[{"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1093/bioinformatics/btz397"}]},"page":"2219-2220","publication_identifier":{"issn":["1367-4803","1460-2059"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"08","extern":"1","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>.","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.","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.","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>","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>.","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>"},"language":[{"iso":"eng"}],"date_updated":"2021-01-12T08:19:25Z","article_processing_charge":"No","author":[{"first_name":"Sébastien","last_name":"Morin","full_name":"Morin, Sébastien"},{"last_name":"Linnet","full_name":"Linnet, Troels E","first_name":"Troels E"},{"last_name":"Lescanne","full_name":"Lescanne, Mathilde","first_name":"Mathilde"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul"},{"last_name":"Thompson","full_name":"Thompson, Gary S","first_name":"Gary S"},{"first_name":"Martin","last_name":"Tollinger","full_name":"Tollinger, Martin"},{"full_name":"Teilum, Kaare","last_name":"Teilum","first_name":"Kaare"},{"first_name":"Stéphane","last_name":"Gagné","full_name":"Gagné, Stéphane"},{"full_name":"Marion, Dominique","last_name":"Marion","first_name":"Dominique"},{"first_name":"Christian","full_name":"Griesinger, Christian","last_name":"Griesinger"},{"last_name":"Blackledge","full_name":"Blackledge, Martin","first_name":"Martin"},{"last_name":"d’Auvergne","full_name":"d’Auvergne, Edward J","first_name":"Edward J"}],"doi":"10.1093/bioinformatics/btu166","publication_status":"published","oa_version":"None","type":"journal_article","status":"public","keyword":["Statistics and Probability","Computational Theory and Mathematics","Biochemistry","Molecular Biology","Computational Mathematics","Computer Science Applications"],"publication":"Bioinformatics","volume":30,"title":"Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data","article_type":"original","_id":"8459","day":"01","publisher":"Oxford University Press","date_published":"2014-08-01T00:00:00Z","issue":"15","year":"2014","abstract":[{"lang":"eng","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."}],"intvolume":"        30","date_created":"2020-09-18T10:08:07Z","quality_controlled":"1"},{"page":"4312-4317","publication":"Angewandte Chemie International Edition","publication_identifier":{"issn":["1433-7851"]},"volume":53,"month":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","title":"Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy","_id":"8460","extern":"1","day":"18","publisher":"Wiley","citation":{"chicago":"Ma, Peixiang, Jens D. Haller, Jérémy Zajakala, Pavel Macek, Astrid C. Sivertsen, Dieter Willbold, Jérôme Boisbouvier, and Paul Schanda. “Probing Transient Conformational States of Proteins by Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.” <i>Angewandte Chemie International Edition</i>. Wiley, 2014. <a href=\"https://doi.org/10.1002/anie.201311275\">https://doi.org/10.1002/anie.201311275</a>.","apa":"Ma, P., Haller, J. D., Zajakala, J., Macek, P., Sivertsen, A. C., Willbold, D., … Schanda, P. (2014). Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.201311275\">https://doi.org/10.1002/anie.201311275</a>","ama":"Ma P, Haller JD, Zajakala J, et al. Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. <i>Angewandte Chemie International Edition</i>. 2014;53(17):4312-4317. doi:<a href=\"https://doi.org/10.1002/anie.201311275\">10.1002/anie.201311275</a>","mla":"Ma, Peixiang, et al. “Probing Transient Conformational States of Proteins by Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.” <i>Angewandte Chemie International Edition</i>, vol. 53, no. 17, Wiley, 2014, pp. 4312–17, doi:<a href=\"https://doi.org/10.1002/anie.201311275\">10.1002/anie.201311275</a>.","short":"P. Ma, J.D. Haller, J. Zajakala, P. Macek, A.C. Sivertsen, D. Willbold, J. Boisbouvier, P. Schanda, Angewandte Chemie International Edition 53 (2014) 4312–4317.","ista":"Ma P, Haller JD, Zajakala J, Macek P, Sivertsen AC, Willbold D, Boisbouvier J, Schanda P. 2014. Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie International Edition. 53(17), 4312–4317.","ieee":"P. Ma <i>et al.</i>, “Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy,” <i>Angewandte Chemie International Edition</i>, vol. 53, no. 17. Wiley, pp. 4312–4317, 2014."},"language":[{"iso":"eng"}],"date_updated":"2021-01-12T08:19:25Z","date_published":"2014-03-18T00:00:00Z","issue":"17","year":"2014","article_processing_charge":"No","author":[{"full_name":"Ma, Peixiang","last_name":"Ma","first_name":"Peixiang"},{"first_name":"Jens D.","last_name":"Haller","full_name":"Haller, Jens D."},{"full_name":"Zajakala, Jérémy","last_name":"Zajakala","first_name":"Jérémy"},{"first_name":"Pavel","full_name":"Macek, Pavel","last_name":"Macek"},{"first_name":"Astrid C.","full_name":"Sivertsen, Astrid C.","last_name":"Sivertsen"},{"last_name":"Willbold","full_name":"Willbold, Dieter","first_name":"Dieter"},{"first_name":"Jérôme","full_name":"Boisbouvier, Jérôme","last_name":"Boisbouvier"},{"first_name":"Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","last_name":"Schanda"}],"doi":"10.1002/anie.201311275","intvolume":"        53","date_created":"2020-09-18T10:08:53Z","publication_status":"published","abstract":[{"lang":"eng","text":"The function of proteins depends on their ability to sample a variety of states differing in structure and free energy. Deciphering how the various thermally accessible conformations are connected, and understanding their structures and relative energies is crucial in rationalizing protein function. Many biomolecular reactions take place within microseconds to milliseconds, and this timescale is therefore of central functional importance. Here we show that R1ρ relaxation dispersion experiments in magic‐angle‐spinning solid‐state NMR spectroscopy make it possible to investigate the thermodynamics and kinetics of such exchange process, and gain insight into structural features of short‐lived states."}],"oa_version":"None","type":"journal_article","quality_controlled":"1","status":"public"},{"publication_identifier":{"issn":["0010-3640"]},"keyword":["Applied Mathematics","General Mathematics"],"page":"748-775","publication":"Communications on Pure and Applied Mathematics","article_type":"original","title":"Arnol′d diffusion in a pendulum lattice","volume":67,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"05","day":"01","publisher":"Wiley","_id":"8500","extern":"1","language":[{"iso":"eng"}],"citation":{"ieee":"V. Kaloshin, M. Levi, and M. Saprykina, “Arnol′d diffusion in a pendulum lattice,” <i>Communications on Pure and Applied Mathematics</i>, vol. 67, no. 5. Wiley, pp. 748–775, 2014.","short":"V. Kaloshin, M. Levi, M. Saprykina, Communications on Pure and Applied Mathematics 67 (2014) 748–775.","ista":"Kaloshin V, Levi M, Saprykina M. 2014. Arnol′d diffusion in a pendulum lattice. Communications on Pure and Applied Mathematics. 67(5), 748–775.","mla":"Kaloshin, Vadim, et al. “Arnol′d Diffusion in a Pendulum Lattice.” <i>Communications on Pure and Applied Mathematics</i>, vol. 67, no. 5, Wiley, 2014, pp. 748–75, doi:<a href=\"https://doi.org/10.1002/cpa.21509\">10.1002/cpa.21509</a>.","apa":"Kaloshin, V., Levi, M., &#38; Saprykina, M. (2014). Arnol′d diffusion in a pendulum lattice. <i>Communications on Pure and Applied Mathematics</i>. Wiley. <a href=\"https://doi.org/10.1002/cpa.21509\">https://doi.org/10.1002/cpa.21509</a>","chicago":"Kaloshin, Vadim, Mark Levi, and Maria Saprykina. “Arnol′d Diffusion in a Pendulum Lattice.” <i>Communications on Pure and Applied Mathematics</i>. Wiley, 2014. <a href=\"https://doi.org/10.1002/cpa.21509\">https://doi.org/10.1002/cpa.21509</a>.","ama":"Kaloshin V, Levi M, Saprykina M. Arnol′d diffusion in a pendulum lattice. <i>Communications on Pure and Applied Mathematics</i>. 2014;67(5):748-775. doi:<a href=\"https://doi.org/10.1002/cpa.21509\">10.1002/cpa.21509</a>"},"issue":"5","year":"2014","date_updated":"2022-08-25T13:58:13Z","date_published":"2014-05-01T00:00:00Z","author":[{"last_name":"Kaloshin","full_name":"Kaloshin, Vadim","first_name":"Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"},{"full_name":"Levi, Mark","last_name":"Levi","first_name":"Mark"},{"first_name":"Maria","full_name":"Saprykina, Maria","last_name":"Saprykina"}],"article_processing_charge":"No","oa_version":"None","quality_controlled":"1","type":"journal_article","doi":"10.1002/cpa.21509","date_created":"2020-09-18T10:47:01Z","intvolume":"        67","publication_status":"published","abstract":[{"text":"The main model studied in this paper is a lattice of pendula with a nearest‐neighbor coupling. If the coupling is weak, then the system is near‐integrable and KAM tori fill most of the phase space. For all KAM trajectories the energy of each pendulum stays within a narrow band for all time. Still, we show that for an arbitrarily weak coupling of a certain localized type, the neighboring pendula can exchange energy. In fact, the energy can be transferred between the pendula in any prescribed way.","lang":"eng"}],"status":"public"},{"publisher":"Independent University of Moscow","arxiv":1,"day":"01","_id":"8501","article_type":"original","title":"Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom","volume":14,"keyword":["General Mathematics"],"publication":"Moscow Mathematical Journal","quality_controlled":"1","date_created":"2020-09-18T10:47:09Z","abstract":[{"text":"In this paper, we study small perturbations of a class of non-convex integrable Hamiltonians with two degrees of freedom, and we prove a result of diffusion for an open and dense set of perturbations, with an optimal time of diffusion which grows linearly with respect to the inverse of the size of the perturbation.","lang":"eng"}],"intvolume":"        14","year":"2014","issue":"2","date_published":"2014-04-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"mla":"Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class of Non-Convex Hamiltonians with Two Degrees of Freedom.” <i>Moscow Mathematical Journal</i>, vol. 14, no. 2, Independent University of Moscow, 2014, pp. 181–203, doi:<a href=\"https://doi.org/10.17323/1609-4514-2014-14-2-181-203\">10.17323/1609-4514-2014-14-2-181-203</a>.","short":"A. Bounemoura, V. Kaloshin, Moscow Mathematical Journal 14 (2014) 181–203.","ista":"Bounemoura A, Kaloshin V. 2014. Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom. Moscow Mathematical Journal. 14(2), 181–203.","ieee":"A. Bounemoura and V. Kaloshin, “Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom,” <i>Moscow Mathematical Journal</i>, vol. 14, no. 2. Independent University of Moscow, pp. 181–203, 2014.","ama":"Bounemoura A, Kaloshin V. Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom. <i>Moscow Mathematical Journal</i>. 2014;14(2):181-203. doi:<a href=\"https://doi.org/10.17323/1609-4514-2014-14-2-181-203\">10.17323/1609-4514-2014-14-2-181-203</a>","chicago":"Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class of Non-Convex Hamiltonians with Two Degrees of Freedom.” <i>Moscow Mathematical Journal</i>. Independent University of Moscow, 2014. <a href=\"https://doi.org/10.17323/1609-4514-2014-14-2-181-203\">https://doi.org/10.17323/1609-4514-2014-14-2-181-203</a>.","apa":"Bounemoura, A., &#38; Kaloshin, V. (2014). Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom. <i>Moscow Mathematical Journal</i>. Independent University of Moscow. <a href=\"https://doi.org/10.17323/1609-4514-2014-14-2-181-203\">https://doi.org/10.17323/1609-4514-2014-14-2-181-203</a>"},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"04","publication_identifier":{"issn":["1609-3321","1609-4514"]},"page":"181-203","external_id":{"arxiv":["1304.3050"]},"status":"public","type":"journal_article","oa_version":"Preprint","publication_status":"published","doi":"10.17323/1609-4514-2014-14-2-181-203","article_processing_charge":"No","author":[{"first_name":"Abed","full_name":"Bounemoura, Abed","last_name":"Bounemoura"},{"full_name":"Kaloshin, Vadim","last_name":"Kaloshin","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628"}],"date_updated":"2021-01-12T08:19:43Z"},{"publication":"Genome Biology and Evolution","page":"1949 - 1955","title":"Long-Term asymmetrical acceleration of protein evolution after gene duplication","month":"08","publist_id":"6797","volume":6,"publisher":"Oxford University Press","day":"01","extern":1,"_id":"852","citation":{"mla":"Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration of Protein Evolution after Gene Duplication.” <i>Genome Biology and Evolution</i>, vol. 6, no. 8, Oxford University Press, 2014, pp. 1949–55, doi:<a href=\"https://doi.org/10.1093/gbe/evu159\">10.1093/gbe/evu159</a>.","ista":"Rosello O, Kondrashov F. 2014. Long-Term asymmetrical acceleration of protein evolution after gene duplication. Genome Biology and Evolution. 6(8), 1949–1955.","ieee":"O. Rosello and F. Kondrashov, “Long-Term asymmetrical acceleration of protein evolution after gene duplication,” <i>Genome Biology and Evolution</i>, vol. 6, no. 8. Oxford University Press, pp. 1949–1955, 2014.","short":"O. Rosello, F. Kondrashov, Genome Biology and Evolution 6 (2014) 1949–1955.","ama":"Rosello O, Kondrashov F. Long-Term asymmetrical acceleration of protein evolution after gene duplication. <i>Genome Biology and Evolution</i>. 2014;6(8):1949-1955. doi:<a href=\"https://doi.org/10.1093/gbe/evu159\">10.1093/gbe/evu159</a>","chicago":"Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration of Protein Evolution after Gene Duplication.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/gbe/evu159\">https://doi.org/10.1093/gbe/evu159</a>.","apa":"Rosello, O., &#38; Kondrashov, F. (2014). Long-Term asymmetrical acceleration of protein evolution after gene duplication. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evu159\">https://doi.org/10.1093/gbe/evu159</a>"},"year":"2014","issue":"8","date_published":"2014-08-01T00:00:00Z","date_updated":"2021-01-12T08:19:51Z","author":[{"last_name":"Rosello","full_name":"Rosello, Oriol P","first_name":"Oriol"},{"full_name":"Fyodor Kondrashov","last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"quality_controlled":0,"type":"journal_article","abstract":[{"text":"Rapid divergence of gene copies after duplication is thought to determine the fate of the copies and evolution of novel protein functions. However, data on howlong the gene copies continue to experience an elevated rate of evolution remain scarce. Standard theory of gene duplications based on some level of genetic redundancy of gene copies predicts that the period of accelerated evolutionmust end relatively quickly. Using a maximum-likelihood approach we estimate preduplication, initial postduplication, and recent postduplication rates of evolution that occurred in themammalian lineage.Wefind that both gene copies experience a similar in magnitude acceleration in their rate of evolution. The copy located in the original genomic position typically returns to the preduplication rates of evolution in a short period of time. The burst of faster evolution of the copy that is located in a new genomic position typically lasts longer. Furthermore, the fast-evolving copies on average continue to evolve faster than the preduplication rates far longer than predicted by standard theory of gene duplications.We hypothesize that the prolonged elevated rates of evolution are determined by functional properties that were acquired during, or soon after, the gene duplication event. ","lang":"eng"}],"date_created":"2018-12-11T11:48:51Z","intvolume":"         6","publication_status":"published","doi":"10.1093/gbe/evu159","status":"public"},{"status":"public","doi":"10.1038/ncomms5868","intvolume":"         5","abstract":[{"text":"The emergence of new genes throughout evolution requires rewiring and extension of regulatory networks. However, the molecular details of how the transcriptional regulation of new gene copies evolves remain largely unexplored. Here we show how duplication of a transcription factor gene allowed the emergence of two independent regulatory circuits. Interestingly, the ancestral transcription factor was promiscuous and could bind different motifs in its target promoters. After duplication, one paralogue evolved increased binding specificity so that it only binds one type of motif, whereas the other copy evolved a decreased activity so that it only activates promoters that contain multiple binding sites. Interestingly, only a few mutations in both the DNA-binding domains and in the promoter binding sites were required to gradually disentangle the two networks. These results reveal how duplication of a promiscuous transcription factor followed by concerted cis and trans mutations allows expansion of a regulatory network.","lang":"eng"}],"publication_status":"published","date_created":"2018-12-11T11:48:52Z","type":"journal_article","quality_controlled":0,"author":[{"last_name":"Pougach","full_name":"Pougach, Ksenia S","first_name":"Ksenia"},{"full_name":"Voet, Arnout R","last_name":"Voet","first_name":"Arnout"},{"first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","full_name":"Fyodor Kondrashov"},{"full_name":"Voordeckers, Karin","last_name":"Voordeckers","first_name":"Karin"},{"first_name":"Joaquin","last_name":"Christiaens","full_name":"Christiaens, Joaquin F"},{"first_name":"Bianka","last_name":"Baying","full_name":"Baying, Bianka"},{"last_name":"Bénès","full_name":"Bénès, Vladimı́r","first_name":"Vladimı́R"},{"first_name":"Ryo","full_name":"Sakai, Ryo","last_name":"Sakai"},{"first_name":"Jan","full_name":"Aerts, Jan A","last_name":"Aerts"},{"full_name":"Zhu, Bo","last_name":"Zhu","first_name":"Bo"},{"first_name":"Patrick","full_name":"Van Dijck, Patrick","last_name":"Van Dijck"},{"first_name":"Kevin","full_name":"Verstrepen, Kevin J","last_name":"Verstrepen"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2021-01-12T08:20:01Z","date_published":"2014-01-01T00:00:00Z","year":"2014","citation":{"chicago":"Pougach, Ksenia, Arnout Voet, Fyodor Kondrashov, Karin Voordeckers, Joaquin Christiaens, Bianka Baying, Vladimı́R Bénès, et al. “Duplication of a Promiscuous Transcription Factor Drives the Emergence of a New Regulatory Network.” <i>Nature Communications</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/ncomms5868\">https://doi.org/10.1038/ncomms5868</a>.","apa":"Pougach, K., Voet, A., Kondrashov, F., Voordeckers, K., Christiaens, J., Baying, B., … Verstrepen, K. (2014). Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms5868\">https://doi.org/10.1038/ncomms5868</a>","ama":"Pougach K, Voet A, Kondrashov F, et al. Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. <i>Nature Communications</i>. 2014;5. doi:<a href=\"https://doi.org/10.1038/ncomms5868\">10.1038/ncomms5868</a>","mla":"Pougach, Ksenia, et al. “Duplication of a Promiscuous Transcription Factor Drives the Emergence of a New Regulatory Network.” <i>Nature Communications</i>, vol. 5, Nature Publishing Group, 2014, doi:<a href=\"https://doi.org/10.1038/ncomms5868\">10.1038/ncomms5868</a>.","ieee":"K. Pougach <i>et al.</i>, “Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network,” <i>Nature Communications</i>, vol. 5. Nature Publishing Group, 2014.","short":"K. Pougach, A. Voet, F. Kondrashov, K. Voordeckers, J. Christiaens, B. Baying, V. Bénès, R. Sakai, J. Aerts, B. Zhu, P. Van Dijck, K. Verstrepen, Nature Communications 5 (2014).","ista":"Pougach K, Voet A, Kondrashov F, Voordeckers K, Christiaens J, Baying B, Bénès V, Sakai R, Aerts J, Zhu B, Van Dijck P, Verstrepen K. 2014. Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nature Communications. 5."},"extern":1,"_id":"856","day":"01","publisher":"Nature Publishing Group","volume":5,"publist_id":"6790","month":"01","title":"Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network","acknowledgement":"K.P. acknowledges financial support from TRIPLE I and a Belspo mobility grant from the Belgian Federal Science Policy Office co-funded by the Marie Curie Actions from the European Commission. Research in the lab of K.J.V. is supported by ERC Starting Grant 241426, HFSP programme grant RGP0050/2013, VIB, EMBO YIP programme, KU Leuven Programme Financing, FWO, and IWT. A.V. acknowledges RIKEN for the FPR grant. The work of F.A.K. was supported by a grant of the HHMI International Early Career Scientist Programme (grant #55007424), the Spanish Ministry of Economy and Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP programme, two grants from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017 (grant #Sev-2012-0208)’ and (grant #BES-2013-064004) funded by the European Regional Development Fund (ERDF), the European Union and the European Research Council (grant #335980_EinME). K.V. is supported by an FWO postdoctoral fellowship. Funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","publication":"Nature Communications"},{"citation":{"ama":"Moroz L, Kocot K, Citarella M, et al. The ctenophore genome and the evolutionary origins of neural systems. <i>Nature</i>. 2014;510(7503):109-114. doi:<a href=\"https://doi.org/10.1038/nature13400\">10.1038/nature13400</a>","chicago":"Moroz, Leonid, Kevin Kocot, Mathew Citarella, Sohn Dosung, Tigran Norekian, Inna Povolotskaya, Anastasia Grigorenko, et al. “The Ctenophore Genome and the Evolutionary Origins of Neural Systems.” <i>Nature</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/nature13400\">https://doi.org/10.1038/nature13400</a>.","apa":"Moroz, L., Kocot, K., Citarella, M., Dosung, S., Norekian, T., Povolotskaya, I., … Kohn, A. (2014). The ctenophore genome and the evolutionary origins of neural systems. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature13400\">https://doi.org/10.1038/nature13400</a>","mla":"Moroz, Leonid, et al. “The Ctenophore Genome and the Evolutionary Origins of Neural Systems.” <i>Nature</i>, vol. 510, no. 7503, Nature Publishing Group, 2014, pp. 109–14, doi:<a href=\"https://doi.org/10.1038/nature13400\">10.1038/nature13400</a>.","short":"L. Moroz, K. Kocot, M. Citarella, S. Dosung, T. Norekian, I. Povolotskaya, A. Grigorenko, C. Dailey, E. Berezikov, K. Buckley, A. Ptitsyn, D. Reshetov, K. Mukherjee, T. Moroz, Y. Bobkova, F. Yu, V. Kapitonov, J. Jurka, Y. Bobkov, J. Swore, D. Girardo, A. Fodor, F. Gusev, R. Sanford, R. Bruders, E. Kittler, C. Mills, J. Rast, R. Derelle, V. Solovyev, F. Kondrashov, B. Swalla, J. Sweedler, E. Rogaev, K. Halanych, A. Kohn, Nature 510 (2014) 109–114.","ieee":"L. Moroz <i>et al.</i>, “The ctenophore genome and the evolutionary origins of neural systems,” <i>Nature</i>, vol. 510, no. 7503. Nature Publishing Group, pp. 109–114, 2014.","ista":"Moroz L, Kocot K, Citarella M, Dosung S, Norekian T, Povolotskaya I, Grigorenko A, Dailey C, Berezikov E, Buckley K, Ptitsyn A, Reshetov D, Mukherjee K, Moroz T, Bobkova Y, Yu F, Kapitonov V, Jurka J, Bobkov Y, Swore J, Girardo D, Fodor A, Gusev F, Sanford R, Bruders R, Kittler E, Mills C, Rast J, Derelle R, Solovyev V, Kondrashov F, Swalla B, Sweedler J, Rogaev E, Halanych K, Kohn A. 2014. The ctenophore genome and the evolutionary origins of neural systems. Nature. 510(7503), 109–114."},"_id":"863","extern":1,"publisher":"Nature Publishing Group","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","day":"01","month":"01","publist_id":"6785","volume":510,"title":"The ctenophore genome and the evolutionary origins of neural systems","acknowledgement":"We thank Friday Harbor Laboratories for facilities during animal collection and Marine Genomics apprenticeships (L.L.M., B.J.S.); E. Dabe, G. Winters, J. Netherton, N. Churches and C. Bostwick for help with animal, tissue, in situ, RNA and DNA assays; and X.-X. Tan, F. Lu and T. Tyazelova for sequencing. We thank F. Nivens for videos and P. L. Williams for database support. This work was supported by NSF (NSF-0744649 and NSF CNS-0821622 to L.L.M.; NSF CHE-1111705 to J.V.S.), NIH (1R01GM097502, R01MH097062, R21RR025699 and 5R21DA030118 to L.L.M.; P30 DA018310 to J.V.S.; R01 AG029360 and 1S10RR027052 to E.I.R.), NASA NNX13AJ31G (to K.M.H., L.L.M. and K.M.K.), NSERC 458115 and 211598 (J.P.R.), University of Florida Opportunity Funds/McKnight Brain Research and Florida Biodiversity Institute (L.L.M.), Rostock Inc./A.V. Chikunov (E.I.R.), grant from Russian Federation Government 14.B25.31.0033 (Resolution No.220) (E.I.R.). F.A.K., I.S.P. and R.D. were supported by HHMI (55007424), EMBO and MINECO (BFU2012-31329 and Sev-2012-0208). Contributions of AU Marine Biology Program 117 and Molette laboratory 22.","publication":"Nature","page":"109 - 114","status":"public","abstract":[{"text":"The origins of neural systems remain unresolved. In contrast to other basal metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived muscular systems. These holoplanktonic predators also have sophisticated ciliated locomotion, behaviour and distinct development. Here we present the draft genome of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore transcriptomes, and show that they are remarkably distinct from other animal genomes in their content of neurogenic, immune and developmental genes. Our integrative analyses place Ctenophora as the earliest lineage within Metazoa. This hypothesis is supported by comparative analysis of multiple gene families, including the apparent absence of HOX genes, canonical microRNA machinery, and reduced immune complement in ctenophores. Although two distinct nervous systems are well recognized in ctenophores, many bilaterian neuron-specific genes and genes of 'classical' neurotransmitter pathways either are absent or, if present, are not expressed in neurons. Our metabolomic and physiological data are consistent with the hypothesis that ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.","lang":"eng"}],"publication_status":"published","date_created":"2018-12-11T11:48:54Z","intvolume":"       510","doi":"10.1038/nature13400","quality_controlled":0,"type":"journal_article","author":[{"last_name":"Moroz","full_name":"Moroz, Leonid L","first_name":"Leonid"},{"first_name":"Kevin","full_name":"Kocot, Kevin M","last_name":"Kocot"},{"last_name":"Citarella","full_name":"Citarella, Mathew R","first_name":"Mathew"},{"first_name":"Sohn","full_name":"Dosung, Sohn","last_name":"Dosung"},{"last_name":"Norekian","full_name":"Norekian, Tigran P","first_name":"Tigran"},{"first_name":"Inna","last_name":"Povolotskaya","full_name":"Povolotskaya, Inna"},{"last_name":"Grigorenko","full_name":"Grigorenko, Anastasia P","first_name":"Anastasia"},{"first_name":"Christopher","last_name":"Dailey","full_name":"Dailey, Christopher A"},{"first_name":"Eugene","last_name":"Berezikov","full_name":"Berezikov, Eugene"},{"full_name":"Buckley, Katherine M","last_name":"Buckley","first_name":"Katherine"},{"full_name":"Ptitsyn, Andrey A","last_name":"Ptitsyn","first_name":"Andrey"},{"full_name":"Reshetov, Denis A","last_name":"Reshetov","first_name":"Denis"},{"first_name":"Krishanu","last_name":"Mukherjee","full_name":"Mukherjee, Krishanu"},{"full_name":"Moroz, Tatiana P","last_name":"Moroz","first_name":"Tatiana"},{"first_name":"Yelena","last_name":"Bobkova","full_name":"Bobkova, Yelena V"},{"full_name":"Yu, Fahong","last_name":"Yu","first_name":"Fahong"},{"first_name":"Vladimir","last_name":"Kapitonov","full_name":"Kapitonov, Vladimir V"},{"first_name":"Jerzy","last_name":"Jurka","full_name":"Jurka, Jerzy W"},{"last_name":"Bobkov","full_name":"Bobkov, Yuriy V","first_name":"Yuriy"},{"first_name":"Joshua","last_name":"Swore","full_name":"Swore, Joshua J"},{"first_name":"David","full_name":"Girardo, David O","last_name":"Girardo"},{"full_name":"Fodor, Alexander","last_name":"Fodor","first_name":"Alexander"},{"first_name":"Fedor","last_name":"Gusev","full_name":"Gusev, Fedor E"},{"first_name":"Rachel","full_name":"Sanford, Rachel S","last_name":"Sanford"},{"last_name":"Bruders","full_name":"Bruders, Rebecca","first_name":"Rebecca"},{"last_name":"Kittler","full_name":"Kittler, Ellen L","first_name":"Ellen"},{"first_name":"Claudia","last_name":"Mills","full_name":"Mills, Claudia E"},{"full_name":"Rast, Jonathan P","last_name":"Rast","first_name":"Jonathan"},{"full_name":"Derelle, Romain","last_name":"Derelle","first_name":"Romain"},{"first_name":"Victor","last_name":"Solovyev","full_name":"Solovyev, Victor"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","full_name":"Fyodor Kondrashov"},{"first_name":"Billie","full_name":"Swalla, Billie J","last_name":"Swalla"},{"first_name":"Jonathan","last_name":"Sweedler","full_name":"Sweedler, Jonathan V"},{"first_name":"Evgeny","full_name":"Rogaev, Evgeny I","last_name":"Rogaev"},{"full_name":"Halanych, Kenneth M","last_name":"Halanych","first_name":"Kenneth"},{"first_name":"Andrea","full_name":"Kohn, Andrea B","last_name":"Kohn"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"date_published":"2014-01-01T00:00:00Z","date_updated":"2021-01-12T08:20:21Z","year":"2014","issue":"7503"},{"volume":87,"publist_id":"6782","month":"02","title":"Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling","page":"571 - 578","publication":"Biochemical Pharmacology","citation":{"chicago":"Koval, Alexey, Peter Vlasov, Polina Shichkova, S Khunderyakova, Yury Markov, J Panchenko, A Volodina, Fyodor Kondrashov, and Vladimir Katanaev. “Anti Leprosy Drug Clofazimine Inhibits Growth of Triple-Negative Breast Cancer Cells via Inhibition of Canonical Wnt Signaling.” <i>Biochemical Pharmacology</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.bcp.2013.12.007\">https://doi.org/10.1016/j.bcp.2013.12.007</a>.","apa":"Koval, A., Vlasov, P., Shichkova, P., Khunderyakova, S., Markov, Y., Panchenko, J., … Katanaev, V. (2014). Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. <i>Biochemical Pharmacology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bcp.2013.12.007\">https://doi.org/10.1016/j.bcp.2013.12.007</a>","ama":"Koval A, Vlasov P, Shichkova P, et al. Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. <i>Biochemical Pharmacology</i>. 2014;87(4):571-578. doi:<a href=\"https://doi.org/10.1016/j.bcp.2013.12.007\">10.1016/j.bcp.2013.12.007</a>","mla":"Koval, Alexey, et al. “Anti Leprosy Drug Clofazimine Inhibits Growth of Triple-Negative Breast Cancer Cells via Inhibition of Canonical Wnt Signaling.” <i>Biochemical Pharmacology</i>, vol. 87, no. 4, Elsevier, 2014, pp. 571–78, doi:<a href=\"https://doi.org/10.1016/j.bcp.2013.12.007\">10.1016/j.bcp.2013.12.007</a>.","ista":"Koval A, Vlasov P, Shichkova P, Khunderyakova S, Markov Y, Panchenko J, Volodina A, Kondrashov F, Katanaev V. 2014. Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. Biochemical Pharmacology. 87(4), 571–578.","short":"A. Koval, P. Vlasov, P. Shichkova, S. Khunderyakova, Y. Markov, J. Panchenko, A. Volodina, F. Kondrashov, V. Katanaev, Biochemical Pharmacology 87 (2014) 571–578.","ieee":"A. Koval <i>et al.</i>, “Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling,” <i>Biochemical Pharmacology</i>, vol. 87, no. 4. Elsevier, pp. 571–578, 2014."},"extern":1,"_id":"865","day":"15","publisher":"Elsevier","author":[{"first_name":"Alexey","full_name":"Koval, Alexey V","last_name":"Koval"},{"full_name":"Vlasov, Peter K","last_name":"Vlasov","first_name":"Peter"},{"last_name":"Shichkova","full_name":"Shichkova, Polina","first_name":"Polina"},{"first_name":"S","full_name":"Khunderyakova, S","last_name":"Khunderyakova"},{"first_name":"Yury","full_name":"Markov, Yury","last_name":"Markov"},{"first_name":"J","last_name":"Panchenko","full_name":"Panchenko, J"},{"last_name":"Volodina","full_name":"Volodina, A","first_name":"A"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","full_name":"Fyodor Kondrashov"},{"first_name":"Vladimir","last_name":"Katanaev","full_name":"Katanaev, Vladimir L"}],"date_updated":"2021-01-12T08:20:24Z","date_published":"2014-02-15T00:00:00Z","issue":"4","year":"2014","status":"public","doi":"10.1016/j.bcp.2013.12.007","publication_status":"published","date_created":"2018-12-11T11:48:55Z","abstract":[{"lang":"eng","text":"Research on existing drugs often discovers novel mechanisms of their action and leads to the expansion of their therapeutic scope and subsequent remarketing. The Wnt signaling pathway is of the immediate therapeutic relevance, as it plays critical roles in cancer development and progression. However, drugs which disrupt this pathway are unavailable despite the high demand. Here we report an attempt to identify antagonists of the Wnt-FZD interaction among the library of the FDA-approved drugs. We performed an in silico screening which brought up several potential antagonists of the ligand-receptor interaction. 14 of these substances were tested using the TopFlash luciferase reporter assay and four of them identified as active and specific inhibitors of the Wnt3a-induced signaling. However, further analysis through GTP-binding and β-catenin stabilization assays showed that the compounds do not target the Wnt-FZD pair, but inhibit the signaling at downstream levels. We further describe the previously unknown inhibitory activity of an anti-leprosy drug clofazimine in the Wnt pathway and provide data demonstrating its efficiency in suppressing growth of Wnt-dependent triple-negative breast cancer cells. These data provide a basis for further investigations of the efficiency of clofazimine in treatment of Wnt-dependent cancers."}],"intvolume":"        87","type":"journal_article","quality_controlled":0},{"license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","extern":"1","language":[{"iso":"eng"}],"citation":{"ieee":"D. Ivankov, A. Finkelstein, and F. Kondrashov, “A structural perspective of compensatory evolution,” <i>Current Opinion in Structural Biology</i>, vol. 26. Elsevier, pp. 104–112, 2014.","ista":"Ivankov D, Finkelstein A, Kondrashov F. 2014. A structural perspective of compensatory evolution. Current Opinion in Structural Biology. 26, 104–112.","short":"D. Ivankov, A. Finkelstein, F. Kondrashov, Current Opinion in Structural Biology 26 (2014) 104–112.","mla":"Ivankov, Dmitry, et al. “A Structural Perspective of Compensatory Evolution.” <i>Current Opinion in Structural Biology</i>, vol. 26, Elsevier, 2014, pp. 104–12, doi:<a href=\"https://doi.org/10.1016/j.sbi.2014.05.004\">10.1016/j.sbi.2014.05.004</a>.","apa":"Ivankov, D., Finkelstein, A., &#38; Kondrashov, F. (2014). A structural perspective of compensatory evolution. <i>Current Opinion in Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2014.05.004\">https://doi.org/10.1016/j.sbi.2014.05.004</a>","chicago":"Ivankov, Dmitry, Alexei Finkelstein, and Fyodor Kondrashov. “A Structural Perspective of Compensatory Evolution.” <i>Current Opinion in Structural Biology</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.sbi.2014.05.004\">https://doi.org/10.1016/j.sbi.2014.05.004</a>.","ama":"Ivankov D, Finkelstein A, Kondrashov F. A structural perspective of compensatory evolution. <i>Current Opinion in Structural Biology</i>. 2014;26:104-112. doi:<a href=\"https://doi.org/10.1016/j.sbi.2014.05.004\">10.1016/j.sbi.2014.05.004</a>"},"page":"104 - 112","acknowledgement":"The work has been supported by a grant of the HHMI International Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness (EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017 (Sev-2012-0208)’ and (BFU2012-31329), the European Union and the European Research Council grant (335980_EinME), RFBR (13-04-00253a), MCB RAS (01201358029) and MES RK Grants.\r\n","month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","type":"journal_article","doi":"10.1016/j.sbi.2014.05.004","publication_status":"published","status":"public","date_updated":"2025-08-05T14:53:21Z","article_processing_charge":"No","author":[{"first_name":"Dmitry","full_name":"Ivankov, Dmitry","last_name":"Ivankov"},{"full_name":"Finkelstein, Alexei","last_name":"Finkelstein","first_name":"Alexei"},{"last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"}],"day":"01","publisher":"Elsevier","_id":"892","publication":"Current Opinion in Structural Biology","title":"A structural perspective of compensatory evolution","volume":26,"publist_id":"6756","main_file_link":[{"url":"https://doi.org/10.1016/j.sbi.2014.05.004","open_access":"1"}],"abstract":[{"lang":"eng","text":"The study of molecular evolution is important because it reveals how protein functions emerge and evolve. Recently, several types of studies indicated that substitutions in molecular evolution occur in a compensatory manner, whereby the occurrence of a substitution depends on the amino acid residues at other sites. However, a molecular or structural basis behind the compensation often remains obscure. Here, we review studies on the interface of structural biology and molecular evolution that revealed novel aspects of compensatory evolution. In many cases structural studies benefit from evolutionary data while structural data often add a functional dimension to the study of molecular evolution."}],"intvolume":"        26","date_created":"2018-12-11T11:49:03Z","year":"2014","date_published":"2014-06-01T00:00:00Z","oa":1,"tmp":{"short":"CC BY-NC-ND (3.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode"}},{"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","month":"03","external_id":{"arxiv":["1309.5662"],"pmid":["24800268"]},"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"article_number":"1784","citation":{"apa":"Takagi, D., Palacci, J. A., Braunschweig, A. B., Shelley, M. J., &#38; Zhang, J. (2014). Hydrodynamic capture of microswimmers into sphere-bound orbits. <i>Soft Matter</i>. Royal Society of Chemistry . <a href=\"https://doi.org/10.1039/c3sm52815d\">https://doi.org/10.1039/c3sm52815d</a>","chicago":"Takagi, Daisuke, Jérémie A Palacci, Adam B. Braunschweig, Michael J. Shelley, and Jun Zhang. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.” <i>Soft Matter</i>. Royal Society of Chemistry , 2014. <a href=\"https://doi.org/10.1039/c3sm52815d\">https://doi.org/10.1039/c3sm52815d</a>.","ama":"Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. Hydrodynamic capture of microswimmers into sphere-bound orbits. <i>Soft Matter</i>. 2014;10(11). doi:<a href=\"https://doi.org/10.1039/c3sm52815d\">10.1039/c3sm52815d</a>","ieee":"D. Takagi, J. A. Palacci, A. B. Braunschweig, M. J. Shelley, and J. Zhang, “Hydrodynamic capture of microswimmers into sphere-bound orbits,” <i>Soft Matter</i>, vol. 10, no. 11. Royal Society of Chemistry , 2014.","short":"D. Takagi, J.A. Palacci, A.B. Braunschweig, M.J. Shelley, J. Zhang, Soft Matter 10 (2014).","ista":"Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. 2014. Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft Matter. 10(11), 1784.","mla":"Takagi, Daisuke, et al. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.” <i>Soft Matter</i>, vol. 10, no. 11, 1784, Royal Society of Chemistry , 2014, doi:<a href=\"https://doi.org/10.1039/c3sm52815d\">10.1039/c3sm52815d</a>."