[{"title":"Zero-error communication over adversarial MACs","external_id":{"arxiv":["2101.12426"]},"year":"2023","doi":"10.1109/tit.2023.3257239","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2101.12426","open_access":"1"}],"author":[{"id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","first_name":"Yihan","orcid":"0000-0002-6465-6258","full_name":"Zhang, Yihan","last_name":"Zhang"}],"keyword":["Computer Science Applications","Information Systems"],"abstract":[{"text":"We consider zero-error communication over a two-transmitter deterministic adversarial multiple access channel (MAC) governed by an adversary who has access to the transmissions of both senders (hence called omniscient ) and aims to maliciously corrupt the communication. None of the encoders, jammer and decoder is allowed to randomize using private or public randomness. This enforces a combinatorial nature of the problem. Our model covers a large family of channels studied in the literature, including all deterministic discrete memoryless noisy or noiseless MACs. In this work, given an arbitrary two-transmitter deterministic omniscient adversarial MAC, we characterize when the capacity region: 1) has nonempty interior (in particular, is two-dimensional); 2) consists of two line segments (in particular, has empty interior); 3) consists of one line segment (in particular, is one-dimensional); 4) or only contains (0,0) (in particular, is zero-dimensional). This extends a recent result by Wang et al. (201 9) from the point-to-point setting to the multiple access setting. Indeed, our converse arguments build upon their generalized Plotkin bound and involve delicate case analysis. One of the technical challenges is to take care of both “joint confusability” and “marginal confusability”. In particular, the treatment of marginal confusability does not follow from the point-to-point results by Wang et al. Our achievability results follow from random coding with expurgation.","lang":"eng"}],"citation":{"chicago":"Zhang, Yihan. “Zero-Error Communication over Adversarial MACs.” <i>IEEE Transactions on Information Theory</i>. Institute of Electrical and Electronics Engineers, 2023. <a href=\"https://doi.org/10.1109/tit.2023.3257239\">https://doi.org/10.1109/tit.2023.3257239</a>.","ieee":"Y. Zhang, “Zero-error communication over adversarial MACs,” <i>IEEE Transactions on Information Theory</i>, vol. 69, no. 7. Institute of Electrical and Electronics Engineers, pp. 4093–4127, 2023.","apa":"Zhang, Y. (2023). Zero-error communication over adversarial MACs. <i>IEEE Transactions on Information Theory</i>. Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/tit.2023.3257239\">https://doi.org/10.1109/tit.2023.3257239</a>","ista":"Zhang Y. 2023. Zero-error communication over adversarial MACs. IEEE Transactions on Information Theory. 69(7), 4093–4127.","short":"Y. Zhang, IEEE Transactions on Information Theory 69 (2023) 4093–4127.","mla":"Zhang, Yihan. “Zero-Error Communication over Adversarial MACs.” <i>IEEE Transactions on Information Theory</i>, vol. 69, no. 7, Institute of Electrical and Electronics Engineers, 2023, pp. 4093–127, doi:<a href=\"https://doi.org/10.1109/tit.2023.3257239\">10.1109/tit.2023.3257239</a>.","ama":"Zhang Y. Zero-error communication over adversarial MACs. <i>IEEE Transactions on Information Theory</i>. 2023;69(7):4093-4127. doi:<a href=\"https://doi.org/10.1109/tit.2023.3257239\">10.1109/tit.2023.3257239</a>"},"publication_status":"published","quality_controlled":"1","oa_version":"Preprint","acknowledgement":"The author would like to thank Amitalok J. Budkuley and Sidharth Jaggi for many helpful discussions at the early stage of this work. He would also like to thank Nir Ailon, Qi Cao, and Chandra Nair for discussions on a related problem regarding zero-error binary adder MACs.\r\nThe work of Yihan Zhang was supported by the European Union’s Horizon 2020 Research and Innovation Programme under Grant 682203-ERC-[Inf-Speed-Tradeoff]","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0018-9448"],"eissn":["1557-9654"]},"_id":"14751","article_processing_charge":"No","date_updated":"2024-01-09T08:45:24Z","volume":69,"oa":1,"arxiv":1,"language":[{"iso":"eng"}],"scopus_import":"1","publisher":"Institute of Electrical and Electronics Engineers","article_type":"original","date_published":"2023-07-01T00:00:00Z","month":"07","date_created":"2024-01-08T13:04:54Z","department":[{"_id":"MaMo"}],"status":"public","intvolume":"        69","type":"journal_article","day":"01","page":"4093-4127","publication":"IEEE Transactions on Information Theory","issue":"7"},{"type":"journal_article","day":"01","status":"public","intvolume":"        24","file_date_updated":"2024-01-10T13:39:42Z","issue":"22","publication":"International Journal of Molecular Sciences","article_type":"original","date_published":"2023-11-01T00:00:00Z","month":"11","language":[{"iso":"eng"}],"publisher":"MDPI","department":[{"_id":"JiFr"}],"has_accepted_license":"1","file":[{"success":1,"content_type":"application/pdf","relation":"main_file","file_id":"14791","creator":"dernst","file_name":"2023_IJMS_Teplova.pdf","file_size":2637784,"date_created":"2024-01-10T13:39:42Z","checksum":"4df7d206ba022b7f54eff1f0aec1659a","date_updated":"2024-01-10T13:39:42Z","access_level":"open_access"}],"date_created":"2024-01-10T09:24:35Z","publication_status":"published","citation":{"mla":"Teplova, Anastasiia, et al. “Phytaspase Is Capable of Detaching the Endoplasmic Reticulum Retrieval Signal from Tobacco Calreticulin-3.” <i>International Journal of Molecular Sciences</i>, vol. 24, no. 22, 16527, MDPI, 2023, doi:<a href=\"https://doi.org/10.3390/ijms242216527\">10.3390/ijms242216527</a>.","ama":"Teplova A, Pigidanov AA, Serebryakova MV, et al. Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. <i>International Journal of Molecular Sciences</i>. 2023;24(22). doi:<a href=\"https://doi.org/10.3390/ijms242216527\">10.3390/ijms242216527</a>","short":"A. Teplova, A.A. Pigidanov, M.V. Serebryakova, S.A. Golyshev, R.A. Galiullina, N.V. Chichkova, A.B. Vartapetian, International Journal of Molecular Sciences 24 (2023).","ista":"Teplova A, Pigidanov AA, Serebryakova MV, Golyshev SA, Galiullina RA, Chichkova NV, Vartapetian AB. 2023. Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. International Journal of Molecular Sciences. 24(22), 16527.","ieee":"A. Teplova <i>et al.</i>, “Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3,” <i>International Journal of Molecular Sciences</i>, vol. 24, no. 22. MDPI, 2023.","apa":"Teplova, A., Pigidanov, A. A., Serebryakova, M. V., Golyshev, S. A., Galiullina, R. A., Chichkova, N. V., &#38; Vartapetian, A. B. (2023). Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms242216527\">https://doi.org/10.3390/ijms242216527</a>","chicago":"Teplova, Anastasiia, Artemii A. Pigidanov, Marina V. Serebryakova, Sergei A. Golyshev, Raisa A. Galiullina, Nina V. Chichkova, and Andrey B. Vartapetian. “Phytaspase Is Capable of Detaching the Endoplasmic Reticulum Retrieval Signal from Tobacco Calreticulin-3.” <i>International Journal of Molecular Sciences</i>. MDPI, 2023. <a href=\"https://doi.org/10.3390/ijms242216527\">https://doi.org/10.3390/ijms242216527</a>."},"author":[{"full_name":"Teplova, Anastasiia","last_name":"Teplova","first_name":"Anastasiia","id":"e3736151-106c-11ec-b916-c2558e2762c6"},{"full_name":"Pigidanov, Artemii A.","last_name":"Pigidanov","first_name":"Artemii A."},{"first_name":"Marina V.","full_name":"Serebryakova, Marina V.","last_name":"Serebryakova"},{"last_name":"Golyshev","full_name":"Golyshev, Sergei A.","first_name":"Sergei A."},{"first_name":"Raisa A.","last_name":"Galiullina","full_name":"Galiullina, Raisa A."},{"last_name":"Chichkova","full_name":"Chichkova, Nina V.","first_name":"Nina V."},{"first_name":"Andrey B.","full_name":"Vartapetian, Andrey B.","last_name":"Vartapetian"}],"keyword":["Inorganic Chemistry","Organic Chemistry","Physical and Theoretical Chemistry","Computer Science Applications","Spectroscopy","Molecular Biology","General Medicine","Catalysis"],"abstract":[{"text":"Soluble chaperones residing in the endoplasmic reticulum (ER) play vitally important roles in folding and quality control of newly synthesized proteins that transiently pass through the ER en route to their final destinations. These soluble residents of the ER are themselves endowed with an ER retrieval signal that enables the cell to bring the escaped residents back from the Golgi. Here, by using purified proteins, we showed that Nicotiana tabacum phytaspase, a plant aspartate-specific protease, introduces two breaks at the C-terminus of the N. tabacum ER resident calreticulin-3. These cleavages resulted in removal of either a dipeptide or a hexapeptide from the C-terminus of calreticulin-3 encompassing part or all of the ER retrieval signal. Consistently, expression of the calreticulin-3 derivative mimicking the phytaspase cleavage product in Nicotiana benthamiana cells demonstrated loss of the ER accumulation of the protein. Notably, upon its escape from the ER, calreticulin-3 was further processed by an unknown protease(s) to generate the free N-terminal (N) domain of calreticulin-3, which was ultimately secreted into the apoplast. Our study thus identified a specific proteolytic enzyme capable of precise detachment of the ER retrieval signal from a plant ER resident protein, with implications for the further fate of the escaped resident.","lang":"eng"}],"volume":24,"oa":1,"date_updated":"2024-01-10T13:41:10Z","article_processing_charge":"Yes","acknowledgement":"We thank C.U.T. Hellen for critically reading the manuscript. The MALDI MS facility and CLSM became available to us in the framework of Moscow State University Development Programs PNG 5.13 and PNR 5.13.\r\nThis work was funded by the Russian Science Foundation, grant numbers 19-14-00010 and 22-14-00071.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","oa_version":"Published Version","_id":"14776","pmid":1,"publication_identifier":{"issn":["1422-0067"]},"doi":"10.3390/ijms242216527","year":"2023","external_id":{"isi":["001113792600001"],"pmid":["38003717"]},"title":"Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3","article_number":"16527","isi":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["580"]},{"type":"journal_article","day":"15","status":"public","intvolume":"       467","publication":"Journal of Computational Physics","date_published":"2022-10-15T00:00:00Z","article_type":"original","month":"10","language":[{"iso":"eng"}],"publisher":"Elsevier","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"date_created":"2022-07-11T12:19:59Z","publication_status":"published","citation":{"ama":"Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. <i>Journal of Computational Physics</i>. 2022;467. doi:<a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">10.1016/j.jcp.2022.111439</a>","mla":"Kalinov, Aleksei, et al. “Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.” <i>Journal of Computational Physics</i>, vol. 467, 111439, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">10.1016/j.jcp.2022.111439</a>.","short":"A. Kalinov, A.I. Osinskiy, S.A. Matveev, W. Otieno, N.V. Brilliantov, Journal of Computational Physics 467 (2022).","ista":"Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. 2022. Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. Journal of Computational Physics. 467, 111439.","ieee":"A. Kalinov, A. I. Osinskiy, S. A. Matveev, W. Otieno, and N. V. Brilliantov, “Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics,” <i>Journal of Computational Physics</i>, vol. 467. Elsevier, 2022.","apa":"Kalinov, A., Osinskiy, A. I., Matveev, S. A., Otieno, W., &#38; Brilliantov, N. V. (2022). Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. <i>Journal of Computational Physics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">https://doi.org/10.1016/j.jcp.2022.111439</a>","chicago":"Kalinov, Aleksei, A.I. Osinskiy, S.A. Matveev, W. Otieno, and N.V. Brilliantov. “Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.” <i>Journal of Computational Physics</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">https://doi.org/10.1016/j.jcp.2022.111439</a>."