[{"file_date_updated":"2021-12-01T14:38:08Z","month":"08","doi":"10.1515/bmt-2013-4181","has_accepted_license":"1","issue":"SI-1-Track-G","article_processing_charge":"No","language":[{"iso":"eng"}],"day":"01","quality_controlled":"1","status":"public","conference":{"location":"Graz, Austria","start_date":"2013-09-19","end_date":"2013-09-21","name":"BMT: Biomedizinische Technik "},"department":[{"_id":"PeJo"}],"oa_version":"Submitted Version","date_published":"2013-08-01T00:00:00Z","external_id":{"isi":["000497714000034"],"pmid":["24042795"]},"oa":1,"intvolume":"        58","isi":1,"corr_author":"1","author":[{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","orcid":"0000-0002-5621-8100","last_name":"Schlögl","full_name":"Schlögl, Alois"},{"full_name":"Jonas, Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"first_name":"C.","last_name":"Schmidt-Hieber","full_name":"Schmidt-Hieber, C."},{"first_name":"S. J.","last_name":"Guzman","full_name":"Guzman, S. J."}],"title":"Stimfit: A fast visualization and analysis environment for cellular neurophysiology","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"De Gruyter","year":"2013","date_updated":"2025-09-30T07:31:23Z","pmid":1,"_id":"10396","citation":{"apa":"Schlögl, A., Jonas, P. M., Schmidt-Hieber, C., &#38; Guzman, S. J. (2013). Stimfit: A fast visualization and analysis environment for cellular neurophysiology. <i>Biomedical Engineering / Biomedizinische Technik</i>. Graz, Austria: De Gruyter. <a href=\"https://doi.org/10.1515/bmt-2013-4181\">https://doi.org/10.1515/bmt-2013-4181</a>","chicago":"Schlögl, Alois, Peter M Jonas, C. Schmidt-Hieber, and S. J. Guzman. “Stimfit: A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” <i>Biomedical Engineering / Biomedizinische Technik</i>. De Gruyter, 2013. <a href=\"https://doi.org/10.1515/bmt-2013-4181\">https://doi.org/10.1515/bmt-2013-4181</a>.","ista":"Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. 2013. Stimfit: A fast visualization and analysis environment for cellular neurophysiology. Biomedical Engineering / Biomedizinische Technik. 58(SI-1-Track-G), 000010151520134181.","mla":"Schlögl, Alois, et al. “Stimfit: A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” <i>Biomedical Engineering / Biomedizinische Technik</i>, vol. 58, no. SI-1-Track-G, 000010151520134181, De Gruyter, 2013, doi:<a href=\"https://doi.org/10.1515/bmt-2013-4181\">10.1515/bmt-2013-4181</a>.","short":"A. Schlögl, P.M. Jonas, C. Schmidt-Hieber, S.J. Guzman, Biomedical Engineering / Biomedizinische Technik 58 (2013).","ieee":"A. Schlögl, P. M. Jonas, C. Schmidt-Hieber, and S. J. Guzman, “Stimfit: A fast visualization and analysis environment for cellular neurophysiology,” <i>Biomedical Engineering / Biomedizinische Technik</i>, vol. 58, no. SI-1-Track-G. De Gruyter, 2013.","ama":"Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. Stimfit: A fast visualization and analysis environment for cellular neurophysiology. <i>Biomedical Engineering / Biomedizinische Technik</i>. 2013;58(SI-1-Track-G). doi:<a href=\"https://doi.org/10.1515/bmt-2013-4181\">10.1515/bmt-2013-4181</a>"},"publication_identifier":{"issn":["0013-5585"],"eissn":["1862-278X"]},"abstract":[{"lang":"eng","text":"Stimfit is a free cross-platform software package for viewing and analyzing electrophysiological data. It supports most standard file types for cellular neurophysiology and other biomedical formats. Its analysis algorithms have been used and validated in several experimental laboratories. Its embedded Python scripting interface makes Stimfit highly extensible and customizable."}],"article_number":"000010151520134181","article_type":"original","publication_status":"published","keyword":["biomedical engineering","data analysis","free software"],"publication":"Biomedical Engineering / Biomedizinische Technik","volume":58,"date_created":"2021-12-01T14:35:35Z","type":"journal_article","file":[{"relation":"main_file","success":1,"file_size":149825,"access_level":"open_access","file_id":"10397","file_name":"Schloegl_Abstract-BMT2013.pdf","checksum":"cdfc5339b530a25d6079f7223f0b1f16","creator":"schloegl","content_type":"application/pdf","date_updated":"2021-12-01T14:38:08Z","date_created":"2021-12-01T14:38:08Z"}],"ddc":["005","610"]},{"type":"journal_article","date_created":"2018-12-11T11:48:43Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"access_level":"open_access","relation":"main_file","file_size":953299,"file_name":"2013_FrontiersPlant_OBrien.pdf","checksum":"fdc25ddd1bf9a99b99f662cdbafeddd4","file_id":"5903","creator":"dernst","date_created":"2019-01-31T10:40:38Z","date_updated":"2020-07-14T12:48:11Z","content_type":"application/pdf"}],"ddc":["580"],"article_number":"451","publication_status":"published","abstract":[{"text":"As sessile organisms, plants have to be able to adapt to a continuously changing environment. Plants that perceive some of these changes as stress signals activate signaling pathways to modulate their development and to enable them to survive. The complex responses to environmental cues are to a large extent mediated by plant hormones that together orchestrate the final plant response. The phytohormone cytokinin is involved in many plant developmental processes. Recently, it has been established that cytokinin plays an important role in stress responses, but does not act alone. Indeed, the hormonal control of plant development and stress adaptation is the outcome of a complex network of multiple synergistic and antagonistic interactions between various hormones. Here, we review the recent findings on the cytokinin function as part of this hormonal network. We focus on the importance of the crosstalk between cytokinin and other hormones, such as abscisic acid, jasmonate, salicylic acid, ethylene, and auxin in the modulation of plant development and stress adaptation. Finally, the impact of the current research in the biotechnological industry will be discussed.","lang":"eng"}],"volume":4,"publication":"Frontiers in Plant Science","_id":"827","date_updated":"2025-09-29T14:33:09Z","citation":{"ama":"O’Brien J, Benková E. Cytokinin cross talking during biotic and abiotic stress responses. <i>Frontiers in Plant Science</i>. 2013;4. doi:<a href=\"https://doi.org/10.3389/fpls.2013.00451\">10.3389/fpls.2013.00451</a>","short":"J. O’Brien, E. Benková, Frontiers in Plant Science 4 (2013).","ieee":"J. O’Brien and E. Benková, “Cytokinin cross talking during biotic and abiotic stress responses,” <i>Frontiers in Plant Science</i>, vol. 4. Frontiers Research Foundation, 2013.","mla":"O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and Abiotic Stress Responses.” <i>Frontiers in Plant Science</i>, vol. 4, 451, Frontiers Research Foundation, 2013, doi:<a href=\"https://doi.org/10.3389/fpls.2013.00451\">10.3389/fpls.2013.00451</a>.","ista":"O’Brien J, Benková E. 2013. Cytokinin cross talking during biotic and abiotic stress responses. Frontiers in Plant Science. 4, 451.","chicago":"O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and Abiotic Stress Responses.” <i>Frontiers in Plant Science</i>. Frontiers Research Foundation, 2013. <a href=\"https://doi.org/10.3389/fpls.2013.00451\">https://doi.org/10.3389/fpls.2013.00451</a>.","apa":"O’Brien, J., &#38; Benková, E. (2013). Cytokinin cross talking during biotic and abiotic stress responses. <i>Frontiers in Plant Science</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fpls.2013.00451\">https://doi.org/10.3389/fpls.2013.00451</a>"},"title":"Cytokinin cross talking during biotic and abiotic stress responses","ec_funded":1,"publisher":"Frontiers Research Foundation","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2013","intvolume":"         4","isi":1,"corr_author":"1","author":[{"first_name":"José","last_name":"O'Brien","full_name":"O'Brien, José"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","full_name":"Benková, Eva"}],"status":"public","quality_controlled":"1","oa_version":"Published Version","department":[{"_id":"EvBe"}],"oa":1,"date_published":"2013-11-19T00:00:00Z","external_id":{"isi":["000331445200001"]},"project":[{"grant_number":"207362","call_identifier":"FP7","name":"Hormonal cross-talk in plant organogenesis","_id":"253FCA6A-B435-11E9-9278-68D0E5697425"}],"publist_id":"6821","has_accepted_license":"1","day":"19","scopus_import":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"month":"11","file_date_updated":"2020-07-14T12:48:11Z","doi":"10.3389/fpls.2013.00451"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Frontiers Research Foundation","title":"Systems approaches to study root architecture dynamics","ec_funded":1,"year":"2013","date_updated":"2025-09-29T14:32:42Z","_id":"828","citation":{"apa":"Cuesta, C., Wabnik, K. T., &#38; Benková, E. (2013). Systems approaches to study root architecture dynamics. <i>Frontiers in Plant Science</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fpls.2013.00537\">https://doi.org/10.3389/fpls.2013.00537</a>","chicago":"Cuesta, Candela, Krzysztof T Wabnik, and Eva Benková. “Systems Approaches to Study Root Architecture Dynamics.” <i>Frontiers in Plant Science</i>. Frontiers Research Foundation, 2013. <a href=\"https://doi.org/10.3389/fpls.2013.00537\">https://doi.org/10.3389/fpls.2013.00537</a>.","mla":"Cuesta, Candela, et al. “Systems Approaches to Study Root Architecture Dynamics.” <i>Frontiers in Plant Science</i>, vol. 4, 537, Frontiers Research Foundation, 2013, doi:<a href=\"https://doi.org/10.3389/fpls.2013.00537\">10.3389/fpls.2013.00537</a>.","ista":"Cuesta C, Wabnik KT, Benková E. 2013. Systems approaches to study root architecture dynamics. Frontiers in Plant Science. 