[{"title":"SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography","_id":"10810","oa_version":"Published Version","citation":{"chicago":"Rubel, Paul, Danilo Pani, Alois Schlögl, Jocelyne Fayn, Fabio Badilini, Peter Macfarlane, and Alpo Varri. “SCP-ECG V3.0: An Enhanced Standard Communication Protocol for Computer-Assisted Electrocardiography.” In <i>2016 Computing in Cardiology Conference</i>, 43:309–12. Computing in Cardiology, 2016. <a href=\"https://doi.org/10.22489/cinc.2016.090-500\">https://doi.org/10.22489/cinc.2016.090-500</a>.","ieee":"P. Rubel <i>et al.</i>, “SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography,” in <i>2016 Computing in Cardiology Conference</i>, Vancouver, Canada, 2016, vol. 43, pp. 309–312.","ista":"Rubel P, Pani D, Schlögl A, Fayn J, Badilini F, Macfarlane P, Varri A. 2016. SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography. 2016 Computing in Cardiology Conference. CinC: Computing in Cardiology vol. 43, 309–312.","short":"P. Rubel, D. Pani, A. Schlögl, J. Fayn, F. Badilini, P. Macfarlane, A. Varri, in:, 2016 Computing in Cardiology Conference, Computing in Cardiology, 2016, pp. 309–312.","mla":"Rubel, Paul, et al. “SCP-ECG V3.0: An Enhanced Standard Communication Protocol for Computer-Assisted Electrocardiography.” <i>2016 Computing in Cardiology Conference</i>, vol. 43, Computing in Cardiology, 2016, pp. 309–12, doi:<a href=\"https://doi.org/10.22489/cinc.2016.090-500\">10.22489/cinc.2016.090-500</a>.","apa":"Rubel, P., Pani, D., Schlögl, A., Fayn, J., Badilini, F., Macfarlane, P., &#38; Varri, A. (2016). SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography. In <i>2016 Computing in Cardiology Conference</i> (Vol. 43, pp. 309–312). Vancouver, Canada: Computing in Cardiology. <a href=\"https://doi.org/10.22489/cinc.2016.090-500\">https://doi.org/10.22489/cinc.2016.090-500</a>","ama":"Rubel P, Pani D, Schlögl A, et al. SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography. In: <i>2016 Computing in Cardiology Conference</i>. Vol 43. Computing in Cardiology; 2016:309-312. doi:<a href=\"https://doi.org/10.22489/cinc.2016.090-500\">10.22489/cinc.2016.090-500</a>"},"publisher":"Computing in Cardiology","status":"public","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The authors are thankful to Drs. Roger Abaecherli, Nikus Kjell, Paul Kligfield, Jay Mason, Patrice Nony, Vito Starc, Anders Thurin and the late Galen Wagner for their in depth review and constructive comments.","publication_status":"published","year":"2016","publication_identifier":{"issn":["2325-887X"]},"month":"03","main_file_link":[{"open_access":"1","url":"https://doi.org/10.22489/cinc.2016.090-500"}],"page":"309-312","department":[{"_id":"CampIT"}],"date_created":"2022-03-03T10:43:10Z","language":[{"iso":"eng"}],"author":[{"first_name":"Paul","last_name":"Rubel","full_name":"Rubel, Paul"},{"first_name":"Danilo","full_name":"Pani, Danilo","last_name":"Pani"},{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","last_name":"Schlögl","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois"},{"first_name":"Jocelyne","last_name":"Fayn","full_name":"Fayn, Jocelyne"},{"first_name":"Fabio","last_name":"Badilini","full_name":"Badilini, Fabio"},{"full_name":"Macfarlane, Peter","last_name":"Macfarlane","first_name":"Peter"},{"last_name":"Varri","full_name":"Varri, Alpo","first_name":"Alpo"}],"date_published":"2016-03-01T00:00:00Z","article_processing_charge":"No","date_updated":"2026-06-18T08:48:07Z","oa":1,"volume":43,"doi":"10.22489/cinc.2016.090-500","conference":{"location":"Vancouver, Canada","start_date":"2016-09-11","name":"CinC: Computing in Cardiology","end_date":"2016-09-14"},"quality_controlled":"1","abstract":[{"lang":"eng","text":"The main goal of the SCP-ECG standard is to address ECG data and related metadata structuring, semantics and syntax, with the objective of facilitating interoperability and thus supporting and promoting the exchange of the relevant information for unary and serial ECG diagnosis. Starting with version V3.0, the standard now also provides support for the storage of continuous, long-term ECG recordings and affords a repository for selected ECG sequences and the related metadata to accommodate stress tests, drug trials and protocol-based ECG recordings. The global and per-lead measurements sections have been extended and three new sections have been introduced for storing beat-by-beat and/or spike-by-spike measurements\r\nand annotations. The used terminology and the provided measurements and annotations have been harmonized with the ISO/IEEE 11073-10102 Annotated ECG standard. Emphasis has also been put on harmonizing the Universal Statement Codes with the CDISC and the categorized AHA statement codes and similarly the drug and implanted devices codes with the ATC and NASPE/BPEG codes. "}],"intvolume":"        43","ddc":["000"],"publication":"2016 Computing in Cardiology Conference","type":"conference","scopus_import":"1"},{"quality_controlled":"1","ec_funded":1,"abstract":[{"text":"With the accelerated development of robot technologies, optimal control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. The idea is that the controller controls the world---the body plus its environment---as reliably as possible. This paper focuses on new lines of self-organization for developmental robotics. We apply the recently developed differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object's internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently discovers how to rotate it. In this way, the robot discovers affordances of objects its body is interacting with.","lang":"eng"}],"conference":{"name":"ALIFE 2016: Conference on the Synthesis and Simulation of Living Systems","end_date":"2016-07-08","location":"Cancun, Mexico","start_date":"2016-07-04"},"type":"conference","scopus_import":"1","corr_author":"1","intvolume":"        28","publication":"15th International Conference on the Synthesis and Simulation of Living Systems","ddc":["610"],"date_published":"2016-09-01T00:00:00Z","article_processing_charge":"No","volume":28,"doi":"10.7551/978-0-262-33936-0-ch029","date_updated":"2025-07-10T11:55:05Z","oa":1,"month":"09","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"language":[{"iso":"eng"}],"date_created":"2020-07-05T22:00:47Z","author":[{"last_name":"Martius","full_name":"Martius, Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S"},{"first_name":"Rafael","full_name":"Hostettler, Rafael","last_name":"Hostettler"},{"first_name":"Alois","last_name":"Knoll","full_name":"Knoll, Alois"},{"first_name":"Ralf","full_name":"Der, Ralf","last_name":"Der"}],"file":[{"content_type":"application/pdf","file_size":678670,"date_created":"2020-07-06T12:59:09Z","checksum":"cff63e7a4b8ac466ba51a9c84153a940","creator":"cziletti","file_name":"2016_ProcALIFE_Martius.pdf","relation":"main_file","file_id":"8096","access_level":"open_access","date_updated":"2020-07-14T12:48:09Z"}],"page":"142-143","year":"2016","publication_identifier":{"isbn":["9780262339360"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","publication_status":"published","license":"https://creativecommons.org/licenses/by/4.0/","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"has_accepted_license":"1","status":"public","publisher":"MIT Press","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"oa_version":"Published Version","_id":"8094","citation":{"ieee":"G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Self-organized control of an tendon driven arm by differential extrinsic plasticity,” in <i>15th International Conference on the Synthesis and Simulation of Living Systems</i>, Cancun, Mexico, 2016, vol. 28, pp. 142–143.","ista":"Martius GS, Hostettler R, Knoll A, Der R. 2016. Self-organized control of an tendon driven arm by differential extrinsic plasticity. 