},"keyword":["Computer Science Applications","Physics and Astronomy (miscellaneous)","Applied Mathematics","Computational Mathematics","Modeling and Simulation","Numerical Analysis"],"author":[{"orcid":"0000-0003-2189-3904","last_name":"Kalinov","full_name":"Kalinov, Aleksei","first_name":"Aleksei","id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02"},{"first_name":"A.I.","full_name":"Osinskiy, A.I.","last_name":"Osinskiy"},{"last_name":"Matveev","full_name":"Matveev, S.A.","first_name":"S.A."},{"first_name":"W.","full_name":"Otieno, W.","last_name":"Otieno"},{"full_name":"Brilliantov, N.V.","last_name":"Brilliantov","first_name":"N.V."}],"abstract":[{"text":"We revisit two basic Direct Simulation Monte Carlo Methods to model aggregation kinetics and extend them for aggregation processes with collisional fragmentation (shattering). We test the performance and accuracy of the extended methods and compare their performance with efficient deterministic finite-difference method applied to the same model. We validate the stochastic methods on the test problems and apply them to verify the existence of oscillating regimes in the aggregation-fragmentation kinetics recently detected in deterministic simulations. We confirm the emergence of steady oscillations of densities in such systems and prove the stability of the\r\noscillations with respect to fluctuations and noise.","lang":"eng"}],"volume":467,"date_updated":"2023-08-03T11:55:06Z","oa":1,"article_processing_charge":"No","arxiv":1,"acknowledgement":"Zhores supercomputer of Skolkovo Institute of Science and Technology [68] has been used in the present research. S.A.M. was supported by Moscow Center for Fundamental and Applied Mathematics (the agreement with the Ministry of Education and Science of the Russian Federation No. 075-15-2019-1624). A.I.O. acknowledges RFBR project No. 20-31-90022. N.V.B. acknowledges the support of the Analytical Center (subsidy agreement 000000D730321P5Q0002, Grant No. 70-2021-00145 02.11.2021).","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","quality_controlled":"1","_id":"11556","publication_identifier":{"issn":["0021-9991"]},"doi":"10.1016/j.jcp.2022.111439","year":"2022","external_id":{"arxiv":["2103.09481"],"isi":["000917225500013"]},"title":"Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics","isi":1,"article_number":"111439","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2103.09481"}],"ddc":["518"]},{"year":"2022","doi":"10.1287/moor.2020.1116","title":"Finite-memory strategies in POMDPs with long-run average objectives","external_id":{"arxiv":["1904.13360"],"isi":["000731918100001"]},"isi":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1904.13360"}],"citation":{"mla":"Chatterjee, Krishnendu, et al. “Finite-Memory Strategies in POMDPs with Long-Run Average Objectives.” <i>Mathematics of Operations Research</i>, vol. 47, no. 1, Institute for Operations Research and the Management Sciences, 2022, pp. 100–19, doi:<a href=\"https://doi.org/10.1287/moor.2020.1116\">10.1287/moor.2020.1116</a>.","ama":"Chatterjee K, Saona Urmeneta RJ, Ziliotto B. Finite-memory strategies in POMDPs with long-run average objectives. <i>Mathematics of Operations Research</i>. 2022;47(1):100-119. doi:<a href=\"https://doi.org/10.1287/moor.2020.1116\">10.1287/moor.2020.1116</a>","ista":"Chatterjee K, Saona Urmeneta RJ, Ziliotto B. 2022. Finite-memory strategies in POMDPs with long-run average objectives. Mathematics of Operations Research. 47(1), 100–119.","short":"K. Chatterjee, R.J. Saona Urmeneta, B. Ziliotto, Mathematics of Operations Research 47 (2022) 100–119.","ieee":"K. Chatterjee, R. J. Saona Urmeneta, and B. Ziliotto, “Finite-memory strategies in POMDPs with long-run average objectives,” <i>Mathematics of Operations Research</i>, vol. 47, no. 1. Institute for Operations Research and the Management Sciences, pp. 100–119, 2022.","apa":"Chatterjee, K., Saona Urmeneta, R. J., &#38; Ziliotto, B. (2022). Finite-memory strategies in POMDPs with long-run average objectives. <i>Mathematics of Operations Research</i>. Institute for Operations Research and the Management Sciences. <a href=\"https://doi.org/10.1287/moor.2020.1116\">https://doi.org/10.1287/moor.2020.1116</a>","chicago":"Chatterjee, Krishnendu, Raimundo J Saona Urmeneta, and Bruno Ziliotto. “Finite-Memory Strategies in POMDPs with Long-Run Average Objectives.” <i>Mathematics of Operations Research</i>. Institute for Operations Research and the Management Sciences, 2022. <a href=\"https://doi.org/10.1287/moor.2020.1116\">https://doi.org/10.1287/moor.2020.1116</a>."},"publication_status":"published","abstract":[{"text":"Partially observable Markov decision processes (POMDPs) are standard models for dynamic systems with probabilistic and nondeterministic behaviour in uncertain environments. We prove that in POMDPs with long-run average objective, the decision maker has approximately optimal strategies with finite memory. This implies notably that approximating the long-run value is recursively enumerable, as well as a weak continuity property of the value with respect to the transition function. ","lang":"eng"}],"keyword":["Management Science and Operations Research","General Mathematics","Computer Science Applications"],"author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","orcid":"0000-0001-5103-038X","full_name":"Saona Urmeneta, Raimundo J","last_name":"Saona Urmeneta","first_name":"Raimundo J"},{"last_name":"Ziliotto","full_name":"Ziliotto, Bruno","first_name":"Bruno"}],"arxiv":1,"article_processing_charge":"No","date_updated":"2023-09-05T13:16:11Z","oa":1,"volume":47,"publication_identifier":{"eissn":["1526-5471"],"issn":["0364-765X"]},"_id":"9311","oa_version":"Preprint","project":[{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"}],"quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"Partially supported by Austrian Science Fund (FWF) NFN Grant No RiSE/SHiNE S11407, by CONICYT Chile through grant PII 20150140, and by ECOS-CONICYT through grant C15E03.