},"language":[{"iso":"eng"}],"scopus_import":"1","extern":"1","article_processing_charge":"No","author":[{"last_name":"Takagi","full_name":"Takagi, Daisuke","first_name":"Daisuke"},{"first_name":"Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","last_name":"Palacci","full_name":"Palacci, Jérémie A"},{"last_name":"Braunschweig","full_name":"Braunschweig, Adam B.","first_name":"Adam B."},{"first_name":"Michael J.","last_name":"Shelley","full_name":"Shelley, Michael J."},{"first_name":"Jun","full_name":"Zhang, Jun","last_name":"Zhang"}],"date_updated":"2023-02-23T13:47:35Z","status":"public","doi":"10.1039/c3sm52815d","publication_status":"published","oa_version":"Preprint","type":"journal_article","volume":10,"title":"Hydrodynamic capture of microswimmers into sphere-bound orbits","article_type":"original","keyword":["General Chemistry","Condensed Matter Physics"],"publication":"Soft Matter","pmid":1,"_id":"9050","day":"21","publisher":"Royal Society of Chemistry ","arxiv":1,"oa":1,"date_published":"2014-03-21T00:00:00Z","issue":"11","year":"2014","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1309.5662"}],"intvolume":"        10","date_created":"2021-02-01T13:43:31Z","abstract":[{"lang":"eng","text":"Self-propelled particles can exhibit surprising non-equilibrium behaviors, and how they interact with obstacles or boundaries remains an important open problem. Here we show that chemically propelled micro-rods can be captured, with little change in their speed, into close orbits around solid spheres resting on or near a horizontal plane. We show that this interaction between sphere and particle is short-range, occurring even for spheres smaller than the particle length, and for a variety of sphere materials. We consider a simple model, based on lubrication theory, of a force- and torque-free swimmer driven by a surface slip (the phoretic propulsion mechanism) and moving near a solid surface. The model demonstrates capture, or movement towards the surface, and yields speeds independent of distance. This study reveals the crucial aspects of activity–driven interactions of self-propelled particles with passive objects, and brings into question the use of colloidal tracers as probes of active matter."}],"quality_controlled":"1"},{"publication_status":"published","doi":"10.1098/rsta.2013.0372","type":"journal_article","oa_version":"Published Version","status":"public","date_updated":"2021-02-22T10:44:16Z","article_processing_charge":"No","author":[{"first_name":"Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","last_name":"Palacci","full_name":"Palacci, Jérémie A"},{"first_name":"S.","last_name":"Sacanna","full_name":"Sacanna, S."},{"first_name":"S.-H.","last_name":"Kim","full_name":"Kim, S.-H."},{"first_name":"G.-R.","full_name":"Yi, G.-R.","last_name":"Yi"},{"first_name":"D. J.","last_name":"Pine","full_name":"Pine, D. J."},{"last_name":"Chaikin","full_name":"Chaikin, P. M.","first_name":"P. M."}],"extern":"1","scopus_import":"1","citation":{"short":"J.A. Palacci, S. Sacanna, S.-H. Kim, G.-R. Yi, D.J. Pine, P.M. Chaikin, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 372 (2014).","ieee":"J. A. Palacci, S. Sacanna, S.-H. Kim, G.-R. Yi, D. J. Pine, and P. M. Chaikin, “Light-activated self-propelled colloids,” <i>Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>, vol. 372, no. 2029. The Royal Society, 2014.","ista":"Palacci JA, Sacanna S, Kim S-H, Yi G-R, Pine DJ, Chaikin PM. 2014. Light-activated self-propelled colloids. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 372(2029), 20130372.","mla":"Palacci, Jérémie A., et al. “Light-Activated Self-Propelled Colloids.” <i>Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>, vol. 372, no. 2029, 20130372, The Royal Society, 2014, doi:<a href=\"https://doi.org/10.1098/rsta.2013.0372\">10.1098/rsta.2013.0372</a>.","apa":"Palacci, J. A., Sacanna, S., Kim, S.-H., Yi, G.-R., Pine, D. J., &#38; Chaikin, P. M. (2014). Light-activated self-propelled colloids. <i>Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsta.2013.0372\">https://doi.org/10.1098/rsta.2013.0372</a>","chicago":"Palacci, Jérémie A, S. Sacanna, S.-H. Kim, G.-R. Yi, D. J. Pine, and P. M. Chaikin. “Light-Activated Self-Propelled Colloids.” <i>Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. The Royal Society, 2014. <a href=\"https://doi.org/10.1098/rsta.2013.0372\">https://doi.org/10.1098/rsta.2013.0372</a>.","ama":"Palacci JA, Sacanna S, Kim S-H, Yi G-R, Pine DJ, Chaikin PM. Light-activated self-propelled colloids. <i>Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. 2014;372(2029). doi:<a href=\"https://doi.org/10.1098/rsta.2013.0372\">10.1098/rsta.2013.0372</a>"},"article_number":"20130372","language":[{"iso":"eng"}],"external_id":{"arxiv":["1410.7278"],"pmid":["25332383"]},"publication_identifier":{"eissn":["1471-2962"],"issn":["1364-503X"]},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","month":"11","date_created":"2021-02-18T14:31:11Z","abstract":[{"lang":"eng","text":"Light-activated self-propelled colloids are synthesized and their active motion is studied using optical microscopy. We propose a versatile route using different photoactive materials, and demonstrate a multiwavelength activation and propulsion. Thanks to the photoelectrochemical properties of two semiconductor materials (α-Fe2O3 and TiO2), a light with an energy higher than the bandgap triggers the reaction of decomposition of hydrogen peroxide and produces a chemical cloud around the particle. It induces a phoretic attraction with neighbouring colloids as well as an osmotic self-propulsion of the particle on the substrate. We use these mechanisms to form colloidal cargos as well as self-propelled particles where the light-activated component is embedded into a dielectric sphere. The particles are self-propelled along a direction otherwise randomized by thermal fluctuations, and exhibit a persistent random walk. For sufficient surface density, the particles spontaneously form ‘living crystals’ which are mobile, break apart and reform. Steering the particle with an external magnetic field, we show that the formation of the dense phase results from the collisions heads-on of the particles. This effect is intrinsically non-equilibrium and a novel principle of organization for systems without detailed balance. Engineering families of particles self-propelled by different wavelength demonstrate a good understanding of both the physics and the chemistry behind the system and points to a general route for designing new families of self-propelled particles."}],"intvolume":"       372","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rsta.2013.0372"}],"quality_controlled":"1","date_published":"2014-11-28T00:00:00Z","year":"2014","issue":"2029","oa":1,"_id":"9166","publisher":"The Royal Society","arxiv":1,"day":"28","pmid":1,"publication":"Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences","keyword":["General Engineering","General Physics and Astronomy","General Mathematics"],"volume":372,"title":"Light-activated self-propelled colloids","article_type":"original"},{"date_updated":"2021-01-12T08:21:57Z","date_published":"2014-05-22T00:00:00Z","issue":"4","year":"2014","author":[{"first_name":"Bo","full_name":"Dong, Bo","last_name":"Dong"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"full_name":"Hayashi, Shigeo","last_name":"Hayashi","first_name":"Shigeo"}],"article_processing_charge":"No","doi":"10.1016/j.celrep.2014.03.066","abstract":[{"lang":"eng","text":"The morphological stability of biological tubes is crucial for the efficient circulation of fluids and gases. Failure of this stability causes irregularly shaped tubes found in multiple pathological conditions. Here, we report that Drosophila mutants of the ESCRT III component Shrub/Vps32 exhibit a strikingly elongated sinusoidal tube phenotype. This is caused by excessive apical membrane synthesis accompanied by the ectopic accumulation and overactivation of Crumbs in swollen endosomes. Furthermore, we demonstrate that the apical extracellular matrix (aECM) of the tracheal tube is a viscoelastic material coupled with the apical membrane. We present a simple mechanical model in which aECM elasticity, apical membrane growth, and their interaction are three vital parameters determining the stability of biological tubes. Our findings demonstrate a mechanical role for the extracellular matrix and suggest that the interaction of the apical membrane and an elastic aECM determines the final morphology of biological tubes independent of cell shape."}],"publication_status":"published","date_created":"2018-12-11T11:49:14Z","intvolume":"         7","oa_version":"None","type":"journal_article","status":"public","acknowledgement":"We thank F. Gao, R.E. Ward, S. Luschnig, T. Okajima, M. Affolter, D. Bilder, E. Knust, T. Tanaka, A. Nakamura, C. Samakovlis, K. Saigo, M. Furuse, the Bloomington Stock Center, Drosophila Genetic Resource Center in Kyoto, Japan, and the Developmental Studies Hybridoma Bank for generously providing antibodies and fly stocks; H. Wada for UAS-3×TagRFP fly and dye injection; Y.H. Zhang for plasmid and protocol for CBP preparation; and J. Prost and J.F. Joanny for their support for the project and discussion. We also thank T. Shibata, Y. Morishita, T. Kondo, and G. Sheng for critically reading the manuscript. This work was supported by a Grant-in-Aid for Scientific Research on Innovative Areas from MEXT Japan to S.H. and the RIKEN Foreign Postdoctoral Researcher Program to B.D.","publication":"Cell Reports","page":"941 - 950","volume":7,"publist_id":"6515","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","title":"Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape","extern":"1","_id":"925","day":"22","publisher":"Cell Press","citation":{"mla":"Dong, Bo, et al. “Balance between Apical Membrane Growth and Luminal Matrix Resistance Determines Epithelial Tubule Shape.” <i>Cell Reports</i>, vol. 7, no. 4, Cell Press, 2014, pp. 941–50, doi:<a href=\"https://doi.org/10.1016/j.celrep.2014.03.066\">10.1016/j.celrep.2014.03.066</a>.","ieee":"B. Dong, E. B. Hannezo, and S. Hayashi, “Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape,” <i>Cell Reports</i>, vol. 7, no. 4. Cell Press, pp. 941–950, 2014.","short":"B. Dong, E.B. Hannezo, S. Hayashi, Cell Reports 7 (2014) 941–950.","ista":"Dong B, Hannezo EB, Hayashi S. 2014. Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape. Cell Reports. 7(4), 941–950.","chicago":"Dong, Bo, Edouard B Hannezo, and Shigeo Hayashi. “Balance between Apical Membrane Growth and Luminal Matrix Resistance Determines Epithelial Tubule Shape.” <i>Cell Reports</i>. Cell Press, 2014. <a href=\"https://doi.org/10.1016/j.celrep.2014.03.066\">https://doi.org/10.1016/j.celrep.2014.03.066</a>.","apa":"Dong, B., Hannezo, E. B., &#38; Hayashi, S. (2014). Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2014.03.066\">https://doi.org/10.1016/j.celrep.2014.03.066</a>","ama":"Dong B, Hannezo EB, Hayashi S. Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape. <i>Cell Reports</i>. 2014;7(4):941-950. doi:<a href=\"https://doi.org/10.1016/j.celrep.2014.03.066\">10.1016/j.celrep.2014.03.066</a>"},"language":[{"iso":"eng"}]},{"date_updated":"2021-01-12T08:21:57Z","date_published":"2014-04-06T00:00:00Z","issue":"93","year":"2014","author":[{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B"},{"full_name":"Prost, Jacques","last_name":"Prost","first_name":"Jacques"},{"first_name":"Jean","last_name":"Joanny","full_name":"Joanny, Jean"}],"article_processing_charge":"No","doi":"10.1098/rsif.2013.0895","abstract":[{"text":"The regulation of cell growth in animal tissues is a question of critical importance: most tissues contain different types of cells in interconversion and the fraction of each type has to be controlled in a precise way, by mechanisms that remain unclear. Here, we provide a theoretical framework for the homeostasis of stem-cell-containing epithelial tissues using mechanical equations, which describe the size of the tissue and kinetic equations, which describe the interconversions of the cell populations. We show that several features, such as the evolution of stem cell fractions during intestinal development, the shape of a developing intestinal wall, as well as the increase in the proliferative compartment in cancer initiation, can be studied and understood from generic modelling which does not rely on a particular regulatory mechanism. Finally, inspired by recent experiments, we propose a model where cell division rates are regulated by the mechanical stresses in the epithelial sheet. We show that pressure-controlled growth can, in addition to the previous features, also explain with few parameters the formation of stem cell compartments as well as the morphologies observed when a colonic crypt becomes cancerous. We also discuss optimal strategies of wound healing, in connection with experiments on the cornea.","lang":"eng"}],"date_created":"2018-12-11T11:49:14Z","publication_status":"published","intvolume":"        11","oa_version":"None","type":"journal_article","status":"public","publication":"Journal of the Royal Society Interface","acknowledgement":"We thank Jens Elgeti and Silvia Fre for fruitful discussions.","volume":11,"publist_id":"6516","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"04","title":"Growth homeostatic regulation and stem cell dynamics in tissues","_id":"926","extern":"1","day":"06","publisher":"Royal Society of London","citation":{"ieee":"E. B. Hannezo, J. Prost, and J. Joanny, “Growth homeostatic regulation and stem cell dynamics in tissues,” <i>Journal of the Royal Society Interface</i>, vol. 11, no. 93. Royal Society of London, 2014.","short":"E.B. Hannezo, J. Prost, J. Joanny, Journal of the Royal Society Interface 11 (2014).","ista":"Hannezo EB, Prost J, Joanny J. 2014. Growth homeostatic regulation and stem cell dynamics in tissues. Journal of the Royal Society Interface. 11(93).","mla":"Hannezo, Edouard B., et al. “Growth Homeostatic Regulation and Stem Cell Dynamics in Tissues.” <i>Journal of the Royal Society Interface</i>, vol. 11, no. 93, Royal Society of London, 2014, doi:<a href=\"https://doi.org/10.1098/rsif.2013.0895\">10.1098/rsif.2013.0895</a>.","ama":"Hannezo EB, Prost J, Joanny J. Growth homeostatic regulation and stem cell dynamics in tissues. <i>Journal of the Royal Society Interface</i>. 2014;11(93). doi:<a href=\"https://doi.org/10.1098/rsif.2013.0895\">10.1098/rsif.2013.0895</a>","apa":"Hannezo, E. B., Prost, J., &#38; Joanny, J. (2014). Growth homeostatic regulation and stem cell dynamics in tissues. <i>Journal of the Royal Society Interface</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rsif.2013.0895\">https://doi.org/10.1098/rsif.2013.0895</a>","chicago":"Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Growth Homeostatic Regulation and Stem Cell Dynamics in Tissues.” <i>Journal of the Royal Society Interface</i>. Royal Society of London, 2014. <a href=\"https://doi.org/10.1098/rsif.2013.0895\">https://doi.org/10.1098/rsif.2013.0895</a>."},"language":[{"iso":"eng"}]},{"author":[{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"first_name":"Jacques","last_name":"Prost","full_name":"Prost, Jacques"},{"full_name":"Joanny, Jean","last_name":"Joanny","first_name":"Jean"}],"article_processing_charge":"No","date_updated":"2021-01-12T08:21:58Z","date_published":"2014-01-01T00:00:00Z","issue":"1","year":"2014","status":"public","doi":"10.1073/pnas.1312076111","abstract":[{"text":"Morphogenesis during embryo development requires the coordination of mechanical forces to generate the macroscopic shapes of organs. We propose a minimal theoretical model, based on cell adhesion and actomyosin contractility, which describes the various shapes of epithelial cells and the bending and buckling of epithelial sheets, as well as the relative stability of cellular tubes and spheres. We show that, to understand these processes, a full 3D description of the cells is needed, but that simple scaling laws can still be derived. The morphologies observed in vivo can be understood as stable points of mechanical equations and the transitions between them are either continuous or discontinuous. We then focus on epithelial sheet bending, a ubiquitous morphogenetic process. We calculate the curvature of an epithelium as a function of actin belt tension as well as of cell-cell and and cell-substrate tension. The model allows for a comparison of the relative stabilities of spherical or cylindrical cellular structures (acini or tubes). Finally, we propose a unique type of buckling instability of epithelia, driven by a flattening of individual cell shapes, and discuss experimental tests to verify our predictions.","lang":"eng"}],"publication_status":"published","date_created":"2018-12-11T11:49:14Z","intvolume":"       111","oa_version":"None","type":"journal_article","volume":111,"publist_id":"6517","month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Theory of epithelial sheet morphology in three dimensions","page":"27 - 32","publication":"PNAS","citation":{"ama":"Hannezo EB, Prost J, Joanny J. Theory of epithelial sheet morphology in three dimensions. <i>PNAS</i>. 2014;111(1):27-32. doi:<a href=\"https://doi.org/10.1073/pnas.1312076111\">10.1073/pnas.1312076111</a>","apa":"Hannezo, E. B., Prost, J., &#38; Joanny, J. (2014). Theory of epithelial sheet morphology in three dimensions. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1312076111\">https://doi.org/10.1073/pnas.1312076111</a>","chicago":"Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Theory of Epithelial Sheet Morphology in Three Dimensions.” <i>PNAS</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1312076111\">https://doi.org/10.1073/pnas.1312076111</a>.","ieee":"E. B. Hannezo, J. Prost, and J. Joanny, “Theory of epithelial sheet morphology in three dimensions,” <i>PNAS</i>, vol. 111, no. 1. National Academy of Sciences, pp. 27–32, 2014.","short":"E.B. Hannezo, J. Prost, J. Joanny, PNAS 111 (2014) 27–32.","ista":"Hannezo EB, Prost J, Joanny J. 2014. Theory of epithelial sheet morphology in three dimensions. PNAS. 111(1), 27–32.","mla":"Hannezo, Edouard B., et al. “Theory of Epithelial Sheet Morphology in Three Dimensions.” <i>PNAS</i>, vol. 111, no. 1, National Academy of Sciences, 2014, pp. 27–32, doi:<a href=\"https://doi.org/10.1073/pnas.1312076111\">10.1073/pnas.1312076111</a>."},"language":[{"iso":"eng"}],"_id":"927","extern":"1","day":"01","publisher":"National Academy of Sciences"},{"article_processing_charge":"No","author":[{"first_name":"Jason T.","full_name":"Huff, Jason T.","last_name":"Huff"},{"full_name":"Zilberman, Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel"}],"department":[{"_id":"DaZi"}],"date_updated":"2021-12-14T08:22:36Z","status":"public","oa_version":"Published Version","type":"journal_article","doi":"10.1016/j.cell.2014.01.029","publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"03","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"external_id":{"pmid":["24630728"]},"page":"1286-1297","language":[{"iso":"eng"}],"citation":{"mla":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>, vol. 156, no. 6, Elsevier, 2014, pp. 1286–97, doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>.","ieee":"J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes,” <i>Cell</i>, vol. 156, no. 6. Elsevier, pp. 1286–1297, 2014.","short":"J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297.","ista":"Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297.","ama":"Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. 