4, 537.","ieee":"C. Cuesta, K. T. Wabnik, and E. Benková, “Systems approaches to study root architecture dynamics,” <i>Frontiers in Plant Science</i>, vol. 4. Frontiers Research Foundation, 2013.","short":"C. Cuesta, K.T. Wabnik, E. Benková, Frontiers in Plant Science 4 (2013).","ama":"Cuesta C, Wabnik KT, Benková E. Systems approaches to study root architecture dynamics. <i>Frontiers in Plant Science</i>. 2013;4. doi:<a href=\"https://doi.org/10.3389/fpls.2013.00537\">10.3389/fpls.2013.00537</a>"},"abstract":[{"text":"The plant root system is essential for providing anchorage to the soil, supplying minerals and water, and synthesizing metabolites. It is a dynamic organ modulated by external cues such as environmental signals, water and nutrients availability, salinity and others. Lateral roots (LRs) are initiated from the primary root post-embryonically, after which they progress through discrete developmental stages which can be independently controlled, providing a high level of plasticity during root system formation. Within this review, main contributions are presented, from the classical forward genetic screens to the more recent high-throughput approaches, combined with computer model predictions, dissecting how LRs and thereby root system architecture is established and developed.","lang":"eng"}],"publication_status":"published","article_number":"537","publication":"Frontiers in Plant Science","volume":4,"date_created":"2018-12-11T11:48:43Z","type":"journal_article","file":[{"content_type":"application/pdf","date_created":"2019-01-31T10:36:43Z","date_updated":"2020-07-14T12:48:11Z","creator":"dernst","file_id":"5902","file_name":"2013_FrontiersPlant_Cuesta.pdf","checksum":"0185b3c4d7df9a94bd3ce5a66d213506","relation":"main_file","file_size":710835,"access_level":"open_access"}],"ddc":["580"],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file_date_updated":"2020-07-14T12:48:11Z","month":"12","doi":"10.3389/fpls.2013.00537","has_accepted_license":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"scopus_import":"1","day":"26","department":[{"_id":"EvBe"}],"oa_version":"Published Version","status":"public","quality_controlled":"1","publist_id":"6820","project":[{"grant_number":"207362","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","name":"Hormonal cross-talk in plant organogenesis","call_identifier":"FP7"}],"external_id":{"isi":["000331533500002"]},"date_published":"2013-12-26T00:00:00Z","oa":1,"isi":1,"intvolume":"         4","author":[{"orcid":"0000-0003-1923-2410","full_name":"Cuesta, Candela","last_name":"Cuesta","first_name":"Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krzysztof T","last_name":"Wabnik","full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"corr_author":"1"},{"issue":"1","language":[{"iso":"eng"}],"article_processing_charge":"No","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2013.02.033","open_access":"1"}],"day":"28","month":"03","doi":"10.1016/j.cell.2013.02.033","intvolume":"       153","author":[{"full_name":"Zemach, Assaf","last_name":"Zemach","first_name":"Assaf"},{"last_name":"Kim","full_name":"Kim, M. Yvonne","first_name":"M. Yvonne"},{"first_name":"Ping-Hung","full_name":"Hsieh, Ping-Hung","last_name":"Hsieh"},{"first_name":"Devin","last_name":"Coleman-Derr","full_name":"Coleman-Derr, Devin"},{"first_name":"Leor","last_name":"Eshed-Williams","full_name":"Eshed-Williams, Leor"},{"first_name":"Ka","last_name":"Thao","full_name":"Thao, Ka"},{"first_name":"Stacey L.","last_name":"Harmer","full_name":"Harmer, Stacey L."},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"page":"193-205","extern":"1","department":[{"_id":"DaZi"}],"oa_version":"Published Version","status":"public","quality_controlled":"1","external_id":{"pmid":["23540698"]},"date_published":"2013-03-28T00:00:00Z","oa":1,"pmid":1,"date_updated":"2021-12-14T08:25:35Z","_id":"9459","citation":{"apa":"Zemach, A., Kim, M. Y., Hsieh, P.-H., Coleman-Derr, D., Eshed-Williams, L., Thao, K., … Zilberman, D. (2013). The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">https://doi.org/10.1016/j.cell.2013.02.033</a>","chicago":"Zemach, Assaf, M. Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor Eshed-Williams, Ka Thao, Stacey L. Harmer, and Daniel Zilberman. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” <i>Cell</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">https://doi.org/10.1016/j.cell.2013.02.033</a>.","ista":"Zemach A, Kim MY, Hsieh P-H, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer SL, Zilberman D. 2013. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 153(1), 193–205.","mla":"Zemach, Assaf, et al. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” <i>Cell</i>, vol. 153, no. 1, Elsevier, 2013, pp. 193–205, doi:<a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">10.1016/j.cell.2013.02.033</a>.","short":"A. Zemach, M.Y. Kim, P.-H. Hsieh, D. Coleman-Derr, L. Eshed-Williams, K. Thao, S.L. Harmer, D. Zilberman, Cell 153 (2013) 193–205.","ieee":"A. Zemach <i>et al.</i>, “The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin,” <i>Cell</i>, vol. 153, no. 1. Elsevier, pp. 193–205, 2013.","ama":"Zemach A, Kim MY, Hsieh P-H, et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. <i>Cell</i>. 2013;153(1):193-205. doi:<a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">10.1016/j.cell.2013.02.033</a>"},"publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"publisher":"Elsevier","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin","year":"2013","date_created":"2021-06-04T12:23:28Z","type":"journal_article","abstract":[{"lang":"eng","text":"Nucleosome remodelers of the DDM1/Lsh family are required for DNA methylation of transposable elements, but the reason for this is unknown. How DDM1 interacts with other methylation pathways, such as small-RNA-directed DNA methylation (RdDM), which is thought to mediate plant asymmetric methylation through DRM enzymes, is also unclear. Here, we show that most asymmetric methylation is facilitated by DDM1 and mediated by the methyltransferase CMT2 separately from RdDM. We find that heterochromatic sequences preferentially require DDM1 for DNA methylation and that this preference depends on linker histone H1. RdDM is instead inhibited by heterochromatin and absolutely requires the nucleosome remodeler DRD1. Together, DDM1 and RdDM mediate nearly all transposon methylation and collaborate to repress transposition and regulate the methylation and expression of genes. Our results indicate that DDM1 provides DNA methyltransferases access to H1-containing heterochromatin to allow stable silencing of transposable elements in cooperation with the RdDM pathway."}],"publication_status":"published","article_type":"original","publication":"Cell","volume":153},{"author":[{"first_name":"Jessica A.","full_name":"Rodrigues, Jessica A.","last_name":"Rodrigues"},{"full_name":"Ruan, Randy","last_name":"Ruan","first_name":"Randy"},{"first_name":"Toshiro","full_name":"Nishimura, Toshiro","last_name":"Nishimura"},{"first_name":"Manoj K.","last_name":"Sharma","full_name":"Sharma, Manoj K."},{"full_name":"Sharma, Rita","last_name":"Sharma","first_name":"Rita"},{"full_name":"Ronald, Pamela C","last_name":"Ronald","first_name":"Pamela C"},{"full_name":"Fischer, Robert L.","last_name":"Fischer","first_name":"Robert L."},{"first_name":"Daniel","full_name":"Zilberman, Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"page":"7934-7939","extern":"1","intvolume":"       110","external_id":{"pmid":["23613580"]},"date_published":"2013-05-07T00:00:00Z","oa":1,"oa_version":"Published Version","department":[{"_id":"DaZi"}],"quality_controlled":"1","status":"public","article_processing_charge":"No","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1306164110"}],"day":"07","issue":"19","doi":"10.1073/pnas.1306164110","month":"05","date_created":"2021-06-07T07:31:02Z","type":"journal_article","keyword":["Multidisciplinary"],"publication":"Proceedings of the National Academy of Sciences","volume":110,"abstract":[{"lang":"eng","text":"Arabidopsis thaliana endosperm, a transient tissue that nourishes the embryo, exhibits extensive localized DNA demethylation on maternally inherited chromosomes. Demethylation mediates parent-of-origin–specific (imprinted) gene expression but is apparently unnecessary for the extensive accumulation of maternally biased small RNA (sRNA) molecules detected in seeds. Endosperm DNA in the distantly related monocots rice and maize is likewise locally hypomethylated, but whether this hypomethylation is generally parent-of-origin specific is unknown. Imprinted expression of sRNA also remains uninvestigated in monocot seeds. Here, we report high-coverage sequencing of the Kitaake rice cultivar that enabled us to show that localized hypomethylation in rice endosperm occurs solely on the maternal genome, preferring regions of high DNA accessibility. Maternally expressed imprinted genes are enriched for hypomethylation at putative promoter regions and transcriptional termini and paternally expressed genes at promoters and gene bodies, mirroring our recent results in A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are expressed from both parental genomes and correlate with hypomethylation. Overlaps between imprinted sRNA loci and imprinted genes expressed from opposite alleles suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling tissues primarily originate from small class II (cut-and-paste) transposable elements, those in endosperm are more uniformly derived, including sequences from other transposon classes, as well as genic and intergenic regions. Our data indicate that the endosperm exhibits a unique pattern of sRNA expression and suggest that localized hypomethylation of maternal endosperm DNA is conserved in flowering plants."