\r\n","month":"02","article_type":"original","date_published":"2022-02-01T00:00:00Z","scopus_import":"1","publisher":"Institute for Operations Research and the Management Sciences","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"KrCh"}],"date_created":"2021-04-08T09:33:31Z","day":"01","type":"journal_article","intvolume":"        47","status":"public","publication":"Mathematics of Operations Research","issue":"1","page":"100-119"},{"ddc":["530"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_number":"04LT02","title":"Explosive transitions in epidemic dynamics","year":"2022","doi":"10.1088/2632-072x/ac99cd","publication_identifier":{"issn":["2632-072X"]},"_id":"12134","oa_version":"Published Version","quality_controlled":"1","acknowledgement":"We acknowledge support from the Volkswagen Foundation under Grant No. 99720 and the German Federal Ministry for Education and Research (BMBF) under Grant No. 16ICR01. This research was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2068—390729961—Cluster of Excellence Physics of Life of TU Dresden.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","volume":3,"date_updated":"2023-02-13T09:15:13Z","oa":1,"abstract":[{"text":"Standard epidemic models exhibit one continuous, second order phase transition to macroscopic outbreaks. However, interventions to control outbreaks may fundamentally alter epidemic dynamics. Here we reveal how such interventions modify the type of phase transition. In particular, we uncover three distinct types of explosive phase transitions for epidemic dynamics with capacity-limited interventions. Depending on the capacity limit, interventions may (i) leave the standard second order phase transition unchanged but exponentially suppress the probability of large outbreaks, (ii) induce a first-order discontinuous transition to macroscopic outbreaks, or (iii) cause a secondary explosive yet continuous third-order transition. These insights highlight inherent limitations in predicting and containing epidemic outbreaks. More generally our study offers a cornerstone example of a third-order explosive phase transition in complex systems.","lang":"eng"}],"author":[{"full_name":"Börner, Georg","last_name":"Börner","first_name":"Georg"},{"first_name":"Malte","full_name":"Schröder, Malte","last_name":"Schröder"},{"id":"40315C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-4271","full_name":"Scarselli, Davide","last_name":"Scarselli","first_name":"Davide"},{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B","last_name":"Budanur","first_name":"Nazmi B"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","first_name":"Björn"},{"first_name":"Marc","last_name":"Timme","full_name":"Timme, Marc"}],"keyword":["Artificial Intelligence","Computer Networks and Communications","Computer Science Applications","Information Systems"],"citation":{"chicago":"Börner, Georg, Malte Schröder, Davide Scarselli, Nazmi B Budanur, Björn Hof, and Marc Timme. “Explosive Transitions in Epidemic Dynamics.” <i>Journal of Physics: Complexity</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.1088/2632-072x/ac99cd\">https://doi.org/10.1088/2632-072x/ac99cd</a>.","apa":"Börner, G., Schröder, M., Scarselli, D., Budanur, N. B., Hof, B., &#38; Timme, M. (2022). Explosive transitions in epidemic dynamics. <i>Journal of Physics: Complexity</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/2632-072x/ac99cd\">https://doi.org/10.1088/2632-072x/ac99cd</a>","ieee":"G. Börner, M. Schröder, D. Scarselli, N. B. Budanur, B. Hof, and M. Timme, “Explosive transitions in epidemic dynamics,” <i>Journal of Physics: Complexity</i>, vol. 3, no. 4. IOP Publishing, 2022.","ista":"Börner G, Schröder M, Scarselli D, Budanur NB, Hof B, Timme M. 2022. Explosive transitions in epidemic dynamics. Journal of Physics: Complexity. 3(4), 04LT02.","short":"G. Börner, M. Schröder, D. Scarselli, N.B. Budanur, B. Hof, M. Timme, Journal of Physics: Complexity 3 (2022).","ama":"Börner G, Schröder M, Scarselli D, Budanur NB, Hof B, Timme M. Explosive transitions in epidemic dynamics. <i>Journal of Physics: Complexity</i>. 2022;3(4). doi:<a href=\"https://doi.org/10.1088/2632-072x/ac99cd\">10.1088/2632-072x/ac99cd</a>","mla":"Börner, Georg, et al. “Explosive Transitions in Epidemic Dynamics.” <i>Journal of Physics: Complexity</i>, vol. 3, no. 4, 04LT02, IOP Publishing, 2022, doi:<a href=\"https://doi.org/10.1088/2632-072x/ac99cd\">10.1088/2632-072x/ac99cd</a>."},"publication_status":"published","file":[{"success":1,"content_type":"application/pdf","relation":"main_file","file_id":"12350","creator":"dernst","file_name":"2022_JourPhysics_Boerner.pdf","file_size":1006106,"date_created":"2023-01-24T07:24:37Z","checksum":"35c5c5cb0eb17ea1b5184755daab9fc9","date_updated":"2023-01-24T07:24:37Z","access_level":"open_access"}],"date_created":"2023-01-12T12:03:43Z","has_accepted_license":"1","department":[{"_id":"BjHo"}],"scopus_import":"1","publisher":"IOP Publishing","language":[{"iso":"eng"}],"month":"10","article_type":"original","date_published":"2022-10-25T00:00:00Z","publication":"Journal of Physics: Complexity","issue":"4","file_date_updated":"2023-01-24T07:24:37Z","intvolume":"         3","status":"public","day":"25","type":"journal_article"},{"article_processing_charge":"Yes (via OA deal)","date_updated":"2023-02-13T09:20:34Z","volume":31,"oa":1,"quality_controlled":"1","project":[{"grant_number":"P28844-B27","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported through the Center for the Physics of Biological Function (PHYe1734030) and by National Institutes of Health Grants R01GM097275 and U01DK127429 (TG). GT acknowledges the support of the Austrian Science Fund grant FWF P28844 and the Human Frontiers Science Program. ","publication_identifier":{"issn":["2452-3100"]},"_id":"12156","citation":{"ieee":"B. Zoller, T. Gregor, and G. Tkačik, “Eukaryotic gene regulation at equilibrium, or non?,” <i>Current Opinion in Systems Biology</i>, vol. 31, no. 9. Elsevier, 2022.","apa":"Zoller, B., Gregor, T., &#38; Tkačik, G. (2022). Eukaryotic gene regulation at equilibrium, or non? <i>Current Opinion in Systems Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">https://doi.org/10.1016/j.coisb.2022.100435</a>","chicago":"Zoller, Benjamin, Thomas Gregor, and Gašper Tkačik. “Eukaryotic Gene Regulation at Equilibrium, or Non?” <i>Current Opinion in Systems Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">https://doi.org/10.1016/j.coisb.2022.100435</a>.","mla":"Zoller, Benjamin, et al. “Eukaryotic Gene Regulation at Equilibrium, or Non?” <i>Current Opinion in Systems Biology</i>, vol. 31, no. 9, 100435, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">10.1016/j.coisb.2022.100435</a>.","ama":"Zoller B, Gregor T, Tkačik G. Eukaryotic gene regulation at equilibrium, or non? <i>Current Opinion in Systems Biology</i>. 