[{"citation":{"ieee":"M. Breuss et al., “Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule stability,” Human Molecular Genetics, vol. 26, no. 2. Oxford University Press, pp. 258–269, 2017.","ista":"Breuss M, Nguyen T, Srivatsan A, Leca I, Tian G, Fritz T, Hansen AH, Musaev D, Mcevoy Venneri J, Kiely J, Rosti R, Scott E, Tan U, Kolodner R, Cowan N, Keays D, Gleeson J. 2017. Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule stability. Human Molecular Genetics. 26(2), 258–269.","short":"M. Breuss, T. Nguyen, A. Srivatsan, I. Leca, G. Tian, T. Fritz, A.H. Hansen, D. Musaev, J. Mcevoy Venneri, J. Kiely, R. Rosti, E. Scott, U. Tan, R. Kolodner, N. Cowan, D. Keays, J. Gleeson, Human Molecular Genetics 26 (2017) 258–269.","chicago":"Breuss, Martin, Thai Nguyen, Anjana Srivatsan, Ines Leca, Guoling Tian, Tanja Fritz, Andi H Hansen, et al. “Uner Tan Syndrome Caused by a Homozygous TUBB2B Mutation Affecting Microtubule Stability.” Human Molecular Genetics. Oxford University Press, 2017. https://doi.org/10.1093/hmg/ddw383.","ama":"Breuss M, Nguyen T, Srivatsan A, et al. Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule stability. Human Molecular Genetics. 2017;26(2):258-269. doi:10.1093/hmg/ddw383","mla":"Breuss, Martin, et al. “Uner Tan Syndrome Caused by a Homozygous TUBB2B Mutation Affecting Microtubule Stability.” Human Molecular Genetics, vol. 26, no. 2, Oxford University Press, 2017, pp. 258–69, doi:10.1093/hmg/ddw383.","apa":"Breuss, M., Nguyen, T., Srivatsan, A., Leca, I., Tian, G., Fritz, T., … Gleeson, J. (2017). Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule stability. Human Molecular Genetics. Oxford University Press. https://doi.org/10.1093/hmg/ddw383"},"article_processing_charge":"No","isi":1,"title":"Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule stability","status":"public","type":"journal_article","doi":"10.1093/hmg/ddw383","external_id":{"isi":["000397066400002"]},"page":"258 - 269","_id":"1016","intvolume":" 26","quality_controlled":"1","department":[{"_id":"SiHi"}],"oa_version":"None","month":"01","publist_id":"6379","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","date_updated":"2023-09-22T09:42:42Z","publication_identifier":{"issn":["09646906"]},"publisher":"Oxford University Press","scopus_import":"1","date_created":"2018-12-11T11:49:42Z","issue":"2","author":[{"full_name":"Breuss, Martin","first_name":"Martin","last_name":"Breuss"},{"last_name":"Nguyen","first_name":"Thai","full_name":"Nguyen, Thai"},{"full_name":"Srivatsan, Anjana","last_name":"Srivatsan","first_name":"Anjana"},{"last_name":"Leca","first_name":"Ines","full_name":"Leca, Ines"},{"first_name":"Guoling","last_name":"Tian","full_name":"Tian, Guoling"},{"last_name":"Fritz","first_name":"Tanja","full_name":"Fritz, Tanja"},{"last_name":"Hansen","first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","full_name":"Hansen, Andi H"},{"full_name":"Musaev, Damir","first_name":"Damir","last_name":"Musaev"},{"first_name":"Jennifer","last_name":"Mcevoy Venneri","full_name":"Mcevoy Venneri, Jennifer"},{"full_name":"Kiely, James","first_name":"James","last_name":"Kiely"},{"first_name":"Rasim","last_name":"Rosti","full_name":"Rosti, Rasim"},{"full_name":"Scott, Eric","first_name":"Eric","last_name":"Scott"},{"full_name":"Tan, Uner","first_name":"Uner","last_name":"Tan"},{"full_name":"Kolodner, Richard","last_name":"Kolodner","first_name":"Richard"},{"first_name":"Nicholas","last_name":"Cowan","full_name":"Cowan, Nicholas"},{"full_name":"Keays, David","first_name":"David","last_name":"Keays"},{"first_name":"Joseph","last_name":"Gleeson","full_name":"Gleeson, Joseph"}],"abstract":[{"text":"The integrity and dynamic properties of the microtubule cytoskeleton are indispensable for the development of the mammalian brain. Consequently, mutations in the genes that encode the structural component (the α/β-tubulin heterodimer) can give rise to severe, sporadic neurodevelopmental disorders. These are commonly referred to as the tubulinopathies. Here we report the addition of recessive quadrupedalism, also known as Uner Tan syndrome (UTS), to the growing list of diseases caused by tubulin variants. Analysis of a consanguineous UTS family identified a biallelic TUBB2B mutation, resulting in a p.R390Q amino acid substitution. In addition to the identifying quadrupedal locomotion, all three patients showed severe cerebellar hypoplasia. None, however, displayed the basal ganglia malformations typically associated with TUBB2B mutations. Functional analysis of the R390Q substitution revealed that it did not affect the ability of β-tubulin to fold or become assembled into the α/β-heterodimer, nor did it influence the incorporation of mutant-containing heterodimers into microtubule polymers. The 390Q mutation in S. cerevisiae TUB2 did not affect growth under basal conditions, but did result in increased sensitivity to microtubule-depolymerizing drugs, indicative of a mild impact of this mutation on microtubule function. The TUBB2B mutation described here represents an unusual recessive mode of inheritance for missense-mediated tubulinopathies and reinforces the sensitivity of the developing cerebellum to microtubule defects.","lang":"eng"}],"volume":26,"date_published":"2017-01-01T00:00:00Z","publication":"Human Molecular Genetics","day":"01","year":"2017","language":[{"iso":"eng"}]},{"pubrep_id":"806","status":"public","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"Tubulins and brain development: The origins of functional specification","isi":1,"article_processing_charge":"No","citation":{"ista":"Breuss M, Leca I, Gstrein T, Hansen AH, Keays D. 2017. Tubulins and brain development: The origins of functional specification. Molecular and Cellular Neuroscience. 84, 58–67.","ieee":"M. Breuss, I. Leca, T. Gstrein, A. H. Hansen, and D. Keays, “Tubulins and brain development: The origins of functional specification,” Molecular and Cellular Neuroscience, vol. 84. Academic Press, pp. 58–67, 2017.","short":"M. Breuss, I. Leca, T. Gstrein, A.H. Hansen, D. Keays, Molecular and Cellular Neuroscience 84 (2017) 58–67.","ama":"Breuss M, Leca I, Gstrein T, Hansen AH, Keays D. Tubulins and brain development: The origins of functional specification. Molecular and Cellular Neuroscience. 2017;84:58-67. doi:10.1016/j.mcn.2017.03.002","chicago":"Breuss, Martin, Ines Leca, Thomas Gstrein, Andi H Hansen, and David Keays. “Tubulins and Brain Development: The Origins of Functional Specification.” Molecular and Cellular Neuroscience. Academic Press, 2017. https://doi.org/10.1016/j.mcn.2017.03.002.","mla":"Breuss, Martin, et al. “Tubulins and Brain Development: The Origins of Functional Specification.” Molecular and Cellular Neuroscience, vol. 84, Academic Press, 2017, pp. 58–67, doi:10.1016/j.mcn.2017.03.002.","apa":"Breuss, M., Leca, I., Gstrein, T., Hansen, A. H., & Keays, D. (2017). Tubulins and brain development: The origins of functional specification. Molecular and Cellular Neuroscience. Academic Press. https://doi.org/10.1016/j.mcn.2017.03.002"},"department":[{"_id":"SiHi"}],"quality_controlled":"1","intvolume":" 84","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","_id":"1017","page":"58 - 67","external_id":{"isi":["000415140700007"]},"doi":"10.1016/j.mcn.2017.03.002","has_accepted_license":"1","publication_identifier":{"issn":["10447431"]},"date_updated":"2023-09-22T09:42:15Z","ddc":["571"],"oa":1,"publication_status":"published","publist_id":"6377","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","month":"10","scopus_import":"1","publisher":"Academic Press","file":[{"content_type":"application/pdf","date_updated":"2018-12-12T10:09:19Z","file_size":1436377,"access_level":"open_access","file_name":"IST-2017-806-v1+2_1-s2.0-S1044743116302500-main_1_.pdf","file_id":"4742","relation":"main_file","date_created":"2018-12-12T10:09:19Z","creator":"system"}],"date_created":"2018-12-11T11:49:42Z","date_published":"2017-10-01T00:00:00Z","abstract":[{"lang":"eng","text":"The development of the vertebrate central nervous system is reliant on a complex cascade of biological processes that include mitotic division, relocation of migrating neurons, and the extension of dendritic and axonal processes. Each of these cellular events requires the diverse functional repertoire of the microtubule cytoskeleton for the generation of forces, assembly of macromolecular complexes and transport of molecules and organelles. The tubulins are a multi-gene family that encode for the constituents of microtubules, and have been implicated in a spectrum of neurological disorders. Evidence is building that different tubulins tune the functional properties of the microtubule cytoskeleton dependent on the cell type, developmental profile and subcellular localisation. Here we review of the origins of the functional specification of the tubulin gene family in the developing brain at a transcriptional, translational, and post-transcriptional level. We remind the reader that tubulins are not just loading controls for your average Western blot."