[{"status":"public","doi":"10.7554/elife.30674","citation":{"mla":"Lyons, David B., and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” <i>ELife</i>, vol. 6, e30674, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/elife.30674\">10.7554/elife.30674</a>.","chicago":"Lyons, David B, and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/elife.30674\">https://doi.org/10.7554/elife.30674</a>.","ieee":"D. B. Lyons and D. Zilberman, “DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017.","short":"D.B. Lyons, D. Zilberman, ELife 6 (2017).","ista":"Lyons DB, Zilberman D. 2017. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 6, e30674.","ama":"Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/elife.30674\">10.7554/elife.30674</a>","apa":"Lyons, D. B., &#38; Zilberman, D. (2017). DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.30674\">https://doi.org/10.7554/elife.30674</a>"},"date_created":"2021-06-02T14:28:58Z","month":"11","_id":"9445","day":"15","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication":"eLife","abstract":[{"lang":"eng","text":"Cytosine methylation regulates essential genome functions across eukaryotes, but the fundamental question of whether nucleosomal or naked DNA is the preferred substrate of plant and animal methyltransferases remains unresolved. Here, we show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome, suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases in vivo. Furthermore, we show that simultaneous mutation of DDM1 and linker histone H1 in Arabidopsis reproduces the strong linker-specific methylation patterns of species that diverged from flowering plants and animals over a billion years ago. Our results indicate that in the absence of remodeling, nucleosomes are strong barriers to DNA methyltransferases. Linker-specific methylation can evolve simply by breaking the connection between nucleosome remodeling and DNA methylation."}],"date_published":"2017-11-15T00:00:00Z","author":[{"last_name":"Lyons","full_name":"Lyons, David B","first_name":"David B"},{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"file_date_updated":"2021-06-02T14:33:36Z","license":"https://creativecommons.org/licenses/by/4.0/","file":[{"checksum":"4cfcdd67511ae4aed3d993550e46e146","file_id":"9446","file_size":1603102,"creator":"cziletti","file_name":"2017_eLife_Lyons.pdf","success":1,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2021-06-02T14:33:36Z","date_created":"2021-06-02T14:33:36Z"}],"volume":6,"scopus_import":"1","quality_controlled":"1","has_accepted_license":"1","publication_status":"published","publisher":"eLife Sciences Publications","extern":"1","intvolume":"         6","article_type":"original","pmid":1,"external_id":{"pmid":["29140247"]},"year":"2017","publication_identifier":{"eissn":["2050-084X"]},"type":"journal_article","ddc":["570"],"oa_version":"Published Version","language":[{"iso":"eng"}],"date_updated":"2021-12-14T07:54:36Z","department":[{"_id":"DaZi"}],"article_processing_charge":"No","title":"DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes","article_number":"e30674"},{"quality_controlled":"1","scopus_import":"1","isi":1,"intvolume":"        34","publisher":"Oxford University Press","publication_status":"published","has_accepted_license":"1","project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF"}],"file_date_updated":"2020-07-14T12:48:15Z","oa":1,"volume":34,"file":[{"date_created":"2018-12-12T10:10:23Z","date_updated":"2020-07-14T12:48:15Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-848-v1+1_2017_Vicoso_GlobalDosage.pdf","file_size":462863,"creator":"system","checksum":"009fd68043211d645ceb9d1de28274f2","file_id":"4810"}],"_id":"945","publist_id":"6472","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"06","author":[{"last_name":"Huylmans","orcid":"0000-0001-8871-4961","first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","full_name":"Huylmans, Ann K"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","full_name":"Macon, Ariana","last_name":"Macon"},{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"issue":"10","date_published":"2017-07-06T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Molecular Biology and Evolution","abstract":[{"lang":"eng","text":"While chromosome-wide dosage compensation of the X chromosome has been found in many species, studies in ZW clades have indicated that compensation of the Z is more localized and/or incomplete. In the ZW Lepidoptera, some species show complete compensation of the Z chromosome, while others lack full equalization, but what drives these inconsistencies is unclear. Here, we compare patterns of male and female gene expression on the Z chromosome of two closely related butterfly species, Papilio xuthus and Papilio machaon, and in multiple tissues of two moths species, Plodia interpunctella and Bombyx mori, which were previously found to differ in the extent to which they equalize Z-linked gene expression between the sexes. We find that, while some species and tissues seem to have incomplete dosage compensation, this is in fact due to the accumulation of male-biased genes and the depletion of female-biased genes on the Z chromosome. Once this is accounted for, the Z chromosome is fully compensated in all four species, through the up-regulation of Z expression in females and in some cases additional down-regulation in males. We further find that both sex-biased genes and Z-linked genes have increased rates of expression divergence in this clade, and that this can lead to fast shifts in patterns of gene expression even between closely related species. Taken together, these results show that the uneven distribution of sex-biased genes on sex chromosomes can confound conclusions about dosage compensation and that Z chromosome-wide dosage compensation is not only possible but ubiquitous among Lepidoptera."}],"status":"public","month":"07","date_created":"2018-12-11T11:49:20Z","citation":{"short":"A.K. Huylmans, A. Macon, B. Vicoso, Molecular Biology and Evolution 34 (2017) 2637–2649.","ieee":"A. K. Huylmans, A. Macon, and B. Vicoso, “Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome,” <i>Molecular Biology and Evolution</i>, vol. 34, no. 10. Oxford University Press, pp. 2637–2649, 2017.","mla":"Huylmans, Ann K., et al. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” <i>Molecular Biology and Evolution</i>, vol. 34, no. 10, Oxford University Press, 2017, pp. 2637–49, doi:<a href=\"https://doi.org/10.1093/molbev/msx190\">10.1093/molbev/msx190</a>.","chicago":"Huylmans, Ann K, Ariana Macon, and Beatriz Vicoso. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/molbev/msx190\">https://doi.org/10.1093/molbev/msx190</a>.","apa":"Huylmans, A. K., Macon, A., &#38; Vicoso, B. (2017). Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msx190\">https://doi.org/10.1093/molbev/msx190</a>","ama":"Huylmans AK, Macon A, Vicoso B. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. <i>Molecular Biology and Evolution</i>. 2017;34(10):2637-2649. doi:<a href=\"https://doi.org/10.1093/molbev/msx190\">10.1093/molbev/msx190</a>","ista":"Huylmans AK, Macon A, Vicoso B. 2017. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. 34(10), 2637–2649."},"doi":"10.1093/molbev/msx190","title":"Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"BeVi"}],"language":[{"iso":"eng"}],"date_updated":"2023-09-26T15:36:34Z","type":"journal_article","page":"2637 - 2649","pubrep_id":"848","oa_version":"Published Version","ddc":["570","576"],"external_id":{"isi":["000411814800016"]},"publication_identifier":{"issn":["07374038"]},"year":"2017"},{"status":"public","date_created":"2018-12-11T11:49:21Z","month":"06","doi":"10.7554/eLife.26792","citation":{"mla":"von Wangenheim, Daniel, et al. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” <i>ELife</i>, vol. 6, e26792, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/eLife.26792\">10.7554/eLife.26792</a>.","chicago":"Wangenheim, Daniel von, Robert Hauschild, Matyas Fendrych, Vanessa Barone, Eva Benková, and Jiří Friml. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/eLife.26792\">https://doi.org/10.7554/eLife.26792</a>.","short":"D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, J. Friml, ELife 6 (2017).","ieee":"D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, and J. Friml, “Live tracking of moving samples in confocal microscopy for vertically grown roots,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017.","ista":"von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. 2017. Live tracking of moving samples in confocal microscopy for vertically grown roots. eLife. 6, e26792.","apa":"von Wangenheim, D., Hauschild, R., Fendrych, M., Barone, V., Benková, E., &#38; Friml, J. (2017). Live tracking of moving samples in confocal microscopy for vertically grown roots. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.26792\">https://doi.org/10.7554/eLife.26792</a>","ama":"von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. Live tracking of moving samples in confocal microscopy for vertically grown roots. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/eLife.26792\">10.7554/eLife.26792</a>"},"day":"19","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publist_id":"6471","_id":"946","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Von Wangenheim","orcid":"0000-0002-6862-1247","id":"49E91952-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","full_name":"Von Wangenheim, Daniel"},{"orcid":"0000-0001-9843-3522","last_name":"Hauschild","full_name":"Hauschild, Robert","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","full_name":"Fendrych, Matyas","last_name":"Fendrych","orcid":"0000-0002-9767-8699"},{"full_name":"Barone, Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","orcid":"0000-0003-2676-3367","last_name":"Barone"},{"full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","last_name":"Benková"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2017-06-19T00:00:00Z","acknowledgement":"Funding: Marie Curie Actions (FP7/2007-2013 no 291734) to Daniel von Wangenheim; Austrian Science Fund (M 2128-B21) to Matyáš Fendrych; Austrian Science Fund (FWF01_I1774S) to Eva Benková; European Research Council (FP7/2007-2013 no 282300) to Jiří Friml. \r\nThe authors are grateful to the Miba Machine Shop at IST Austria for their contribution to the microscope setup and to Yvonne Kemper for reading, understanding and correcting the manuscript.