2014;156(6):1286-1297. doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>","chicago":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>.","apa":"Huff, J. T., &#38; Zilberman, D. (2014). Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>"},"scopus_import":"1","extern":"1","oa":1,"issue":"6","year":"2014","date_published":"2014-03-13T00:00:00Z","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2014.01.029"}],"intvolume":"       156","date_created":"2021-06-04T12:00:16Z","abstract":[{"text":"Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints.","lang":"eng"}],"title":"Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes","article_type":"original","volume":156,"publication":"Cell","pmid":1,"day":"13","publisher":"Elsevier","_id":"9458"},{"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1418564111","open_access":"1"}],"abstract":[{"text":"Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction.","lang":"eng"}],"date_created":"2021-06-07T07:23:43Z","intvolume":"       111","oa":1,"issue":"45","year":"2014","date_published":"2014-11-11T00:00:00Z","pmid":1,"day":"11","publisher":"National Academy of Sciences","_id":"9479","title":"The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes","article_type":"original","volume":111,"publication":"Proceedings of the National Academy of Sciences","status":"public","oa_version":"Published Version","type":"journal_article","doi":"10.1073/pnas.1418564111","publication_status":"published","article_processing_charge":"No","author":[{"first_name":"Zsuzsanna","full_name":"Mérai, Zsuzsanna","last_name":"Mérai"},{"first_name":"Nina","full_name":"Chumak, Nina","last_name":"Chumak"},{"first_name":"Marcelina","last_name":"García-Aguilar","full_name":"García-Aguilar, Marcelina"},{"first_name":"Tzung-Fu","last_name":"Hsieh","full_name":"Hsieh, Tzung-Fu"},{"first_name":"Toshiro","last_name":"Nishimura","full_name":"Nishimura, Toshiro"},{"first_name":"Vera K.","last_name":"Schoft","full_name":"Schoft, Vera K."},{"first_name":"János","last_name":"Bindics","full_name":"Bindics, János"},{"first_name":"Lucyna","last_name":"Ślusarz","full_name":"Ślusarz, Lucyna"},{"last_name":"Arnoux","full_name":"Arnoux, Stéphanie","first_name":"Stéphanie"},{"first_name":"Susanne","last_name":"Opravil","full_name":"Opravil, Susanne"},{"first_name":"Karl","full_name":"Mechtler, Karl","last_name":"Mechtler"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel","full_name":"Zilberman, Daniel","last_name":"Zilberman"},{"last_name":"Fischer","full_name":"Fischer, Robert L.","first_name":"Robert L."},{"last_name":"Tamaru","full_name":"Tamaru, Hisashi","first_name":"Hisashi"}],"department":[{"_id":"DaZi"}],"date_updated":"2021-12-14T08:23:26Z","language":[{"iso":"eng"}],"citation":{"mla":"Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45, National Academy of Sciences, 2014, pp. 16166–71, doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>.","ista":"Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 111(45), 16166–16171.","short":"Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft, J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L. Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014) 16166–16171.","ieee":"Z. Mérai <i>et al.</i>, “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45. National Academy of Sciences, pp. 16166–16171, 2014.","chicago":"Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh, Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>.","apa":"Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft, V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>","ama":"Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(45):16166-16171. doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>"},"scopus_import":"1","extern":"1","month":"11","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"external_id":{"pmid":["25344531"]},"page":"16166-16171"},{"abstract":[{"text":"Transposons are selfish genetic sequences that can increase their copy number and inflict substantial damage on their hosts. To combat these genomic parasites, plants have evolved multiple pathways to identify and silence transposons by methylating their DNA. Plants have also evolved mechanisms to limit the collateral damage from the antitransposon machinery. In this review, we examine recent developments that have elucidated many of the molecular workings of these pathways. We also highlight the evidence that the methylation and demethylation pathways interact, indicating that plants have a highly sophisticated, integrated system of transposon defense that has an important role in the regulation of gene expression.","lang":"eng"}],"intvolume":"        19","date_created":"2021-06-07T14:38:09Z","quality_controlled":"1","date_published":"2014-05-04T00:00:00Z","year":"2014","issue":"5","pmid":1,"_id":"9519","publisher":"Elsevier","day":"04","volume":19,"article_type":"review","title":"DNA methylation as a system of plant genomic immunity","publication":"Trends in Plant Science","status":"public","publication_status":"published","doi":"10.1016/j.tplants.2014.01.014","type":"journal_article","oa_version":"None","article_processing_charge":"No","author":[{"first_name":"M. Yvonne","full_name":"Kim, M. Yvonne","last_name":"Kim"},{"first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman"}],"date_updated":"2021-12-14T08:24:48Z","department":[{"_id":"DaZi"}],"citation":{"mla":"Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” <i>Trends in Plant Science</i>, vol. 19, no. 5, Elsevier, 2014, pp. 320–26, doi:<a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">10.1016/j.tplants.2014.01.014</a>.","ieee":"M. Y. Kim and D. Zilberman, “DNA methylation as a system of plant genomic immunity,” <i>Trends in Plant Science</i>, vol. 19, no. 5. Elsevier, pp. 320–326, 2014.","short":"M.Y. Kim, D. Zilberman, Trends in Plant Science 19 (2014) 320–326.","ista":"Kim MY, Zilberman D. 2014. DNA methylation as a system of plant genomic immunity. Trends in Plant Science. 19(5), 320–326.","ama":"Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity. <i>Trends in Plant Science</i>. 2014;19(5):320-326. doi:<a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">10.1016/j.tplants.2014.01.014</a>","chicago":"Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” <i>Trends in Plant Science</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">https://doi.org/10.1016/j.tplants.2014.01.014</a>.","apa":"Kim, M. Y., &#38; Zilberman, D. (2014). DNA methylation as a system of plant genomic immunity. <i>Trends in Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">https://doi.org/10.1016/j.tplants.2014.01.014</a>"},"language":[{"iso":"eng"}],"extern":"1","scopus_import":"1","month":"05","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"320-326","external_id":{"pmid":["24618094 "]},"publication_identifier":{"eissn":["1878-4372"],"issn":["1360-1385"]}},{"doi":"10.37236/3752","publication_status":"published","oa_version":"Published Version","type":"journal_article","status":"public","date_updated":"2023-02-23T14:02:12Z","author":[{"first_name":"Catherine","last_name":"Greenhill","full_name":"Greenhill, Catherine"},{"orcid":"0000-0002-4003-7567","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","first_name":"Matthew Alan","full_name":"Kwan, Matthew Alan","last_name":"Kwan"},{"first_name":"David","full_name":"Wind, David","last_name":"Wind"}],"article_processing_charge":"No","scopus_import":"1","extern":"1","article_number":"P1.45","citation":{"mla":"Greenhill, Catherine, et al. “On the Number of Spanning Trees in Random Regular Graphs.” <i>The Electronic Journal of Combinatorics</i>, vol. 21, no. 1, P1.45, The Electronic Journal of Combinatorics, 2014, doi:<a href=\"https://doi.org/10.37236/3752\">10.37236/3752</a>.","ista":"Greenhill C, Kwan MA, Wind D. 2014. On the number of spanning trees in random regular graphs. The Electronic Journal of Combinatorics. 21(1), P1.45.","short":"C. Greenhill, M.A. Kwan, D. Wind, The Electronic Journal of Combinatorics 21 (2014).","ieee":"C. Greenhill, M. A. Kwan, and D. Wind, “On the number of spanning trees in random regular graphs,” <i>The Electronic Journal of Combinatorics</i>, vol. 21, no. 1. The Electronic Journal of Combinatorics, 2014.","ama":"Greenhill C, Kwan MA, Wind D. On the number of spanning trees in random regular graphs. <i>The Electronic Journal of Combinatorics</i>. 2014;21(1). doi:<a href=\"https://doi.org/10.37236/3752\">10.37236/3752</a>","chicago":"Greenhill, Catherine, Matthew Alan Kwan, and David Wind. “On the Number of Spanning Trees in Random Regular Graphs.” <i>The Electronic Journal of Combinatorics</i>. The Electronic Journal of Combinatorics, 2014. <a href=\"https://doi.org/10.37236/3752\">https://doi.org/10.37236/3752</a>.","apa":"Greenhill, C., Kwan, M. A., &#38; Wind, D. (2014). On the number of spanning trees in random regular graphs. <i>The Electronic Journal of Combinatorics</i>. The Electronic Journal of Combinatorics. <a href=\"https://doi.org/10.37236/3752\">https://doi.org/10.37236/3752</a>"},"language":[{"iso":"eng"}],"external_id":{"arxiv":["1309.6710"]},"publication_identifier":{"eissn":["1077-8926"]},"month":"02","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"open_access":"1","url":"https://doi.org/10.37236/3752"}],"abstract":[{"lang":"eng","text":"Let d≥3 be a fixed integer. We give an asympotic formula for the expected number of spanning trees in a uniformly random d-regular graph with n vertices. (The asymptotics are as n→∞, restricted to even n if d is odd.) We also obtain the asymptotic distribution of the number of spanning trees in a uniformly random cubic graph, and conjecture that the corresponding result holds for arbitrary (fixed) d. Numerical evidence is presented which supports our conjecture."