15th International Conference on the Synthesis and Simulation of Living Systems. ALIFE 2016: Conference on the Synthesis and Simulation of Living Systems vol. 28, 142–143.","chicago":"Martius, Georg S, Rafael Hostettler, Alois Knoll, and Ralf Der. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” In <i>15th International Conference on the Synthesis and Simulation of Living Systems</i>, 28:142–43. MIT Press, 2016. <a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">https://doi.org/10.7551/978-0-262-33936-0-ch029</a>.","mla":"Martius, Georg S., et al. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” <i>15th International Conference on the Synthesis and Simulation of Living Systems</i>, vol. 28, MIT Press, 2016, pp. 142–43, doi:<a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">10.7551/978-0-262-33936-0-ch029</a>.","short":"G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, 15th International Conference on the Synthesis and Simulation of Living Systems, MIT Press, 2016, pp. 142–143.","apa":"Martius, G. S., Hostettler, R., Knoll, A., &#38; Der, R. (2016). Self-organized control of an tendon driven arm by differential extrinsic plasticity. In <i>15th International Conference on the Synthesis and Simulation of Living Systems</i> (Vol. 28, pp. 142–143). Cancun, Mexico: MIT Press. <a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">https://doi.org/10.7551/978-0-262-33936-0-ch029</a>","ama":"Martius GS, Hostettler R, Knoll A, Der R. Self-organized control of an tendon driven arm by differential extrinsic plasticity. In: <i>15th International Conference on the Synthesis and Simulation of Living Systems</i>. Vol 28. MIT Press; 2016:142-143. doi:<a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">10.7551/978-0-262-33936-0-ch029</a>"},"title":"Self-organized control of an tendon driven arm by differential extrinsic plasticity","file_date_updated":"2020-07-14T12:48:09Z"},{"article_processing_charge":"No","date_published":"2016-10-27T00:00:00Z","oa":1,"date_updated":"2021-12-14T07:55:30Z","volume":538,"doi":"10.1038/nature20110","article_type":"letter_note","abstract":[{"text":"The discovery of introns four decades ago was one of the most unexpected findings in molecular biology. Introns are sequences interrupting genes that must be removed as part of messenger RNA production. Genome sequencing projects have shown that most eukaryotic genes contain at least one intron, and frequently many. Comparison of these genomes reveals a history of long evolutionary periods during which few introns were gained, punctuated by episodes of rapid, extensive gain. However, although several detailed mechanisms for such episodic intron generation have been proposed, none has been empirically supported on a genomic scale. Here we show how short, non-autonomous DNA transposons independently generated hundreds to thousands of introns in the prasinophyte Micromonas pusilla and the pelagophyte Aureococcus anophagefferens. Each transposon carries one splice site. The other splice site is co-opted from the gene sequence that is duplicated upon transposon insertion, allowing perfect splicing out of the RNA. The distributions of sequences that can be co-opted are biased with respect to codons, and phasing of transposon-generated introns is similarly biased. These transposons insert between pre-existing nucleosomes, so that multiple nearby insertions generate nucleosome-sized intervening segments. Thus, transposon insertion and sequence co-option may explain the intron phase biases and prevalence of nucleosome-sized exons observed in eukaryotes. Overall, the two independent examples of proliferating elements illustrate a general DNA transposon mechanism that can plausibly account for episodes of rapid, extensive intron gain during eukaryotic evolution.","lang":"eng"}],"quality_controlled":"1","publication":"Nature","intvolume":"       538","type":"journal_article","scopus_import":"1","year":"2016","extern":"1","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"issue":"7626","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5684705/"}],"month":"10","page":"533-536","author":[{"first_name":"Jason T.","full_name":"Huff, Jason T.","last_name":"Huff"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"},{"last_name":"Roy","full_name":"Roy, Scott W.","first_name":"Scott W."}],"department":[{"_id":"DaZi"}],"language":[{"iso":"eng"}],"date_created":"2021-06-04T11:34:55Z","external_id":{"pmid":["27760113"]},"publisher":"Springer Nature ","status":"public","day":"27","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","title":"Mechanism for DNA transposons to generate introns on genomic scales","_id":"9456","oa_version":"Submitted Version","pmid":1,"citation":{"mla":"Huff, Jason T., et al. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.” <i>Nature</i>, vol. 538, no. 7626, Springer Nature , 2016, pp. 533–36, doi:<a href=\"https://doi.org/10.1038/nature20110\">10.1038/nature20110</a>.","short":"J.T. Huff, D. Zilberman, S.W. Roy, Nature 538 (2016) 533–536.","ieee":"J. T. Huff, D. Zilberman, and S. W. Roy, “Mechanism for DNA transposons to generate introns on genomic scales,” <i>Nature</i>, vol. 538, no. 7626. Springer Nature , pp. 533–536, 2016.","ista":"Huff JT, Zilberman D, Roy SW. 2016. Mechanism for DNA transposons to generate introns on genomic scales. Nature. 538(7626), 533–536.","chicago":"Huff, Jason T., Daniel Zilberman, and Scott W. Roy. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.” <i>Nature</i>. Springer Nature , 2016. <a href=\"https://doi.org/10.1038/nature20110\">https://doi.org/10.1038/nature20110</a>.","ama":"Huff JT, Zilberman D, Roy SW. Mechanism for DNA transposons to generate introns on genomic scales. <i>Nature</i>. 2016;538(7626):533-536. doi:<a href=\"https://doi.org/10.1038/nature20110\">10.1038/nature20110</a>","apa":"Huff, J. T., Zilberman, D., &#38; Roy, S. W. (2016). Mechanism for DNA transposons to generate introns on genomic scales. <i>Nature</i>. Springer Nature . <a href=\"https://doi.org/10.1038/nature20110\">https://doi.org/10.1038/nature20110</a>"}},{"author":[{"first_name":"Ping-Hung","last_name":"Hsieh","full_name":"Hsieh, Ping-Hung"},{"last_name":"He","full_name":"He, Shengbo","first_name":"Shengbo"},{"last_name":"Buttress","full_name":"Buttress, Toby","first_name":"Toby"},{"first_name":"Hongbo","full_name":"Gao, Hongbo","last_name":"Gao"},{"last_name":"Couchman","full_name":"Couchman, Matthew","first_name":"Matthew"},{"first_name":"Robert L.","full_name":"Fischer, Robert L.","last_name":"Fischer"},{"last_name":"Zilberman","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel"},{"full_name":"Feng, Xiaoqi","last_name":"Feng","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"}],"department":[{"_id":"DaZi"},{"_id":"XiFe"}],"language":[{"iso":"eng"}],"date_created":"2021-06-07T06:21:39Z","page":"15132-15137","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1619074114"}],"month":"12","issue":"52","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"year":"2016","extern":"1","type":"journal_article","scopus_import":"1","publication":"Proceedings of the National Academy of Sciences","intvolume":"       113","abstract":[{"lang":"eng","text":"Cytosine DNA methylation regulates the expression of eukaryotic genes and transposons. Methylation is copied by methyltransferases after DNA replication, which results