\r\n#BioimagingFacility","publication":"eLife","abstract":[{"lang":"eng","text":"Roots navigate through soil integrating environmental signals to orient their growth. The Arabidopsis root is a widely used model for developmental, physiological and cell biological studies. Live imaging greatly aids these efforts, but the horizontal sample position and continuous root tip displacement present significant difficulties. Here, we develop a confocal microscope setup for vertical sample mounting and integrated directional illumination. We present TipTracker – a custom software for automatic tracking of diverse moving objects usable on various microscope setups. Combined, this enables observation of root tips growing along the natural gravity vector over prolonged periods of time, as well as the ability to induce rapid gravity or light stimulation. We also track migrating cells in the developing zebrafish embryo, demonstrating the utility of this system in the acquisition of high-resolution data sets of dynamic samples. We provide detailed descriptions of the tools enabling the easy implementation on other microscopes."}],"oa":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"_id":"2572ED28-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular basis of root growth inhibition by auxin","grant_number":"M02128"},{"call_identifier":"FWF","name":"Hormone cross-talk drives nutrient dependent plant development","grant_number":"I 1774-B16","_id":"2542D156-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-07-14T12:48:15Z","volume":6,"file":[{"file_id":"5315","checksum":"9af3398cb0d81f99d79016a616df22e9","file_size":19581847,"creator":"system","file_name":"IST-2017-847-v1+1_elife-26792-v2.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:48:15Z","relation":"main_file","access_level":"open_access","date_created":"2018-12-12T10:17:57Z"}],"quality_controlled":"1","isi":1,"scopus_import":"1","ec_funded":1,"intvolume":"         6","publication_status":"published","has_accepted_license":"1","publisher":"eLife Sciences Publications","year":"2017","external_id":{"isi":["000404728300001"]},"type":"journal_article","pubrep_id":"847","oa_version":"Published Version","ddc":["570"],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"date_updated":"2025-05-07T11:12:33Z","language":[{"iso":"eng"}],"title":"Live tracking of moving samples in confocal microscopy for vertically grown roots","article_processing_charge":"Yes","department":[{"_id":"JiFr"},{"_id":"Bio"},{"_id":"CaHe"},{"_id":"EvBe"}],"related_material":{"record":[{"status":"public","relation":"popular_science","id":"5566"}]},"article_number":"e26792"},{"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"oa":1,"volume":96,"ec_funded":1,"quality_controlled":"1","scopus_import":"1","isi":1,"publisher":"American Institute of Physics","publication_status":"published","intvolume":"        96","status":"public","citation":{"short":"D. De Martino, F. Capuani, A. De Martino,  Physical Review E Statistical Nonlinear and Soft Matter Physics  96 (2017).","ieee":"D. De Martino, F. Capuani, and A. De Martino, “Quantifying the entropic cost of cellular growth control,” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>, vol. 96, no. 1. American Institute of Physics, 2017.","mla":"De Martino, Daniele, et al. “Quantifying the Entropic Cost of Cellular Growth Control.” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>, vol. 96, no. 1, 010401, American Institute of Physics, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.010401\">10.1103/PhysRevE.96.010401</a>.","chicago":"De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Quantifying the Entropic Cost of Cellular Growth Control.” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. American Institute of Physics, 2017. <a href=\"https://doi.org/10.1103/PhysRevE.96.010401\">https://doi.org/10.1103/PhysRevE.96.010401</a>.","ama":"De Martino D, Capuani F, De Martino A. Quantifying the entropic cost of cellular growth control. <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. 2017;96(1). doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.010401\">10.1103/PhysRevE.96.010401</a>","apa":"De Martino, D., Capuani, F., &#38; De Martino, A. (2017). Quantifying the entropic cost of cellular growth control. <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.96.010401\">https://doi.org/10.1103/PhysRevE.96.010401</a>","ista":"De Martino D, Capuani F, De Martino A. 2017. Quantifying the entropic cost of cellular growth control.  Physical Review E Statistical Nonlinear and Soft Matter Physics . 96(1), 010401."},"doi":"10.1103/PhysRevE.96.010401","date_created":"2018-12-11T11:49:21Z","month":"07","day":"10","_id":"947","publist_id":"6470","publication":" Physical Review E Statistical Nonlinear and Soft Matter Physics ","abstract":[{"text":"Viewing the ways a living cell can organize its metabolism as the phase space of a physical system, regulation can be seen as the ability to reduce the entropy of that space by selecting specific cellular configurations that are, in some sense, optimal. Here we quantify the amount of regulation required to control a cell's growth rate by a maximum-entropy approach to the space of underlying metabolic phenotypes, where a configuration corresponds to a metabolic flux pattern as described by genome-scale models. We link the mean growth rate achieved by a population of cells to the minimal amount of metabolic regulation needed to achieve it through a phase diagram that highlights how growth suppression can be as costly (in regulatory terms) as growth enhancement. Moreover, we provide an interpretation of the inverse temperature β controlling maximum-entropy distributions based on the underlying growth dynamics. Specifically, we show that the asymptotic value of β for a cell population can be expected to depend on (i) the carrying capacity of the environment, (ii) the initial size of the colony, and (iii) the probability distribution from which the inoculum was sampled. Results obtained for E. coli and human cells are found to be remarkably consistent with empirical evidence.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"1","date_published":"2017-07-10T00:00:00Z","author":[{"last_name":"De Martino","orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","full_name":"De Martino, Daniele"},{"full_name":"Capuani, Fabrizio","first_name":"Fabrizio","last_name":"Capuani"},{"last_name":"De Martino","full_name":"De Martino, Andrea","first_name":"Andrea"}],"date_updated":"2023-09-22T10:03:50Z","language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"GaTk"}],"title":"Quantifying the entropic cost of cellular growth control","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.00219"}],"article_number":"010401","year":"2017","publication_identifier":{"issn":["24700045"]},"external_id":{"isi":["000405194200002"]},"type":"journal_article","oa_version":"Submitted Version"},{"language":[{"iso":"eng"}],"date_updated":"2024-03-25T23:30:19Z","conference":{"end_date":"2017-10-06","location":"Pune, India","start_date":"2017-10-03","name":"ATVA: Automated Technology for Verification and Analysis"},"title":"JTDec: A tool for tree decompositions in soot","department":[{"_id":"KrCh"}],"related_material":{"record":[{"id":"8934","relation":"dissertation_contains","status":"public"}]},"article_processing_charge":"No","external_id":{"isi":["000723567800004"]},"publication_identifier":{"issn":["03029743"]},"year":"2017","oa_version":"Submitted Version","ddc":["005"],"type":"conference","page":"59 - 66","pubrep_id":"845","volume":10482,"file":[{"date_created":"2018-12-12T10:10:45Z","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:48:16Z","content_type":"application/pdf","file_name":"IST-2017-845-v1+1_2017_Chatterjee_JTDec.pdf","file_size":948514,"creator":"system","file_id":"4835","checksum":"a0d9f5f94dc594c4e71e78525c9942f1"}],"file_date_updated":"2020-07-14T12:48:16Z","project":[{"call_identifier":"FWF","grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"oa":1,"intvolume":"     10482","has_accepted_license":"1","publication_status":"published","publisher":"Springer","quality_controlled":"1","isi":1,"scopus_import":"1","ec_funded":1,"date_created":"2018-12-11T11:49:22Z","month":"01","doi":"10.1007/978-3-319-68167-2_4","citation":{"ista":"Chatterjee K, Goharshady AK, Pavlogiannis A. 2017. JTDec: A tool for tree decompositions in soot. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 10482, 59–66.","ama":"Chatterjee K, Goharshady AK, Pavlogiannis A. JTDec: A tool for tree decompositions in soot. In: D’Souza D, ed. Vol 10482. Springer; 2017:59-66. doi:<a href=\"https://doi.org/10.1007/978-3-319-68167-2_4\">10.1007/978-3-319-68167-2_4</a>","apa":"Chatterjee, K., Goharshady, A. K., &#38; Pavlogiannis, A. (2017). JTDec: A tool for tree decompositions in soot. In D. D’Souza (Ed.) (Vol. 10482, pp. 59–66). Presented at the ATVA: Automated Technology for Verification and Analysis, Pune, India: Springer. <a href=\"https://doi.org/10.1007/978-3-319-68167-2_4\">https://doi.org/10.1007/978-3-319-68167-2_4</a>","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Andreas Pavlogiannis. “JTDec: A Tool for Tree Decompositions in Soot.” edited by Deepak D’Souza, 10482:59–66. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-68167-2_4\">https://doi.org/10.1007/978-3-319-68167-2_4</a>.","mla":"Chatterjee, Krishnendu, et al. <i>JTDec: A Tool for Tree Decompositions in Soot</i>. Edited by Deepak D’Souza, vol. 10482, Springer, 2017, pp. 59–66, doi:<a href=\"https://doi.org/10.1007/978-3-319-68167-2_4\">10.1007/978-3-319-68167-2_4</a>.","short":"K. Chatterjee, A.K. Goharshady, A. Pavlogiannis, in:, D. D’Souza (Ed.), Springer, 2017, pp. 59–66.","ieee":"K. Chatterjee, A. K. Goharshady, and A. Pavlogiannis, “JTDec: A tool for tree decompositions in soot,” presented at the ATVA: Automated Technology for Verification and Analysis, Pune, India, 2017, vol. 10482, pp. 59–66."