}],"article_type":"original","publication_status":"published","citation":{"chicago":"Rodrigues, Jessica A., Randy Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, Pamela C Ronald, Robert L. Fischer, and Daniel Zilberman. “Imprinted Expression of Genes and Small RNA Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1306164110\">https://doi.org/10.1073/pnas.1306164110</a>.","apa":"Rodrigues, J. A., Ruan, R., Nishimura, T., Sharma, M. K., Sharma, R., Ronald, P. C., … Zilberman, D. (2013). Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1306164110\">https://doi.org/10.1073/pnas.1306164110</a>","ieee":"J. A. Rodrigues <i>et al.</i>, “Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 110, no. 19. National Academy of Sciences, pp. 7934–7939, 2013.","short":"J.A. Rodrigues, R. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 110 (2013) 7934–7939.","ista":"Rodrigues JA, Ruan R, Nishimura T, Sharma MK, Sharma R, Ronald PC, Fischer RL, Zilberman D. 2013. Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. Proceedings of the National Academy of Sciences. 110(19), 7934–7939.","mla":"Rodrigues, Jessica A., et al. “Imprinted Expression of Genes and Small RNA Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 110, no. 19, National Academy of Sciences, 2013, pp. 7934–39, doi:<a href=\"https://doi.org/10.1073/pnas.1306164110\">10.1073/pnas.1306164110</a>.","ama":"Rodrigues JA, Ruan R, Nishimura T, et al. Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. 2013;110(19):7934-7939. doi:<a href=\"https://doi.org/10.1073/pnas.1306164110\">10.1073/pnas.1306164110</a>"},"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"pmid":1,"date_updated":"2021-12-14T08:26:44Z","_id":"9481","year":"2013","publisher":"National Academy of Sciences","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm"},{"department":[{"_id":"DaZi"},{"_id":"XiFe"}],"oa_version":"Published Version","quality_controlled":"1","status":"public","external_id":{"pmid":["23410937"]},"date_published":"2013-02-11T00:00:00Z","oa":1,"intvolume":"        24","author":[{"orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","last_name":"Feng","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"},{"full_name":"Zilberman, Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"last_name":"Dickinson","full_name":"Dickinson, Hugh","first_name":"Hugh"}],"page":"215-225","extern":"1","month":"02","doi":"10.1016/j.devcel.2013.01.014","issue":"3","article_processing_charge":"No","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2013.01.014"}],"day":"11","abstract":[{"text":"Plants undergo alternation of generation in which reproductive cells develop in the plant body (\"sporophytic generation\") and then differentiate into a multicellular gamete-forming \"gametophytic generation.\" Different populations of helper cells assist in this transgenerational journey, with somatic tissues supporting early development and single nurse cells supporting gametogenesis. New data reveal a two-way relationship between early reproductive cells and their helpers involving complex epigenetic and signaling networks determining cell number and fate. Later, the egg cell plays a central role in specifying accessory cells, whereas in both gametophytes, companion cells contribute non-cell-autonomously to the epigenetic landscape of the gamete genomes.","lang":"eng"}],"article_type":"review","publication_status":"published","publication":"Developmental Cell","volume":24,"date_created":"2021-06-08T06:14:50Z","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","title":"A conversation across generations: Soma-germ cell crosstalk in plants","year":"2013","pmid":1,"date_updated":"2023-05-08T11:00:59Z","_id":"9520","citation":{"ama":"Feng X, Zilberman D, Dickinson H. A conversation across generations: Soma-germ cell crosstalk in plants. <i>Developmental Cell</i>. 2013;24(3):215-225. doi:<a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">10.1016/j.devcel.2013.01.014</a>","chicago":"Feng, Xiaoqi, Daniel Zilberman, and Hugh Dickinson. “A Conversation across Generations: Soma-Germ Cell Crosstalk in Plants.” <i>Developmental Cell</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">https://doi.org/10.1016/j.devcel.2013.01.014</a>.","apa":"Feng, X., Zilberman, D., &#38; Dickinson, H. (2013). A conversation across generations: Soma-germ cell crosstalk in plants. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">https://doi.org/10.1016/j.devcel.2013.01.014</a>","ieee":"X. Feng, D. Zilberman, and H. Dickinson, “A conversation across generations: Soma-germ cell crosstalk in plants,” <i>Developmental Cell</i>, vol. 24, no. 3. Elsevier, pp. 215–225, 2013.","short":"X. Feng, D. Zilberman, H. Dickinson, Developmental Cell 24 (2013) 215–225.","mla":"Feng, Xiaoqi, et al. “A Conversation across Generations: Soma-Germ Cell Crosstalk in Plants.” <i>Developmental Cell</i>, vol. 24, no. 3, Elsevier, 2013, pp. 215–25, doi:<a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">10.1016/j.devcel.2013.01.014</a>.","ista":"Feng X, Zilberman D, Dickinson H. 2013. A conversation across generations: Soma-germ cell crosstalk in plants. Developmental Cell. 24(3), 215–225."},"publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]}},{"department":[{"_id":"KrCh"}],"abstract":[{"text":"Cooperative behavior, where one individual incurs a cost to help another, is a wide spread phenomenon. Here we study direct reciprocity in the context of the alternating Prisoner's Dilemma. We consider all strategies that can be implemented by one and two-state automata. We calculate the payoff matrix of all pairwise encounters in the presence of noise. We explore deterministic selection dynamics with and without mutation. Using different error rates and payoff values, we observe convergence to a small number of distinct equilibria. Two of them are uncooperative strict Nash equilibria representing always-defect (ALLD) and Grim. The third equilibrium is mixed and represents a cooperative alliance of several strategies, dominated by a strategy which we call Forgiver. Forgiver cooperates whenever the opponent has cooperated; it defects once when the opponent has defected, but subsequently Forgiver attempts to re-establish cooperation even if the opponent has defected again. Forgiver is not an evolutionarily stable strategy, but the alliance, which it rules, is asymptotically stable. For a wide range of parameter values the most commonly observed outcome is convergence to the mixed equilibrium, dominated by Forgiver. Our results show that although forgiving might incur a short-term loss it can lead to a long-term gain. Forgiveness facilitates stable cooperation in the presence of exploitation and noise.","lang":"eng"}],"oa_version":"Published Version","status":"public","date_published":"2013-12-12T00:00:00Z","date_created":"2021-07-28T15:45:07Z","type":"research_data_reference","author":[{"last_name":"Zagorsky","full_name":"Zagorsky, Benjamin","first_name":"Benjamin"},{"id":"4A918E98-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","last_name":"Reiter","full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"related_material":{"record":[{"relation":"used_in_publication","id":"2247","status":"public"}]},"publisher":"Public Library of Science","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Forgiver triumphs in alternating prisoner's dilemma ","month":"12","doi":"10.1371/journal.pone.0080814.s001","year":"2013","date_updated":"2025-09-29T14:30:03Z","_id":"9749","article_processing_charge":"No","citation":{"apa":"Zagorsky, B., Reiter, J., Chatterjee, K., &#38; Nowak, M. (2013). Forgiver triumphs in alternating prisoner’s dilemma . Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">https://doi.org/10.1371/journal.pone.0080814.s001</a>","chicago":"Zagorsky, Benjamin, Johannes Reiter, Krishnendu Chatterjee, and Martin Nowak. “Forgiver Triumphs in Alternating Prisoner’s Dilemma .” Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">https://doi.org/10.1371/journal.pone.0080814.s001</a>.","mla":"Zagorsky, Benjamin, et al. <i>Forgiver Triumphs in Alternating Prisoner’s Dilemma </i>. Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">10.1371/journal.pone.0080814.s001</a>.","ista":"Zagorsky B, Reiter J, Chatterjee K, Nowak M. 2013. Forgiver triumphs in alternating prisoner’s dilemma , Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">10.1371/journal.pone.0080814.s001</a>.","ieee":"B. Zagorsky, J. Reiter, K. Chatterjee, and M. Nowak, “Forgiver triumphs in alternating prisoner’s dilemma .” Public Library of Science, 2013.","short":"B. Zagorsky, J. Reiter, K. Chatterjee, M. Nowak, (2013).","ama":"Zagorsky B, Reiter J, Chatterjee K, Nowak M. Forgiver triumphs in alternating prisoner’s dilemma . 