2022;31(9). doi:<a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">10.1016/j.coisb.2022.100435</a>","short":"B. Zoller, T. Gregor, G. Tkačik, Current Opinion in Systems Biology 31 (2022).","ista":"Zoller B, Gregor T, Tkačik G. 2022. Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology. 31(9), 100435."},"publication_status":"published","keyword":["Applied Mathematics","Computer Science Applications","Drug Discovery","General Biochemistry","Genetics and Molecular Biology","Modeling and Simulation"],"author":[{"first_name":"Benjamin","full_name":"Zoller, Benjamin","last_name":"Zoller"},{"full_name":"Gregor, Thomas","last_name":"Gregor","first_name":"Thomas"},{"orcid":"1","full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"Models of transcriptional regulation that assume equilibrium binding of transcription factors have been less successful at predicting gene expression from sequence in eukaryotes than in bacteria. This could be due to the non-equilibrium nature of eukaryotic regulation. Unfortunately, the space of possible non-equilibrium mechanisms is vast and predominantly uninteresting. The key question is therefore how this space can be navigated efficiently, to focus on mechanisms and models that are biologically relevant. In this review, we advocate for the normative role of theory—theory that prescribes rather than just describes—in providing such a focus. Theory should expand its remit beyond inferring mechanistic models from data, towards identifying non-equilibrium gene regulatory schemes that may have been evolutionarily selected, despite their energy consumption, because they are precise, reliable, fast, or otherwise outperform regulation at equilibrium. We illustrate our reasoning by toy examples for which we provide simulation code."}],"article_number":"100435","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"year":"2022","doi":"10.1016/j.coisb.2022.100435","title":"Eukaryotic gene regulation at equilibrium, or non?","file_date_updated":"2023-01-24T12:14:10Z","publication":"Current Opinion in Systems Biology","issue":"9","type":"journal_article","day":"01","status":"public","intvolume":"        31","department":[{"_id":"GaTk"}],"has_accepted_license":"1","file":[{"date_created":"2023-01-24T12:14:10Z","checksum":"97ef01e0cc60cdc84f45640a0f248fb0","file_name":"2022_CurrentBiology_Zoller.pdf","file_size":2214944,"date_updated":"2023-01-24T12:14:10Z","access_level":"open_access","success":1,"creator":"dernst","file_id":"12362","content_type":"application/pdf","relation":"main_file"}],"date_created":"2023-01-12T12:08:51Z","article_type":"original","date_published":"2022-09-01T00:00:00Z","month":"09","language":[{"iso":"eng"}],"scopus_import":"1","publisher":"Elsevier"},{"related_material":{"link":[{"relation":"software","url":"https://github.com/ratschlab/scim"}]},"main_file_link":[{"url":"https://doi.org/10.1093/bioinformatics/btaa843","open_access":"1"}],"external_id":{"pmid":["33381818"]},"title":"SCIM: Universal single-cell matching with unpaired feature sets","year":"2020","doi":"10.1093/bioinformatics/btaa843","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","quality_controlled":"1","pmid":1,"_id":"14125","publication_identifier":{"eissn":["1367-4811"]},"extern":"1","volume":36,"oa":1,"date_updated":"2023-09-11T10:21:00Z","article_processing_charge":"No","keyword":["Computational Mathematics","Computational Theory and Mathematics","Computer Science Applications","Molecular Biology","Biochemistry","Statistics and Probability"],"author":[{"first_name":"Stefan G","full_name":"Stark, Stefan G","last_name":"Stark"},{"full_name":"Ficek, Joanna","last_name":"Ficek","first_name":"Joanna"},{"first_name":"Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"first_name":"Ximena","last_name":"Bonilla","full_name":"Bonilla, Ximena"},{"first_name":"Stéphane","last_name":"Chevrier","full_name":"Chevrier, Stéphane"},{"first_name":"Franziska","full_name":"Singer, Franziska","last_name":"Singer"},{"first_name":"Rudolf","last_name":"Aebersold","full_name":"Aebersold, Rudolf"},{"last_name":"Al-Quaddoomi","full_name":"Al-Quaddoomi, Faisal S","first_name":"Faisal S"},{"first_name":"Jonas","full_name":"Albinus, Jonas","last_name":"Albinus"},{"full_name":"Alborelli, Ilaria","last_name":"Alborelli","first_name":"Ilaria"},{"last_name":"Andani","full_name":"Andani, Sonali","first_name":"Sonali"},{"first_name":"Per-Olof","last_name":"Attinger","full_name":"Attinger, Per-Olof"},{"first_name":"Marina","full_name":"Bacac, Marina","last_name":"Bacac"},{"first_name":"Daniel","last_name":"Baumhoer","full_name":"Baumhoer, Daniel"},{"last_name":"Beck-Schimmer","full_name":"Beck-Schimmer, Beatrice","first_name":"Beatrice"},{"first_name":"Niko","full_name":"Beerenwinkel, Niko","last_name":"Beerenwinkel"},{"first_name":"Christian","full_name":"Beisel, Christian","last_name":"Beisel"},{"first_name":"Lara","full_name":"Bernasconi, Lara","last_name":"Bernasconi"},{"first_name":"Anne","full_name":"Bertolini, Anne","last_name":"Bertolini"},{"first_name":"Bernd","last_name":"Bodenmiller","full_name":"Bodenmiller, Bernd"},{"first_name":"Ximena","last_name":"Bonilla","full_name":"Bonilla, Ximena"},{"first_name":"Ruben","last_name":"Casanova","full_name":"Casanova, Ruben"},{"first_name":"Stéphane","last_name":"Chevrier","full_name":"Chevrier, Stéphane"},{"full_name":"Chicherova, Natalia","last_name":"Chicherova","first_name":"Natalia"},{"last_name":"D'Costa","full_name":"D'Costa, Maya","first_name":"Maya"},{"full_name":"Danenberg, Esther","last_name":"Danenberg","first_name":"Esther"},{"full_name":"Davidson, Natalie","last_name":"Davidson","first_name":"Natalie"},{"last_name":"gan","full_name":"gan, Monica-Andreea