},"status":"public","alternative_title":["LNCS"],"editor":[{"first_name":"Deepak","full_name":"D'Souza, Deepak","last_name":"D'Souza"}],"date_published":"2017-01-01T00:00:00Z","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"full_name":"Goharshady, Amir","first_name":"Amir","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","last_name":"Goharshady"},{"orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"The notion of treewidth of graphs has been exploited for faster algorithms for several problems arising in verification and program analysis. Moreover, various notions of balanced tree decompositions have been used for improved algorithms supporting dynamic updates and analysis of concurrent programs. In this work, we present a tool for constructing tree-decompositions of CFGs obtained from Java methods, which is implemented as an extension to the widely used Soot framework. The experimental results show that our implementation on real-world Java benchmarks is very efficient. Our tool also provides the first implementation for balancing tree-decompositions. In summary, we present the first tool support for exploiting treewidth in the static analysis problems on Java programs."}],"_id":"949","publist_id":"6468","day":"01"},{"ddc":["000"],"oa_version":"Published Version","pubrep_id":"844","type":"conference","external_id":{"arxiv":["1705.01433"]},"publication_identifier":{"issn":["1868-8969"]},"year":"2017","article_number":"17","related_material":{"record":[{"status":"public","id":"6752","relation":"later_version"}]},"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"title":"Infinite-duration bidding games","language":[{"iso":"eng"}],"date_updated":"2023-08-29T07:02:13Z","conference":{"start_date":"2017-09-05","name":"CONCUR: Concurrency Theory","end_date":"2017-09-07","location":"Berlin, Germany"},"abstract":[{"text":"Two-player games on graphs are widely studied in formal methods as they model the interaction between a system and its environment. The game is played by moving a token throughout a graph to produce an infinite path. There are several common modes to determine how the players move the token through the graph; e.g., in turn-based games the players alternate turns in moving the token. We study the bidding mode of moving the token, which, to the best of our knowledge, has never been studied in infinite-duration games. Both players have separate budgets, which sum up to $1$. In each turn, a bidding takes place. Both players submit bids simultaneously, and a bid is legal if it does not exceed the available budget. The winner of the bidding pays his bid to the other player and moves the token. For reachability objectives, repeated bidding games have been studied and are called Richman games. There, a central question is the existence and computation of threshold budgets; namely, a value t\\in [0,1] such that if\\PO's budget exceeds $t$, he can win the game, and if\\PT's budget exceeds 1-t, he can win the game. We focus on parity games and mean-payoff games. We show the existence of threshold budgets in these games, and reduce the problem of finding them to Richman games. We also determine the strategy-complexity of an optimal strategy. Our most interesting result shows that memoryless strategies suffice for mean-payoff bidding games. \r\n","lang":"eng"}],"author":[{"orcid":"0000-0001-5588-8287","last_name":"Avni","full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy"},{"orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chonev","first_name":"Ventsislav K","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","full_name":"Chonev, Ventsislav K"}],"date_published":"2017-09-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6466","_id":"950","day":"01","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"doi":"10.4230/LIPIcs.CONCUR.2017.21","citation":{"ieee":"G. Avni, T. A. Henzinger, and V. K. Chonev, “Infinite-duration bidding games,” presented at the CONCUR: Concurrency Theory, Berlin, Germany, 2017, vol. 85.","short":"G. Avni, T.A. Henzinger, V.K. Chonev, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Avni, Guy, et al. <i>Infinite-Duration Bidding Games</i>. Vol. 85, 17, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2017.21\">10.4230/LIPIcs.CONCUR.2017.21</a>.","chicago":"Avni, Guy, Thomas A Henzinger, and Ventsislav K Chonev. “Infinite-Duration Bidding Games,” Vol. 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2017.21\">https://doi.org/10.4230/LIPIcs.CONCUR.2017.21</a>.","ama":"Avni G, Henzinger TA, Chonev VK. Infinite-duration bidding games. In: Vol 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2017.21\">10.4230/LIPIcs.CONCUR.2017.21</a>","apa":"Avni, G., Henzinger, T. A., &#38; Chonev, V. K. (2017). Infinite-duration bidding games (Vol. 85). Presented at the CONCUR: Concurrency Theory, Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2017.21\">https://doi.org/10.4230/LIPIcs.CONCUR.2017.21</a>","ista":"Avni G, Henzinger TA, Chonev VK. 2017. Infinite-duration bidding games. CONCUR: Concurrency Theory, LIPIcs, vol. 85, 17."},"date_created":"2018-12-11T11:49:22Z","month":"09","status":"public","alternative_title":["LIPIcs"],"publication_status":"published","has_accepted_license":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","intvolume":"        85","arxiv":1,"scopus_import":1,"quality_controlled":"1","file":[{"file_size":335170,"creator":"system","checksum":"6d5cccf755207b91ccbef95d8275b013","file_id":"5318","date_created":"2018-12-12T10:18:00Z","access_level":"open_access","date_updated":"2020-07-14T12:48:16Z","relation":"main_file","content_type":"application/pdf","file_name":"IST-2017-844-v1+1_concur-cr.pdf"}],"volume":85,"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"file_date_updated":"2020-07-14T12:48:16Z","oa":1},{"oa_version":"Published Version","ddc":["570"],"type":"journal_article","external_id":{"pmid":["28486944"]},"year":"2017","publication_identifier":{"issn":["1474-760X"],"eissn":["1465-6906"]},"pmid":1,"article_number":"87","title":"An evolutionary case for functional gene body methylation in plants and animals","department":[{"_id":"DaZi"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"date_updated":"2021-12-14T07:55:02Z","author":[{"last_name":"Zilberman","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel"}],"issue":"1","date_published":"2017-05-09T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"Methylation in the bodies of active genes is common in animals and vascular plants. Evolutionary patterns indicate homeostatic functions for this type of methylation."}],"publication":"Genome Biology","_id":"9506","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"09","date_created":"2021-06-07T12:27:39Z","month":"05","citation":{"ista":"Zilberman D. 2017. An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. 18(1), 87.","apa":"Zilberman, D. (2017). An evolutionary case for functional gene body methylation in plants and animals. <i>Genome Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13059-017-1230-2\">https://doi.org/10.1186/s13059-017-1230-2</a>","ama":"Zilberman D. An evolutionary case for functional gene body methylation in plants and animals. <i>Genome Biology</i>. 2017;18(1). doi:<a href=\"https://doi.org/10.1186/s13059-017-1230-2\">10.1186/s13059-017-1230-2</a>","mla":"Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation in Plants and Animals.” <i>Genome Biology</i>, vol. 18, no. 1, 87, Springer Nature, 2017, doi:<a href=\"https://doi.org/10.1186/s13059-017-1230-2\">10.1186/s13059-017-1230-2</a>.","chicago":"Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation in Plants and Animals.” <i>Genome Biology</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1186/s13059-017-1230-2\">https://doi.org/10.1186/s13059-017-1230-2</a>.","ieee":"D. Zilberman, “An evolutionary case for functional gene body methylation in plants and animals,” <i>Genome Biology</i>, vol. 18, no. 1. Springer Nature, 2017.","short":"D. Zilberman, Genome Biology 18 (2017)."},"doi":"10.1186/s13059-017-1230-2","status":"public","intvolume":"        18","extern":"1","publisher":"Springer Nature","publication_status":"published","has_accepted_license":"1","quality_controlled":"1","scopus_import":"1","volume":18,"file":[{"file_id":"9507","checksum":"5a455ad914e7d225b1baa4ab07fd925e","creator":"asandaue","file_size":278183,"file_name":"2017_GenomeBiology_Zilberman.pdf","success":1,"content_type":"application/pdf","date_updated":"2021-06-07T12:31:36Z","relation":"main_file","access_level":"open_access","date_created":"2021-06-07T12:31:36Z"}],"oa":1,"file_date_updated":"2021-06-07T12:31:36Z"},{"related_material":{"record":[{"id":"9856","relation":"research_data","status":"public"},{"status":"public","id":"9857","relation":"research_data"},{"id":"9858","relation":"research_data","status":"public"}]},"article_processing_charge":"No","department":[{"_id":"NiBa"}],"title":"Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti","article_number":"e2001894","date_updated":"2023-09-22T10:02:52Z","language":[{"iso":"eng"}],"pubrep_id":"843","type":"journal_article","ddc":["576"],"oa_version":"Published Version","year":"2017","publication_identifier":{"issn":["15449173"]},"external_id":{"isi":["000402520000012"]},"scopus_import":"1","quality_controlled":"1","isi":1,"publication_status":"published","publisher":"Public Library of Science","has_accepted_license":"1","intvolume":"        15","file_date_updated":"2020-07-14T12:48:16Z","oa":1,"file":[{"creator":"system","file_size":5541206,"checksum":"107d290bd1159ec77b734eb2824b01c8","file_id":"4691","date_created":"2018-12-12T10:08:30Z","relation":"main_file","date_updated":"2020-07-14T12:48:16Z","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-843-v1+1_journal.pbio.2001894.pdf"}],"volume":15,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"30","publist_id":"6464","_id":"951","publication":"PLoS