in faithful transmission of methylation patterns during cell division and, at least in flowering plants, across generations. Transgenerational inheritance is mediated by a small group of cells that includes gametes and their progenitors. However, methylation is usually analyzed in somatic tissues that do not contribute to the next generation, and the mechanisms of transgenerational inheritance are inferred from such studies. To gain a better understanding of how DNA methylation is inherited, we analyzed purified Arabidopsis thaliana sperm and vegetative cells-the cell types that comprise pollen-with mutations in the DRM, CMT2, and CMT3 methyltransferases. We find that DNA methylation dependency on these enzymes is similar in sperm, vegetative cells, and somatic tissues, although DRM activity extends into heterochromatin in vegetative cells, likely reflecting transcription of heterochromatic transposons in this cell type. We also show that lack of histone H1, which elevates heterochromatic DNA methylation in somatic tissues, does not have this effect in pollen. Instead, levels of CG methylation in wild-type sperm and vegetative cells, as well as in wild-type microspores from which both pollen cell types originate, are substantially higher than in wild-type somatic tissues and similar to those of H1-depleted roots. Our results demonstrate that the mechanisms of methylation maintenance are similar between pollen and somatic cells, but the efficiency of CG methylation is higher in pollen, allowing methylation patterns to be accurately inherited across generations."}],"quality_controlled":"1","article_type":"original","volume":113,"doi":"10.1073/pnas.1619074114","oa":1,"date_updated":"2023-05-08T11:00:40Z","article_processing_charge":"No","date_published":"2016-12-27T00:00:00Z","citation":{"apa":"Hsieh, P.-H., He, S., Buttress, T., Gao, H., Couchman, M., Fischer, R. L., … Feng, X. (2016). Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1619074114\">https://doi.org/10.1073/pnas.1619074114</a>","ama":"Hsieh P-H, He S, Buttress T, et al. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(52):15132-15137. doi:<a href=\"https://doi.org/10.1073/pnas.1619074114\">10.1073/pnas.1619074114</a>","ista":"Hsieh P-H, He S, Buttress T, Gao H, Couchman M, Fischer RL, Zilberman D, Feng X. 2016. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. Proceedings of the National Academy of Sciences. 113(52), 15132–15137.","ieee":"P.-H. Hsieh <i>et al.</i>, “Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52. National Academy of Sciences, pp. 15132–15137, 2016.","chicago":"Hsieh, Ping-Hung, Shengbo He, Toby Buttress, Hongbo Gao, Matthew Couchman, Robert L. Fischer, Daniel Zilberman, and Xiaoqi Feng. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1619074114\">https://doi.org/10.1073/pnas.1619074114</a>.","short":"P.-H. Hsieh, S. He, T. Buttress, H. Gao, M. Couchman, R.L. Fischer, D. Zilberman, X. Feng, Proceedings of the National Academy of Sciences 113 (2016) 15132–15137.","mla":"Hsieh, Ping-Hung, et al. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15132–37, doi:<a href=\"https://doi.org/10.1073/pnas.1619074114\">10.1073/pnas.1619074114</a>."},"pmid":1,"_id":"9473","oa_version":"Published Version","title":"Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues","publication_status":"published","day":"27","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"National Academy of Sciences","external_id":{"pmid":["27956643"]}},{"year":"2016","extern":"1","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"12","keyword":["Multidisciplinary"],"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1619047114","open_access":"1"}],"issue":"52","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"date_created":"2021-06-07T07:10:59Z","language":[{"iso":"eng"}],"author":[{"full_name":"Park, Kyunghyuk","last_name":"Park","first_name":"Kyunghyuk"},{"full_name":"Kim, M. Yvonne","last_name":"Kim","first_name":"M. Yvonne"},{"last_name":"Vickers","full_name":"Vickers, Martin","first_name":"Martin"},{"full_name":"Park, Jin-Sup","last_name":"Park","first_name":"Jin-Sup"},{"first_name":"Youbong","full_name":"Hyun, Youbong","last_name":"Hyun"},{"full_name":"Okamoto, Takashi","last_name":"Okamoto","first_name":"Takashi"},{"first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649"},{"last_name":"Fischer","full_name":"Fischer, Robert L.","first_name":"Robert L."},{"orcid":"0000-0002-4008-1234","last_name":"Feng","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi"},{"last_name":"Choi","full_name":"Choi, Yeonhee","first_name":"Yeonhee"},{"last_name":"Scholten","full_name":"Scholten, Stefan","first_name":"Stefan"}],"page":"15138-15143","date_published":"2016-12-27T00:00:00Z","article_processing_charge":"No","doi":"10.1073/pnas.1619047114","volume":113,"date_updated":"2023-05-08T11:00:07Z","oa":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"Cytosine methylation is a DNA modification with important regulatory functions in eukaryotes. In flowering plants, sexual reproduction is accompanied by extensive DNA demethylation, which is required for proper gene expression in the endosperm, a nutritive extraembryonic seed tissue. Endosperm arises from a fusion of a sperm cell carried in the pollen and a female central cell. Endosperm DNA demethylation is observed specifically on the chromosomes inherited from the central cell in Arabidopsis thaliana, rice, and maize, and requires the DEMETER DNA demethylase in Arabidopsis. DEMETER is expressed in the central cell before fertilization, suggesting that endosperm demethylation patterns are inherited from the central cell. Down-regulation of the MET1 DNA methyltransferase has also been proposed to contribute to central cell demethylation. However, with the exception of three maize genes, central cell DNA methylation has not been directly measured, leaving the origin and mechanism of endosperm demethylation uncertain. Here, we report genome-wide analysis of DNA methylation in the central cells of Arabidopsis and rice—species that diverged 150 million years ago—as well as in rice egg cells. We find that DNA demethylation in both species is initiated in central cells, which requires DEMETER in Arabidopsis. However, we do not observe a global reduction of CG methylation that would be indicative of lowered MET1 activity; on the contrary, CG methylation efficiency is elevated in female gametes compared with nonsexual tissues. Our results demonstrate that locus-specific, active DNA demethylation in the central cell is the origin of maternal chromosome hypomethylation in the endosperm."}],"article_type":"original","type":"journal_article","scopus_import":"1","intvolume":"       113","publication":"Proceedings of the National Academy of Sciences","title":"DNA demethylation is initiated in the central cells of Arabidopsis and rice","oa_version":"Published Version","_id":"9477","citation":{"short":"K. Park, M.Y. Kim, M. Vickers, J.-S. Park, Y. Hyun, T. Okamoto, D. Zilberman, R.L. Fischer, X. Feng, Y. Choi, S. Scholten, Proceedings of the National Academy of Sciences 113 (2016) 15138–15143.","mla":"Park, Kyunghyuk, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15138–43, doi:<a href=\"https://doi.org/10.1073/pnas.1619047114\">10.1073/pnas.1619047114</a>.","ieee":"K. Park <i>et al.