}],"volume":84,"author":[{"last_name":"Breuss","first_name":"Martin","full_name":"Breuss, Martin"},{"full_name":"Leca, Ines","first_name":"Ines","last_name":"Leca"},{"last_name":"Gstrein","first_name":"Thomas","full_name":"Gstrein, Thomas"},{"full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","last_name":"Hansen","first_name":"Andi H"},{"full_name":"Keays, David","first_name":"David","last_name":"Keays"}],"file_date_updated":"2018-12-12T10:09:19Z","year":"2017","language":[{"iso":"eng"}],"day":"01","publication":"Molecular and Cellular Neuroscience"},{"type":"journal_article","status":"public","title":"Light regulated expression of sensor histidine kinase CKI1 controls cytokinin related development","isi":1,"citation":{"short":"T. Dobisova, V. Hrdinova, C. Cuesta, S. Michlickova, I. Urbankova, R. Hejatkova, P. Zadnikova, M. Pernisová, E. Benková, J. Hejátko, Plant Physiology 174 (2017) 387–404.","chicago":"Dobisova, Tereza, Vendula Hrdinova, Candela Cuesta, Sarka Michlickova, Ivana Urbankova, Romana Hejatkova, Petra Zadnikova, Markéta Pernisová, Eva Benková, and Jan Hejátko. “Light Regulated Expression of Sensor Histidine Kinase CKI1 Controls Cytokinin Related Development.” Plant Physiology. American Society of Plant Biologists, 2017. https://doi.org/10.1104/pp.16.01964.","ama":"Dobisova T, Hrdinova V, Cuesta C, et al. Light regulated expression of sensor histidine kinase CKI1 controls cytokinin related development. Plant Physiology. 2017;174(1):387-404. doi:10.1104/pp.16.01964","mla":"Dobisova, Tereza, et al. “Light Regulated Expression of Sensor Histidine Kinase CKI1 Controls Cytokinin Related Development.” Plant Physiology, vol. 174, no. 1, American Society of Plant Biologists, 2017, pp. 387–404, doi:10.1104/pp.16.01964.","apa":"Dobisova, T., Hrdinova, V., Cuesta, C., Michlickova, S., Urbankova, I., Hejatkova, R., … Hejátko, J. (2017). Light regulated expression of sensor histidine kinase CKI1 controls cytokinin related development. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.01964","ista":"Dobisova T, Hrdinova V, Cuesta C, Michlickova S, Urbankova I, Hejatkova R, Zadnikova P, Pernisová M, Benková E, Hejátko J. 2017. Light regulated expression of sensor histidine kinase CKI1 controls cytokinin related development. Plant Physiology. 174(1), 387–404.","ieee":"T. Dobisova et al., “Light regulated expression of sensor histidine kinase CKI1 controls cytokinin related development,” Plant Physiology, vol. 174, no. 1. American Society of Plant Biologists, pp. 387–404, 2017."},"article_processing_charge":"No","department":[{"_id":"EvBe"}],"quality_controlled":"1","intvolume":" 174","_id":"1018","page":"387 - 404","external_id":{"isi":["000402057200028"]},"doi":"10.1104/pp.16.01964","date_updated":"2023-09-22T09:41:48Z","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6375","oa_version":"None","month":"05","scopus_import":"1","publisher":"American Society of Plant Biologists","date_created":"2018-12-11T11:49:43Z","date_published":"2017-05-17T00:00:00Z","volume":174,"abstract":[{"text":"In plants, the multistep phosphorelay (MSP) pathway mediates a range of regulatory processes, including those activated by cytokinins. The crosstalk between cytokinin response and light is known for a long time. However, the molecular mechanism underlying the interactionbetween light and cytokinin signaling remains elusive. In the screen for upstream regulators we identified a LONG PALE HYPOCOTYL (LPH) gene whose activity is indispensable for spatiotemporally correct expression of CYTOKININ INDEPENDENT-1 (CKI1), encoding the constitutively active sensor histidine kinase that activates MSP signaling. lph is a new allele of HEME OXYGENASE 1 (HY1) which encodes the key protein in the biosynthesis of phytochromobilin, a cofactor of photoconvertiblephytochromes. Our analysis confirmed the light-dependent regulation oftheCKI1 expression pattern. We show that CKI1 expression is under the control of phytochrome A (phyA), functioning as a dual (both positive and negative) regulator of CKI1 expression, presumably via the phyA-regulated transcription factors PHYTOCHROME INTERACTING FACTOR 3 (PIF3) and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1). Changes in CKI1 expression observed in lph/hy1-7 and phy mutants correlatewithmisregulation of MSP signaling, changedcytokinin sensitivity and developmental aberrations,previously shown to be associated with cytokinin and/or CKI1 action. Besides that, we demonstrate novel role of phyA-dependent CKI1 expression in the hypocotyl elongation and hook development during skotomorphogenesis. Based on these results, we propose that the light-dependent regulation of CKI1 provides a plausible mechanistic link underlying the well-known interaction between light- and cytokinin-controlled plant development.","lang":"eng"}],"author":[{"full_name":"Dobisova, Tereza","last_name":"Dobisova","first_name":"Tereza"},{"last_name":"Hrdinova","first_name":"Vendula","full_name":"Hrdinova, Vendula"},{"id":"33A3C818-F248-11E8-B48F-1D18A9856A87","full_name":"Cuesta, Candela","orcid":"0000-0003-1923-2410","first_name":"Candela","last_name":"Cuesta"},{"last_name":"Michlickova","first_name":"Sarka","full_name":"Michlickova, Sarka"},{"full_name":"Urbankova, Ivana","first_name":"Ivana","last_name":"Urbankova"},{"full_name":"Hejatkova, Romana","first_name":"Romana","last_name":"Hejatkova"},{"full_name":"Zadnikova, Petra","last_name":"Zadnikova","first_name":"Petra"},{"full_name":"Pernisová, Markéta","first_name":"Markéta","last_name":"Pernisová"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková"},{"full_name":"Hejátko, Jan","last_name":"Hejátko","first_name":"Jan"}],"issue":"1","year":"2017","language":[{"iso":"eng"}],"day":"17","publication":"Plant Physiology"},{"external_id":{"isi":["000405397800004"]},"doi":"10.1038/hdy.2017.12","intvolume":" 119","page":"27 - 34","_id":"1019","quality_controlled":"1","department":[{"_id":"BeVi"}],"citation":{"mla":"Argyridou, Eliza, et al. “X-Linkage Is Not a General Inhibitor of Tissue-Specific Gene Expression in Drosophila Melanogaster.” Heredity, vol. 119, no. 1, Nature Publishing Group, 2017, pp. 27–34, doi:10.1038/hdy.2017.12.","apa":"Argyridou, E., Huylmans, A. K., Königer, A., & Parsch, J. (2017). X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster. Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2017.12","short":"E. Argyridou, A.K. Huylmans, A. Königer, J. Parsch, Heredity 119 (2017) 27–34.","ama":"Argyridou E, Huylmans AK, Königer A, Parsch J. X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster. Heredity. 2017;119(1):27-34. doi:10.1038/hdy.2017.12","chicago":"Argyridou, Eliza, Ann K Huylmans, Annabella Königer, and John Parsch. “X-Linkage Is Not a General Inhibitor of Tissue-Specific Gene Expression in Drosophila Melanogaster.” Heredity. Nature Publishing Group, 2017. https://doi.org/10.1038/hdy.2017.12.","ieee":"E. Argyridou, A. K. Huylmans, A. Königer, and J. Parsch, “X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster,” Heredity, vol. 119, no. 1. Nature Publishing Group, pp. 27–34, 2017.","ista":"Argyridou E, Huylmans AK, Königer A, Parsch J. 2017. X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster. Heredity. 119(1), 27–34."},"article_processing_charge":"No","isi":1,"title":"X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster","type":"journal_article","status":"public","oa_version":"None","month":"07","related_material":{"record":[{"status":"public","id":"9861","relation":"research_data"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6374","publication_status":"published","publication_identifier":{"issn":["0018067X"]},"date_updated":"2023-09-22T09:41:21Z","date_created":"2018-12-11T11:49:43Z","publisher":"Nature Publishing Group","scopus_import":"1","publication":"Heredity","year":"2017","language":[{"iso":"eng"}],"day":"01","issue":"1","author":[{"last_name":"Argyridou","first_name":"Eliza","full_name":"Argyridou, Eliza"},{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","full_name":"Huylmans, Ann K","last_name":"Huylmans","first_name":"Ann K","orcid":"0000-0001-8871-4961"},{"full_name":"Königer, Annabella","last_name":"Königer","first_name":"Annabella"},{"full_name":"Parsch, John","first_name":"John","last_name":"Parsch"}],"date_published":"2017-07-01T00:00:00Z","abstract":[{"lang":"eng","text":"As a consequence of its difference in copy number between males and females, the X chromosome is subject to unique evolutionary forces and gene regulatory mechanisms. Previous studies of Drosophila melanogaster have shown that the expression of X-linked, testis-specific reporter genes is suppressed in the male germline. However, it is not known whether this phenomenon is restricted to testis-expressed genes or if it is a more general property of genes with tissue-specific expression, which are also underrepresented on the X chromosome. To test this, we compared the expression of three tissue-specific reporter genes (ovary, accessory gland and Malpighian tubule) inserted at various autosomal and X-chromosomal locations. In contrast to testis-specific reporter genes, we found no reduction of X-linked expression in any of the other tissues. In accessory gland and Malpighian tubule, we detected higher expression of the X-linked reporter genes, which suggests that they are at least partially dosage compensated. We found no difference in the tissue-specificity of X-linked and autosomal reporter genes. These findings indicate that, in general, the X chromosome is not a detrimental environment for tissue-specific gene expression and that the suppression of X-linked expression is limited to the male germline."