2013. doi:<a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">10.1371/journal.pone.0080814.s001</a>"},"day":"12"},{"abstract":[{"text":"High relatedness among interacting individuals has generally been considered a precondition for the evolution of altruism. However, kin-selection theory also predicts the evolution of altruism when relatedness is low, as long as the cost of the altruistic act is minor compared to its benefit. Here, we demonstrate evidence for a low-cost altruistic act in bacteria. We investigated Escherichia coli responding to the attack of an obligately lytic phage by committing suicide in order to prevent parasite transmission to nearby relatives. We found that bacterial suicide provides large benefits to survivors at marginal costs to committers. The cost of suicide was low because infected cells are moribund, rapidly dying upon phage infection, such that no more opportunity for reproduction remains. As a consequence of its marginal cost, host suicide was selectively favoured even when relatedness between committers and survivors approached zero. Altogether, our findings demonstrate that low-cost suicide can evolve with ease, represents an effective host-defence strategy, and seems to be widespread among microbes. Moreover, low-cost suicide might also occur in higher organisms as exemplified by infected social insect workers leaving the colony to die in isolation.","lang":"eng"}],"department":[{"_id":"CaGu"}],"oa_version":"Published Version","status":"public","oa":1,"date_published":"2013-03-21T00:00:00Z","type":"research_data_reference","date_created":"2021-07-30T08:08:09Z","related_material":{"record":[{"status":"public","id":"2853","relation":"used_in_publication"}]},"author":[{"full_name":"Refardt, Dominik","last_name":"Refardt","first_name":"Dominik"},{"first_name":"Tobias","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kümmerli, Rolf","last_name":"Kümmerli","first_name":"Rolf"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Dryad","month":"03","title":"Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection","doi":"10.5061/dryad.b1q2n","year":"2013","_id":"9751","date_updated":"2025-09-29T13:41:12Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.b1q2n"}],"day":"21","article_processing_charge":"No","citation":{"ama":"Refardt D, Bergmiller T, Kümmerli R. Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection. 2013. doi:<a href=\"https://doi.org/10.5061/dryad.b1q2n\">10.5061/dryad.b1q2n</a>","ista":"Refardt D, Bergmiller T, Kümmerli R. 2013. Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection, Dryad, <a href=\"https://doi.org/10.5061/dryad.b1q2n\">10.5061/dryad.b1q2n</a>.","mla":"Refardt, Dominik, et al. <i>Data from: Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection</i>. Dryad, 2013, doi:<a href=\"https://doi.org/10.5061/dryad.b1q2n\">10.5061/dryad.b1q2n</a>.","short":"D. Refardt, T. Bergmiller, R. Kümmerli, (2013).","ieee":"D. Refardt, T. Bergmiller, and R. Kümmerli, “Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection.” Dryad, 2013.","apa":"Refardt, D., Bergmiller, T., &#38; Kümmerli, R. (2013). Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection. Dryad. <a href=\"https://doi.org/10.5061/dryad.b1q2n\">https://doi.org/10.5061/dryad.b1q2n</a>","chicago":"Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “Data from: Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection.” Dryad, 2013. <a href=\"https://doi.org/10.5061/dryad.b1q2n\">https://doi.org/10.5061/dryad.b1q2n</a>."}},{"oa":1,"date_published":"2013-10-01T00:00:00Z","abstract":[{"lang":"eng","text":"Short-read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate among recent, non-equilibrium histories. We address both the assembly and inference challenges. We develop a bioinformatic pipeline for generating outgroup-rooted alignments of orthologous sequence blocks from de novo low-coverage short-read data for a small number of genomes, and show how such sequence blocks can be used to fit explicit models of population divergence and admixture in a likelihood framework. To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding insect (the oak gallwasp Biorhiza pallida) which, in common with many other taxa, was restricted during Pleistocene ice ages to a longitudinal series of southern refugia spanning theWestern Palaearctic. Our analysis of sequence blocks sampled from a single genome from each of three major glacial refugia reveals support for an unexpected history dominated by recent admixture. Despite the fact that 80% of the genome is affected by admixture during the last glacial cycle, we are able to infer the deeper divergence history of these populations. These inferences are robust to variation in block length, mutation model, and the sampling location of individual genomes within refugia. This combination of de novo assembly and numerical likelihood calculation provides a powerful framework for estimating recent population history that can be applied to any organism without the need for prior genetic resources."}],"oa_version":"Published Version","department":[{"_id":"NiBa"}],"status":"public","related_material":{"record":[{"status":"public","id":"2170","relation":"used_in_publication"}]},"author":[{"first_name":"Jack","last_name":"Hearn","full_name":"Hearn, Jack"},{"full_name":"Stone, Graham","last_name":"Stone","first_name":"Graham"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"},{"full_name":"Lohse, Konrad","last_name":"Lohse","first_name":"Konrad"},{"last_name":"Bunnefeld","full_name":"Bunnefeld, Lynsey","first_name":"Lynsey"}],"type":"research_data_reference","date_created":"2021-07-30T08:31:22Z","doi":"10.5061/dryad.r3r60","year":"2013","publisher":"Dryad","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"10","title":"Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies","main_file_link":[{"url":"https://doi.org/10.5061/dryad.r3r60","open_access":"1"}],"day":"01","article_processing_charge":"No","citation":{"ama":"Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies. 2013. doi:<a href=\"https://doi.org/10.5061/dryad.r3r60\">10.5061/dryad.r3r60</a>","apa":"Hearn, J., Stone, G., Barton, N. H., Lohse, K., &#38; Bunnefeld, L. (2013). Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies. Dryad. <a href=\"https://doi.org/10.5061/dryad.r3r60\">https://doi.org/10.5061/dryad.r3r60</a>","chicago":"Hearn, Jack, Graham Stone, Nicholas H Barton, Konrad Lohse, and Lynsey Bunnefeld. “Data from: Likelihood-Based Inference of Population History from Low Coverage de Novo Genome Assemblies.” Dryad, 2013. <a href=\"https://doi.org/10.5061/dryad.r3r60\">https://doi.org/10.5061/dryad.r3r60</a>.","ista":"Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. 2013. Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies, Dryad, <a href=\"https://doi.org/10.5061/dryad.r3r60\">10.5061/dryad.r3r60</a>.","mla":"Hearn, Jack, et al. <i>Data from: Likelihood-Based Inference of Population History from Low Coverage de Novo Genome Assemblies</i>. Dryad, 2013, doi:<a href=\"https://doi.org/10.5061/dryad.r3r60\">10.5061/dryad.r3r60</a>.","ieee":"J. Hearn, G. Stone, N. H. Barton, K. Lohse, and L. Bunnefeld, “Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies.” Dryad, 2013.","short":"J. Hearn, G. Stone, N.H. Barton, K. Lohse, L. Bunnefeld, (2013)."},"_id":"9754","date_updated":"2025-09-29T11:38:51Z"},{"_id":"6440","date_updated":"2020-07-14T23:06:19Z","has_accepted_license":"1","day":"13","publication_identifier":{"issn":["2664-1690"]},"citation":{"apa":"Henzinger, T. A., Payer, H., &#38; Sezgin, A. (2013). <i>Replacing competition with cooperation to achieve scalable lock-free FIFO queues </i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-124-v1-1\">https://doi.org/10.15479/AT:IST-2013-124-v1-1</a>","chicago":"Henzinger, Thomas A, Hannes Payer, and Ali Sezgin. <i>Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues </i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-124-v1-1\">https://doi.org/10.15479/AT:IST-2013-124-v1-1</a>.","mla":"Henzinger, Thomas A., et al. <i>Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues </i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-124-v1-1\">10.15479/AT:IST-2013-124-v1-1</a>.","ista":"Henzinger TA, Payer H, Sezgin A. 2013. Replacing competition with cooperation to achieve scalable lock-free FIFO queues , IST Austria, 23p.","short":"T.A. Henzinger, H. Payer, A. Sezgin, Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues , IST Austria, 2013.","ieee":"T. A. Henzinger, H. Payer, and A. Sezgin, <i>Replacing competition with cooperation to achieve scalable lock-free FIFO queues </i>. IST Austria, 2013.","ama":"Henzinger TA, Payer H, Sezgin A. <i>Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues </i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-124-v1-1\">10.15479/AT:IST-2013-124-v1-1</a>"},"pubrep_id":"124","language":[{"iso":"eng"}],"title":"Replacing competition with cooperation to achieve scalable lock-free FIFO queues ","month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"IST Austria","file_date_updated":"2020-07-14T12:47:30Z","year":"2013","doi":"10.15479/AT:IST-2013-124-v1-1","type":"technical_report","alternative_title":["IST Austria Technical Report"],"date_created":"2019-05-13T14:13:27Z","page":"23","ddc":["000","005"],"file":[{"date_created":"2019-05-13T14:11:39Z","date_updated":"2020-07-14T12:47:30Z","content_type":"application/pdf","creator":"dernst","file_name":"2013_TechRep_Henzinger.pdf","checksum":"a219ba4eada6cd62befed52262ee15d4","file_id":"6441","access_level":"open_access","relation":"main_file","file_size":549684}],"author":[{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Payer, Hannes","last_name":"Payer","first_name":"Hannes"},{"last_name":"Sezgin","full_name":"Sezgin, Ali","first_name":"Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","status":"public","abstract":[{"text":"In order to guarantee that each method of a data structure updates the logical state exactly once, al-most all non-blocking implementations employ Compare-And-Swap (CAS) based synchronization. For FIFO  queue  implementations  this  translates  into  concurrent  enqueue  or  dequeue  methods competing among themselves to update the same variable, the tail or the head, respectively, leading to high contention and poor scalability. Recent non-blocking queue implementations try to alleviate high contentionby increasing the number of contention points, all the while using CAS-based synchronization. Furthermore, obtaining a wait-free implementation with competition is achieved by additional synchronization which leads to further degradation of performance.In this paper we formalize the notion of competitiveness of a synchronizing statement which can beused as a measure for the scalability of concurrent implementations.  