Biology","abstract":[{"lang":"eng","text":"Dengue-suppressing Wolbachia strains are promising tools for arbovirus control, particularly as they have the potential to self-spread following local introductions. To test this, we followed the frequency of the transinfected Wolbachia strain wMel through Ae. aegypti in Cairns, Australia, following releases at 3 nonisolated locations within the city in early 2013. Spatial spread was analysed graphically using interpolation and by fitting a statistical model describing the position and width of the wave. For the larger 2 of the 3 releases (covering 0.97 km2 and 0.52 km2), we observed slow but steady spatial spread, at about 100–200 m per year, roughly consistent with theoretical predictions. In contrast, the smallest release (0.11 km2) produced erratic temporal and spatial dynamics, with little evidence of spread after 2 years. This is consistent with the prediction concerning fitness-decreasing Wolbachia transinfections that a minimum release area is needed to achieve stable local establishment and spread in continuous habitats. Our graphical and likelihood analyses produced broadly consistent estimates of wave speed and wave width. Spread at all sites was spatially heterogeneous, suggesting that environmental heterogeneity will affect large-scale Wolbachia transformations of urban mosquito populations. The persistence and spread of Wolbachia in release areas meeting minimum area requirements indicates the promise of successful large-scale population transfo"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"5","date_published":"2017-05-30T00:00:00Z","author":[{"last_name":"Schmidt","first_name":"Tom","full_name":"Schmidt, Tom"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"last_name":"Rasic","full_name":"Rasic, Gordana","first_name":"Gordana"},{"last_name":"Turley","first_name":"Andrew","full_name":"Turley, Andrew"},{"last_name":"Montgomery","first_name":"Brian","full_name":"Montgomery, Brian"},{"full_name":"Iturbe Ormaetxe, Inaki","first_name":"Inaki","last_name":"Iturbe Ormaetxe"},{"full_name":"Cook, Peter","first_name":"Peter","last_name":"Cook"},{"first_name":"Peter","full_name":"Ryan, Peter","last_name":"Ryan"},{"last_name":"Ritchie","full_name":"Ritchie, Scott","first_name":"Scott"},{"first_name":"Ary","full_name":"Hoffmann, Ary","last_name":"Hoffmann"},{"first_name":"Scott","full_name":"O’Neill, Scott","last_name":"O’Neill"},{"last_name":"Turelli","first_name":"Michael","full_name":"Turelli, Michael"}],"status":"public","doi":"10.1371/journal.pbio.2001894","citation":{"mla":"Schmidt, Tom, et al. “Local Introduction and Heterogeneous Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” <i>PLoS Biology</i>, vol. 15, no. 5, e2001894, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2001894\">10.1371/journal.pbio.2001894</a>.","chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Local Introduction and Heterogeneous Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” <i>PLoS Biology</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pbio.2001894\">https://doi.org/10.1371/journal.pbio.2001894</a>.","short":"T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, PLoS Biology 15 (2017).","ieee":"T. Schmidt <i>et al.</i>, “Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti,” <i>PLoS Biology</i>, vol. 15, no. 5. Public Library of Science, 2017.","ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. 15(5), e2001894.","ama":"Schmidt T, Barton NH, Rasic G, et al. Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. <i>PLoS Biology</i>. 2017;15(5). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2001894\">10.1371/journal.pbio.2001894</a>","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2001894\">https://doi.org/10.1371/journal.pbio.2001894</a>"},"month":"05","date_created":"2018-12-11T11:49:22Z"},{"status":"public","citation":{"ieee":"M. Turelli and N. H. Barton, “Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti,” <i>Theoretical Population Biology</i>, vol. 115. Elsevier, pp. 45–60, 2017.","short":"M. Turelli, N.H. Barton, Theoretical Population Biology 115 (2017) 45–60.","mla":"Turelli, Michael, and Nicholas H. Barton. “Deploying Dengue-Suppressing Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” <i>Theoretical Population Biology</i>, vol. 115, Elsevier, 2017, pp. 45–60, doi:<a href=\"https://doi.org/10.1016/j.tpb.2017.03.003\">10.1016/j.tpb.2017.03.003</a>.","chicago":"Turelli, Michael, and Nicholas H Barton. “Deploying Dengue-Suppressing Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” <i>Theoretical Population Biology</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.tpb.2017.03.003\">https://doi.org/10.1016/j.tpb.2017.03.003</a>.","ama":"Turelli M, Barton NH. Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. <i>Theoretical Population Biology</i>. 2017;115:45-60. doi:<a href=\"https://doi.org/10.1016/j.tpb.2017.03.003\">10.1016/j.tpb.2017.03.003</a>","apa":"Turelli, M., &#38; Barton, N. H. (2017). Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. <i>Theoretical Population Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tpb.2017.03.003\">https://doi.org/10.1016/j.tpb.2017.03.003</a>","ista":"Turelli M, Barton NH. 2017. Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. 115, 45–60."},"doi":"10.1016/j.tpb.2017.03.003","month":"06","date_created":"2018-12-11T11:49:22Z","day":"01","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"publist_id":"6463","_id":"952","publication":"Theoretical Population Biology","abstract":[{"lang":"eng","text":"A novel strategy for controlling the spread of arboviral diseases such as dengue, Zika and chikungunya is to transform mosquito populations with virus-suppressing Wolbachia. In general, Wolbachia transinfected into mosquitoes induce fitness costs through lower viability or fecundity. These maternally inherited bacteria also produce a frequency-dependent advantage for infected females by inducing cytoplasmic incompatibility (CI), which kills the embryos produced by uninfected females mated to infected males. These competing effects, a frequency-dependent advantage and frequency-independent costs, produce bistable Wolbachia frequency dynamics. Above a threshold frequency, denoted pˆ, CI drives fitness-decreasing Wolbachia transinfections through local populations; but below pˆ, infection frequencies tend to decline to zero. If pˆ is not too high, CI also drives spatial spread once infections become established over sufficiently large areas. We illustrate how simple models provide testable predictions concerning the spatial and temporal dynamics of Wolbachia introductions, focusing on rate of spatial spread, the shape of spreading waves, and the conditions for initiating spread from local introductions. First, we consider the robustness of diffusion-based predictions to incorporating two important features of wMel-Aedes aegypti biology that may be inconsistent with the diffusion approximations, namely fast local dynamics induced by complete CI (i.e., all embryos produced from incompatible crosses die) and long-tailed, non-Gaussian dispersal. With complete CI, our numerical analyses show that long-tailed dispersal changes wave-width predictions only slightly; but it can significantly reduce wave speed relative to the diffusion prediction; it also allows smaller local introductions to initiate spatial spread. Second, we use approximations for pˆ and dispersal distances to predict the outcome of 2013 releases of wMel-infected Aedes aegypti in Cairns, Australia, Third, we describe new data from Ae. aegypti populations near Cairns, Australia that demonstrate long-distance dispersal and provide an approximate lower bound on pˆ for wMel in northeastern Australia. Finally, we apply our analyses to produce operational guidelines for efficient transformation of vector populations over large areas. We demonstrate that even very slow spatial spread, on the order of 10-20 m/month (as predicted), can produce area-wide population transformation within a few years following initial releases covering about 20-30% of the target area."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2017-06-01T00:00:00Z","author":[{"last_name":"Turelli","first_name":"Michael","full_name":"Turelli, Michael"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"oa":1,"file_date_updated":"2020-07-14T12:48:16Z","file":[{"file_id":"6327","checksum":"9aeff86fa7de69f7a15cf4fc60d57d01","creator":"dernst","file_size":2073856,"file_name":"2017_TheoreticalPopulationBio_Turelli.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:48:16Z","relation":"main_file","access_level":"open_access","date_created":"2019-04-17T06:39:45Z"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","volume":115,"scopus_import":"1","quality_controlled":"1","publisher":"Elsevier","publication_status":"published","has_accepted_license":"1","intvolume":"       115","pmid":1,"year":"2017","publication_identifier":{"issn":["00405809"]},"external_id":{"pmid":["28411063"]},"pubrep_id":"972","page":"45 - 60","type":"journal_article","ddc":["576"],"oa_version":"Submitted Version","date_updated":"2023-09-22T10:02:21Z","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"article_processing_charge":"No","title":"Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti"},{"article_number":"20162864","title":"The sources of adaptive evolution","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454256/"}],"department":[{"_id":"NiBa"}],"article_processing_charge":"No","date_updated":"2023-09-22T10:01:48Z","language":[{"iso":"eng"}],"oa_version":"Submitted Version","type":"journal_article","year":"2017","external_id":{"isi":["000405148800021"],"pmid":["28566483"]},"pmid":1,"intvolume":"       284","publisher":"Royal Society, The","publication_status":"published","isi":1,"scopus_import":"1","quality_controlled":"1","volume":284,"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2017-05-31T00:00:00Z","author":[{"last_name":"Charlesworth","first_name":"Deborah","full_name":"Charlesworth, Deborah"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"first_name":"Brian","full_name":"Charlesworth, Brian","last_name":"Charlesworth"}],"issue":"1855","abstract":[{"text":"The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis. Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today's understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed.","lang":"eng"}],"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","day":"31","publist_id":"6462","_id":"953","date_created":"2018-12-11T11:49:23Z","month":"05","doi":"10.1098/rspb.2016.2864","citation":{"ista":"Charlesworth D, Barton NH, Charlesworth B. 2017. The sources of adaptive evolution. Proceedings of the Royal Society of London Series B Biological Sciences. 284(1855), 20162864.","ama":"Charlesworth D, Barton NH, Charlesworth B. The sources of adaptive evolution. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2017;284(1855). doi:<a href=\"https://doi.org/10.1098/rspb.2016.2864\">10.1098/rspb.2016.2864</a>","apa":"Charlesworth, D., Barton, N. H., &#38; Charlesworth, B. (2017). The sources of adaptive evolution. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rspb.2016.2864\">https://doi.org/10.1098/rspb.2016.2864</a>","chicago":"Charlesworth, Deborah, Nicholas H Barton, and Brian Charlesworth. “The Sources of Adaptive Evolution.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, The, 2017. <a href=\"https://doi.org/10.1098/rspb.2016.2864\">https://doi.org/10.1098/rspb.2016.2864</a>.","mla":"Charlesworth, Deborah, et al. “The Sources of Adaptive Evolution.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 284, no. 1855, 20162864, Royal Society, The, 2017, doi:<a href=\"https://doi.org/10.1098/rspb.2016.2864\">10.1098/rspb.2016.2864</a>.","short":"D. Charlesworth, N.H. Barton, B. Charlesworth, Proceedings of the Royal Society of London Series B Biological Sciences 284 (2017).","ieee":"D. Charlesworth, N. H. Barton, and B. Charlesworth, “The sources of adaptive evolution,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 284, no. 1855. Royal Society, The, 2017."},"status":"public"},{"author":[{"last_name":"Lagator","first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato"},{"full_name":"Paixao, Tiago","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","last_name":"Paixao"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"full_name":"Bollback, Jonathan P","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","last_name":"Bollback"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","full_name":"Guet, Calin C"}],"date_published":"2017-05-18T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Understanding the relation between genotype and phenotype remains a major challenge. The difficulty of predicting individual mutation effects, and particularly the interactions between them, has prevented the development of a comprehensive theory that links genotypic changes to their phenotypic effects. We show that a general thermodynamic framework for gene regulation, based on a biophysical understanding of protein-DNA binding, accurately predicts the sign of epistasis in a canonical cis-regulatory element consisting of overlapping RNA polymerase and repressor binding sites. Sign and magnitude of individual mutation effects are sufficient to predict the sign of epistasis and its environmental dependence. Thus, the thermodynamic model offers the correct null prediction for epistasis between mutations across DNA-binding sites. Our results indicate that a predictive theory for the effects of cis-regulatory mutations is possible from first principles, as long as the essential molecular mechanisms and the constraints these impose on a biological system are accounted for.","lang":"eng"}],"publication":"eLife","publist_id":"6460","_id":"954","day":"18","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"month":"05","date_created":"2018-12-11T11:49:23Z","citation":{"ista":"Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. 2017. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 6, e25192.","apa":"Lagator, M., Paixao, T., Barton, N. H., Bollback, J. P., &#38; Guet, C. C. (2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.25192\">https://doi.org/10.7554/eLife.25192</a>","ama":"Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature of epistasis in a canonical cis-regulatory element. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/eLife.25192\">10.7554/eLife.25192</a>","chicago":"Lagator, Mato, Tiago Paixao, Nicholas H Barton, Jonathan P Bollback, and Calin C Guet. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/eLife.25192\">https://doi.org/10.7554/eLife.25192</a>.","mla":"Lagator, Mato, et al. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” <i>ELife</i>, vol. 6, e25192, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/eLife.25192\">10.7554/eLife.25192</a>.","short":"M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017).","ieee":"M. Lagator, T. Paixao, N. H. Barton, J. P. Bollback, and C. C. Guet, “On the mechanistic nature of epistasis in a canonical cis-regulatory element,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017."},"doi":"10.7554/eLife.25192","status":"public","intvolume":"         6","publication_status":"published","publisher":"eLife Sciences Publications","has_accepted_license":"1","isi":1,"quality_controlled":"1","scopus_import":"1","ec_funded":1,"volume":6,"file":[{"content_type":"application/pdf","file_name":"IST-2017-841-v1+1_elife-25192-v2.pdf","date_created":"2018-12-12T10:17:49Z","date_updated":"2020-07-14T12:48:16Z","access_level":"open_access","relation":"main_file","creator":"system","file_size":2441529,"checksum":"59cdd4400fb41280122d414fea971546","file_id":"5306"},{"file_size":3752660,"creator":"system","file_id":"5307","checksum":"b69024880558b858eb8c5d47a92b6377","content_type":"application/pdf","file_name":"IST-2017-841-v1+2_elife-25192-figures-v2.pdf","date_created":"2018-12-12T10:17:50Z","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:48:16Z"}],"file_date_updated":"2020-07-14T12:48:16Z","oa":1,"project":[{"call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440"}],"oa_version":"Published Version","ddc":["576"],"type":"journal_article","pubrep_id":"841","external_id":{"isi":["000404024800001"]},"publication_identifier":{"issn":["2050084X"]},"year":"2017","article_number":"e25192","title":"On the mechanistic nature of epistasis in a canonical cis-regulatory element","department":[{"_id":"CaGu"},{"_id":"NiBa"},{"_id":"JoBo"}],"article_processing_charge":"Yes","language":[{"iso":"eng"}],"date_updated":"2023-09-22T10:01:17Z"},{"date_updated":"2025-05-28T11:42:50Z","language":[{"iso":"eng"}],"title":"Evolution of new regulatory functions on biophysically realistic fitness landscapes","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6071"}]},"article_processing_charge":"Yes (in subscription journal)","article_number":"216","publication_identifier":{"issn":["20411723"]},"year":"2017","external_id":{"isi":["000407198800005"]},"type":"journal_article","pubrep_id":"864","oa_version":"Published Version","ddc":["539","576"],"oa":1,"file_date_updated":"2020-07-14T12:48:16Z","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"}],"volume":8,"file":[{"date_created":"2018-12-12T10:14:14Z","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:48:16Z","content_type":"application/pdf","file_name":"IST-2017-864-v1+1_s41467-017-00238-8.pdf","file_size":998157,"creator":"system","checksum":"29a1b5db458048d3bd5c67e0e2a56818","file_id":"5064"},{"access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:48:16Z","date_created":"2018-12-12T10:14:15Z","file_name":"IST-2017-864-v1+2_41467_2017_238_MOESM1_ESM.pdf","content_type":"application/pdf","checksum":"7b78401e52a576cf3e6bbf8d0abadc17","file_id":"5065","creator":"system","file_size":9715993}],"quality_controlled":"1","scopus_import":"1","isi":1,"ec_funded":1,"intvolume":"         8","publication_status":"published","publisher":"Nature Publishing Group","has_accepted_license":"1","status":"public","date_created":"2018-12-11T11:49:23Z","month":"08","citation":{"mla":"Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” <i>Nature Communications</i>, vol. 8, no. 1, 216, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-00238-8\">10.1038/s41467-017-00238-8</a>.","chicago":"Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-00238-8\">https://doi.org/10.1038/s41467-017-00238-8</a>.","short":"T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications 8 (2017).","ieee":"T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new regulatory functions on biophysically realistic fitness landscapes,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","ista":"Friedlander T, Prizak R, Barton NH, Tkačik G. 2017. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 8(1), 216.","apa":"Friedlander, T., Prizak, R., Barton, N. H., &#38; Tkačik, G. (2017). Evolution of new regulatory functions on biophysically realistic fitness landscapes. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-00238-8\">https://doi.org/10.1038/s41467-017-00238-8</a>","ama":"Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions on biophysically realistic fitness landscapes. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-00238-8\">10.1038/s41467-017-00238-8</a>"},"doi":"10.1038/s41467-017-00238-8","day":"09","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"955","publist_id":"6459","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Friedlander","first_name":"Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","full_name":"Friedlander, Tamar"},{"last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik"}],"date_published":"2017-08-09T00:00:00Z","issue":"1","abstract":[{"text":"Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge. We show that specialization of new network components is usually slow, but can be drastically accelerated in the presence of regulatory crosstalk and mutations that promote promiscuous interactions between network components.","lang":"eng"}],"publication":"Nature Communications"},{"department":[{"_id":"JaMa"}],"article_processing_charge":"No","title":"Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance","main_file_link":[{"url":"https://arxiv.org/abs/1609.01254","open_access":"1"}],"date_updated":"2023-09-22T10:00:18Z","language":[{"iso":"eng"}],"page":"1810 - 1869","type":"journal_article","oa_version":"Submitted Version","year":"2017","publication_identifier":{"issn":["00221236"]},"external_id":{"isi":["000406082300005"]},"isi":1,"scopus_import":"1","quality_controlled":"1","publisher":"Academic Press","publication_status":"published","intvolume":"       273","oa":1,"volume":273,"day":"01","publist_id":"6452","_id":"956","publication":"Journal of Functional Analysis","abstract":[{"lang":"eng","text":"We study a class of ergodic quantum Markov semigroups on finite-dimensional unital C⁎-algebras. These semigroups have a unique stationary state σ, and we are concerned with those that satisfy a quantum detailed balance condition with respect to σ. We show that the evolution on the set of states that is given by such a quantum Markov semigroup is gradient flow for the relative entropy with respect to σ in a particular Riemannian metric on the set of states. This metric is a non-commutative analog of the 2-Wasserstein metric, and in several interesting cases we are able to show, in analogy with work of Otto on gradient flows with respect to the classical 2-Wasserstein metric, that the relative entropy is strictly and uniformly convex with respect to the Riemannian metric introduced here. As a consequence, we obtain a number of new inequalities for the decay of relative entropy for ergodic quantum Markov semigroups with detailed balance."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"5","author":[{"full_name":"Carlen, Eric","first_name":"Eric","last_name":"Carlen"},{"full_name":"Maas, Jan","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","last_name":"Maas"}],"date_published":"2017-09-01T00:00:00Z","status":"public","doi":"10.1016/j.jfa.2017.05.003","citation":{"short":"E. Carlen, J. Maas, Journal of Functional Analysis 273 (2017) 1810–1869.","ieee":"E. Carlen and J. Maas, “Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance,” <i>Journal of Functional Analysis</i>, vol. 273, no. 5. Academic Press, pp. 1810–1869, 2017.","mla":"Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for Quantum Markov Semigroups with Detailed Balance.” <i>Journal of Functional Analysis</i>, vol. 273, no. 5, Academic Press, 2017, pp. 1810–69, doi:<a href=\"https://doi.org/10.1016/j.jfa.2017.05.003\">10.1016/j.jfa.2017.05.003</a>.","chicago":"Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for Quantum Markov Semigroups with Detailed Balance.” <i>Journal of Functional Analysis</i>. Academic Press, 2017. <a href=\"https://doi.org/10.1016/j.jfa.2017.05.003\">https://doi.org/10.1016/j.jfa.2017.05.003</a>.","apa":"Carlen, E., &#38; Maas, J. (2017). Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. <i>Journal of Functional Analysis</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jfa.2017.05.003\">https://doi.org/10.1016/j.jfa.2017.05.003</a>","ama":"Carlen E, Maas J. Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. <i>Journal of Functional Analysis</i>. 2017;273(5):1810-1869. doi:<a href=\"https://doi.org/10.1016/j.jfa.2017.05.003\">10.1016/j.jfa.2017.05.003</a>","ista":"Carlen E, Maas J. 2017. Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. Journal of Functional Analysis. 273(5), 1810–1869."},"date_created":"2018-12-11T11:49:24Z","month":"09"},{"abstract":[{"text":"Small molecule biosensors based on Forster resonance energy transfer (FRET) enable small molecule signaling to be monitored with high spatial and temporal resolution in complex cellular environments. FRET sensors can be constructed by fusing a pair of fluorescent proteins to a suitable recognition domain, such as a member of the solute-binding protein (SBP) superfamily. However, naturally occurring SBPs may be unsuitable for incorporation into FRET sensors due to their low thermostability, which may preclude imaging under physiological conditions, or because the positions of their N- and C-termini may be suboptimal for fusion of fluorescent proteins, which may limit the dynamic range of the resulting sensors. Here, we show how these problems can be overcome using ancestral protein reconstruction and circular permutation. Ancestral protein reconstruction, used as a protein engineering strategy, leverages phylogenetic information to improve the thermostability of proteins, while circular permutation enables the termini of an SBP to be repositioned to maximize the dynamic range of the resulting FRET sensor. We also provide a protocol for cloning the engineered SBPs into FRET sensor constructs using Golden Gate assembly and discuss considerations for in situ characterization of the FRET sensors.","lang":"eng"}],"publication":"Synthetic Protein Switches","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Clifton","full_name":"Clifton, Ben","first_name":"Ben"},{"last_name":"Whitfield","full_name":"Whitfield, Jason","first_name":"Jason"},{"last_name":"Sanchez Romero","full_name":"Sanchez Romero, Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","first_name":"Inmaculada"},{"first_name":"Michel","full_name":"Herde, Michel","last_name":"Herde"},{"last_name":"Henneberger","first_name":"Christian","full_name":"Henneberger, Christian"},{"full_name":"Janovjak, Harald L","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","last_name":"Janovjak"},{"full_name":"Jackson, Colin","first_name":"Colin","last_name":"Jackson"}],"date_published":"2017-03-15T00:00:00Z","day":"15","publist_id":"6451","_id":"957","doi":"10.1007/978-1-4939-6940-1_5","citation":{"mla":"Clifton, Ben, et al. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” <i>Synthetic Protein Switches</i>, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 71–87, doi:<a href=\"https://doi.org/10.1007/978-1-4939-6940-1_5\">10.1007/978-1-4939-6940-1_5</a>.","chicago":"Clifton, Ben, Jason Whitfield, Inmaculada Sanchez-Romero, Michel Herde, Christian Henneberger, Harald L Janovjak, and Colin Jackson. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” In <i>Synthetic Protein Switches</i>, edited by Viktor Stein, 1596:71–87. Synthetic Protein Switches. Springer, 2017. <a href=\"https://doi.org/10.1007/978-1-4939-6940-1_5\">https://doi.org/10.1007/978-1-4939-6940-1_5</a>.","short":"B. Clifton, J. Whitfield, I. Sanchez-Romero, M. Herde, C. Henneberger, H.L. Janovjak, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 71–87.","ieee":"B. Clifton <i>et al.</i>, “Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors,” in <i>Synthetic Protein Switches</i>, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 71–87.","ista":"Clifton B, Whitfield J, Sanchez-Romero I, Herde M, Henneberger C, Janovjak HL, Jackson C. 2017.Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 71–87.","apa":"Clifton, B., Whitfield, J., Sanchez-Romero, I., Herde, M., Henneberger, C., Janovjak, H. L., &#38; Jackson, C. (2017). Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In V. Stein (Ed.), <i>Synthetic Protein Switches</i> (Vol. 1596, pp. 71–87). Springer. <a href=\"https://doi.org/10.1007/978-1-4939-6940-1_5\">https://doi.org/10.1007/978-1-4939-6940-1_5</a>","ama":"Clifton B, Whitfield J, Sanchez-Romero I, et al. Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Stein V, ed. <i>Synthetic Protein Switches</i>. Vol 1596. Synthetic Protein Switches. Springer; 2017:71-87. doi:<a href=\"https://doi.org/10.1007/978-1-4939-6940-1_5\">10.1007/978-1-4939-6940-1_5</a>"},"month":"03","date_created":"2018-12-11T11:49:24Z","editor":[{"full_name":"Stein, Viktor","first_name":"Viktor","last_name":"Stein"}],"alternative_title":["Methods in Molecular Biology"],"status":"public","publisher":"Springer","publication_status":"published","intvolume":"      1596","scopus_import":1,"quality_controlled":"1","volume":1596,"project":[{"grant_number":"RGY0084/2012","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","_id":"255BFFFA-B435-11E9-9278-68D0E5697425"}],"oa_version":"None","page":"71 - 87","type":"book_chapter","year":"2017","publication_identifier":{"issn":["10643745"]},"series_title":"Synthetic Protein Switches","department":[{"_id":"HaJa"}],"title":"Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors","date_updated":"2021-01-12T08:22:13Z","language":[{"iso":"eng"}]},{"page":"93-99","type":"journal_article","oa_version":"Preprint","article_type":"original","year":"2017","publication_identifier":{"issn":["1571-0653"]},"external_id":{"arxiv":["1609.08136"]},"article_processing_charge":"No","title":"Resilience for the Littlewood-Offord problem","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1609.08136"}],"date_updated":"2023-02-23T14:01:26Z","language":[{"iso":"eng"}],"day":"01","_id":"9574","publication":"Electronic Notes in Discrete Mathematics","abstract":[{"text":"Consider the sum X(ξ)=∑ni=1aiξi, where a=(ai)ni=1 is a sequence of non-zero reals and ξ=(ξi)ni=1 is a sequence of i.i.d. Rademacher random variables (that is, Pr[ξi=1]=Pr[ξi=−1]=1/2). The classical Littlewood-Offord problem asks for the best possible upper bound on the concentration probabilities Pr[X=x]. In this paper we study a resilience version of the Littlewood-Offord problem: how many of the ξi is an adversary typically allowed to change without being able to force concentration on a particular value? We solve this problem asymptotically, and present a few interesting open problems.","lang":"eng"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_published":"2017-08-01T00:00:00Z","author":[{"full_name":"Bandeira, Afonso S.","first_name":"Afonso S.","last_name":"Bandeira"},{"last_name":"Ferber","first_name":"Asaf","full_name":"Ferber, Asaf"},{"full_name":"Kwan, Matthew Alan","first_name":"Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","orcid":"0000-0002-4003-7567","last_name":"Kwan"}],"status":"public","doi":"10.1016/j.endm.2017.06.025","citation":{"ieee":"A. S. Bandeira, A. Ferber, and M. A. Kwan, “Resilience for the Littlewood-Offord problem,” <i>Electronic Notes in Discrete Mathematics</i>, vol. 61. Elsevier, pp. 93–99, 2017.","short":"A.S. Bandeira, A. Ferber, M.A. Kwan, Electronic Notes in Discrete Mathematics 61 (2017) 93–99.","mla":"Bandeira, Afonso S., et al. “Resilience for the Littlewood-Offord Problem.” <i>Electronic Notes in Discrete Mathematics</i>, vol. 61, Elsevier, 2017, pp. 93–99, doi:<a href=\"https://doi.org/10.1016/j.endm.2017.06.025\">10.1016/j.endm.2017.06.025</a>.","chicago":"Bandeira, Afonso S., Asaf Ferber, and Matthew Alan Kwan. “Resilience for the Littlewood-Offord Problem.” <i>Electronic Notes in Discrete Mathematics</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.endm.2017.06.025\">https://doi.org/10.1016/j.endm.2017.06.025</a>.","ama":"Bandeira AS, Ferber A, Kwan MA. Resilience for the Littlewood-Offord problem. <i>Electronic Notes in Discrete Mathematics</i>. 