}],"volume":119},{"type":"journal_article","status":"public","title":"Disordered cellulose based nanostructures for enhanced light scattering","isi":1,"citation":{"apa":"Caixeiro, S., Peruzzo, M., Onelli, O., Vignolini, S., & Sapienza, R. (2017). Disordered cellulose based nanostructures for enhanced light scattering. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.6b15986","mla":"Caixeiro, Soraya, et al. “Disordered Cellulose Based Nanostructures for Enhanced Light Scattering.” ACS Applied Materials and Interfaces, vol. 9, no. 9, American Chemical Society, 2017, pp. 7885–90, doi:10.1021/acsami.6b15986.","ama":"Caixeiro S, Peruzzo M, Onelli O, Vignolini S, Sapienza R. Disordered cellulose based nanostructures for enhanced light scattering. ACS Applied Materials and Interfaces. 2017;9(9):7885-7890. doi:10.1021/acsami.6b15986","chicago":"Caixeiro, Soraya, Matilda Peruzzo, Olimpia Onelli, Silvia Vignolini, and Riccardo Sapienza. “Disordered Cellulose Based Nanostructures for Enhanced Light Scattering.” ACS Applied Materials and Interfaces. American Chemical Society, 2017. https://doi.org/10.1021/acsami.6b15986.","short":"S. Caixeiro, M. Peruzzo, O. Onelli, S. Vignolini, R. Sapienza, ACS Applied Materials and Interfaces 9 (2017) 7885–7890.","ista":"Caixeiro S, Peruzzo M, Onelli O, Vignolini S, Sapienza R. 2017. Disordered cellulose based nanostructures for enhanced light scattering. ACS Applied Materials and Interfaces. 9(9), 7885–7890.","ieee":"S. Caixeiro, M. Peruzzo, O. Onelli, S. Vignolini, and R. Sapienza, “Disordered cellulose based nanostructures for enhanced light scattering,” ACS Applied Materials and Interfaces, vol. 9, no. 9. American Chemical Society, pp. 7885–7890, 2017."},"article_processing_charge":"No","department":[{"_id":"JoFi"}],"quality_controlled":"1","acknowledgement":"This research was funded by the EPSRC (EP/M027961/1), the Leverhulme Trust (RPG-2014-238), Royal Society (RG140457), the BBSRC David Phillips fellowship (BB/K014617/1), and the European Research Council (ERC-2014-STG H2020 639088). All data created during this research are provided in full in the results section and Supporting Information. They are openly available from figshare and can be accessed at ref 30.","intvolume":" 9","page":"7885 - 7890","_id":"1020","external_id":{"isi":["000396186000002"]},"doi":"10.1021/acsami.6b15986","publication_identifier":{"issn":["19448244"]},"date_updated":"2023-09-22T09:40:14Z","oa":1,"publication_status":"published","publist_id":"6372","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","month":"03","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1702.01415","open_access":"1"}],"publisher":"American Chemical Society","date_created":"2018-12-11T11:49:44Z","date_published":"2017-03-08T00:00:00Z","abstract":[{"text":"Cellulose is the most abundant biopolymer on Earth. Cellulose fibers, such as the one extracted form cotton or woodpulp, have been used by humankind for hundreds of years to make textiles and paper. Here we show how, by engineering light-matter interaction, we can optimize light scattering using exclusively cellulose nanocrystals. The produced material is sustainable, biocompatible, and when compared to ordinary microfiber-based paper, it shows enhanced scattering strength (×4), yielding a transport mean free path as low as 3.5 μm in the visible light range. The experimental results are in a good agreement with the theoretical predictions obtained with a diffusive model for light propagation.","lang":"eng"}],"volume":9,"author":[{"full_name":"Caixeiro, Soraya","last_name":"Caixeiro","first_name":"Soraya"},{"full_name":"Peruzzo, Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628","first_name":"Matilda","last_name":"Peruzzo"},{"last_name":"Onelli","first_name":"Olimpia","full_name":"Onelli, Olimpia"},{"full_name":"Vignolini, Silvia","last_name":"Vignolini","first_name":"Silvia"},{"full_name":"Sapienza, Riccardo","last_name":"Sapienza","first_name":"Riccardo"}],"issue":"9","year":"2017","language":[{"iso":"eng"}],"day":"08","publication":"ACS Applied Materials and Interfaces"},{"publication":"Journal of Fluid Mechanics","year":"2017","language":[{"iso":"eng"}],"day":"25","author":[{"last_name":"Lopez Alonso","first_name":"Jose M","orcid":"0000-0002-0384-2022","id":"40770848-F248-11E8-B48F-1D18A9856A87","full_name":"Lopez Alonso, Jose M"},{"first_name":"Marc","last_name":"Avila","full_name":"Avila, Marc"}],"date_published":"2017-04-25T00:00:00Z","volume":817,"abstract":[{"lang":"eng","text":"Most flows in nature and engineering are turbulent because of their large velocities and spatial scales. Laboratory experiments on rotating quasi-Keplerian flows, for which the angular velocity decreases radially but the angular momentum increases, are however laminar at Reynolds numbers exceeding one million. This is in apparent contradiction to direct numerical simulations showing that in these experiments turbulence transition is triggered by the axial boundaries. We here show numerically that as the Reynolds number increases, turbulence becomes progressively confined to the boundary layers and the flow in the bulk fully relaminarizes. Our findings support that turbulence is unlikely to occur in isothermal constant-density quasi-Keplerian flows."}],"date_created":"2018-12-11T11:49:44Z","project":[{"name":"Information processing and computation in fish groups","_id":"255008E4-B435-11E9-9278-68D0E5697425","grant_number":"RGP0065/2012"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.05527"}],"publisher":"Cambridge University Press","publication_status":"published","oa":1,"publication_identifier":{"issn":["00221120"]},"date_updated":"2023-09-22T09:39:46Z","oa_version":"Submitted Version","month":"04","publist_id":"6371","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","department":[{"_id":"BjHo"}],"external_id":{"isi":["000398179100006"]},"doi":"10.1017/jfm.2017.109","intvolume":" 817","page":"21 - 34","_id":"1021","title":"Boundary layer turbulence in experiments on quasi Keplerian flows","type":"journal_article","status":"public","citation":{"mla":"Lopez Alonso, Jose M., and Marc Avila. “Boundary Layer Turbulence in Experiments on Quasi Keplerian Flows.” Journal of Fluid Mechanics, vol. 817, Cambridge University Press, 2017, pp. 21–34, doi:10.1017/jfm.2017.109.","apa":"Lopez Alonso, J. M., & Avila, M. (2017). Boundary layer turbulence in experiments on quasi Keplerian flows. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.109","ama":"Lopez Alonso JM, Avila M. Boundary layer turbulence in experiments on quasi Keplerian flows. Journal of Fluid Mechanics. 2017;817:21-34. doi:10.1017/jfm.2017.109","short":"J.M. Lopez Alonso, M. Avila, Journal of Fluid Mechanics 817 (2017) 21–34.","chicago":"Lopez Alonso, Jose M, and Marc Avila. “Boundary Layer Turbulence in Experiments on Quasi Keplerian Flows.” Journal of Fluid Mechanics. Cambridge University Press, 2017. https://doi.org/10.1017/jfm.2017.109.","ista":"Lopez Alonso JM, Avila M. 2017. Boundary layer turbulence in experiments on quasi Keplerian flows. Journal of Fluid Mechanics. 817, 21–34.","ieee":"J. M. Lopez Alonso and M. Avila, “Boundary layer turbulence in experiments on quasi Keplerian flows,” Journal of Fluid Mechanics, vol. 817. Cambridge University Press, pp. 21–34, 2017."},"article_processing_charge":"No","isi":1},{"oa":1,"publication_status":"published","publication_identifier":{"issn":["00358711"]},"date_updated":"2023-09-22T09:40:55Z","oa_version":"Submitted Version","month":"01","publist_id":"6373","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","acknowledgement":"Part of this work has been supported by the 7th Framework Programme for Research of the European Commission, under FETOpen grant number 255827 (CGL Computational Geometry Learning) and ERC advanced grant, URSAT (Understanding Random Systems via Algebraic Topology) number 320422.","department":[{"_id":"HeEd"}],"external_id":{"isi":["000395170200039"]},"doi":"10.1093/mnras/stw2862","intvolume":" 465","page":"4281 - 4310","_id":"1022","title":"The topology of the cosmic web in terms of persistent Betti numbers","status":"public","type":"journal_article","citation":{"ista":"Pranav P, Edelsbrunner H, Van De Weygaert R, Vegter G, Kerber M, Jones B, Wintraecken M. 2017. The topology of the cosmic web in terms of persistent Betti numbers. Monthly Notices of the Royal Astronomical Society. 