We present a new queue implementation, the Speculative Pairing (SP) queue, which, as we show, decreases competitiveness by using Fetch-And-Increment (FAI) instead of CAS. We prove that the SP queue is linearizable and lock-free.We also show that replacing CAS with FAI leads to wait-freedom for dequeue methods without an adverse effect on performance.  In fact, our experiments suggest that the SP queue can perform and scale better than the state-of-the-art queue implementations.","lang":"eng"}],"department":[{"_id":"ToHe"}],"oa_version":"Published Version","oa":1,"date_published":"2013-06-13T00:00:00Z"},{"day":"01","article_processing_charge":"No","language":[{"iso":"eng"}],"scopus_import":"1","issue":"2","doi":"10.1007/s10703-012-0170-4","month":"04","page":"142 - 174","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"last_name":"De Alfaro","full_name":"De Alfaro, Luca","first_name":"Luca"},{"full_name":"Faella, Marco","last_name":"Faella","first_name":"Marco"},{"first_name":"Ritankar","full_name":"Majumdar, Ritankar","last_name":"Majumdar"},{"first_name":"Vishwanath","last_name":"Raman","full_name":"Raman, Vishwanath"}],"acknowledgement":"This research was supported in part by the National Science Foundation CAREER award CCR-0132780, by the ONR grant N00014-02-1-0671, by the National Science Foundation grants CCR-0427202 and CCR-0234690, and by the ARP award TO.030.MM.D.","isi":1,"intvolume":"        42","publist_id":"3583","external_id":{"isi":["000316677500002"]},"date_published":"2013-04-01T00:00:00Z","oa_version":"None","department":[{"_id":"KrCh"}],"status":"public","quality_controlled":"1","citation":{"ama":"Chatterjee K, De Alfaro L, Faella M, Majumdar R, Raman V. Code aware resource management. <i>Formal Methods in System Design</i>. 2013;42(2):142-174. doi:<a href=\"https://doi.org/10.1007/s10703-012-0170-4\">10.1007/s10703-012-0170-4</a>","ista":"Chatterjee K, De Alfaro L, Faella M, Majumdar R, Raman V. 2013. Code aware resource management. Formal Methods in System Design. 42(2), 142–174.","mla":"Chatterjee, Krishnendu, et al. “Code Aware Resource Management.” <i>Formal Methods in System Design</i>, vol. 42, no. 2, Springer, 2013, pp. 142–74, doi:<a href=\"https://doi.org/10.1007/s10703-012-0170-4\">10.1007/s10703-012-0170-4</a>.","short":"K. Chatterjee, L. De Alfaro, M. Faella, R. Majumdar, V. Raman, Formal Methods in System Design 42 (2013) 142–174.","ieee":"K. Chatterjee, L. De Alfaro, M. Faella, R. Majumdar, and V. Raman, “Code aware resource management,” <i>Formal Methods in System Design</i>, vol. 42, no. 2. Springer, pp. 142–174, 2013.","apa":"Chatterjee, K., De Alfaro, L., Faella, M., Majumdar, R., &#38; Raman, V. (2013). Code aware resource management. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-012-0170-4\">https://doi.org/10.1007/s10703-012-0170-4</a>","chicago":"Chatterjee, Krishnendu, Luca De Alfaro, Marco Faella, Ritankar Majumdar, and Vishwanath Raman. “Code Aware Resource Management.” <i>Formal Methods in System Design</i>. Springer, 2013. <a href=\"https://doi.org/10.1007/s10703-012-0170-4\">https://doi.org/10.1007/s10703-012-0170-4</a>."},"_id":"3116","date_updated":"2025-09-29T13:24:54Z","year":"2013","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Springer","title":"Code aware resource management","type":"journal_article","date_created":"2018-12-11T12:01:29Z","volume":42,"publication":"Formal Methods in System Design","publication_status":"published","abstract":[{"lang":"eng","text":"Multithreaded programs coordinate their interaction through synchronization primitives like mutexes and semaphores, which are managed by an OS-provided resource manager. We propose algorithms for the automatic construction of code-aware resource managers for multithreaded embedded applications. Such managers use knowledge about the structure and resource usage (mutex and semaphore usage) of the threads to guarantee deadlock freedom and progress while managing resources in an efficient way. Our algorithms compute managers as winning strategies in certain infinite games, and produce a compact code description of these strategies. We have implemented the algorithms in the tool Cynthesis. Given a multithreaded program in C, the tool produces C code implementing a code-aware resource manager. We show in experiments that Cynthesis produces compact resource managers within a few minutes on a set of embedded benchmarks with up to 6 threads. © 2012 Springer Science+Business Media, LLC."}]},{"date_created":"2018-12-11T12:02:19Z","type":"journal_article","file":[{"file_id":"5873","checksum":"ecd859fe52a562193027d428b5524a8d","file_name":"2013_PNAS_Dubuis.pdf","file_size":1670548,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:46:06Z","date_created":"2019-01-22T13:53:23Z","creator":"dernst"}],"ddc":["570"],"abstract":[{"text":"Cells in a developing embryo have no direct way of &quot;measuring&quot; their physical position. Through a variety of processes, however, the expression levels of multiple genes come to be correlated with position, and these expression levels thus form a code for &quot;positional information.&quot; We show how to measure this information, in bits, using the gap genes in the Drosophila embryo as an example. Individual genes carry nearly two bits of information, twice as much as expected if the expression patterns consisted only of on/off domains separated by sharp boundaries. Taken together, four gap genes carry enough information to define a cell's location with an error bar of ~1% along the anterior-posterior axis of the embryo. This precision is nearly enough for each cell to have a unique identity, which is the maximum information the system can use, and is nearly constant along the length of the embryo. We argue that this constancy is a signature of optimality in the transmission of information from primary morphogen inputs to the output of the gap gene network.","lang":"eng"}],"publication_status":"published","publication":"PNAS","volume":110,"pmid":1,"date_updated":"2025-09-29T13:24:21Z","_id":"3261","citation":{"ama":"Dubuis J, Tkačik G, Wieschaus E, Gregor T, Bialek W. Positional information, in bits. <i>PNAS</i>. 2013;110(41):16301-16308. doi:<a href=\"https://doi.org/10.1073/pnas.1315642110\">10.1073/pnas.1315642110</a>","apa":"Dubuis, J., Tkačik, G., Wieschaus, E., Gregor, T., &#38; Bialek, W. (2013). Positional information, in bits. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1315642110\">https://doi.org/10.1073/pnas.1315642110</a>","chicago":"Dubuis, Julien, Gašper Tkačik, Eric Wieschaus, Thomas Gregor, and William Bialek. “Positional Information, in Bits.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1315642110\">https://doi.org/10.1073/pnas.1315642110</a>.","ista":"Dubuis J, Tkačik G, Wieschaus E, Gregor T, Bialek W. 2013. Positional information, in bits. PNAS. 110(41), 16301–16308.","mla":"Dubuis, Julien, et al. “Positional Information, in Bits.” <i>PNAS</i>, vol. 110, no. 41, National Academy of Sciences, 2013, pp. 16301–08, doi:<a href=\"https://doi.org/10.1073/pnas.1315642110\">10.1073/pnas.1315642110</a>.","ieee":"J. Dubuis, G. Tkačik, E. Wieschaus, T. Gregor, and W. Bialek, “Positional information, in bits,” <i>PNAS</i>, vol. 110, no. 41. National Academy of Sciences, pp. 16301–16308, 2013.","short":"J. Dubuis, G. Tkačik, E. Wieschaus, T. Gregor, W. Bialek, PNAS 110 (2013) 16301–16308."},"title":"Positional information, in bits","publisher":"National Academy of Sciences","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2013","intvolume":"       110","isi":1,"author":[{"first_name":"Julien","last_name":"Dubuis","full_name":"Dubuis, Julien"},{"orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wieschaus, Eric","last_name":"Wieschaus","first_name":"Eric"},{"first_name":"Thomas","full_name":"Gregor, Thomas","last_name":"Gregor"},{"last_name":"Bialek","full_name":"Bialek, William","first_name":"William"}],"page":"16301 - 16308","status":"public","quality_controlled":"1","oa_version":"Published Version","department":[{"_id":"GaTk"}],"date_published":"2013-10-08T00:00:00Z","publist_id":"3387","external_id":{"pmid":["24089448"],"isi":["000325395600021"]},"oa":1,"has_accepted_license":"1","issue":"41","scopus_import":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"day":"08","file_date_updated":"2020-07-14T12:46:06Z","month":"10","doi":"10.1073/pnas.1315642110"},{"author":[{"first_name":"Novi","last_name":"Quadrianto","full_name":"Quadrianto, Novi"},{"first_name":"Christoph","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"page":"1069 - 1069","editor":[{"first_name":"Werner","full_name":"Dubitzky, Werner","last_name":"Dubitzky"},{"first_name":"Olaf","last_name":"Wolkenhauer","full_name":"Wolkenhauer, Olaf"},{"first_name":"Kwang","full_name":"Cho, Kwang","last_name":"Cho"},{"full_name":"Yokota, Hiroki","last_name":"Yokota","first_name":"Hiroki"}],"date_created":"2018-12-11T12:02:39Z","intvolume":"         3","type":"encyclopedia_article","publication":"Encyclopedia of Systems Biology","date_published":"2013-01-01T00:00:00Z","publist_id":"3314","volume":3,"status":"public","quality_controlled":"1","department":[{"_id":"ChLa"}],"oa_version":"None","publication_status":"published","citation":{"chicago":"Quadrianto, Novi, and Christoph Lampert. “Kernel Based Learning.” In <i>Encyclopedia of Systems Biology</i>, edited by Werner Dubitzky, Olaf Wolkenhauer, Kwang Cho, and Hiroki Yokota, 3:1069–1069. Springer, 2013. <a href=\"https://doi.org/10.1007/978-1-4419-9863-7_604\">https://doi.org/10.1007/978-1-4419-9863-7_604</a>.","apa":"Quadrianto, N., &#38; Lampert, C. (2013). Kernel based learning. In W. Dubitzky, O. Wolkenhauer, K. Cho, &#38; H. Yokota (Eds.), <i>Encyclopedia of Systems Biology</i> (Vol. 