2017;61:93-99. doi:<a href=\"https://doi.org/10.1016/j.endm.2017.06.025\">10.1016/j.endm.2017.06.025</a>","apa":"Bandeira, A. S., Ferber, A., &#38; Kwan, M. A. (2017). Resilience for the Littlewood-Offord problem. <i>Electronic Notes in Discrete Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.endm.2017.06.025\">https://doi.org/10.1016/j.endm.2017.06.025</a>","ista":"Bandeira AS, Ferber A, Kwan MA. 2017. Resilience for the Littlewood-Offord problem. Electronic Notes in Discrete Mathematics. 61, 93–99."},"month":"08","date_created":"2021-06-21T06:31:10Z","quality_controlled":"1","scopus_import":"1","publication_status":"published","publisher":"Elsevier","arxiv":1,"extern":"1","intvolume":"        61","oa":1,"volume":61},{"volume":1596,"quality_controlled":"1","scopus_import":1,"intvolume":"      1596","publication_status":"published","publisher":"Springer","alternative_title":["Methods in Molecular Biology"],"status":"public","editor":[{"full_name":"Stein, Viktor","first_name":"Viktor","last_name":"Stein"}],"date_created":"2018-12-11T11:49:24Z","month":"05","doi":"10.1007/978-1-4939-6940-1_6","citation":{"apa":"Mitchell, J., Zhang, W., Herde, M., Henneberger, C., Janovjak, H. L., O’Mara, M., &#38; Jackson, C. (2017). Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In V. Stein (Ed.), <i>Synthetic Protein Switches</i> (Vol. 1596, pp. 89–99). Springer. <a href=\"https://doi.org/10.1007/978-1-4939-6940-1_6\">https://doi.org/10.1007/978-1-4939-6940-1_6</a>","ama":"Mitchell J, Zhang W, Herde M, et al. Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In: Stein V, ed. <i>Synthetic Protein Switches</i>. Vol 1596. Synthetic Protein Switches. Springer; 2017:89-99. doi:<a href=\"https://doi.org/10.1007/978-1-4939-6940-1_6\">10.1007/978-1-4939-6940-1_6</a>","ista":"Mitchell J, Zhang W, Herde M, Henneberger C, Janovjak HL, O’Mara M, Jackson C. 2017.Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 89–99.","short":"J. Mitchell, W. Zhang, M. Herde, C. Henneberger, H.L. Janovjak, M. O’Mara, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 89–99.","ieee":"J. Mitchell <i>et al.</i>, “Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment,” in <i>Synthetic Protein Switches</i>, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 89–99.","chicago":"Mitchell, Joshua, William Zhang, Michel Herde, Christian Henneberger, Harald L Janovjak, Megan O’Mara, and Colin Jackson. “Method for Developing Optical Sensors Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.” In <i>Synthetic Protein Switches</i>, edited by Viktor Stein, 1596:89–99. Synthetic Protein Switches. Springer, 2017. <a href=\"https://doi.org/10.1007/978-1-4939-6940-1_6\">https://doi.org/10.1007/978-1-4939-6940-1_6</a>.","mla":"Mitchell, Joshua, et al. “Method for Developing Optical Sensors Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.” <i>Synthetic Protein Switches</i>, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 89–99, doi:<a href=\"https://doi.org/10.1007/978-1-4939-6940-1_6\">10.1007/978-1-4939-6940-1_6</a>."},"day":"15","_id":"958","publist_id":"6450","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Joshua","full_name":"Mitchell, Joshua","last_name":"Mitchell"},{"full_name":"Zhang, William","first_name":"William","last_name":"Zhang"},{"full_name":"Herde, Michel","first_name":"Michel","last_name":"Herde"},{"last_name":"Henneberger","first_name":"Christian","full_name":"Henneberger, Christian"},{"full_name":"Janovjak, Harald L","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","last_name":"Janovjak"},{"first_name":"Megan","full_name":"O'Mara, Megan","last_name":"O'Mara"},{"last_name":"Jackson","full_name":"Jackson, Colin","first_name":"Colin"}],"date_published":"2017-05-15T00:00:00Z","publication":"Synthetic Protein Switches","abstract":[{"lang":"eng","text":"Biosensors that exploit Forster resonance energy transfer (FRET) can be used to visualize biological and physiological processes and are capable of providing detailed information in both spatial and temporal dimensions. In a FRET-based biosensor, substrate binding is associated with a change in the relative positions of two fluorophores, leading to a change in FRET efficiency that may be observed in the fluorescence spectrum. As a result, their design requires a ligand-binding protein that exhibits a conformational change upon binding. However, not all ligand-binding proteins produce responsive sensors upon conjugation to fluorescent proteins or dyes, and identifying the optimum locations for the fluorophores often involves labor-intensive iterative design or high-throughput screening. Combining the genetic fusion of a fluorescent protein to the ligand-binding protein with site-specific covalent attachment of a fluorescent dye can allow fine control over the positions of the two fluorophores, allowing the construction of very sensitive sensors. This relies upon the accurate prediction of the locations of the two fluorophores in bound and unbound states. In this chapter, we describe a method for computational identification of dye-attachment sites that allows the use of cysteine modification to attach synthetic dyes that can be paired with a fluorescent protein for the purposes of creating FRET sensors."}],"date_updated":"2021-01-12T08:22:13Z","language":[{"iso":"eng"}],"title":"Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment","department":[{"_id":"HaJa"}],"series_title":"Synthetic Protein Switches","publication_identifier":{"issn":["10643745"]},"year":"2017","type":"book_chapter","page":"89 - 99","oa_version":"None"},{"publication_status":"published","publisher":"Elsevier","extern":"1","intvolume":"       319","arxiv":1,"quality_controlled":"1","scopus_import":"1","volume":319,"oa":1,"abstract":[{"lang":"eng","text":"Consider the sum  X(ξ)=∑ni=1aiξi , where  a=(ai)ni=1  is a sequence of non-zero reals and  ξ=(ξi)ni=1  is a sequence of i.i.d. Rademacher random variables (that is,  Pr[ξi=1]=Pr[ξi=−1]=1/2 ). The classical Littlewood-Offord problem asks for the best possible upper bound on the concentration probabilities  Pr[X=x] . In this paper we study a resilience version of the Littlewood-Offord problem: how many of the  ξi  is an adversary typically allowed to change without being able to force concentration on a particular value? We solve this problem asymptotically, and present a few interesting open problems."}],"publication":"Advances in Mathematics","date_published":"2017-10-15T00:00:00Z","author":[{"full_name":"Bandeira, Afonso S.","first_name":"Afonso S.","last_name":"Bandeira"},{"full_name":"Ferber, Asaf","first_name":"Asaf","last_name":"Ferber"},{"id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","first_name":"Matthew Alan","full_name":"Kwan, Matthew Alan","last_name":"Kwan","orcid":"0000-0002-4003-7567"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9588","day":"15","doi":"10.1016/j.aim.2017.08.031","citation":{"mla":"Bandeira, Afonso S., et al. “Resilience for the Littlewood–Offord Problem.” <i>Advances in Mathematics</i>, vol. 319, Elsevier, 2017, pp. 292–312, doi:<a href=\"https://doi.org/10.1016/j.aim.2017.08.031\">10.1016/j.aim.2017.08.031</a>.","chicago":"Bandeira, Afonso S., Asaf Ferber, and Matthew Alan Kwan. “Resilience for the Littlewood–Offord Problem.” <i>Advances in Mathematics</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.aim.2017.08.031\">https://doi.org/10.1016/j.aim.2017.08.031</a>.","ieee":"A. S. Bandeira, A. Ferber, and M. A. Kwan, “Resilience for the Littlewood–Offord problem,” <i>Advances in Mathematics</i>, vol. 319. Elsevier, pp. 292–312, 2017.","short":"A.S. Bandeira, A. Ferber, M.A. Kwan, Advances in Mathematics 319 (2017) 292–312.","ista":"Bandeira AS, Ferber A, Kwan MA. 2017. Resilience for the Littlewood–Offord problem. Advances in Mathematics. 319, 292–312.","ama":"Bandeira AS, Ferber A, Kwan MA. Resilience for the Littlewood–Offord problem. <i>Advances in Mathematics</i>. 2017;319:292-312. doi:<a href=\"https://doi.org/10.1016/j.aim.2017.08.031\">10.1016/j.aim.2017.08.031</a>","apa":"Bandeira, A. S., Ferber, A., &#38; Kwan, M. A. (2017). Resilience for the Littlewood–Offord problem. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2017.08.031\">https://doi.org/10.1016/j.aim.2017.08.031</a>"},"month":"10","date_created":"2021-06-22T11:51:27Z","status":"public","article_processing_charge":"No","main_file_link":[{"url":"https://arxiv.org/abs/1609.08136","open_access":"1"}],"title":"Resilience for the Littlewood–Offord problem","language":[{"iso":"eng"}],"date_updated":"2023-02-23T14:01:57Z","oa_version":"Preprint","page":"292-312","type":"journal_article","article_type":"original","external_id":{"arxiv":["1609.08136"]},"publication_identifier":{"issn":["0001-8708"]},"year":"2017"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Greenhill","full_name":"Greenhill, Catherine","first_name":"Catherine"},{"first_name":"Mikhail","full_name":"Isaev, Mikhail","last_name":"Isaev"},{"orcid":"0000-0002-4003-7567","last_name":"Kwan","full_name":"Kwan, Matthew Alan","first_name":"Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3"},{"last_name":"McKay","full_name":"McKay, Brendan D.","first_name":"Brendan D."