465(4), 4281–4310.","ieee":"P. Pranav et al., “The topology of the cosmic web in terms of persistent Betti numbers,” Monthly Notices of the Royal Astronomical Society, vol. 465, no. 4. Oxford University Press, pp. 4281–4310, 2017.","ama":"Pranav P, Edelsbrunner H, Van De Weygaert R, et al. The topology of the cosmic web in terms of persistent Betti numbers. Monthly Notices of the Royal Astronomical Society. 2017;465(4):4281-4310. doi:10.1093/mnras/stw2862","chicago":"Pranav, Pratyush, Herbert Edelsbrunner, Rien Van De Weygaert, Gert Vegter, Michael Kerber, Bernard Jones, and Mathijs Wintraecken. “The Topology of the Cosmic Web in Terms of Persistent Betti Numbers.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stw2862.","short":"P. Pranav, H. Edelsbrunner, R. Van De Weygaert, G. Vegter, M. Kerber, B. Jones, M. Wintraecken, Monthly Notices of the Royal Astronomical Society 465 (2017) 4281–4310.","mla":"Pranav, Pratyush, et al. “The Topology of the Cosmic Web in Terms of Persistent Betti Numbers.” Monthly Notices of the Royal Astronomical Society, vol. 465, no. 4, Oxford University Press, 2017, pp. 4281–310, doi:10.1093/mnras/stw2862.","apa":"Pranav, P., Edelsbrunner, H., Van De Weygaert, R., Vegter, G., Kerber, M., Jones, B., & Wintraecken, M. (2017). The topology of the cosmic web in terms of persistent Betti numbers. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stw2862"},"article_processing_charge":"No","isi":1,"publication":"Monthly Notices of the Royal Astronomical Society","language":[{"iso":"eng"}],"year":"2017","day":"01","author":[{"full_name":"Pranav, Pratyush","last_name":"Pranav","first_name":"Pratyush"},{"first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Van De Weygaert, Rien","last_name":"Van De Weygaert","first_name":"Rien"},{"last_name":"Vegter","first_name":"Gert","full_name":"Vegter, Gert"},{"first_name":"Michael","last_name":"Kerber","full_name":"Kerber, Michael"},{"first_name":"Bernard","last_name":"Jones","full_name":"Jones, Bernard"},{"orcid":"0000-0002-7472-2220","first_name":"Mathijs","last_name":"Wintraecken","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","full_name":"Wintraecken, Mathijs"}],"date_published":"2017-01-01T00:00:00Z","abstract":[{"lang":"eng","text":"We introduce a multiscale topological description of the Megaparsec web-like cosmic matter distribution. Betti numbers and topological persistence offer a powerful means of describing the rich connectivity structure of the cosmic web and of its multiscale arrangement of matter and galaxies. Emanating from algebraic topology and Morse theory, Betti numbers and persistence diagrams represent an extension and deepening of the cosmologically familiar topological genus measure and the related geometric Minkowski functionals. In addition to a description of the mathematical background, this study presents the computational procedure for computing Betti numbers and persistence diagrams for density field filtrations. The field may be computed starting from a discrete spatial distribution of galaxies or simulation particles. The main emphasis of this study concerns an extensive and systematic exploration of the imprint of different web-like morphologies and different levels of multiscale clustering in the corresponding computed Betti numbers and persistence diagrams. To this end, we use Voronoi clustering models as templates for a rich variety of web-like configurations and the fractal-like Soneira-Peebles models exemplify a range of multiscale configurations. We have identified the clear imprint of cluster nodes, filaments, walls, and voids in persistence diagrams, along with that of the nested hierarchy of structures in multiscale point distributions. We conclude by outlining the potential of persistent topology for understanding the connectivity structure of the cosmic web, in large simulations of cosmic structure formation and in the challenging context of the observed galaxy distribution in large galaxy surveys."}],"volume":465,"issue":"4","date_created":"2018-12-11T11:49:44Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.04519"}],"publisher":"Oxford University Press"},{"file_date_updated":"2018-12-12T10:15:29Z","author":[{"id":"4D902E6A-F248-11E8-B48F-1D18A9856A87","full_name":"Nemish, Yuriy","last_name":"Nemish","first_name":"Yuriy","orcid":"0000-0002-7327-856X"}],"date_published":"2017-02-06T00:00:00Z","abstract":[{"text":"We consider products of independent square non-Hermitian random matrices. More precisely, let X1,…, Xn be independent N × N random matrices with independent entries (real or complex with independent real and imaginary parts) with zero mean and variance 1/N. Soshnikov-O’Rourke [19] and Götze-Tikhomirov [15] showed that the empirical spectral distribution of the product of n random matrices with iid entries converges to (equation found). We prove that if the entries of the matrices X1,…, Xn are independent (but not necessarily identically distributed) and satisfy uniform subexponential decay condition, then in the bulk the convergence of the ESD of X1,…, Xn to (0.1) holds up to the scale N–1/2+ε.","lang":"eng"}],"volume":22,"publication":"Electronic Journal of Probability","language":[{"iso":"eng"}],"year":"2017","day":"06","publisher":"Institute of Mathematical Statistics","file":[{"file_name":"IST-2017-802-v1+1_euclid.ejp.1487991681.pdf","file_size":742275,"access_level":"open_access","date_updated":"2018-12-12T10:15:29Z","content_type":"application/pdf","creator":"system","date_created":"2018-12-12T10:15:29Z","relation":"main_file","file_id":"5149"}],"scopus_import":"1","date_created":"2018-12-11T11:49:44Z","has_accepted_license":"1","article_number":"22","month":"02","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6370","oa":1,"publication_status":"published","publication_identifier":{"issn":["10836489"]},"ddc":["510"],"date_updated":"2023-09-22T09:27:51Z","article_processing_charge":"No","citation":{"ista":"Nemish Y. 2017. Local law for the product of independent non-Hermitian random matrices with independent entries. Electronic Journal of Probability. 22, 22.","ieee":"Y. Nemish, “Local law for the product of independent non-Hermitian random matrices with independent entries,” Electronic Journal of Probability, vol. 22. Institute of Mathematical Statistics, 2017.","chicago":"Nemish, Yuriy. “Local Law for the Product of Independent Non-Hermitian Random Matrices with Independent Entries.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/17-EJP38.","ama":"Nemish Y. Local law for the product of independent non-Hermitian random matrices with independent entries. Electronic Journal of Probability. 2017;22. doi:10.1214/17-EJP38","short":"Y. Nemish, Electronic Journal of Probability 22 (2017).","apa":"Nemish, Y. (2017). Local law for the product of independent non-Hermitian random matrices with independent entries. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/17-EJP38","mla":"Nemish, Yuriy. “Local Law for the Product of Independent Non-Hermitian Random Matrices with Independent Entries.” Electronic Journal of Probability, vol. 22, 22, Institute of Mathematical Statistics, 2017, doi:10.1214/17-EJP38."},"isi":1,"title":"Local law for the product of independent non-Hermitian random matrices with independent entries","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"pubrep_id":"802","type":"journal_article","status":"public","external_id":{"isi":["000396611900022"]},"doi":"10.1214/17-EJP38","intvolume":" 22","license":"https://creativecommons.org/licenses/by/4.0/","_id":"1023","quality_controlled":"1","department":[{"_id":"LaEr"}]},{"year":"2017","language":[{"iso":"eng"}],"day":"17","publication":"Auxins and Cytokinins in Plant Biology","file_date_updated":"2019-10-15T07:47:05Z","date_published":"2017-03-17T00:00:00Z","volume":1569,"abstract":[{"lang":"eng","text":"The history of auxin and cytokinin biology including the initial discoveries by father–son duo Charles Darwin and Francis Darwin (1880), and Gottlieb Haberlandt (1919) is a beautiful demonstration of unceasing continuity of research. Novel findings are integrated into existing hypotheses and models and deepen our understanding of biological principles. At the same time new questions are triggered and hand to hand with this new methodologies are developed to address these new challenges."