit connectivity in superconducting qubit devices restricts most applications to the hardware's native topology. Here we show a quantum approximate optimization algorithm (QAOA) on nonplanar random regular graphs with up to 40 nodes enabled by a machine learning-based error mitigation. We use a swap network with careful decision-variable-to-qubit mapping and a feed-forward neural network to optimize a depth-two QAOA on up to 40 qubits. We observe a meaningful parameter optimization for the largest graph which requires running quantum circuits with 958 two-qubit gates. Our paper emphasizes the need to mitigate samples, and not only expectation values, in quantum approximate optimization. These results are a step towards executing quantum approximate optimization at a scale that is not classically simulable. Reaching such system sizes is key to properly understanding the true potential of heuristic algorithms like QAOA."}],"scopus_import":"1","publication":"Physical Review Research","year":"2024","date_created":"2024-03-17T23:00:59Z","citation":{"mla":"Sack, Stefan, and Daniel J. Egger. “Large-Scale Quantum Approximate Optimization on Nonplanar Graphs with Machine Learning Noise Mitigation.” <i>Physical Review Research</i>, vol. 6, no. 1, 013223, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.6.013223\">10.1103/PhysRevResearch.6.013223</a>.","short":"S. Sack, D.J. Egger, Physical Review Research 6 (2024).","ieee":"S. Sack and D. J. Egger, “Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation,” <i>Physical Review Research</i>, vol. 6, no. 1. American Physical Society, 2024.","chicago":"Sack, Stefan, and Daniel J. Egger. “Large-Scale Quantum Approximate Optimization on Nonplanar Graphs with Machine Learning Noise Mitigation.” <i>Physical Review Research</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevResearch.6.013223\">https://doi.org/10.1103/PhysRevResearch.6.013223</a>.","apa":"Sack, S., &#38; Egger, D. J. (2024). Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.6.013223\">https://doi.org/10.1103/PhysRevResearch.6.013223</a>","ista":"Sack S, Egger DJ. 2024. Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation. Physical Review Research. 6(1), 013223.","ama":"Sack S, Egger DJ. Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation. <i>Physical Review Research</i>. 2024;6(1). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.6.013223\">10.1103/PhysRevResearch.6.013223</a>"},"date_updated":"2026-10-16T12:12:26Z","author":[{"full_name":"Sack, Stefan","orcid":"0000-0001-5400-8508","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","first_name":"Stefan","last_name":"Sack"},{"full_name":"Egger, Daniel J.","last_name":"Egger","first_name":"Daniel J."}],"researchdata_availability":"no","volume":6,"publication_identifier":{"eissn":["2643-1564"]},"article_type":"original","intvolume":"         6","issue":"1","article_number":"013223","quality_controlled":"1","_id":"15122","department":[{"_id":"MaSe"}],"acknowledgement":"S.H.S. acknowledges support from the IBM Ph.D. fellowship 2022 in quantum computing. The authors also thank M. Serbyn, R. Kueng, R. A. Medina, and S. Woerner for fruitful discussions.","external_id":{"arxiv":["2307.14427"]},"month":"03","oa_version":"Published Version","publisher":"American Physical Society","fulldoi":"https://doi.org/10.1103/PhysRevResearch.6.013223","arxiv":1,"file":[{"success":1,"date_updated":"2024-03-19T07:16:38Z","relation":"main_file","file_name":"2024_PhysicalReviewResearch_Sack.pdf","access_level":"open_access","date_created":"2024-03-19T07:16:38Z","content_type":"application/pdf","file_id":"15123","file_size":2777593,"checksum":"274c9f1b15b3547a10a03f39e4ccc582","creator":"dernst"}],"project":[{"name":"IBM PhD Nomination Fellowship - Stefan Sack","_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d"}],"title":"Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation","publication_status":"published","type":"journal_article","ddc":["530"],"status":"public","corr_author":"1","supplementarymaterial":"yes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"Yes","has_accepted_license":"1","file_date_updated":"2024-03-19T07:16:38Z","oa":1}]