}],"date_created":"2021-06-23T06:29:35Z","intvolume":"        21","quality_controlled":"1","date_published":"2014-02-28T00:00:00Z","issue":"1","year":"2014","oa":1,"_id":"9594","day":"28","publisher":"The Electronic Journal of Combinatorics","arxiv":1,"publication":"The Electronic Journal of Combinatorics","volume":21,"article_type":"original","title":"On the number of spanning trees in random regular graphs"},{"day":"14","publisher":"American Physiological Society","arxiv":1,"_id":"96","title":"Coherent operations and screening in multielectron spin qubits","publist_id":"7958","volume":112,"publication":"APS Physics, Physical Review Letters","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1306.2720","open_access":"1"}],"intvolume":"       112","abstract":[{"lang":"eng","text":"Multielectron spin qubits are demonstrated, and performance examined by comparing coherent exchange oscillations in coupled single-electron and multielectron quantum dots, measured in the same device. Fast (&gt;1 GHz) exchange oscillations with a quality factor Q∼15 are found for the multielectron case, compared to Q∼2 for the single-electron case, the latter consistent with experiments in the literature. A model of dephasing that includes voltage and hyperfine noise is developed that is in good agreement with both single- and multielectron data, though in both cases additional exchange-independent dephasing is needed to obtain quantitative agreement across a broad parameter range."}],"date_created":"2018-12-11T11:44:36Z","oa":1,"issue":"2","year":"2014","date_published":"2014-01-14T00:00:00Z","language":[{"iso":"eng"}],"article_number":"026801","citation":{"ama":"Higginbotham AP, Kuemmeth F, Hanson M, Gossard A, Marcus C. Coherent operations and screening in multielectron spin qubits. <i>APS Physics, Physical Review Letters</i>. 2014;112(2). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.112.026801\">10.1103/PhysRevLett.112.026801</a>","chicago":"Higginbotham, Andrew P, Ferdinand Kuemmeth, Micah Hanson, Arthur Gossard, and Charles Marcus. “Coherent Operations and Screening in Multielectron Spin Qubits.” <i>APS Physics, Physical Review Letters</i>. American Physiological Society, 2014. <a href=\"https://doi.org/10.1103/PhysRevLett.112.026801\">https://doi.org/10.1103/PhysRevLett.112.026801</a>.","apa":"Higginbotham, A. P., Kuemmeth, F., Hanson, M., Gossard, A., &#38; Marcus, C. (2014). Coherent operations and screening in multielectron spin qubits. <i>APS Physics, Physical Review Letters</i>. American Physiological Society. <a href=\"https://doi.org/10.1103/PhysRevLett.112.026801\">https://doi.org/10.1103/PhysRevLett.112.026801</a>","mla":"Higginbotham, Andrew P., et al. “Coherent Operations and Screening in Multielectron Spin Qubits.” <i>APS Physics, Physical Review Letters</i>, vol. 112, no. 2, 026801, American Physiological Society, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.112.026801\">10.1103/PhysRevLett.112.026801</a>.","ieee":"A. P. Higginbotham, F. Kuemmeth, M. Hanson, A. Gossard, and C. Marcus, “Coherent operations and screening in multielectron spin qubits,” <i>APS Physics, Physical Review Letters</i>, vol. 112, no. 2. American Physiological Society, 2014.","short":"A.P. Higginbotham, F. Kuemmeth, M. Hanson, A. Gossard, C. Marcus, APS Physics, Physical Review Letters 112 (2014).","ista":"Higginbotham AP, Kuemmeth F, Hanson M, Gossard A, Marcus C. 2014. Coherent operations and screening in multielectron spin qubits. APS Physics, Physical Review Letters. 112(2), 026801."},"extern":"1","month":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1306.2720"]},"acknowledgement":"The research is supported by the Intelligence Advanced Research Projects Activity (IARPA), through the Army Research Office Grant No. W911NF-12-1-0354, the DARPA QuEST Program, the Department of Energy, Office of Science, and the Danish National Research Foundation.","status":"public","oa_version":"Preprint","type":"journal_article","doi":"10.1103/PhysRevLett.112.026801","publication_status":"published","author":[{"orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P"},{"full_name":"Kuemmeth, Ferdinand","last_name":"Kuemmeth","first_name":"Ferdinand"},{"full_name":"Hanson, Micah","last_name":"Hanson","first_name":"Micah"},{"last_name":"Gossard","full_name":"Gossard, Arthur","first_name":"Arthur"},{"first_name":"Charles","last_name":"Marcus","full_name":"Marcus, Charles"}],"date_updated":"2021-01-12T08:22:14Z"},{"pmid":1,"ddc":["570"],"day":"01","publisher":"Elsevier","_id":"9655","article_type":"original","title":"Correlative light- and electron microscopy with chemical tags","volume":186,"publication":"Journal of Structural Biology","quality_controlled":"1","intvolume":"       186","abstract":[{"text":"Correlative microscopy incorporates the specificity of fluorescent protein labeling into high-resolution electron micrographs. Several approaches exist for correlative microscopy, most of which have used the green fluorescent protein (GFP) as the label for light microscopy. Here we use chemical tagging and synthetic fluorophores instead, in order to achieve protein-specific labeling, and to perform multicolor imaging. We show that synthetic fluorophores preserve their post-embedding fluorescence in the presence of uranyl acetate. Post-embedding fluorescence is of such quality that the specimen can be prepared with identical protocols for scanning electron microscopy (SEM) and transmission electron microscopy (TEM); this is particularly valuable when singular or otherwise difficult samples are examined. We show that synthetic fluorophores give bright, well-resolved signals in super-resolution light microscopy, enabling us to superimpose light microscopic images with a precision of up to 25 nm in the x–y plane on electron micrographs. To exemplify the preservation quality of our new method we visualize the molecular arrangement of cadherins in adherens junctions of mouse epithelial cells.","lang":"eng"}],"date_created":"2021-07-14T09:05:42Z","oa":1,"tmp":{"short":"CC BY-NC-ND (3.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode"},"issue":"2","year":"2014","date_published":"2014-05-01T00:00:00Z","language":[{"iso":"eng"}],"has_accepted_license":"1","citation":{"ama":"Perkovic M, Kunz M, Endesfelder U, et al. Correlative light- and electron microscopy with chemical tags. <i>Journal of Structural Biology</i>. 2014;186(2):205-213. doi:<a href=\"https://doi.org/10.1016/j.jsb.2014.03.018\">10.1016/j.jsb.2014.03.018</a>","apa":"Perkovic, M., Kunz, M., Endesfelder, U., Bunse, S., Wigge, C., Yu, Z., … Frangakis, A. S. (2014). Correlative light- and electron microscopy with chemical tags. <i>Journal of Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsb.2014.03.018\">https://doi.org/10.1016/j.jsb.2014.03.018</a>","chicago":"Perkovic, Mario, Michael Kunz, Ulrike Endesfelder, Stefanie Bunse, Christoph Wigge, Zhou Yu, Victor-Valentin Hodirnau, et al. “Correlative Light- and Electron Microscopy with Chemical Tags.” <i>Journal of Structural Biology</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.jsb.2014.03.018\">https://doi.org/10.1016/j.jsb.2014.03.018</a>.","ieee":"M. Perkovic <i>et al.</i>, “Correlative light- and electron microscopy with chemical tags,” <i>Journal of Structural Biology</i>, vol. 186, no. 2. Elsevier, pp. 205–213, 2014.","ista":"Perkovic M, Kunz M, Endesfelder U, Bunse S, Wigge C, Yu Z, Hodirnau V-V, Scheffer MP, Seybert A, Malkusch S, Schuman EM, Heilemann M, Frangakis AS. 2014. Correlative light- and electron microscopy with chemical tags. Journal of Structural Biology. 186(2), 205–213.","short":"M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V.-V. Hodirnau, M.P. Scheffer, A. Seybert, S. Malkusch, E.M. Schuman, M. Heilemann, A.S. Frangakis, Journal of Structural Biology 186 (2014) 205–213.","mla":"Perkovic, Mario, et al. “Correlative Light- and Electron Microscopy with Chemical Tags.” <i>Journal of Structural Biology</i>, vol. 186, no. 2, Elsevier, 2014, pp. 205–13, doi:<a href=\"https://doi.org/10.1016/j.jsb.2014.03.018\">10.1016/j.jsb.2014.03.018</a>."},"file_date_updated":"2021-07-22T08:06:34Z","scopus_import":"1","extern":"1","month":"05","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publication_identifier":{"issn":["1047-8477"]},"external_id":{"pmid":["24698954"]},"file":[{"relation":"main_file","checksum":"a322991b43cdc5935c99db88d285aa3a","file_size":3454628,"file_name":"2014_JournalOfStructuralBiology_Perkovic.pdf","date_updated":"2021-07-22T08:06:34Z","creator":"asandaue","content_type":"application/pdf","file_id":"9701","success":1,"access_level":"open_access","date_created":"2021-07-22T08:06:34Z"}],"page":"205-213","status":"public","oa_version":"Published Version","type":"journal_article","doi":"10.1016/j.jsb.2014.03.018","publication_status":"published","article_processing_charge":"No","author":[{"full_name":"Perkovic, Mario","last_name":"Perkovic","first_name":"Mario"},{"first_name":"Michael","full_name":"Kunz, Michael","last_name":"Kunz"},{"first_name":"Ulrike","full_name":"Endesfelder, Ulrike","last_name":"Endesfelder"},{"first_name":"Stefanie","last_name":"Bunse","full_name":"Bunse, Stefanie"},{"first_name":"Christoph","full_name":"Wigge, Christoph","last_name":"Wigge"},{"full_name":"Yu, Zhou","last_name":"Yu","first_name":"Zhou"},{"first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau"},{"full_name":"Scheffer, Margot P.","last_name":"Scheffer","first_name":"Margot P."},{"first_name":"Anja","last_name":"Seybert","full_name":"Seybert, Anja"},{"last_name":"Malkusch","full_name":"Malkusch, Sebastian","first_name":"Sebastian"},{"full_name":"Schuman, Erin M.","last_name":"Schuman","first_name":"Erin M."},{"full_name":"Heilemann, Mike","last_name":"Heilemann","first_name":"Mike"},{"last_name":"Frangakis","full_name":"Frangakis, Achilleas S.","first_name":"Achilleas S."}],"date_updated":"2021-07-22T08:26:32Z"}]