3, pp. 1069–1069). Springer. <a href=\"https://doi.org/10.1007/978-1-4419-9863-7_604\">https://doi.org/10.1007/978-1-4419-9863-7_604</a>","short":"N. Quadrianto, C. Lampert, in:, W. Dubitzky, O. Wolkenhauer, K. Cho, H. Yokota (Eds.), Encyclopedia of Systems Biology, Springer, 2013, pp. 1069–1069.","ieee":"N. Quadrianto and C. Lampert, “Kernel based learning,” in <i>Encyclopedia of Systems Biology</i>, vol. 3, W. Dubitzky, O. Wolkenhauer, K. Cho, and H. Yokota, Eds. Springer, 2013, pp. 1069–1069.","ista":"Quadrianto N, Lampert C. 2013.Kernel based learning. In: Encyclopedia of Systems Biology. vol. 3, 1069–1069.","mla":"Quadrianto, Novi, and Christoph Lampert. “Kernel Based Learning.” <i>Encyclopedia of Systems Biology</i>, edited by Werner Dubitzky et al., vol. 3, Springer, 2013, pp. 1069–1069, doi:<a href=\"https://doi.org/10.1007/978-1-4419-9863-7_604\">10.1007/978-1-4419-9863-7_604</a>.","ama":"Quadrianto N, Lampert C. Kernel based learning. In: Dubitzky W, Wolkenhauer O, Cho K, Yokota H, eds. <i>Encyclopedia of Systems Biology</i>. Vol 3. Springer; 2013:1069-1069. doi:<a href=\"https://doi.org/10.1007/978-1-4419-9863-7_604\">10.1007/978-1-4419-9863-7_604</a>"},"language":[{"iso":"eng"}],"day":"01","date_updated":"2021-01-12T07:42:38Z","_id":"3321","year":"2013","doi":"10.1007/978-1-4419-9863-7_604","month":"01","title":"Kernel based learning","publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"quality_controlled":"1","status":"public","oa_version":"Preprint","department":[{"_id":"LaEr"}],"date_published":"2013-10-16T00:00:00Z","external_id":{"arxiv":["1105.0506"],"isi":["000326323400006"]},"publist_id":"4198","oa":1,"intvolume":"        15","isi":1,"author":[{"last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Søren","full_name":"Fournais, Søren","last_name":"Fournais"},{"first_name":"Jan","full_name":"Solovej, Jan","last_name":"Solovej"}],"arxiv":1,"page":"2093 - 2113","month":"10","doi":"10.4171/JEMS/416","issue":"6","language":[{"iso":"eng"}],"article_processing_charge":"No","day":"16","main_file_link":[{"url":"http://arxiv.org/abs/1105.0506","open_access":"1"}],"abstract":[{"lang":"eng","text":"We consider non-interacting particles subject to a fixed external potential V and a self-generated magnetic field B. The total energy includes the field energy β∫B2 and we minimize over all particle states and magnetic fields. In the case of spin-1/2 particles this minimization leads to the coupled Maxwell-Pauli system. The parameter β tunes the coupling strength between the field and the particles and it effectively determines the strength of the field. We investigate the stability and the semiclassical asymptotics, h→0, of the total ground state energy E(β,h,V). The relevant parameter measuring the field strength in the semiclassical limit is κ=βh. We are not able to give the exact leading order semiclassical asymptotics uniformly in κ or even for fixed κ. We do however give upper and lower bounds on E with almost matching dependence on κ. In the simultaneous limit h→0 and κ→∞ we show that the standard non-magnetic Weyl asymptotics holds. The same result also holds for the spinless case, i.e. where the Pauli operator is replaced by the Schrödinger operator."}],"publication_status":"published","publication":"Journal of the European Mathematical Society","volume":15,"date_created":"2018-12-11T11:59:07Z","type":"journal_article","title":"Stability and semiclassics in self-generated fields","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"EMS Press","year":"2013","date_updated":"2026-07-06T11:56:35Z","_id":"2698","citation":{"ama":"Erdös L, Fournais S, Solovej J. Stability and semiclassics in self-generated fields. <i>Journal of the European Mathematical Society</i>. 2013;15(6):2093-2113. doi:<a href=\"https://doi.org/10.4171/JEMS/416\">10.4171/JEMS/416</a>","ista":"Erdös L, Fournais S, Solovej J. 2013. Stability and semiclassics in self-generated fields. Journal of the European Mathematical Society. 15(6), 2093–2113.","mla":"Erdös, László, et al. “Stability and Semiclassics in Self-Generated Fields.” <i>Journal of the European Mathematical Society</i>, vol. 15, no. 6, EMS Press, 2013, pp. 2093–113, doi:<a href=\"https://doi.org/10.4171/JEMS/416\">10.4171/JEMS/416</a>.","ieee":"L. Erdös, S. Fournais, and J. Solovej, “Stability and semiclassics in self-generated fields,” <i>Journal of the European Mathematical Society</i>, vol. 15, no. 6. EMS Press, pp. 2093–2113, 2013.","short":"L. Erdös, S. Fournais, J. Solovej, Journal of the European Mathematical Society 15 (2013) 2093–2113.","apa":"Erdös, L., Fournais, S., &#38; Solovej, J. (2013). Stability and semiclassics in self-generated fields. <i>Journal of the European Mathematical Society</i>. EMS Press. <a href=\"https://doi.org/10.4171/JEMS/416\">https://doi.org/10.4171/JEMS/416</a>","chicago":"Erdös, László, Søren Fournais, and Jan Solovej. “Stability and Semiclassics in Self-Generated Fields.” <i>Journal of the European Mathematical Society</i>. EMS Press, 2013. <a href=\"https://doi.org/10.4171/JEMS/416\">https://doi.org/10.4171/JEMS/416</a>."}},{"ddc":["000","004"],"file":[{"checksum":"bdbb520de91751fe0136309ad4ef67e4","file_name":"IST-2014-197-v1+1_main-queue-verification.pdf","file_id":"4721","access_level":"open_access","file_size":337059,"relation":"main_file","date_created":"2018-12-12T10:08:58Z","date_updated":"2020-07-14T12:45:39Z","content_type":"application/pdf","creator":"system"}],"related_material":{"record":[{"id":"1832","relation":"later_version","status":"public"}]},"date_created":"2018-12-11T11:57:01Z","type":"conference","series_title":"Lecture Notes in Computer Science","volume":8052,"abstract":[{"lang":"eng","text":"Linearizability of concurrent data structures is usually proved by monolithic simulation arguments relying on identifying the so-called linearization points. Regrettably, such proofs, whether manual or automatic, are often complicated and scale poorly to advanced non-blocking concurrency patterns, such as helping and optimistic updates.\r\nIn response, we propose a more modular way of checking linearizability of concurrent queue algorithms that does not involve identifying linearization points. We reduce the task of proving linearizability with respect to the queue specification to establishing four basic properties, each of which can be proved independently by simpler arguments. As a demonstration of our approach, we verify the Herlihy and Wing queue, an algorithm that is challenging to verify by a simulation proof."}],"publication_status":"published","pubrep_id":"197","citation":{"ama":"Henzinger TA, Sezgin A, Vafeiadis V. Aspect-oriented linearizability proofs. 2013;8052:242-256. doi:<a href=\"https://doi.org/10.1007/978-3-642-40184-8_18\">10.1007/978-3-642-40184-8_18</a>","apa":"Henzinger, T. A., Sezgin, A., &#38; Vafeiadis, V. (2013). Aspect-oriented linearizability proofs. Presented at the CONCUR: Concurrency Theory, Buenos Aires, Argentina: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.1007/978-3-642-40184-8_18\">https://doi.org/10.1007/978-3-642-40184-8_18</a>","chicago":"Henzinger, Thomas A, Ali Sezgin, and Viktor Vafeiadis. “Aspect-Oriented Linearizability Proofs.” Lecture Notes in Computer Science. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013. <a href=\"https://doi.org/10.1007/978-3-642-40184-8_18\">https://doi.org/10.1007/978-3-642-40184-8_18</a>.","ista":"Henzinger TA, Sezgin A, Vafeiadis V. 2013. Aspect-oriented linearizability proofs. 8052, 242–256.","mla":"Henzinger, Thomas A., et al. <i>Aspect-Oriented Linearizability Proofs</i>. Vol. 8052, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 242–56, doi:<a href=\"https://doi.org/10.1007/978-3-642-40184-8_18\">10.1007/978-3-642-40184-8_18</a>.","ieee":"T. A. Henzinger, A. Sezgin, and V. Vafeiadis, “Aspect-oriented linearizability proofs,” vol. 8052. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 242–256, 2013.","short":"T.A. Henzinger, A. Sezgin, V. Vafeiadis, 8052 (2013) 242–256."},"date_updated":"2026-07-06T13:24:04Z","_id":"2328","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","title":"Aspect-oriented linearizability proofs","ec_funded":1,"author":[{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sezgin, Ali","last_name":"Sezgin","first_name":"Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vafeiadis, Viktor","last_name":"Vafeiadis","first_name":"Viktor"}],"page":"242 - 256","alternative_title":["LNCS"],"intvolume":"      8052","publist_id":"4598","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"date_published":"2013-08-01T00:00:00Z","oa":1,"department":[{"_id":"ToHe"}],"oa_version":"Submitted Version","quality_controlled":"1","status":"public","conference":{"location":"Buenos Aires, Argentina","start_date":"2013-08-27","end_date":"2013-08-30","name":"CONCUR: Concurrency Theory"},"language":[{"iso":"eng"}],"scopus_import":1,"day":"01","has_accepted_license":"1","doi":"10.1007/978-3-642-40184-8_18","file_date_updated":"2020-07-14T12:45:39Z","month":"08"},{"title":"Computing the M most probable modes of a graphical model","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Journal of Machine Learning Research","year":"2013","date_updated":"2026-07-06T13:43:58Z","_id":"2901","citation":{"chicago":"Chen, Chao, Vladimir Kolmogorov, Zhu Yan, Dimitris Metaxas, and Christoph Lampert. “Computing the M Most Probable Modes of a Graphical Model.” In <i>Proceedings of the 16th International Conference on Artificial Intelligence and Statistics</i>, 31:161–69. Journal of Machine Learning Research, 2013.","apa":"Chen, C., Kolmogorov, V., Yan, Z., Metaxas, D., &#38; Lampert, C. (2013). Computing the M most probable modes of a graphical model. In <i>Proceedings of the 16th International