</i>, “DNA demethylation is initiated in the central cells of Arabidopsis and rice,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52. National Academy of Sciences, pp. 15138–15143, 2016.","chicago":"Park, Kyunghyuk, M. Yvonne Kim, Martin Vickers, Jin-Sup Park, Youbong Hyun, Takashi Okamoto, Daniel Zilberman, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1619047114\">https://doi.org/10.1073/pnas.1619047114</a>.","ista":"Park K, Kim MY, Vickers M, Park J-S, Hyun Y, Okamoto T, Zilberman D, Fischer RL, Feng X, Choi Y, Scholten S. 2016. DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences. 113(52), 15138–15143.","ama":"Park K, Kim MY, Vickers M, et al. DNA demethylation is initiated in the central cells of Arabidopsis and rice. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(52):15138-15143. doi:<a href=\"https://doi.org/10.1073/pnas.1619047114\">10.1073/pnas.1619047114</a>","apa":"Park, K., Kim, M. Y., Vickers, M., Park, J.-S., Hyun, Y., Okamoto, T., … Scholten, S. (2016). DNA demethylation is initiated in the central cells of Arabidopsis and rice. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1619047114\">https://doi.org/10.1073/pnas.1619047114</a>"},"pmid":1,"external_id":{"pmid":["27956642"]},"status":"public","publisher":"National Academy of Sciences","day":"27","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published"},{"publication_status":"published","acknowledgement":"DFG Cluster of Excellence EXC 1077/1 (Hearing4all) and  LU 1196/5-1 (JL and TM), People Programme (Marie Curie Actions) FP7/2007-2013 grant agreement no. 291734 (CS)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","publist_id":"6469","publisher":"Neural Information Processing Systems Foundation","status":"public","citation":{"apa":"Monk, T., Savin, C., &#38; Lücke, J. (2016). Neurons equipped with intrinsic plasticity learn stimulus intensity statistics (Vol. 29, pp. 4285–4293). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine: Neural Information Processing Systems Foundation.","ama":"Monk T, Savin C, Lücke J. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. In: Vol 29. Neural Information Processing Systems Foundation; 2016:4285-4293.","ieee":"T. Monk, C. Savin, and J. Lücke, “Neurons equipped with intrinsic plasticity learn stimulus intensity statistics,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine, 2016, vol. 29, pp. 4285–4293.","chicago":"Monk, Travis, Cristina Savin, and Jörg Lücke. “Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics,” 29:4285–93. Neural Information Processing Systems Foundation, 2016.","ista":"Monk T, Savin C, Lücke J. 2016. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 4285–4293.","mla":"Monk, Travis, et al. <i>Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics</i>. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 4285–93.","short":"T. Monk, C. Savin, J. Lücke, in:, Neural Information Processing Systems Foundation, 2016, pp. 4285–4293."},"_id":"948","oa_version":"None","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"title":"Neurons equipped with intrinsic plasticity learn stimulus intensity statistics","intvolume":"        29","type":"conference","scopus_import":"1","conference":{"location":"Barcelona, Spaine","start_date":"2016-12-05","name":"NIPS: Neural Information Processing Systems","end_date":"2016-12-10"},"ec_funded":1,"abstract":[{"lang":"eng","text":"Experience constantly shapes neural circuits through a variety of plasticity mechanisms. While the functional roles of some plasticity mechanisms are well-understood, it remains unclear how changes in neural excitability contribute to learning. Here, we develop a normative interpretation of intrinsic plasticity (IP) as a key component of unsupervised learning. We introduce a novel generative mixture model that accounts for the class-specific statistics of stimulus intensities, and we derive a neural circuit that learns the input classes and their intensities. We will analytically show that inference and learning for our generative model can be achieved by a neural circuit with intensity-sensitive neurons equipped with a specific form of IP. Numerical experiments verify our analytical derivations and show robust behavior for artificial and natural stimuli. Our results link IP to non-trivial input statistics, in particular the statistics of stimulus intensities for classes to which a neuron is sensitive. More generally, our work paves the way toward new classification algorithms that are robust to intensity variations."}],"quality_controlled":"1","oa":1,"date_updated":"2025-06-03T11:18:32Z","volume":29,"article_processing_charge":"No","date_published":"2016-01-01T00:00:00Z","page":"4285 - 4293","author":[{"full_name":"Monk, Travis","last_name":"Monk","first_name":"Travis"},{"last_name":"Savin","full_name":"Savin, Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina"},{"first_name":"Jörg","last_name":"Lücke","full_name":"Lücke, Jörg"}],"department":[{"_id":"GaTk"}],"date_created":"2018-12-11T11:49:21Z","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://papers.nips.cc/paper/6582-neurons-equipped-with-intrinsic-plasticity-learn-stimulus-intensity-statistics","open_access":"1"}],"month":"01","alternative_title":["Advances in Neural Information Processing Systems"],"year":"2016"},{"oa":1,"publisher":"Dryad","date_updated":"2025-09-22T08:59:29Z","status":"public","doi":"10.5061/dryad.cq7t1","article_processing_charge":"No","date_published":"2016-05-06T00:00:00Z","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"06","abstract":[{"lang":"eng","text":"Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination in vivo. The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline."}],"title":"Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss","year":"2016","citation":{"apa":"Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M., … Paxton, R. (2016). Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Dryad. <a href=\"https://doi.org/10.5061/dryad.cq7t1\">https://doi.org/10.5061/dryad.cq7t1</a>","ama":"Mcmahon D, Natsopoulou M, Doublet V, et al. Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss. 2016. doi:<a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>","chicago":"Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Data from: Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.cq7t1\">https://doi.org/10.5061/dryad.cq7t1</a>.","ieee":"D. Mcmahon <i>et al.</i>, “Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss.” Dryad, 2016.","ista":"Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring A, Paxton R. 2016. Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss, Dryad, <a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>.","short":"D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A. Gogol Döring, R. Paxton, (2016).","mla":"Mcmahon, Dino, et al. <i>Data from: Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss</i>. Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>."},"author":[{"last_name":"Mcmahon","full_name":"Mcmahon, Dino","first_name":"Dino"},{"first_name":"Myrsini","last_name":"Natsopoulou","full_name":"Natsopoulou, Myrsini"},{"last_name":"Doublet","full_name":"Doublet, Vincent","first_name":"Vincent"},{"full_name":"Fürst, Matthias","last_name":"Fürst","orcid":"0000-0002-3712-925X","first_name":"Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Weging","full_name":"Weging, Silvio","first_name":"Silvio"},{"last_name":"Brown","full_name":"Brown, Mark","first_name":"Mark"},{"last_name":"Gogol Döring","full_name":"Gogol Döring, Andreas","first_name":"Andreas"},{"full_name":"Paxton, Robert","last_name":"Paxton","first_name":"Robert"}],"department":[{"_id":"SyCr"}],"date_created":"2021-07-23T08:30:38Z","related_material":{"record":[{"relation":"used_in_publication","id":"1262","status":"public"}]},"oa_version":"Published Version","_id":"9704","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.cq7t1"}],"month":"05"},{"title":"Data from: How does epistasis influence the response to selection?","year":"2016","department":[{"_id":"NiBa"}],"related_material":{"record":[{"relation":"used_in_publication","id":"1199","status":"public"}]},"date_created":"2021-07-23T11:45:47Z","citation":{"chicago":"Barton, Nicholas H. “Data from: How Does Epistasis Influence the Response to Selection?” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.s5s7r\">https://doi.org/10.5061/dryad.s5s7r</a>.","ista":"Barton NH. 2016. Data from: How does epistasis influence the response to selection?, Dryad, <a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>.","ieee":"N. H. Barton, “Data from: How does epistasis influence the response to selection?” Dryad, 2016.","short":"N.H. Barton, (2016).","mla":"Barton, Nicholas H. <i>Data from: How Does Epistasis Influence the Response to Selection?</i> Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>.","apa":"Barton, N. H. (2016). Data from: How does epistasis influence the response to selection? Dryad. <a href=\"https://doi.org/10.5061/dryad.s5s7r\">https://doi.org/10.5061/dryad.s5s7r</a>","ama":"Barton NH. Data from: How does epistasis influence the response to selection? 2016. doi:<a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>"},"author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"_id":"9710","oa_version":"Published Version","month":"09","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.s5s7r"}],"date_updated":"2025-04-15T07:11:02Z","oa":1,"publisher":"Dryad","doi":"10.5061/dryad.s5s7r","status":"public","date_published":"2016-09-23T00:00:00Z","article_processing_charge":"No","type":"research_data_reference","day":"23","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects."}]},{"year":"2016","title":"Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees","oa_version":"Published Version","_id":"9720","main_file_link":[{"url":"https://doi.org/10.5061/dryad.4b565","open_access":"1"}],"month":"01","author":[{"full_name":"Mcmahon, Dino","last_name":"Mcmahon","first_name":"Dino"},{"orcid":"0000-0002-3712-925X","last_name":"Fürst","full_name":"Fürst, Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"last_name":"Caspar","full_name":"Caspar, Jesicca","first_name":"Jesicca"},{"first_name":"Panagiotis","last_name":"Theodorou","full_name":"Theodorou, Panagiotis"},{"last_name":"Brown","full_name":"Brown, Mark","first_name":"Mark"},{"full_name":"Paxton, Robert","last_name":"Paxton","first_name":"Robert"}],"citation":{"short":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, (2016).","mla":"Mcmahon, Dino, et al. <i>Data from: A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees</i>. Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.4b565\">10.5061/dryad.4b565</a>.","ieee":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees.” Dryad, 2016.","ista":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2016. Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees, Dryad, <a href=\"https://doi.org/10.5061/dryad.4b565\">10.5061/dryad.4b565</a>.","chicago":"Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark Brown, and Robert Paxton. “Data from: A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.4b565\">https://doi.org/10.5061/dryad.4b565</a>.","ama":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees. 2016. doi:<a href=\"https://doi.org/10.5061/dryad.4b565\">10.5061/dryad.4b565</a>","apa":"Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., &#38; Paxton, R. (2016). Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees. Dryad. <a href=\"https://doi.org/10.5061/dryad.4b565\">https://doi.org/10.5061/dryad.4b565</a>"},"date_created":"2021-07-26T09:14:19Z","department":[{"_id":"SyCr"}],"related_material":{"record":[{"id":"1855","status":"public","relation":"used_in_publication"}]},"article_processing_charge":"No","date_published":"2016-01-22T00:00:00Z","oa":1,"publisher":"Dryad","date_updated":"2025-09-23T07:26:23Z","doi":"10.5061/dryad.4b565","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"22","abstract":[{"lang":"eng","text":"Summary: Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. This study aims to attain a detailed understanding of the current and ongoing risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses. Within a structured large-scale national survey across 26 independent sites, we quantify the prevalence and pathogen loads of multiple RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus spp.) populations. We then construct models that compare virus prevalence between wild and managed pollinators. Multiple RNA viruses associated with honeybees are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees is a significant predictor of virus prevalence in bumblebees, but we remain cautious in speculating over the principle direction of pathogen transmission. We demonstrate species-specific differences in prevalence, indicating significant variation in disease susceptibility or tolerance. Pathogen loads within individual bumblebees may be high and in the case of at least one RNA virus, prevalence is higher in wild bumblebees than in managed honeybee populations. Our findings indicate widespread transmission of RNA viruses between managed and wild bee pollinators, pointing to an interconnected network of potential disease pressures within and among pollinator species. In the context of the biodiversity crisis, our study emphasizes the importance of targeting a wide range of pathogens and defining host associations when considering potential drivers of population decline."}],"type":"research_data_reference"},{"publisher":"Public Library of Science","date_updated":"2025-09-22T09:55:08Z","doi":"10.1371/journal.pbio.2000234.s016","status":"public","article_processing_charge":"No","type":"research_data_reference","day":"27","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Simulation study to test the robustness of ABC in face of recent times of divergence","year":"2016","citation":{"ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Simulation study to test the robustness of ABC in face of recent times of divergence, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>.","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">https://doi.org/10.1371/journal.pbio.2000234.s016</a>.","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Simulation study to test the robustness of ABC in face of recent times of divergence.” Public Library of Science, 2016.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","mla":"Roux, Camille, et al. <i>Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>.","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Simulation study to test the robustness of ABC in face of recent times of divergence. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">https://doi.org/10.1371/journal.pbio.2000234.s016</a>","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Simulation study to test the robustness of ABC in face of recent times of divergence. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>"},"author":[{"full_name":"Roux, Camille","last_name":"Roux","first_name":"Camille"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","full_name":"Fraisse, Christelle"},{"last_name":"Romiguier","full_name":"Romiguier, Jonathan","first_name":"Jonathan"},{"last_name":"Anciaux","full_name":"Anciaux, Youann","first_name":"Youann"},{"first_name":"Nicolas","last_name":"Galtier","full_name":"Galtier, Nicolas"},{"last_name":"Bierne","full_name":"Bierne, Nicolas","first_name":"Nicolas"}],"date_created":"2021-08-10T08:20:17Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1158"}]},"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"_id":"9862","oa_version":"Published Version","month":"12"},{"day":"27","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","article_processing_charge":"No","date_updated":"2025-09-22T09:55:09Z","publisher":"Public Library of Science","status":"public","doi":"10.1371/journal.pbio.2000234.s017","oa_version":"Published Version","_id":"9863","month":"12","related_material":{"record":[{"status":"public","id":"1158","relation":"used_in_publication"}]},"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"date_created":"2021-08-10T08:22:52Z","author":[{"full_name":"Roux, Camille","last_name":"Roux","first_name":"Camille"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"first_name":"Jonathan","full_name":"Romiguier, Jonathan","last_name":"Romiguier"},{"first_name":"Youann","last_name":"Anciaux","full_name":"Anciaux, Youann"},{"last_name":"Galtier","full_name":"Galtier, Nicolas","first_name":"Nicolas"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"}],"citation":{"apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Accessions of surveyed individuals, geographic locations and summary statistics. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">https://doi.org/10.1371/journal.pbio.2000234.s017</a>","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Accessions of surveyed individuals, geographic locations and summary statistics. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Accessions of surveyed individuals, geographic locations and summary statistics.” Public Library of Science, 2016.","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">https://doi.org/10.1371/journal.pbio.2000234.s017</a>.","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Accessions of surveyed individuals, geographic locations and summary statistics, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>.","mla":"Roux, Camille, et al. <i>Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016)."},"year":"2016","title":"Accessions of surveyed individuals, geographic locations and summary statistics"},{"day":"14","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima."}],"type":"research_data_reference","date_published":"2016-12-14T00:00:00Z","article_processing_charge":"No","date_updated":"2025-07-10T11:49:59Z","oa":1,"publisher":"The Royal Society","status":"public","doi":"10.6084/m9.figshare.4315652.v1","_id":"9864","oa_version":"Published Version","month":"12","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.4315652.v1","open_access":"1"}],"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"date_created":"2021-08-10T08:29:47Z","related_material":{"record":[{"relation":"used_in_publication","id":"1077","status":"public"}]},"author":[{"full_name":"Fernandes Redondo, Rodrigo A","orcid":"0000-0002-5837-2793","last_name":"Fernandes Redondo","first_name":"Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87"},{"id":"2A181218-F248-11E8-B48F-1D18A9856A87","first_name":"Harold","orcid":"0000-0002-5985-7653","last_name":"de Vladar","full_name":"de Vladar, Harold"},{"last_name":"Włodarski","full_name":"Włodarski, Tomasz","first_name":"Tomasz"},{"last_name":"Bollback","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P"}],"citation":{"ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. 2016. doi:<a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., &#38; Bollback, J. P. (2016). Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. The Royal Society. <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">https://doi.org/10.6084/m9.figshare.4315652.v1</a>","mla":"Fernandes Redondo, Rodrigo A., et al. <i>Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family</i>. The Royal Society, 2016, doi:<a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>.","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016).","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family.” The Royal Society, 2016.","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family, The Royal Society, <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>.","chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">https://doi.org/10.6084/m9.figshare.4315652.v1</a>."},"year":"2016","title":"Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"09","type":"research_data_reference","date_published":"2016-12-09T00:00:00Z","article_processing_charge":"No","status":"public","doi":"10.1371/journal.pcbi.1005218.s009","date_updated":"2025-09-22T09:53:16Z","publisher":"Public Library of Science","month":"12","_id":"9866","oa_version":"Published Version","related_material":{"record":[{"id":"1167","status":"public","relation":"used_in_publication"}]},"department":[{"_id":"AnKi"}],"date_created":"2021-08-10T08:37:20Z","citation":{"ama":"Zagórski MP, Burda Z, Wacław B. ZIP-archived directory containing all data and computer programs. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">10.1371/journal.pcbi.1005218.s009</a>","apa":"Zagórski, M. P., Burda, Z., &#38; Wacław, B. (2016). ZIP-archived directory containing all data and computer programs. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">https://doi.org/10.1371/journal.pcbi.1005218.s009</a>","mla":"Zagórski, Marcin P., et al. <i>ZIP-Archived Directory Containing All Data and Computer Programs</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">10.1371/journal.pcbi.1005218.s009</a>.","short":"M.P. Zagórski, Z. Burda, B. Wacław, (2016).","chicago":"Zagórski, Marcin P, Zdzisław Burda, and Bartłomiej Wacław. “ZIP-Archived Directory Containing All Data and Computer Programs.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">https://doi.org/10.1371/journal.pcbi.1005218.s009</a>.","ieee":"M. P. Zagórski, Z. Burda, and B. Wacław, “ZIP-archived directory containing all data and computer programs.” Public Library of Science, 2016.","ista":"Zagórski MP, Burda Z, Wacław B. 2016. ZIP-archived directory containing all data and computer programs, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">10.1371/journal.pcbi.1005218.s009</a>."},"author":[{"orcid":"0000-0001-7896-7762","last_name":"Zagórski","full_name":"Zagórski, Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin P"},{"first_name":"Zdzisław","last_name":"Burda","full_name":"Burda, Zdzisław"},{"last_name":"Wacław","full_name":"Wacław, Bartłomiej","first_name":"Bartłomiej"}],"year":"2016","title":"ZIP-archived directory containing all data and computer programs"},{"abstract":[{"lang":"eng","text":"In the beginning of our experiment, subjects were asked to read a few pages on their computer screens that would explain the rules of the subsequent game. Here, we provide these instructions, translated from German."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"04","type":"research_data_reference","article_processing_charge":"No","doi":"10.1371/journal.pone.0163867.s008","status":"public","publisher":"Public Library of Science","date_updated":"2025-09-22T08:27:00Z","month":"10","_id":"9867","oa_version":"Published Version","author":[{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe","full_name":"Hilbe, Christian"},{"first_name":"Kristin","full_name":"Hagel, Kristin","last_name":"Hagel"},{"full_name":"Milinski, Manfred","last_name":"Milinski","first_name":"Manfred"}],"citation":{"ieee":"C. Hilbe, K. Hagel, and M. Milinski, “Experimental game instructions.” Public Library of Science, 2016.","chicago":"Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Experimental Game Instructions.