Dră","first_name":"Monica-Andreea Dră"},{"last_name":"Dummer","full_name":"Dummer, Reinhard","first_name":"Reinhard"},{"full_name":"Engler, Stefanie","last_name":"Engler","first_name":"Stefanie"},{"first_name":"Martin","last_name":"Erkens","full_name":"Erkens, Martin"},{"last_name":"Eschbach","full_name":"Eschbach, Katja","first_name":"Katja"},{"last_name":"Esposito","full_name":"Esposito, Cinzia","first_name":"Cinzia"},{"first_name":"André","last_name":"Fedier","full_name":"Fedier, André"},{"first_name":"Pedro","full_name":"Ferreira, Pedro","last_name":"Ferreira"},{"full_name":"Ficek, Joanna","last_name":"Ficek","first_name":"Joanna"},{"last_name":"Frei","full_name":"Frei, Anja L","first_name":"Anja L"},{"last_name":"Frey","full_name":"Frey, Bruno","first_name":"Bruno"},{"first_name":"Sandra","full_name":"Goetze, Sandra","last_name":"Goetze"},{"first_name":"Linda","full_name":"Grob, Linda","last_name":"Grob"},{"first_name":"Gabriele","full_name":"Gut, Gabriele","last_name":"Gut"},{"first_name":"Detlef","full_name":"Günther, Detlef","last_name":"Günther"},{"last_name":"Haberecker","full_name":"Haberecker, Martina","first_name":"Martina"},{"last_name":"Haeuptle","full_name":"Haeuptle, Pirmin","first_name":"Pirmin"},{"last_name":"Heinzelmann-Schwarz","full_name":"Heinzelmann-Schwarz, Viola","first_name":"Viola"},{"full_name":"Herter, Sylvia","last_name":"Herter","first_name":"Sylvia"},{"full_name":"Holtackers, Rene","last_name":"Holtackers","first_name":"Rene"},{"first_name":"Tamara","full_name":"Huesser, Tamara","last_name":"Huesser"},{"last_name":"Irmisch","full_name":"Irmisch, Anja","first_name":"Anja"},{"first_name":"Francis","full_name":"Jacob, Francis","last_name":"Jacob"},{"first_name":"Andrea","last_name":"Jacobs","full_name":"Jacobs, Andrea"},{"full_name":"Jaeger, Tim M","last_name":"Jaeger","first_name":"Tim M"},{"first_name":"Katharina","full_name":"Jahn, Katharina","last_name":"Jahn"},{"first_name":"Alva R","full_name":"James, Alva R","last_name":"James"},{"full_name":"Jermann, Philip M","last_name":"Jermann","first_name":"Philip M"},{"last_name":"Kahles","full_name":"Kahles, André","first_name":"André"},{"first_name":"Abdullah","last_name":"Kahraman","full_name":"Kahraman, Abdullah"},{"first_name":"Viktor H","last_name":"Koelzer","full_name":"Koelzer, Viktor H"},{"first_name":"Werner","last_name":"Kuebler","full_name":"Kuebler, Werner"},{"first_name":"Jack","last_name":"Kuipers","full_name":"Kuipers, Jack"},{"first_name":"Christian P","full_name":"Kunze, Christian P","last_name":"Kunze"},{"last_name":"Kurzeder","full_name":"Kurzeder, Christian","first_name":"Christian"},{"full_name":"Lehmann, Kjong-Van","last_name":"Lehmann","first_name":"Kjong-Van"},{"full_name":"Levesque, Mitchell","last_name":"Levesque","first_name":"Mitchell"},{"last_name":"Lugert","full_name":"Lugert, Sebastian","first_name":"Sebastian"},{"full_name":"Maass, Gerd","last_name":"Maass","first_name":"Gerd"},{"first_name":"Markus","last_name":"Manz","full_name":"Manz, Markus"},{"first_name":"Philipp","full_name":"Markolin, Philipp","last_name":"Markolin"},{"first_name":"Julien","last_name":"Mena","full_name":"Mena, Julien"},{"full_name":"Menzel, Ulrike","last_name":"Menzel","first_name":"Ulrike"},{"first_name":"Julian M","full_name":"Metzler, Julian M","last_name":"Metzler"},{"full_name":"Miglino, Nicola","last_name":"Miglino","first_name":"Nicola"},{"last_name":"Milani","full_name":"Milani, Emanuela S","first_name":"Emanuela S"},{"last_name":"Moch","full_name":"Moch, Holger","first_name":"Holger"},{"first_name":"Simone","last_name":"Muenst","full_name":"Muenst, Simone"},{"full_name":"Murri, Riccardo","last_name":"Murri","first_name":"Riccardo"},{"first_name":"Charlotte KY","last_name":"Ng","full_name":"Ng, Charlotte KY"},{"first_name":"Stefan","full_name":"Nicolet, Stefan","last_name":"Nicolet"},{"last_name":"Nowak","full_name":"Nowak, Marta","first_name":"Marta"},{"last_name":"Pedrioli","full_name":"Pedrioli, Patrick GA","first_name":"Patrick GA"},{"last_name":"Pelkmans","full_name":"Pelkmans, Lucas","first_name":"Lucas"},{"first_name":"Salvatore","full_name":"Piscuoglio, Salvatore","last_name":"Piscuoglio"},{"first_name":"Michael","full_name":"Prummer, Michael","last_name":"Prummer"},{"last_name":"Ritter","full_name":"Ritter, Mathilde","first_name":"Mathilde"},{"first_name":"Christian","full_name":"Rommel, Christian","last_name":"Rommel"},{"last_name":"Rosano-González","full_name":"Rosano-González, María L","first_name":"María L"},{"first_name":"Gunnar","full_name":"Rätsch, Gunnar","last_name":"Rätsch"},{"last_name":"Santacroce","full_name":"Santacroce, Natascha","first_name":"Natascha"},{"first_name":"Jacobo Sarabia del","full_name":"Castillo, Jacobo Sarabia del","last_name":"Castillo"},{"first_name":"Ramona","last_name":"Schlenker","full_name":"Schlenker, Ramona"},{"first_name":"Petra C","last_name":"Schwalie","full_name":"Schwalie, Petra C"},{"last_name":"Schwan","full_name":"Schwan, Severin","first_name":"Severin"},{"last_name":"Schär","full_name":"Schär, Tobias","first_name":"Tobias"},{"first_name":"Gabriela","full_name":"Senti, Gabriela","last_name":"Senti"},{"first_name":"Franziska","full_name":"Singer, Franziska","last_name":"Singer"},{"full_name":"Sivapatham, Sujana","last_name":"Sivapatham","first_name":"Sujana"},{"last_name":"Snijder","full_name":"Snijder, Berend","first_name":"Berend"},{"first_name":"Bettina","full_name":"Sobottka, Bettina","last_name":"Sobottka"},{"first_name":"Vipin T","last_name":"Sreedharan","full_name":"Sreedharan, Vipin