Conference on Artificial Intelligence and Statistics</i> (Vol. 31, pp. 161–169). Scottsdale, AZ, United States: Journal of Machine Learning Research.","short":"C. Chen, V. Kolmogorov, Z. Yan, D. Metaxas, C. Lampert, in:, Proceedings of the 16th International Conference on Artificial Intelligence and Statistics, Journal of Machine Learning Research, 2013, pp. 161–169.","ieee":"C. Chen, V. Kolmogorov, Z. Yan, D. Metaxas, and C. Lampert, “Computing the M most probable modes of a graphical model,” in <i>Proceedings of the 16th International Conference on Artificial Intelligence and Statistics</i>, Scottsdale, AZ, United States, 2013, vol. 31, pp. 161–169.","ista":"Chen C, Kolmogorov V, Yan Z, Metaxas D, Lampert C. 2013. Computing the M most probable modes of a graphical model. Proceedings of the 16th International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Uncertainty in Artificial Intelligence, PMLR, vol. 31, 161–169.","mla":"Chen, Chao, et al. “Computing the M Most Probable Modes of a Graphical Model.” <i>Proceedings of the 16th International Conference on Artificial Intelligence and Statistics</i>, vol. 31, Journal of Machine Learning Research, 2013, pp. 161–69.","ama":"Chen C, Kolmogorov V, Yan Z, Metaxas D, Lampert C. Computing the M most probable modes of a graphical model. In: <i>Proceedings of the 16th International Conference on Artificial Intelligence and Statistics</i>. Vol 31. Journal of Machine Learning Research; 2013:161-169."},"abstract":[{"lang":"eng","text":" We introduce the M-modes problem for graphical models: predicting the M label configurations of highest probability that are at the same time local maxima of the probability landscape. M-modes have multiple possible applications: because they are intrinsically diverse, they provide a principled alternative to non-maximum suppression techniques for structured prediction, they can act as codebook vectors for quantizing the configuration space, or they can form component centers for mixture model approximation. We present two algorithms for solving the M-modes problem. The first algorithm solves the problem in polynomial time when the underlying graphical model is a simple chain. The second algorithm solves the problem for junction chains. In synthetic and real dataset, we demonstrate how M-modes can improve the performance of prediction. We also use the generated modes as a tool to understand the topography of the probability distribution of configurations, for example with relation to the training set size and amount of noise in the data. "}],"publication_status":"published","publication":"Proceedings of the 16th International Conference on Artificial Intelligence and Statistics","volume":31,"date_created":"2018-12-11T12:00:14Z","type":"conference","month":"01","das_tickbox":"1","scopus_import":"1","language":[{"iso":"eng"}],"article_processing_charge":"No","day":"01","main_file_link":[{"url":"http://jmlr.org/proceedings/papers/v31/chen13a.html","open_access":"1"}],"conference":{"end_date":"2013-05-01","name":"AISTATS: Conference on Uncertainty in Artificial Intelligence","location":"Scottsdale, AZ, United States","start_date":"2013-04-29"},"quality_controlled":"1","status":"public","department":[{"_id":"HeEd"},{"_id":"VlKo"},{"_id":"ChLa"}],"oa_version":"None","date_published":"2013-01-01T00:00:00Z","publist_id":"3846","oa":1,"alternative_title":["PMLR"],"intvolume":"        31","author":[{"id":"3E92416E-F248-11E8-B48F-1D18A9856A87","first_name":"Chao","last_name":"Chen","full_name":"Chen, Chao"},{"first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Yan","full_name":"Yan, Zhu","first_name":"Zhu"},{"last_name":"Metaxas","full_name":"Metaxas, Dimitris","first_name":"Dimitris"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","first_name":"Christoph"}],"page":"161 - 169"},{"_id":"2818","date_updated":"2026-07-06T13:45:52Z","citation":{"short":"K. Rajan, O. Marre, G. Tkačik, Neural Computation 25 (2013) 1661–1692.","ieee":"K. Rajan, O. Marre, and G. Tkačik, “Learning quadratic receptive fields from neural responses to natural stimuli,” <i>Neural Computation</i>, vol. 25, no. 7. MIT Press, pp. 1661–1692, 2013.","mla":"Rajan, Kanaka, et al. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” <i>Neural Computation</i>, vol. 25, no. 7, MIT Press, 2013, pp. 1661–92, doi:<a href=\"https://doi.org/10.1162/NECO_a_00463\">10.1162/NECO_a_00463</a>.","ista":"Rajan K, Marre O, Tkačik G. 2013. Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. 25(7), 1661–1692.","chicago":"Rajan, Kanaka, Olivier Marre, and Gašper Tkačik. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” <i>Neural Computation</i>. MIT Press, 2013. <a href=\"https://doi.org/10.1162/NECO_a_00463\">https://doi.org/10.1162/NECO_a_00463</a>.","apa":"Rajan, K., Marre, O., &#38; Tkačik, G. (2013). Learning quadratic receptive fields from neural responses to natural stimuli. <i>Neural Computation</i>. MIT Press. <a href=\"https://doi.org/10.1162/NECO_a_00463\">https://doi.org/10.1162/NECO_a_00463</a>","ama":"Rajan K, Marre O, Tkačik G. Learning quadratic receptive fields from neural responses to natural stimuli. <i>Neural Computation</i>. 2013;25(7):1661-1692. doi:<a href=\"https://doi.org/10.1162/NECO_a_00463\">10.1162/NECO_a_00463</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"MIT Press","title":"Learning quadratic receptive fields from neural responses to natural stimuli","year":"2013","type":"journal_article","date_created":"2018-12-11T11:59:45Z","publication_status":"published","abstract":[{"text":"Models of neural responses to stimuli with complex spatiotemporal correlation structure often assume that neurons are selective for only a small number of linear projections of a potentially high-dimensional input. In this review, we explore recent modeling approaches where the neural response depends on the quadratic form of the input rather than on its linear projection, that is, the neuron is sensitive to the local covariance structure of the signal preceding the spike. To infer this quadratic dependence in the presence of arbitrary (e.g., naturalistic) stimulus distribution, we review several inference methods, focusing in particular on two information theory–based approaches (maximization of stimulus energy and of noise entropy) and two likelihood-based approaches (Bayesian spike-triggered covariance and extensions of generalized linear models). We analyze the formal relationship between the likelihood-based and information-based approaches to demonstrate how they lead to consistent inference. We demonstrate the practical feasibility of these procedures by using model neurons responding to a flickering variance stimulus.","lang":"eng"}],"volume":25,"publication":"Neural Computation","issue":"7","main_file_link":[{"url":"http://arxiv.org/abs/1209.0121","open_access":"1"}],"day":"01","article_processing_charge":"No","language":[{"iso":"eng"}],"scopus_import":"1","month":"07","doi":"10.1162/NECO_a_00463","das_tickbox":"1","isi":1,"intvolume":"        25","arxiv":1,"page":"1661 - 1692","author":[{"first_name":"Kanaka","full_name":"Rajan, Kanaka","last_name":"Rajan"},{"last_name":"Marre","full_name":"Marre, Olivier","first_name":"Olivier"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik"}],"oa_version":"Preprint","department":[{"_id":"GaTk"}],"status":"public","quality_controlled":"1","oa":1,"external_id":{"isi":["000319903700001"],"arxiv":["1209.0121"]},"publist_id":"3983","date_published":"2013-07-01T00:00:00Z"},{"date_updated":"2026-07-06T13:38:59Z","_id":"2859","citation":{"apa":"Bendich, P., Edelsbrunner, H., Morozov, D., &#38; Patel, A. (2013). Homology and robustness of level and interlevel sets. <i>Homology, Homotopy and Applications</i>. International Press of Boston. <a href=\"https://doi.org/10.4310/HHA.2013.v15.n1.a3\">https://doi.org/10.4310/HHA.2013.v15.n1.a3</a>","chicago":"Bendich, Paul, Herbert Edelsbrunner, Dmitriy Morozov, and Amit Patel. “Homology and Robustness of Level and Interlevel Sets.” <i>Homology, Homotopy and Applications</i>. International Press of Boston, 2013. <a href=\"https://doi.org/10.4310/HHA.2013.v15.n1.a3\">https://doi.org/10.4310/HHA.2013.v15.n1.a3</a>.","ista":"Bendich P, Edelsbrunner H, Morozov D, Patel A. 2013. Homology and robustness of level and interlevel sets. Homology, Homotopy and Applications. 15(1), 51–72.","mla":"Bendich, Paul, et al. “Homology and Robustness of Level and Interlevel Sets.” <i>Homology, Homotopy and Applications</i>, vol. 15, no. 1, International Press of Boston, 2013, pp. 51–72, doi:<a href=\"https://doi.org/10.4310/HHA.2013.v15.n1.a3\">10.4310/HHA.2013.v15.n1.a3</a>.","ieee":"P. Bendich, H. Edelsbrunner, D. Morozov, and A. Patel, “Homology and robustness of level and interlevel sets,” <i>Homology, Homotopy and Applications</i>, vol. 15, no. 1. International Press of Boston, pp. 51–72, 2013.","short":"P. Bendich, H. Edelsbrunner, D. Morozov, A. Patel, Homology, Homotopy and Applications 15 (2013) 51–72.","ama":"Bendich P, Edelsbrunner H, Morozov D, Patel A. Homology and robustness of level and interlevel sets. <i>Homology, Homotopy and Applications</i>. 2013;15(1):51-72. doi:<a href=\"https://doi.org/10.4310/HHA.2013.v15.n1.a3\">10.4310/HHA.2013.v15.n1.a3</a>"},"title":"Homology and robustness of level and interlevel sets","publisher":"International Press of Boston","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","date_created":"2018-12-11T11:59:58Z","type":"journal_article","abstract":[{"lang":"eng","text":"Given a continuous function f:X-R on a topological space, we consider the preimages of intervals and their homology groups and show how to read the ranks of these groups from the extended persistence diagram of f. In addition, we quantify the robustness of the homology classes under perturbations of f using well groups, and we show how to read the ranks of these groups from the same extended persistence diagram. The special case X=R3 has ramifications in the fields of medical imaging and scientific visualization."