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">https://doi.org/10.1371/journal.pone.0163867.s008</a>.","ista":"Hilbe C, Hagel K, Milinski M. 2016. Experimental game instructions, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">10.1371/journal.pone.0163867.s008</a>.","short":"C. Hilbe, K. Hagel, M. Milinski, (2016).","mla":"Hilbe, Christian, et al. <i>Experimental Game Instructions</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">10.1371/journal.pone.0163867.s008</a>.","apa":"Hilbe, C., Hagel, K., &#38; Milinski, M. (2016). Experimental game instructions. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">https://doi.org/10.1371/journal.pone.0163867.s008</a>","ama":"Hilbe C, Hagel K, Milinski M. Experimental game instructions. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">10.1371/journal.pone.0163867.s008</a>"},"date_created":"2021-08-10T08:42:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1322"}]},"department":[{"_id":"KrCh"}],"year":"2016","title":"Experimental game instructions"},{"date_published":"2016-10-04T00:00:00Z","article_processing_charge":"No","doi":"10.1371/journal.pone.0163867.s009","status":"public","date_updated":"2025-09-22T08:27:00Z","publisher":"Public Library of Science","abstract":[{"text":"The raw data file containing the experimental decisions of all our study subjects.","lang":"eng"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"04","type":"research_data_reference","year":"2016","title":"Experimental data","month":"10","_id":"9868","oa_version":"Published Version","related_material":{"record":[{"id":"1322","status":"public","relation":"used_in_publication"}]},"date_created":"2021-08-10T08:45:00Z","department":[{"_id":"KrCh"}],"author":[{"first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe"},{"first_name":"Kristin","last_name":"Hagel","full_name":"Hagel, Kristin"},{"last_name":"Milinski","full_name":"Milinski, Manfred","first_name":"Manfred"}],"citation":{"ama":"Hilbe C, Hagel K, Milinski M. Experimental data. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">10.1371/journal.pone.0163867.s009</a>","apa":"Hilbe, C., Hagel, K., &#38; Milinski, M. (2016). Experimental data. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">https://doi.org/10.1371/journal.pone.0163867.s009</a>","mla":"Hilbe, Christian, et al. <i>Experimental Data</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">10.1371/journal.pone.0163867.s009</a>.","short":"C. Hilbe, K. Hagel, M. Milinski, (2016).","ista":"Hilbe C, Hagel K, Milinski M. 2016. Experimental data, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">10.1371/journal.pone.0163867.s009</a>.","ieee":"C. Hilbe, K. Hagel, and M. Milinski, “Experimental data.” Public Library of Science, 2016.","chicago":"Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Experimental Data.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">https://doi.org/10.1371/journal.pone.0163867.s009</a>."}},{"type":"research_data_reference","abstract":[{"lang":"eng","text":"A lower bound on the error of a positional estimator with limited positional information is derived."}],"day":"27","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","doi":"10.1371/journal.pone.0163628.s001","publisher":"Public Library of Science","date_updated":"2025-09-22T08:46:14Z","article_processing_charge":"No","date_published":"2016-09-27T00:00:00Z","author":[{"first_name":"Patrick","last_name":"Hillenbrand","full_name":"Hillenbrand, Patrick"},{"first_name":"Ulrich","last_name":"Gerland","full_name":"Gerland, Ulrich"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik"}],"citation":{"ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Error bound on an estimator of position, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">10.1371/journal.pone.0163628.s001</a>.","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Error bound on an estimator of position.” Public Library of Science, 2016.","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Error Bound on an Estimator of Position.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">https://doi.org/10.1371/journal.pone.0163628.s001</a>.","mla":"Hillenbrand, Patrick, et al. <i>Error Bound on an Estimator of Position</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">10.1371/journal.pone.0163628.s001</a>.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","apa":"Hillenbrand, P., Gerland, U., &#38; Tkačik, G. (2016). Error bound on an estimator of position. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">https://doi.org/10.1371/journal.pone.0163628.s001</a>","ama":"Hillenbrand P, Gerland U, Tkačik G. Error bound on an estimator of position. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">10.1371/journal.pone.0163628.s001</a>"},"date_created":"2021-08-10T08:53:48Z","related_material":{"record":[{"id":"1270","status":"public","relation":"used_in_publication"}]},"department":[{"_id":"GaTk"}],"month":"09","_id":"9869","oa_version":"Published Version","title":"Error bound on an estimator of position","year":"2016"},{"date_published":"2016-09-27T00:00:00Z","article_processing_charge":"No","date_updated":"2025-09-22T08:46:14Z","publisher":"Public Library of Science","doi":"10.1371/journal.pone.0163628.s002","status":"public","day":"27","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"text":"The effect of noise in the input field on an Ising model is approximated. Furthermore, methods to compute positional information in an Ising model by transfer matrices and Monte Carlo sampling are outlined.","lang":"eng"}],"type":"research_data_reference","year":"2016","title":"Computation of positional information in an Ising model","_id":"9870","oa_version":"Published Version","month":"09","department":[{"_id":"GaTk"}],"related_material":{"record":[{"status":"public","id":"1270","relation":"used_in_publication"}]},"date_created":"2021-08-10T09:23:45Z","author":[{"last_name":"Hillenbrand","full_name":"Hillenbrand, Patrick","first_name":"Patrick"},{"first_name":"Ulrich","full_name":"Gerland, Ulrich","last_name":"Gerland"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik"}],"citation":{"ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in an Ising model.” Public Library of Science, 2016.","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in an Ising Model.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">https://doi.org/10.1371/journal.pone.0163628.s002</a>.","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information in an Ising model, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">10.1371/journal.pone.0163628.s002</a>.","mla":"Hillenbrand, Patrick, et al. <i>Computation of Positional Information in an Ising Model</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">10.1371/journal.pone.0163628.s002</a>.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","apa":"Hillenbrand, P., Gerland, U., &#38; Tkačik, G. (2016). 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Computation of positional information in a discrete morphogen field. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">https://doi.org/10.1371/journal.pone.0163628.s003</a>","ama":"Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in a discrete morphogen field. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">10.1371/journal.pone.0163628.s003</a>","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information in a discrete morphogen field, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">10.1371/journal.pone.0163628.s003</a>.","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in a Discrete Morphogen Field.