}],"date_published":"2017-06-01T00:00:00Z","abstract":[{"lang":"eng","text":"We give an asymptotic expression for the expected number of spanning trees in a random graph with a given degree sequence , provided that the number of edges is at least , where  is the maximum degree. A key part of our argument involves establishing a concentration result for a certain family of functions over random trees with given degrees, using Prüfer codes."}],"publication":"European Journal of Combinatorics","day":"01","_id":"9589","month":"06","date_created":"2021-06-22T12:18:59Z","doi":"10.1016/j.ejc.2017.02.003","citation":{"ista":"Greenhill C, Isaev M, Kwan MA, McKay BD. 2017. The average number of spanning trees in sparse graphs with given degrees. European Journal of Combinatorics. 63, 6–25.","apa":"Greenhill, C., Isaev, M., Kwan, M. A., &#38; McKay, B. D. (2017). The average number of spanning trees in sparse graphs with given degrees. <i>European Journal of Combinatorics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ejc.2017.02.003\">https://doi.org/10.1016/j.ejc.2017.02.003</a>","ama":"Greenhill C, Isaev M, Kwan MA, McKay BD. The average number of spanning trees in sparse graphs with given degrees. <i>European Journal of Combinatorics</i>. 2017;63:6-25. doi:<a href=\"https://doi.org/10.1016/j.ejc.2017.02.003\">10.1016/j.ejc.2017.02.003</a>","chicago":"Greenhill, Catherine, Mikhail Isaev, Matthew Alan Kwan, and Brendan D. McKay. “The Average Number of Spanning Trees in Sparse Graphs with given Degrees.” <i>European Journal of Combinatorics</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.ejc.2017.02.003\">https://doi.org/10.1016/j.ejc.2017.02.003</a>.","mla":"Greenhill, Catherine, et al. “The Average Number of Spanning Trees in Sparse Graphs with given Degrees.” <i>European Journal of Combinatorics</i>, vol. 63, Elsevier, 2017, pp. 6–25, doi:<a href=\"https://doi.org/10.1016/j.ejc.2017.02.003\">10.1016/j.ejc.2017.02.003</a>.","short":"C. Greenhill, M. Isaev, M.A. Kwan, B.D. McKay, European Journal of Combinatorics 63 (2017) 6–25.","ieee":"C. Greenhill, M. Isaev, M. A. Kwan, and B. D. McKay, “The average number of spanning trees in sparse graphs with given degrees,” <i>European Journal of Combinatorics</i>, vol. 63. Elsevier, pp. 6–25, 2017."},"status":"public","arxiv":1,"intvolume":"        63","extern":"1","publication_status":"published","publisher":"Elsevier","scopus_import":"1","quality_controlled":"1","volume":63,"oa":1,"oa_version":"Published Version","type":"journal_article","page":"6-25","publication_identifier":{"issn":["0195-6698"]},"year":"2017","external_id":{"arxiv":["1606.01586"]},"article_type":"original","title":"The average number of spanning trees in sparse graphs with given degrees","main_file_link":[{"url":"https://doi.org/10.1016/j.ejc.2017.02.003","open_access":"1"}],"article_processing_charge":"No","date_updated":"2023-02-23T14:02:00Z","language":[{"iso":"eng"}]},{"external_id":{"isi":["000404546400004"]},"publication_identifier":{"issn":["24700045"]},"year":"2017","oa_version":"Submitted Version","page":"062419","type":"journal_article","language":[{"iso":"eng"}],"date_updated":"2023-09-22T09:59:01Z","article_processing_charge":"No","department":[{"_id":"GaTk"}],"main_file_link":[{"url":"https://arxiv.org/pdf/1703.00853.pdf","open_access":"1"}],"title":"Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics","citation":{"ista":"De Martino D. 2017. Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics.  Physical Review E Statistical Nonlinear and Soft Matter Physics . 95(6), 062419.","apa":"De Martino, D. (2017). Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.95.062419\">https://doi.org/10.1103/PhysRevE.95.062419</a>","ama":"De Martino D. Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. 2017;95(6):062419. doi:<a href=\"https://doi.org/10.1103/PhysRevE.95.062419\">10.1103/PhysRevE.95.062419</a>","chicago":"De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary Metabolic Network Models via Thermodynamics.” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. American Institute of Physics, 2017. <a href=\"https://doi.org/10.1103/PhysRevE.95.062419\">https://doi.org/10.1103/PhysRevE.95.062419</a>.","mla":"De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary Metabolic Network Models via Thermodynamics.” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>, vol. 95, no. 6, American Institute of Physics, 2017, p. 062419, doi:<a href=\"https://doi.org/10.1103/PhysRevE.95.062419\">10.1103/PhysRevE.95.062419</a>.","short":"D. De Martino,  Physical Review E Statistical Nonlinear and Soft Matter Physics  95 (2017) 062419.","ieee":"D. De Martino, “Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics,” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>, vol. 95, no. 6. American Institute of Physics, p. 062419, 2017."},"doi":"10.1103/PhysRevE.95.062419","month":"06","date_created":"2018-12-11T11:49:25Z","status":"public","abstract":[{"lang":"eng","text":"In this work it is shown that scale-free tails in metabolic flux distributions inferred in stationary models are an artifact due to reactions involved in thermodynamically unfeasible cycles, unbounded by physical constraints and in principle able to perform work without expenditure of free energy. After implementing thermodynamic constraints by removing such loops, metabolic flux distributions scale meaningfully with the physical limiting factors, acquiring in turn a richer multimodal structure potentially leading to symmetry breaking while optimizing for objective functions."}],"publication":" Physical Review E Statistical Nonlinear and Soft Matter Physics ","author":[{"orcid":"0000-0002-5214-4706","last_name":"De Martino","full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele"}],"issue":"6","date_published":"2017-06-28T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"959","publist_id":"6446","day":"28","volume":95,"oa":1,"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"publisher":"American Institute of Physics","publication_status":"published","intvolume":"        95","ec_funded":1,"isi":1,"scopus_import":"1","quality_controlled":"1"},{"type":"journal_article","page":"155-171","oa_version":"Preprint","year":"2017","publication_identifier":{"issn":["0895-4801"],"eissn":["1095-7146"]},"external_id":{"arxiv":["1507.07960"]},"article_type":"original","title":"Bounded-degree spanning trees in randomly perturbed graphs","main_file_link":[{"url":"https://arxiv.org/abs/1507.07960","open_access":"1"}],"article_processing_charge":"No","date_updated":"2023-02-23T14:02:05Z","language":[{"iso":"eng"}],"day":"12","_id":"9590","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"full_name":"Krivelevich, Michael","first_name":"Michael","last_name":"Krivelevich"},{"orcid":"0000-0002-4003-7567","last_name":"Kwan","full_name":"Kwan, Matthew Alan","first_name":"Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3"},{"last_name":"Sudakov","first_name":"Benny","full_name":"Sudakov, Benny"}],"issue":"1","date_published":"2017-01-12T00:00:00Z","publication":"SIAM Journal on Discrete Mathematics","abstract":[{"text":"We show that for any fixed dense graph G and bounded-degree tree T on the same number of vertices, a modest random perturbation of G will typically contain a copy of T . This combines the viewpoints of the well-studied problems of embedding trees into fixed dense graphs and into random graphs, and extends a sizeable body of existing research on randomly perturbed graphs. Specifically, we show that there is c=c(α,Δ) such that if G is an n-vertex graph with minimum degree at least αn, and T is an n-vertex tree with maximum degree at most Δ , then if we add cn uniformly random edges to G, the resulting graph will contain T asymptotically almost surely (as n→∞ ). Our proof uses a lemma concerning the decomposition of a dense graph into super-regular pairs of comparable sizes, which may be of independent interest.","lang":"eng"}],"status":"public","month":"01","date_created":"2021-06-22T12:26:25Z","citation":{"apa":"Krivelevich, M., Kwan, M. A., &#38; Sudakov, B. (2017). Bounded-degree spanning trees in randomly perturbed graphs. <i>SIAM Journal on Discrete Mathematics</i>. Society for Industrial &#38; Applied Mathematics. <a href=\"https://doi.org/10.1137/15m1032910\">https://doi.org/10.1137/15m1032910</a>","ama":"Krivelevich M, Kwan MA, Sudakov B. Bounded-degree spanning trees in randomly perturbed graphs. <i>SIAM Journal on Discrete Mathematics</i>. 2017;31(1):155-171. doi:<a href=\"https://doi.org/10.1137/15m1032910\">10.1137/15m1032910</a>","ista":"Krivelevich M, Kwan MA, Sudakov B. 2017. Bounded-degree spanning trees in randomly perturbed graphs. SIAM Journal on Discrete Mathematics. 31(1), 155–171.","short":"M. Krivelevich, M.A. Kwan, B. Sudakov, SIAM Journal on Discrete Mathematics 31 (2017) 155–171.","ieee":"M. Krivelevich, M. A. Kwan, and B. Sudakov, “Bounded-degree spanning trees in randomly perturbed graphs,” <i>SIAM Journal on Discrete Mathematics</i>, vol. 31, no. 1. Society for Industrial &#38; Applied Mathematics, pp. 155–171, 2017.","mla":"Krivelevich, Michael, et al. “Bounded-Degree Spanning Trees in Randomly Perturbed Graphs.” <i>SIAM Journal on Discrete Mathematics</i>, vol. 31, no. 1, Society for Industrial &#38; Applied Mathematics, 2017, pp. 155–71, doi:<a href=\"https://doi.org/10.1137/15m1032910\">10.1137/15m1032910</a>.","chicago":"Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Bounded-Degree Spanning Trees in Randomly Perturbed Graphs.” <i>SIAM Journal on Discrete Mathematics</i>. Society for Industrial &#38; Applied Mathematics, 2017. <a href=\"https://doi.org/10.1137/15m1032910\">https://doi.org/10.1137/15m1032910</a>."},"doi":"10.1137/15m1032910","scopus_import":"1","quality_controlled":"1","arxiv":1,"intvolume":"        31","extern":"1","publication_status":"published","publisher":"Society for Industrial & Applied Mathematics","oa":1,"volume":31}]