T"},{"last_name":"Stark","full_name":"Stark, Stefan","first_name":"Stefan"},{"first_name":"Daniel J","last_name":"Stekhoven","full_name":"Stekhoven, Daniel J"},{"first_name":"Alexandre PA","last_name":"Theocharides","full_name":"Theocharides, Alexandre PA"},{"full_name":"Thomas, Tinu M","last_name":"Thomas","first_name":"Tinu M"},{"last_name":"Tolnay","full_name":"Tolnay, Markus","first_name":"Markus"},{"full_name":"Tosevski, Vinko","last_name":"Tosevski","first_name":"Vinko"},{"first_name":"Nora C","last_name":"Toussaint","full_name":"Toussaint, Nora C"},{"full_name":"Tuncel, Mustafa A","last_name":"Tuncel","first_name":"Mustafa A"},{"first_name":"Marina","full_name":"Tusup, Marina","last_name":"Tusup"},{"full_name":"Drogen, Audrey Van","last_name":"Drogen","first_name":"Audrey Van"},{"full_name":"Vetter, Marcus","last_name":"Vetter","first_name":"Marcus"},{"last_name":"Vlajnic","full_name":"Vlajnic, Tatjana","first_name":"Tatjana"},{"first_name":"Sandra","last_name":"Weber","full_name":"Weber, Sandra"},{"first_name":"Walter P","last_name":"Weber","full_name":"Weber, Walter P"},{"last_name":"Wegmann","full_name":"Wegmann, Rebekka","first_name":"Rebekka"},{"first_name":"Michael","last_name":"Weller","full_name":"Weller, Michael"},{"first_name":"Fabian","last_name":"Wendt","full_name":"Wendt, Fabian"},{"full_name":"Wey, Norbert","last_name":"Wey","first_name":"Norbert"},{"last_name":"Wicki","full_name":"Wicki, Andreas","first_name":"Andreas"},{"first_name":"Bernd","last_name":"Wollscheid","full_name":"Wollscheid, Bernd"},{"last_name":"Yu","full_name":"Yu, Shuqing","first_name":"Shuqing"},{"first_name":"Johanna","full_name":"Ziegler, Johanna","last_name":"Ziegler"},{"first_name":"Marc","full_name":"Zimmermann, Marc","last_name":"Zimmermann"},{"full_name":"Zoche, Martin","last_name":"Zoche","first_name":"Martin"},{"last_name":"Zuend","full_name":"Zuend, Gregor","first_name":"Gregor"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"full_name":"Lehmann, Kjong-Van","last_name":"Lehmann","first_name":"Kjong-Van"}],"abstract":[{"text":"Motivation: Recent technological advances have led to an increase in the production and availability of single-cell data. The ability to integrate a set of multi-technology measurements would allow the identification of biologically or clinically meaningful observations through the unification of the perspectives afforded by each technology. In most cases, however, profiling technologies consume the used cells and thus pairwise correspondences between datasets are lost. Due to the sheer size single-cell datasets can acquire, scalable algorithms that are able to universally match single-cell measurements carried out in one cell to its corresponding sibling in another technology are needed.\r\nResults: We propose Single-Cell data Integration via Matching (SCIM), a scalable approach to recover such correspondences in two or more technologies. SCIM assumes that cells share a common (low-dimensional) underlying structure and that the underlying cell distribution is approximately constant across technologies. It constructs a technology-invariant latent space using an autoencoder framework with an adversarial objective. Multi-modal datasets are integrated by pairing cells across technologies using a bipartite matching scheme that operates on the low-dimensional latent representations. We evaluate SCIM on a simulated cellular branching process and show that the cell-to-cell matches derived by SCIM reflect the same pseudotime on the simulated dataset. Moreover, we apply our method to two real-world scenarios, a melanoma tumor sample and a human bone marrow sample, where we pair cells from a scRNA dataset to their sibling cells in a CyTOF dataset achieving 90% and 78% cell-matching accuracy for each one of the samples, respectively.","lang":"eng"}],"publication_status":"published","citation":{"ama":"Stark SG, Ficek J, Locatello F, et al. SCIM: Universal single-cell matching with unpaired feature sets. <i>Bioinformatics</i>. 2020;36(Supplement_2):i919-i927. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btaa843\">10.1093/bioinformatics/btaa843</a>","mla":"Stark, Stefan G., et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” <i>Bioinformatics</i>, vol. 36, no. Supplement_2, Oxford University Press, 2020, pp. i919–27, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btaa843\">10.1093/bioinformatics/btaa843</a>.","short":"S.G. Stark, J. Ficek, F. Locatello, X. Bonilla, S. Chevrier, F. Singer, R. Aebersold, F.S. Al-Quaddoomi, J. Albinus, I. Alborelli, S. Andani, P.-O. Attinger, M. Bacac, D. Baumhoer, B. Beck-Schimmer, N. Beerenwinkel, C. Beisel, L. Bernasconi, A. Bertolini, B. Bodenmiller, X. Bonilla, R. Casanova, S. Chevrier, N. Chicherova, M. D’Costa, E. Danenberg, N. Davidson, M.-A.D. gan, R. Dummer, S. Engler, M. Erkens, K. Eschbach, C. Esposito, A. Fedier, P. Ferreira, J. Ficek, A.L. Frei, B. Frey, S. Goetze, L. Grob, G. Gut, D. Günther, M. Haberecker, P. Haeuptle, V. Heinzelmann-Schwarz, S. Herter, R. Holtackers, T. Huesser, A. Irmisch, F. Jacob, A. Jacobs, T.M. Jaeger, K. Jahn, A.R. James, P.M. Jermann, A. Kahles, A. Kahraman, V.H. Koelzer, W. Kuebler, J. Kuipers, C.P. Kunze, C. Kurzeder, K.-V. Lehmann, M. Levesque, S. Lugert, G. Maass, M. Manz, P. Markolin, J. Mena, U. Menzel, J.M. Metzler, N. Miglino, E.S. Milani, H. Moch, S. Muenst, R. Murri, C.K. Ng, S. Nicolet, M. Nowak, P.G. Pedrioli, L. Pelkmans, S. Piscuoglio, M. Prummer, M. Ritter, C. Rommel, M.L. Rosano-González, G. Rätsch, N. Santacroce, J.S. del Castillo, R. Schlenker, P.C. Schwalie, S. Schwan, T. Schär, G. Senti, F. Singer, S. Sivapatham, B. Snijder, B. Sobottka, V.T. Sreedharan, S. Stark, D.J. Stekhoven, A.P. Theocharides, T.M. Thomas, M. Tolnay, V. Tosevski, N.C. Toussaint, M.A. Tuncel, M. Tusup, A.V. Drogen, M. Vetter, T. Vlajnic, S. Weber, W.P. Weber, R. Wegmann, M. Weller, F. Wendt, N. Wey, A. Wicki, B. Wollscheid, S. Yu, J. Ziegler, M. Zimmermann, M. Zoche, G. Zuend, G. Rätsch, K.-V. Lehmann, Bioinformatics 36 (2020) i919–i927.","ista":"Stark SG et al. 2020. SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. 