}],"author":[{"id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","full_name":"Hurny, Andrej","first_name":"Andrej","last_name":"Hurny","orcid":"0000-0003-3638-1426"},{"first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"}],"project":[{"name":"Hormone cross-talk drives nutrient dependent plant development","_id":"2542D156-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I 1774-B16"}],"date_created":"2018-12-11T11:49:45Z","publisher":"Springer","file":[{"relation":"main_file","creator":"system","date_created":"2018-12-12T10:14:18Z","file_id":"5068","file_size":840646,"access_level":"open_access","file_name":"IST-2018-1019-v1+1_Hurny_MethodsMolBiol_2017.pdf","content_type":"application/pdf","date_updated":"2019-10-15T07:47:05Z"}],"scopus_import":1,"related_material":{"record":[{"id":"539","relation":"dissertation_contains","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6369","month":"03","oa_version":"Submitted Version","publication_identifier":{"issn":["10643745"]},"ddc":["575"],"date_updated":"2024-03-25T23:30:09Z","oa":1,"publication_status":"published","alternative_title":["Methods in Molecular Biology"],"has_accepted_license":"1","intvolume":" 1569","_id":"1024","page":"1 - 29","doi":"10.1007/978-1-4939-6831-2_1","department":[{"_id":"EvBe"}],"quality_controlled":"1","citation":{"mla":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” Auxins and Cytokinins in Plant Biology, vol. 1569, Springer, 2017, pp. 1–29, doi:10.1007/978-1-4939-6831-2_1.","apa":"Hurny, A., & Benková, E. (2017). Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. Springer. https://doi.org/10.1007/978-1-4939-6831-2_1","chicago":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” Auxins and Cytokinins in Plant Biology. Springer, 2017. https://doi.org/10.1007/978-1-4939-6831-2_1.","short":"A. Hurny, E. Benková, Auxins and Cytokinins in Plant Biology 1569 (2017) 1–29.","ama":"Hurny A, Benková E. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 2017;1569:1-29. doi:10.1007/978-1-4939-6831-2_1","ieee":"A. Hurny and E. Benková, “Methodological advances in auxin and cytokinin biology,” Auxins and Cytokinins in Plant Biology, vol. 1569. Springer, pp. 1–29, 2017.","ista":"Hurny A, Benková E. 2017. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 1569, 1–29."},"pubrep_id":"1019","type":"journal_article","status":"public","title":"Methodological advances in auxin and cytokinin biology"},{"department":[{"_id":"CaHe"}],"quality_controlled":"1","_id":"1025","page":"43 - 44","intvolume":" 543","doi":"10.1038/nature21502","external_id":{"isi":["000395671500025"]},"status":"public","type":"journal_article","title":"Cell biology: Stretched divisions","isi":1,"citation":{"short":"C.-P.J. Heisenberg, Nature 543 (2017) 43–44.","ama":"Heisenberg C-PJ. Cell biology: Stretched divisions. Nature. 2017;543(7643):43-44. doi:10.1038/nature21502","chicago":"Heisenberg, Carl-Philipp J. “Cell Biology: Stretched Divisions.” Nature. Nature Publishing Group, 2017. https://doi.org/10.1038/nature21502.","mla":"Heisenberg, Carl-Philipp J. “Cell Biology: Stretched Divisions.” Nature, vol. 543, no. 7643, Nature Publishing Group, 2017, pp. 43–44, doi:10.1038/nature21502.","apa":"Heisenberg, C.-P. J. (2017). Cell biology: Stretched divisions. Nature. Nature Publishing Group. https://doi.org/10.1038/nature21502","ista":"Heisenberg C-PJ. 2017. Cell biology: Stretched divisions. Nature. 543(7643), 43–44.","ieee":"C.-P. J. Heisenberg, “Cell biology: Stretched divisions,” Nature, vol. 543, no. 7643. Nature Publishing Group, pp. 43–44, 2017."},"article_processing_charge":"No","date_updated":"2023-09-22T09:26:59Z","publication_identifier":{"issn":["00280836"]},"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6367","month":"03","oa_version":"None","date_created":"2018-12-11T11:49:45Z","scopus_import":"1","publisher":"Nature Publishing Group","day":"02","language":[{"iso":"eng"}],"year":"2017","publication":"Nature","volume":543,"abstract":[{"text":"Many organ surfaces are covered by a protective epithelial-cell layer. It emerges that such layers are maintained by cell stretching that triggers cell division mediated by the force-sensitive ion-channel protein Piezo1. See Letter p.118","lang":"eng"}],"date_published":"2017-03-02T00:00:00Z","author":[{"first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"issue":"7643"},{"scopus_import":"1","publisher":"Elsevier","project":[{"grant_number":"RGY0084/2012","_id":"255BFFFA-B435-11E9-9278-68D0E5697425","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)"},{"call_identifier":"FP7","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"W1232-B24","name":"Molecular Drug Targets","_id":"255A6082-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:49:45Z","article_type":"original","date_published":"2017-12-01T00:00:00Z","volume":48,"abstract":[{"lang":"eng","text":"The optogenetic revolution enabled spatially-precise and temporally-precise control over protein function, signaling pathway activation, and animal behavior with tremendous success in the dissection of signaling networks and neural circuits. Very recently, optogenetic methods have been paired with optical reporters in novel drug screening platforms. In these all-optical platforms, light remotely activated ion channels and kinases thereby obviating the use of electrophysiology or reagents. Consequences were remarkable operational simplicity, throughput, and cost-effectiveness that culminated in the identification of new drug candidates. These blueprints for all-optical assays also revealed potential pitfalls and inspire all-optical variants of other screens, such as those that aim at better understanding dynamic drug action or orphan protein function."}],"author":[{"full_name":"Agus, Viviana","first_name":"Viviana","last_name":"Agus"},{"full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315"}],"ec_funded":1,"language":[{"iso":"eng"}],"year":"2017","day":"01","publication":"Current Opinion in Biotechnology","status":"public","type":"journal_article","title":"Optogenetic methods in drug screening: Technologies and applications","isi":1,"article_processing_charge":"No","citation":{"ista":"Agus V, Janovjak HL. 2017. Optogenetic methods in drug screening: Technologies and applications. Current Opinion in Biotechnology. 48, 8–14.","ieee":"V. Agus and H. L. Janovjak, “Optogenetic methods in drug screening: Technologies and applications,” Current Opinion in Biotechnology, vol. 48. Elsevier, pp. 8–14, 2017.","ama":"Agus V, Janovjak HL. Optogenetic methods in drug screening: Technologies and applications. Current Opinion in Biotechnology. 2017;48:8-14. doi:10.1016/j.copbio.2017.02.006","short":"V. Agus, H.L. Janovjak, Current Opinion in Biotechnology 48 (2017) 8–14.","chicago":"Agus, Viviana, and Harald L Janovjak. “Optogenetic Methods in Drug Screening: Technologies and Applications.” Current Opinion in Biotechnology. Elsevier, 2017. https://doi.org/10.1016/j.copbio.2017.02.006.","mla":"Agus, Viviana, and Harald L. Janovjak. “Optogenetic Methods in Drug Screening: Technologies and Applications.” Current Opinion in Biotechnology, vol. 48, Elsevier, 2017, pp. 8–14, doi:10.1016/j.copbio.2017.02.006.","apa":"Agus, V., & Janovjak, H. L. (2017). Optogenetic methods in drug screening: Technologies and applications. Current Opinion in Biotechnology. Elsevier. https://doi.org/10.1016/j.copbio.2017.02.006"},"department":[{"_id":"HaJa"}],"quality_controlled":"1","acknowledgement":"This work was supported by grants of the European Union Seventh Framework Programme (CIG-303564), the Human Frontier Science Program (RGY0084_2012), and the Austrian Science Fund FWF (W1232 MolecularDrugTargets).","intvolume":" 48","_id":"1026","page":"8 - 14","external_id":{"isi":["000418313200003"]},"doi":"10.1016/j.copbio.2017.02.006","publication_identifier":{"issn":["09581669"]},"date_updated":"2023-09-22T09:26:06Z","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6365","oa_version":"None","month":"12"},{"publisher":"Elsevier","file":[{"content_type":"application/pdf","date_updated":"2019-01-18T09:57:57Z","access_level":"open_access","file_size":858338,"file_name":"2017_CurrentOpinion_Lukaciinova.pdf","file_id":"5846","relation":"main_file","creator":"dernst","date_created":"2019-01-18T09:57:57Z","success":1}],"scopus_import":"1","date_created":"2018-12-11T11:49:45Z","project":[{"name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22","call_identifier":"FWF"},{"name":"Optimality principles in responses to antibiotics","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"303507"},{"name":"Revealing the fundamental limits of cell growth","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013"}],"article_type":"original","file_date_updated":"2019-01-18T09:57:57Z","author":[{"last_name":"Lukacisinova","first_name":"Marta","orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisinova, Marta"},{"orcid":"0000-0003-4398-476X","last_name":"Bollenbach","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias"}],"abstract":[{"text":"The rising prevalence of antibiotic resistant bacteria is an increasingly serious public health challenge. To address this problem, recent work ranging from clinical studies to theoretical modeling has provided valuable insights into the mechanisms of resistance, its emergence and spread, and ways to counteract it. A deeper understanding of the underlying dynamics of resistance evolution will require a combination of experimental and theoretical expertise from different disciplines and new technology for studying evolution in the laboratory. Here, we review recent advances in the quantitative understanding of the mechanisms and evolution of antibiotic resistance. We focus on key theoretical concepts and new technology that enables well-controlled experiments. We further highlight key challenges that can be met in the near future to ultimately develop effective strategies for combating resistance.","lang":"eng"}],"volume":46,"date_published":"2017-08-01T00:00:00Z","publication":"Current Opinion in Biotechnology","day":"01","year":"2017","language":[{"iso":"eng"}],"ec_funded":1,"citation":{"ista":"Lukacisinova M, Bollenbach MT. 2017. Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. 46, 90–97.","ieee":"M. Lukacisinova and M. T. Bollenbach, “Toward a quantitative understanding of antibiotic resistance evolution,” Current Opinion in Biotechnology, vol. 46. Elsevier, pp. 90–97, 2017.","chicago":"Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative Understanding of Antibiotic Resistance Evolution.” Current Opinion in Biotechnology. Elsevier, 2017. https://doi.org/10.1016/j.copbio.2017.02.013.","short":"M. Lukacisinova, M.T. Bollenbach, Current Opinion in Biotechnology 46 (2017) 90–97.","ama":"Lukacisinova M, Bollenbach MT. Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. 2017;46:90-97. doi:10.1016/j.copbio.2017.02.013","mla":"Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative Understanding of Antibiotic Resistance Evolution.” Current Opinion in Biotechnology, vol. 46, Elsevier, 2017, pp. 90–97, doi:10.1016/j.copbio.2017.02.013.","apa":"Lukacisinova, M., & Bollenbach, M. T. (2017). Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. Elsevier. https://doi.org/10.1016/j.copbio.2017.02.013"},"article_processing_charge":"Yes (in subscription journal)","isi":1,"title":"Toward a quantitative understanding of antibiotic resistance evolution","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"type":"journal_article","status":"public","pubrep_id":"801","doi":"10.1016/j.copbio.2017.02.013","external_id":{"isi":["000408077400015"]},"page":"90 - 97","_id":"1027","intvolume":" 46","quality_controlled":"1","department":[{"_id":"ToBo"}],"has_accepted_license":"1","month":"08","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"relation":"dissertation_contains","id":"6263","status":"public"}]},"publist_id":"6364","publication_status":"published","oa":1,"date_updated":"2024-03-25T23:30:15Z","ddc":["570"]},{"publist_id":"6362","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"relation":"dissertation_contains","id":"418","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7680"}]},"month":"03","oa_version":"Published Version","ddc":["540"],"date_updated":"2024-03-25T23:30:08Z","publication_identifier":{"issn":["14337851"]},"publication_status":"published","oa":1,"has_accepted_license":"1","_id":"1028","page":"4608-4611","intvolume":" 56","doi":"10.1002/anie.201611998","external_id":{"isi":["000398154000038"]},"department":[{"_id":"CaGu"},{"_id":"HaJa"}],"acknowledgement":"This work was supported by a grant from the European Union􏰝s Seventh Framework Programme (CIG-303564). E.R. was supported by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF), W1232) and a FemTech fellowship (Austrian Research Promotion Agency, 3580812)","quality_controlled":"1","isi":1,"article_processing_charge":"No","citation":{"short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie - International Edition 56 (2017) 4608–4611.","chicago":"Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” Angewandte Chemie - International Edition. Wiley-Blackwell, 2017. https://doi.org/10.1002/anie.201611998.","ama":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. 2017;56(16):4608-4611. doi:10.1002/anie.201611998","mla":"Kainrath, Stephanie, et al. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” Angewandte Chemie - International Edition, vol. 56, no. 16, Wiley-Blackwell, 2017, pp. 4608–11, doi:10.1002/anie.201611998.","apa":"Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak, H. L. (2017). Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. Wiley-Blackwell. https://doi.org/10.1002/anie.201611998","ieee":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Green-light-induced inactivation of receptor signaling using cobalamin-binding domains,” Angewandte Chemie - International Edition, vol. 56, no. 16. Wiley-Blackwell, pp. 4608–4611, 2017.","ista":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. 56(16), 4608–4611."},"type":"journal_article","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Green-light-induced inactivation of receptor signaling using cobalamin-binding domains","day":"20","language":[{"iso":"eng"}],"year":"2017","publication":"Angewandte Chemie - International Edition","ec_funded":1,"issue":"16","file_date_updated":"2019-01-18T09:39:55Z","abstract":[{"text":"Optogenetics and photopharmacology provide spatiotemporally precise control over protein interactions and protein function in cells and animals. Optogenetic methods that are sensitive to green light and can be used to break protein complexes are not broadly available but would enable multichromatic experiments with previously inaccessible biological targets. Herein, we repurposed cobalamin (vitamin B12) binding domains of bacterial CarH transcription factors for green-light-induced receptor dissociation. In cultured cells, we observed oligomerization-induced cell signaling for the fibroblast growth factor receptor 1 fused to cobalamin-binding domains in the dark that was rapidly eliminated upon illumination. In zebrafish embryos expressing fusion receptors, green light endowed control over aberrant fibroblast growth factor signaling during development. Green-light-induced domain dissociation and light-inactivated receptors will critically expand the optogenetic toolbox for control of biological processes.","lang":"eng"}],"volume":56,"date_published":"2017-03-20T00:00:00Z","author":[{"id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","full_name":"Kainrath, Stephanie","first_name":"Stephanie","last_name":"Kainrath"},{"full_name":"Stadler, Manuela","last_name":"Stadler","first_name":"Manuela"},{"last_name":"Gschaider-Reichhart","first_name":"Eva","orcid":"0000-0002-7218-7738","full_name":"Gschaider-Reichhart, Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","last_name":"Distel","full_name":"Distel, Martin"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L","first_name":"Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315"}],"project":[{"name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564","call_identifier":"FP7"},{"_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets [do not use to be deleted]","grant_number":"W1232-B24","call_identifier":"FWF"}],"date_created":"2018-12-11T11:49:46Z","file":[{"relation":"main_file","creator":"dernst","date_created":"2019-01-18T09:39:55Z","file_id":"5845","access_level":"open_access","file_size":2614942,"file_name":"2017_communications_Kainrath.pdf","content_type":"application/pdf","date_updated":"2019-01-18T09:39:55Z","success":1}],"publisher":"Wiley-Blackwell","scopus_import":"1"},{"scopus_import":"1","publisher":"Public Library of Science","file":[{"file_size":3429381,"access_level":"open_access","file_name":"IST-2017-800-v1+1_journal.pone.0174066.pdf","content_type":"application/pdf","date_updated":"2018-12-12T10:09:47Z","relation":"main_file","creator":"system","date_created":"2018-12-12T10:09:47Z","file_id":"4772"}],"date_created":"2018-12-11T11:49:46Z","author":[{"first_name":"Martin","last_name":"Lukacisin","orcid":"0000-0001-6549-4177","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisin, Martin"},{"full_name":"Landon, Matthieu","last_name":"Landon","first_name":"Matthieu"},{"last_name":"Jajoo","first_name":"Rishi","full_name":"Jajoo, Rishi"}],"volume":12,"abstract":[{"lang":"eng","text":"RNA Polymerase II pauses and backtracks during transcription, with many consequences for gene expression and cellular physiology. Here, we show that the energy required to melt double-stranded nucleic acids in the transcription bubble predicts pausing in Saccharomyces cerevisiae far more accurately than nucleosome roadblocks do. In addition, the same energy difference also determines when the RNA polymerase backtracks instead of continuing to move forward. This data-driven model corroborates—in a genome wide and quantitative manner—previous evidence that sequence-dependent thermodynamic features of nucleic acids influence both transcriptional pausing and backtracking."}],"date_published":"2017-03-16T00:00:00Z","file_date_updated":"2018-12-12T10:09:47Z","issue":"3","publication":"PLoS One","day":"16","year":"2017","language":[{"iso":"eng"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast","status":"public","type":"journal_article","pubrep_id":"800","citation":{"ieee":"M. Lukacisin, M. Landon, and R. Jajoo, “Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast,” PLoS One, vol. 12, no. 3. Public Library of Science, 2017.","ista":"Lukacisin M, Landon M, Jajoo R. 2017. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. 12(3), e0174066.","apa":"Lukacisin, M., Landon, M., & Jajoo, R. (2017). Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0174066","mla":"Lukacisin, Martin, et al. “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” PLoS One, vol. 12, no. 3, e0174066, Public Library of Science, 2017, doi:10.1371/journal.pone.0174066.","chicago":"Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” PLoS One. Public Library of Science, 2017. https://doi.org/10.1371/journal.pone.0174066.","short":"M. Lukacisin, M. Landon, R. Jajoo, PLoS One 12 (2017).","ama":"Lukacisin M, Landon M, Jajoo R. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. 2017;12(3). doi:10.1371/journal.pone.0174066"},"article_processing_charge":"Yes","isi":1,"quality_controlled":"1","department":[{"_id":"ToBo"}],"doi":"10.1371/journal.pone.0174066","external_id":{"isi":["000396318300121"]},"_id":"1029","intvolume":" 12","article_number":"e0174066","has_accepted_license":"1","publication_status":"published","oa":1,"date_updated":"2024-03-25T23:30:03Z","ddc":["570"],"publication_identifier":{"issn":["19326203"]},"month":"03","oa_version":"Published Version","related_material":{"record":[{"id":"5556","relation":"popular_science","status":"public"},{"status":"public","id":"6392","relation":"dissertation_contains"}]},"publist_id":"6361","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"citation":{"short":"M. Villányi, Informationspraxis 3 (2017).","ama":"Villányi M. Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library. Informationspraxis. 2017;3(1). doi:10.11588/ip.2017.1.35227","chicago":"Villányi, Márton. “Ein Freies Bibliothekssystem Für Wissenschaftliche Bibliotheken – Werkstattbericht Der IST Austria Library.” Informationspraxis. Verein Informationspraxis , 2017. https://doi.org/10.11588/ip.2017.1.35227.","apa":"Villányi, M. (2017). Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library. Informationspraxis. Verein Informationspraxis . https://doi.org/10.11588/ip.2017.1.35227","mla":"Villányi, Márton. “Ein Freies Bibliothekssystem Für Wissenschaftliche Bibliotheken – Werkstattbericht Der IST Austria Library.” Informationspraxis, vol. 3, no. 1, Verein Informationspraxis , 2017, doi:10.11588/ip.2017.1.35227.","ista":"Villányi M. 2017. Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library. Informationspraxis. 3(1).","ieee":"M. Villányi, “Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library,” Informationspraxis, vol. 3, no. 1. Verein Informationspraxis , 2017."},"article_processing_charge":"No","title":"Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"pubrep_id":"799","type":"journal_article","status":"public","popular_science":"1","doi":"10.11588/ip.2017.1.35227","intvolume":" 3","_id":"1030","department":[{"_id":"E-Lib"}],"has_accepted_license":"1","month":"01","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6360","oa":1,"publication_status":"published","publication_identifier":{"issn":["2297-3249"]},"date_updated":"2023-10-18T07:49:29Z","ddc":["020"],"publisher":"Verein Informationspraxis ","file":[{"date_updated":"2018-12-12T10:08:20Z","content_type":"application/pdf","file_name":"IST-2017-799-v1+1_35227-112025-1-PB.pdf","file_size":201163,"access_level":"open_access","file_id":"4680","date_created":"2018-12-12T10:08:20Z","creator":"system","relation":"main_file"}],"article_type":"original","date_created":"2018-12-11T11:49:46Z","file_date_updated":"2018-12-12T10:08:20Z","issue":"1","author":[{"full_name":"Villányi, Márton","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","first_name":"Márton","last_name":"Villányi","orcid":"0000-0001-8126-0426"}],"date_published":"2017-01-01T00:00:00Z","volume":3,"abstract":[{"text":"Auf der Suche nach einem Bibliothekssystem entschied sich die Forschungseinrichtung IST Austria im Jahr 2014 für das Open-Source-Produkt Koha. In einem ersten Schritt wurden zunächst Grundfunktionen aktiviert um im Anschluss diverse zusätzliche Tools zum Einsatz zu bringen. Die große Flexibilität des Systems erlaubt maßgeschneiderte Lösungen für unterschiedlichste Institutionen. Trotz Herausforderungen kann die Bibliothek auf eine erfolgreiche Implementierung zurückblicken.","lang":"ger"},{"text":"IST Austria was looking for a new library system until 2014 when the research institute decided\r\nto implement Koha. The library first activated basic functions of the open-source product and\r\nthen brought additional tools into operation. The high flexibility of the system allows customized\r\nsolutions for different institutions. Although the library faced some challenges, it can now look\r\nback on a successful implementation.","lang":"eng"}],"publication":"Informationspraxis","language":[{"iso":"eng"}],"year":"2017","day":"01"},{"publisher":"Association for Computing Machinery","file":[{"success":1,"file_id":"10421","checksum":"faa3f7b3fe8aab84b50ed805c26a0ee5","relation":"main_file","date_created":"2021-12-07T08:06:28Z","creator":"cchlebak","content_type":"application/pdf","date_updated":"2021-12-07T08:06:28Z","access_level":"open_access","file_size":460188,"file_name":"2017_ACMProgLang_Chatterjee.pdf"}],"scopus_import":"1","article_type":"original","date_created":"2021-12-05T23:01:48Z","project":[{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"}],"issue":"POPL","file_date_updated":"2021-12-07T08:06:28Z","volume":2,"abstract":[{"text":"A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graph where the edges are labeled with different types of opening and closing parentheses, and the reachability information is computed via paths whose parentheses are properly matched. We present new results for Dyck reachability problems with applications to alias analysis and data-dependence analysis. Our main contributions, that include improved upper bounds as well as lower bounds that establish optimality guarantees, are as follows: First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph with n nodes and m edges, we present: (i) an algorithm with worst-case running time O(m + n · α(n)), where α(n) is the inverse Ackermann function, improving the previously known O(n2) time bound; (ii) a matching lower bound that shows that our algorithm is optimal wrt to worst-case complexity; and (iii) an optimal average-case upper bound of O(m) time, improving the previously known O(m · logn) bound. Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtain analysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is only linear, and only wrt the number of call sites. Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean Matrix Multiplication, which is a long-standing open problem. Thus we establish that the existing combinatorial algorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the same hardness holds for graphs of constant treewidth. Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependence analysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform all existing methods on the two problems, over real-world benchmarks.","lang":"eng"}],"date_published":"2017-12-27T00:00:00Z","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Choudhary, Bhavya","last_name":"Choudhary","first_name":"Bhavya"},{"orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"}],"day":"27","year":"2017","language":[{"iso":"eng"}],"publication":"Proceedings of the ACM on Programming Languages","ec_funded":1,"article_processing_charge":"No","citation":{"chicago":"Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. “Optimal Dyck Reachability for Data-Dependence and Alias Analysis.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158118.","short":"K. Chatterjee, B. Choudhary, A. Pavlogiannis, Proceedings of the ACM on Programming Languages 2 (2017).","ama":"Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158118","mla":"Chatterjee, Krishnendu, et al. “Optimal Dyck Reachability for Data-Dependence and Alias Analysis.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 30, Association for Computing Machinery, 2017, doi:10.1145/3158118.","apa":"Chatterjee, K., Choudhary, B., & Pavlogiannis, A. (2017). Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158118","ista":"Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. 2(POPL), 30.","ieee":"K. Chatterjee, B. Choudhary, and A. Pavlogiannis, “Optimal Dyck reachability for data-dependence and Alias analysis,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017."},"status":"public","type":"journal_article","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Optimal Dyck reachability for data-dependence and Alias analysis","_id":"10416","intvolume":" 2","doi":"10.1145/3158118","external_id":{"arxiv":["1910.00241"]},"department":[{"_id":"KrCh"}],"acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Start grant (279307: Graph Games).