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">https://doi.org/10.1371/journal.pone.0163628.s003</a>.","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in a discrete morphogen field.” Public Library of Science, 2016.","mla":"Hillenbrand, Patrick, et al. <i>Computation of Positional Information in a Discrete Morphogen Field</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">10.1371/journal.pone.0163628.s003</a>.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016)."},"department":[{"_id":"GaTk"}],"related_material":{"record":[{"status":"public","id":"1270","relation":"used_in_publication"}]},"date_created":"2021-08-10T09:27:35Z","article_processing_charge":"No","publisher":"Public Library of Science","date_updated":"2025-09-22T08:46:14Z","doi":"10.1371/journal.pone.0163628.s003","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"27","abstract":[{"lang":"eng","text":"The positional information in a discrete morphogen field with Gaussian noise is computed."}],"type":"research_data_reference"},{"article_processing_charge":"No","date_updated":"2025-09-22T09:10:03Z","publisher":"Public Library of Science","status":"public","doi":"10.1371/journal.pgen.1005974.s015","day":"19","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","year":"2016","title":"Quantification of the growth rate reduction as a consequence of age-specific mortality","_id":"9873","oa_version":"Published Version","month":"04","date_created":"2021-08-10T09:42:34Z","department":[{"_id":"CaGu"}],"related_material":{"record":[{"relation":"used_in_publication","id":"1250","status":"public"}]},"citation":{"ieee":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, and M. Ackermann, “Quantification of the growth rate reduction as a consequence of age-specific mortality.” Public Library of Science, 2016.","chicago":"Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette Bigosch, and Martin Ackermann. “Quantification of the Growth Rate Reduction as a Consequence of Age-Specific Mortality.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pgen.1005974.s015\">https://doi.org/10.1371/journal.pgen.1005974.s015</a>.","ista":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. 2016. Quantification of the growth rate reduction as a consequence of age-specific mortality, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pgen.1005974.s015\">10.1371/journal.pgen.1005974.s015</a>.","mla":"Boehm, Alex, et al. <i>Quantification of the Growth Rate Reduction as a Consequence of Age-Specific Mortality</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005974.s015\">10.1371/journal.pgen.1005974.s015</a>.","short":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, M. Ackermann, (2016).","apa":"Boehm, A., Arnoldini, M., Bergmiller, T., Röösli, T., Bigosch, C., &#38; Ackermann, M. (2016). Quantification of the growth rate reduction as a consequence of age-specific mortality. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1005974.s015\">https://doi.org/10.1371/journal.pgen.1005974.s015</a>","ama":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. Quantification of the growth rate reduction as a consequence of age-specific mortality. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005974.s015\">10.1371/journal.pgen.1005974.s015</a>"},"author":[{"last_name":"Boehm","full_name":"Boehm, Alex","first_name":"Alex"},{"last_name":"Arnoldini","full_name":"Arnoldini, Markus","first_name":"Markus"},{"orcid":"0000-0001-5396-4346","last_name":"Bergmiller","full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"},{"last_name":"Röösli","full_name":"Röösli, Thomas","first_name":"Thomas"},{"first_name":"Colette","last_name":"Bigosch","full_name":"Bigosch, Colette"},{"last_name":"Ackermann","full_name":"Ackermann, Martin","first_name":"Martin"}]},{"title":"Inference algorithms for pattern-based CRFs on sequence data","related_material":{"record":[{"status":"public","id":"2272","relation":"earlier_version"}]},"citation":{"ieee":"V. Kolmogorov and R. Takhanov, “Inference algorithms for pattern-based CRFs on sequence data,” <i>Algorithmica</i>, vol. 76, no. 1. Springer, pp. 17–46, 2016.","chicago":"Kolmogorov, Vladimir, and Rustem Takhanov. “Inference Algorithms for Pattern-Based CRFs on Sequence Data.” <i>Algorithmica</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s00453-015-0017-7\">https://doi.org/10.1007/s00453-015-0017-7</a>.","ista":"Kolmogorov V, Takhanov R. 2016. Inference algorithms for pattern-based CRFs on sequence data. Algorithmica. 76(1), 17–46.","mla":"Kolmogorov, Vladimir, and Rustem Takhanov. “Inference Algorithms for Pattern-Based CRFs on Sequence Data.” <i>Algorithmica</i>, vol. 76, no. 1, Springer, 2016, pp. 17–46, doi:<a href=\"https://doi.org/10.1007/s00453-015-0017-7\">10.1007/s00453-015-0017-7</a>.","short":"V. Kolmogorov, R. Takhanov, Algorithmica 76 (2016) 17–46.","apa":"Kolmogorov, V., &#38; Takhanov, R. (2016). Inference algorithms for pattern-based CRFs on sequence data. <i>Algorithmica</i>. Springer. <a href=\"https://doi.org/10.1007/s00453-015-0017-7\">https://doi.org/10.1007/s00453-015-0017-7</a>","ama":"Kolmogorov V, Takhanov R. Inference algorithms for pattern-based CRFs on sequence data. <i>Algorithmica</i>. 2016;76(1):17-46. doi:<a href=\"https://doi.org/10.1007/s00453-015-0017-7\">10.1007/s00453-015-0017-7</a>"},"project":[{"call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"oa_version":"Preprint","_id":"1794","status":"public","publisher":"Springer","external_id":{"arxiv":["1210.0508"],"isi":["000381149500002"]},"isi":1,"publication_status":"published","publist_id":"5316","day":"01","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"This work has been partially supported by the European Research Council under the European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no. 616160.","year":"2016","date_created":"2018-12-11T11:54:02Z","language":[{"iso":"eng"}],"department":[{"_id":"VlKo"}],"author":[{"last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"},{"id":"2CCAC26C-F248-11E8-B48F-1D18A9856A87","first_name":"Rustem","last_name":"Takhanov","full_name":"Takhanov, Rustem"}],"page":"17 - 46","month":"09","main_file_link":[{"url":"http://arxiv.org/abs/1210.0508","open_access":"1"}],"issue":"1","volume":76,"doi":"10.1007/s00453-015-0017-7","date_updated":"2025-09-29T14:28:47Z","oa":1,"date_published":"2016-09-01T00:00:00Z","article_processing_charge":"No","type":"journal_article","scopus_import":"1","arxiv":1,"intvolume":"        76","corr_author":"1","publication":"Algorithmica","quality_controlled":"1","ec_funded":1,"abstract":[{"text":"We consider Conditional random fields (CRFs) with pattern-based potentials defined on a chain. In this model the energy of a string (labeling) (Formula presented.) is the sum of terms over intervals [i, j] where each term is non-zero only if the substring (Formula presented.) equals a prespecified pattern w. Such CRFs can be naturally applied to many sequence tagging problems. We present efficient algorithms for the three standard inference tasks in a CRF, namely computing (i) the partition function, (ii) marginals, and (iii) computing the MAP. Their complexities are respectively (Formula presented.), (Formula presented.) and (Formula presented.) where L is the combined length of input patterns, (Formula presented.) is the maximum length of a pattern, and D is the input alphabet. This improves on the previous algorithms of Ye et al. (NIPS, 2009) whose complexities are respectively (Formula presented.), (Formula presented.) and (Formula presented.), where (Formula presented.) is the number of input patterns. In addition, we give an efficient algorithm for sampling, and revisit the case of MAP with non-positive weights.","lang":"eng"}]}]