36(Supplement_2), i919–i927.","ieee":"S. G. Stark <i>et al.</i>, “SCIM: Universal single-cell matching with unpaired feature sets,” <i>Bioinformatics</i>, vol. 36, no. Supplement_2. Oxford University Press, pp. i919–i927, 2020.","apa":"Stark, S. G., Ficek, J., Locatello, F., Bonilla, X., Chevrier, S., Singer, F., … Lehmann, K.-V. (2020). SCIM: Universal single-cell matching with unpaired feature sets. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/btaa843\">https://doi.org/10.1093/bioinformatics/btaa843</a>","chicago":"Stark, Stefan G, Joanna Ficek, Francesco Locatello, Ximena Bonilla, Stéphane Chevrier, Franziska Singer, Rudolf Aebersold, et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” <i>Bioinformatics</i>. Oxford University Press, 2020. <a href=\"https://doi.org/10.1093/bioinformatics/btaa843\">https://doi.org/10.1093/bioinformatics/btaa843</a>."},"date_created":"2023-08-21T12:28:20Z","department":[{"_id":"FrLo"}],"language":[{"iso":"eng"}],"publisher":"Oxford University Press","scopus_import":"1","article_type":"original","date_published":"2020-12-01T00:00:00Z","month":"12","page":"i919-i927","issue":"Supplement_2","publication":"Bioinformatics","status":"public","intvolume":"        36","type":"journal_article","day":"01"},{"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1093/bioinformatics/btz397"}]},"title":"Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data","doi":"10.1093/bioinformatics/btu166","year":"2014","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","quality_controlled":"1","_id":"8459","extern":"1","publication_identifier":{"issn":["1367-4803","1460-2059"]},"volume":30,"date_updated":"2021-01-12T08:19:25Z","article_processing_charge":"No","author":[{"first_name":"Sébastien","full_name":"Morin, Sébastien","last_name":"Morin"},{"full_name":"Linnet, Troels E","last_name":"Linnet","first_name":"Troels E"},{"full_name":"Lescanne, Mathilde","last_name":"Lescanne","first_name":"Mathilde"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda"},{"last_name":"Thompson","full_name":"Thompson, Gary S","first_name":"Gary S"},{"last_name":"Tollinger","full_name":"Tollinger, Martin","first_name":"Martin"},{"last_name":"Teilum","full_name":"Teilum, Kaare","first_name":"Kaare"},{"last_name":"Gagné","full_name":"Gagné, Stéphane","first_name":"Stéphane"},{"full_name":"Marion, Dominique","last_name":"Marion","first_name":"Dominique"},{"full_name":"Griesinger, Christian","last_name":"Griesinger","first_name":"Christian"},{"first_name":"Martin","last_name":"Blackledge","full_name":"Blackledge, Martin"},{"last_name":"d’Auvergne","full_name":"d’Auvergne, Edward J","first_name":"Edward J"}],"keyword":["Statistics and Probability","Computational Theory and Mathematics","Biochemistry","Molecular Biology","Computational Mathematics","Computer Science Applications"],"abstract":[{"text":"Nuclear magnetic resonance (NMR) is a powerful tool for observing the motion of biomolecules at the atomic level. One technique, the analysis of relaxation dispersion phenomenon, is highly suited for studying the kinetics and thermodynamics of biological processes. Built on top of the relax computational environment for NMR dynamics is a new dispersion analysis designed to be comprehensive, accurate and easy-to-use. The software supports more models, both numeric and analytic, than current solutions. An automated protocol, available for scripting and driving the graphical user interface (GUI), is designed to simplify the analysis of dispersion data for NMR spectroscopists. Decreases in optimization time are granted by parallelization for running on computer clusters and by skipping an initial grid search by using parameters from one solution as the starting point for another —using analytic model results for the numeric models, taking advantage of model nesting, and using averaged non-clustered results for the clustered analysis.","lang":"eng"}],"publication_status":"published","citation":{"mla":"Morin, Sébastien, et al. “Relax: The Analysis of Biomolecular Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” <i>Bioinformatics</i>, vol. 30, no. 15, Oxford University Press, 2014, pp. 2219–20, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btu166\">10.1093/bioinformatics/btu166</a>.","ama":"Morin S, Linnet TE, Lescanne M, et al. Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. <i>Bioinformatics</i>. 2014;30(15):2219-2220. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btu166\">10.1093/bioinformatics/btu166</a>","ista":"Morin S, Linnet TE, Lescanne M, Schanda P, Thompson GS, Tollinger M, Teilum K, Gagné S, Marion D, Griesinger C, Blackledge M, d’Auvergne EJ. 2014. Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics. 30(15), 2219–2220.","short":"S. Morin, T.E. Linnet, M. Lescanne, P. Schanda, G.S. Thompson, M. Tollinger, K. Teilum, S. Gagné, D. Marion, C. Griesinger, M. Blackledge, E.J. d’Auvergne, Bioinformatics 30 (2014) 2219–2220.","apa":"Morin, S., Linnet, T. E., Lescanne, M., Schanda, P., Thompson, G. S., Tollinger, M., … d’Auvergne, E. J. (2014). Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/btu166\">https://doi.org/10.1093/bioinformatics/btu166</a>","ieee":"S. Morin <i>et al.</i>, “Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data,” <i>Bioinformatics</i>, vol. 30, no. 15. Oxford University Press, pp. 2219–2220, 2014.","chicago":"Morin, Sébastien, Troels E Linnet, Mathilde Lescanne, Paul Schanda, Gary S Thompson, Martin Tollinger, Kaare Teilum, et al. “Relax: The Analysis of Biomolecular Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” <i>Bioinformatics</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/bioinformatics/btu166\">https://doi.org/10.1093/bioinformatics/btu166</a>."},"date_created":"2020-09-18T10:08:07Z","language":[{"iso":"eng"}],"publisher":"Oxford University Press","article_type":"original","date_published":"2014-08-01T00:00:00Z","month":"08","page":"2219-2220","issue":"15","publication":"Bioinformatics","status":"public","intvolume":"        30","type":"journal_article","day":"01"}]