}],"publication_status":"published","publication":"Homology, Homotopy and Applications","volume":15,"issue":"1","scopus_import":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"day":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1102.3389v1"}],"month":"05","das_tickbox":"1","doi":"10.4310/HHA.2013.v15.n1.a3","intvolume":"        15","isi":1,"author":[{"first_name":"Paul","full_name":"Bendich, Paul","last_name":"Bendich","id":"43F6EC54-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Morozov","full_name":"Morozov, Dmitriy","first_name":"Dmitriy"},{"first_name":"Amit","last_name":"Patel","full_name":"Patel, Amit","id":"34A254A0-F248-11E8-B48F-1D18A9856A87"}],"page":"51 - 72","arxiv":1,"quality_controlled":"1","status":"public","department":[{"_id":"HeEd"}],"oa_version":"Preprint","date_published":"2013-05-01T00:00:00Z","publist_id":"3930","external_id":{"arxiv":["1102.3389"],"isi":["000322423600003"]},"oa":1},{"abstract":[{"text":"The problem of packing ellipsoids of different sizes and shapes into an ellipsoidal container so as to minimize a measure of overlap between ellipsoids is considered. A bilevel optimization formulation is given, together with an algorithm for the general case and a simpler algorithm for the special case in which all ellipsoids are in fact spheres. Convergence results are proved and computational experience is described and illustrated. The motivating application-chromosome organization in the human cell nucleus-is discussed briefly, and some illustrative results are presented.","lang":"eng"}],"publication_status":"published","publication":"SIAM Review","volume":55,"date_created":"2018-12-11T11:56:44Z","type":"journal_article","title":"Packing ellipsoids with overlap","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Society for Industrial and Applied Mathematics","year":"2013","date_updated":"2026-07-06T13:58:55Z","_id":"2280","citation":{"chicago":"Uhler, Caroline, and Stephen Wright. “Packing Ellipsoids with Overlap.” <i>SIAM Review</i>. Society for Industrial and Applied Mathematics, 2013. <a href=\"https://doi.org/10.1137/120872309\">https://doi.org/10.1137/120872309</a>.","apa":"Uhler, C., &#38; Wright, S. (2013). Packing ellipsoids with overlap. <i>SIAM Review</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/120872309\">https://doi.org/10.1137/120872309</a>","short":"C. Uhler, S. Wright, SIAM Review 55 (2013) 671–706.","ieee":"C. Uhler and S. Wright, “Packing ellipsoids with overlap,” <i>SIAM Review</i>, vol. 55, no. 4. Society for Industrial and Applied Mathematics, pp. 671–706, 2013.","mla":"Uhler, Caroline, and Stephen Wright. “Packing Ellipsoids with Overlap.” <i>SIAM Review</i>, vol. 55, no. 4, Society for Industrial and Applied Mathematics, 2013, pp. 671–706, doi:<a href=\"https://doi.org/10.1137/120872309\">10.1137/120872309</a>.","ista":"Uhler C, Wright S. 2013. Packing ellipsoids with overlap. SIAM Review. 55(4), 671–706.","ama":"Uhler C, Wright S. Packing ellipsoids with overlap. <i>SIAM Review</i>. 2013;55(4):671-706. doi:<a href=\"https://doi.org/10.1137/120872309\">10.1137/120872309</a>"},"status":"public","quality_controlled":"1","department":[{"_id":"CaUh"}],"oa_version":"Preprint","date_published":"2013-11-07T00:00:00Z","publist_id":"4655","external_id":{"arxiv":["1204.0235"],"isi":["000327502800002"]},"oa":1,"intvolume":"        55","isi":1,"author":[{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","last_name":"Uhler","full_name":"Uhler, Caroline","first_name":"Caroline"},{"full_name":"Wright, Stephen","last_name":"Wright","first_name":"Stephen"}],"arxiv":1,"page":"671 - 706","month":"11","das_tickbox":"1","doi":"10.1137/120872309","issue":"4","scopus_import":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"day":"07","main_file_link":[{"url":"http://arxiv.org/abs/1204.0235","open_access":"1"}]},{"issue":"1","has_accepted_license":"1","day":"14","scopus_import":"1","language":[{"iso":"eng"}],"article_processing_charge":"No","month":"10","file_date_updated":"2020-07-14T12:45:37Z","doi":"10.1186/1471-2148-13-225","das_tickbox":"1","intvolume":"        13","isi":1,"corr_author":"1","acknowledgement":"The study was funded by the European Research Council (Marie Curie ERG 036569) and Marie Curie IEF 302204 to LVU\r\nCC BY 2.0\r\n","author":[{"last_name":"Tragust","full_name":"Tragust, Simon","first_name":"Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87"},{"id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883","full_name":"Ugelvig, Line V","last_name":"Ugelvig","first_name":"Line V"},{"first_name":"Michel","full_name":"Chapuisat, Michel","last_name":"Chapuisat"},{"full_name":"Heinze, Jürgen","last_name":"Heinze","first_name":"Jürgen"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"}],"quality_controlled":"1","status":"public","oa_version":"Published Version","department":[{"_id":"SyCr"}],"oa":1,"date_published":"2013-10-14T00:00:00Z","project":[{"call_identifier":"FP7","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","_id":"25DC711C-B435-11E9-9278-68D0E5697425","grant_number":"243071"},{"grant_number":"CR-118/3-1","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","name":"Host-Parasite Coevolution"},{"grant_number":"302004","_id":"25DDF0F0-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach"}],"publist_id":"4647","external_id":{"isi":["000326620500001"]},"_id":"2284","date_updated":"2026-07-28T09:35:11Z","pubrep_id":"402","citation":{"chicago":"Tragust, Simon, Line V Ugelvig, Michel Chapuisat, Jürgen Heinze, and Sylvia Cremer. “Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies.” <i>BMC Evolutionary Biology</i>. BioMed Central, 2013. <a href=\"https://doi.org/10.1186/1471-2148-13-225\">https://doi.org/10.1186/1471-2148-13-225</a>.","apa":"Tragust, S., Ugelvig, L. V., Chapuisat, M., Heinze, J., &#38; Cremer, S. (2013). Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. <i>BMC Evolutionary Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2148-13-225\">https://doi.org/10.1186/1471-2148-13-225</a>","ieee":"S. Tragust, L. V. Ugelvig, M. Chapuisat, J. Heinze, and S. Cremer, “Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies,” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1. BioMed Central, 2013.","short":"S. Tragust, L.V. Ugelvig, M. Chapuisat, J. Heinze, S. Cremer, BMC Evolutionary Biology 13 (2013).","ista":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. 2013. Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. BMC Evolutionary Biology. 13(1), 225.","mla":"Tragust, Simon, et al. “Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies.” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1, 225, BioMed Central, 2013, doi:<a href=\"https://doi.org/10.1186/1471-2148-13-225\">10.1186/1471-2148-13-225</a>.","ama":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. <i>BMC Evolutionary Biology</i>. 2013;13(1). doi:<a href=\"https://doi.org/10.1186/1471-2148-13-225\">10.1186/1471-2148-13-225</a>"},"title":"Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"BioMed Central","year":"2013","type":"journal_article","date_created":"2018-12-11T11:56:46Z","related_material":{"record":[{"relation":"research_data","id":"9753","status":"public"}]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"file_name":"IST-2016-402-v1+1_1471-2148-13-225.pdf","checksum":"c16ef36f2a10786a7885e19c4528d707","file_id":"5026","access_level":"open_access","relation":"main_file","file_size":281736,"date_updated":"2020-07-14T12:45:37Z","date_created":"2018-12-12T10:13:41Z","content_type":"application/pdf","creator":"system"}],"ddc":["570"],"article_number":"225","publication_status":"published","abstract":[{"text":"Background: The brood of ants and other social insects is highly susceptible to pathogens, particularly those that penetrate the soft larval and pupal cuticle. We here test whether the presence of a pupal cocoon, which occurs in some ant species but not in others, affects the sanitary brood care and fungal infection patterns after exposure to the entomopathogenic fungus Metarhizium brunneum. We use a) a comparative approach analysing four species with either naked or cocooned pupae and b) a within-species analysis of a single ant species, in which both pupal types co-exist in the same colony. Results: We found that the presence of a cocoon did not compromise fungal pathogen detection by the ants and that species with cocooned pupae increased brood grooming after pathogen exposure. All tested ant species further removed brood from their nests, which was predominantly expressed towards larvae and naked pupae treated with the live fungal pathogen. In contrast, cocooned pupae exposed to live fungus were not removed at higher rates than cocooned pupae exposed to dead fungus or a sham control. Consistent with this, exposure to the live fungus caused high numbers of infections and fungal outgrowth in larvae and naked pupae, but not in cocooned pupae. Moreover, the ants consistently removed the brood prior to fungal outgrowth, ensuring a clean brood chamber. Conclusion: Our study suggests that the pupal cocoon has a protective effect against fungal infection, causing an adaptive change in sanitary behaviours by the ants. It further demonstrates that brood removal-originally described for honeybees as &quot;hygienic behaviour&quot;-is a widespread sanitary behaviour in ants, which likely has important implications on disease dynamics in social insect colonies.","lang":"eng"}],"volume":13,"publication":"BMC Evolutionary Biology"}]