\r\n","quality_controlled":"1","arxiv":1,"has_accepted_license":"1","article_number":"30","related_material":{"record":[{"relation":"earlier_version","id":"5455","status":"public"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","month":"12","ddc":["000"],"date_updated":"2023-02-23T12:27:13Z","publication_identifier":{"eissn":["2475-1421"]},"oa":1,"publication_status":"published","conference":{"location":"Los Angeles, CA, United States","start_date":"2018-01-07","name":"POPL: Programming Languages","end_date":"2018-01-13"}},{"month":"12","oa_version":"Published Version","related_material":{"record":[{"relation":"earlier_version","id":"5448","status":"public"},{"relation":"earlier_version","id":"5456","status":"public"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","oa":1,"conference":{"location":"Los Angeles, CA, United States","name":"POPL: Programming Languages","end_date":"2018-01-13","start_date":"2018-01-07"},"date_updated":"2023-02-23T12:27:16Z","publication_identifier":{"eissn":["2475-1421"]},"arxiv":1,"article_number":"31","doi":"10.1145/3158119","external_id":{"arxiv":["1610.01188"]},"_id":"10417","intvolume":" 2","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF\r\nNFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Czech\r\nScience Foundation grant GBP202/12/G061.","quality_controlled":"1","department":[{"_id":"KrCh"}],"article_processing_charge":"No","citation":{"short":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Proceedings of the ACM on Programming Languages 2 (2017).","ama":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158119","chicago":"Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. “Data-Centric Dynamic Partial Order Reduction.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158119.","apa":"Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K. (2017). Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158119","mla":"Chalupa, Marek, et al. “Data-Centric Dynamic Partial Order Reduction.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 31, Association for Computing Machinery, 2017, doi:10.1145/3158119.","ista":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2(POPL), 31.","ieee":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, “Data-centric dynamic partial order reduction,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017."},"title":"Data-centric dynamic partial order reduction","status":"public","type":"journal_article","publication":"Proceedings of the ACM on Programming Languages","day":"27","language":[{"iso":"eng"}],"year":"2017","ec_funded":1,"issue":"POPL","author":[{"first_name":"Marek","last_name":"Chalupa","full_name":"Chalupa, Marek"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sinha","first_name":"Nishant","full_name":"Sinha, Nishant"},{"last_name":"Vaidya","first_name":"Kapil","full_name":"Vaidya, Kapil"}],"volume":2,"abstract":[{"text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\n\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.","lang":"eng"}],"date_published":"2017-12-27T00:00:00Z","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"}],"date_created":"2021-12-05T23:01:49Z","article_type":"original","publisher":"Association for Computing Machinery","main_file_link":[{"url":"https://dl.acm.org/doi/10.1145/3158119","open_access":"1"}],"scopus_import":"1"},{"article_number":"33","arxiv":1,"publication_identifier":{"eissn":["2475-1421"]},"date_updated":"2021-12-07T08:04:14Z","conference":{"location":"Los Angeles, CA, United States","name":"POPL: Programming Languages","start_date":"2018-01-07","end_date":"2018-01-13"},"oa":1,"publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","month":"12","type":"journal_article","status":"public","title":"A new proof rule for almost-sure termination","article_processing_charge":"No","citation":{"mla":"Mciver, Annabelle, et al. “A New Proof Rule for Almost-Sure Termination.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 33, Association for Computing Machinery, 2017, doi:10.1145/3158121.","apa":"Mciver, A., Morgan, C., Kaminski, B. L., & Katoen, J. P. (2017). A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158121","short":"A. Mciver, C. Morgan, B.L. Kaminski, J.P. Katoen, Proceedings of the ACM on Programming Languages 2 (2017).","ama":"Mciver A, Morgan C, Kaminski BL, Katoen JP. A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158121","chicago":"Mciver, Annabelle, Carroll Morgan, Benjamin Lucien Kaminski, and Joost P Katoen. “A New Proof Rule for Almost-Sure Termination.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158121.","ieee":"A. Mciver, C. Morgan, B. L. Kaminski, and J. P. Katoen, “A new proof rule for almost-sure termination,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017.","ista":"Mciver A, Morgan C, Kaminski BL, Katoen JP. 2017. A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. 2(POPL), 33."},"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"quality_controlled":"1","acknowledgement":"McIver and Morgan are grateful to David Basin and the Information Security Group at ETH Zürich for hosting a six-month stay in Switzerland, during part of which this work began. And thanks particularly to Andreas Lochbihler, who shared with us the probabilistic termination problem that led to it. They acknowledge the support of ARC grant DP140101119. Part of this work was carried out during the Workshop on Probabilistic Programming Semantics\r\nat McGill University’s Bellairs Research Institute on Barbados organised by Alexandra Silva and\r\nPrakash Panangaden. Kaminski and Katoen are grateful to Sebastian Junges for spotting a flaw in §5.4.","intvolume":" 2","_id":"10418","external_id":{"arxiv":["1711.03588"]},"doi":"10.1145/3158121","date_published":"2017-12-07T00:00:00Z","abstract":[{"lang":"eng","text":"We present a new proof rule for proving almost-sure termination of probabilistic programs, including those that contain demonic non-determinism. An important question for a probabilistic program is whether the probability mass of all its diverging runs is zero, that is that it terminates \"almost surely\". Proving that can be hard, and this paper presents a new method for doing so. It applies directly to the program's source code, even if the program contains demonic choice. Like others, we use variant functions (a.k.a. \"super-martingales\") that are real-valued and decrease randomly on each loop iteration; but our key innovation is that the amount as well as the probability of the decrease are parametric. We prove the soundness of the new rule, indicate where its applicability goes beyond existing rules, and explain its connection to classical results on denumerable (non-demonic) Markov chains."}],"volume":2,"author":[{"last_name":"Mciver","first_name":"Annabelle","full_name":"Mciver, Annabelle"},{"full_name":"Morgan, Carroll","first_name":"Carroll","last_name":"Morgan"},{"first_name":"Benjamin Lucien","last_name":"Kaminski","full_name":"Kaminski, Benjamin Lucien"},{"last_name":"Katoen","first_name":"Joost P","id":"4524F760-F248-11E8-B48F-1D18A9856A87","full_name":"Katoen, Joost P"}],"issue":"POPL","language":[{"iso":"eng"}],"year":"2017","day":"07","publication":"Proceedings of the ACM on Programming Languages","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://dl.acm.org/doi/10.1145/3158121"}],"publisher":"Association for Computing Machinery","date_created":"2021-12-05T23:01:49Z","article_type":"original"},{"ec_funded":1,"publication":"Evolution","day":"01","language":[{"iso":"eng"}],"year":"2017","author":[{"first_name":"Hildegard","last_name":"Uecker","orcid":"0000-0001-9435-2813","full_name":"Uecker, Hildegard","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"text":"Severe environmental change can drive a population extinct unless the population adapts in time to the new conditions (“evolutionary rescue”). How does biparental sexual reproduction influence the chances of population persistence compared to clonal reproduction or selfing? In this article, we set up a one‐locus two‐allele model for adaptation in diploid species, where rescue is contingent on the establishment of the mutant homozygote. Reproduction can occur by random mating, selfing, or clonally. Random mating generates and destroys the rescue mutant; selfing is efficient at generating it but at the same time depletes the heterozygote, which can lead to a low mutant frequency in the standing genetic variation. Due to these (and other) antagonistic effects, we find a nontrivial dependence of population survival on the rate of sex/selfing, which is strongly influenced by the dominance coefficient of the mutation before and after the environmental change. Importantly, since mating with the wild‐type breaks the mutant homozygote up, a slow decay of the wild‐type population size can impede rescue in randomly mating populations.","lang":"eng"}],"volume":71,"date_published":"2017-04-01T00:00:00Z","issue":"4","date_created":"2018-12-11T11:49:57Z","project":[{"name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7"}],"scopus_import":"1","publisher":"Wiley-Blackwell","main_file_link":[{"open_access":"1","url":"http://biorxiv.org/content/early/2016/10/14/081042"}],"oa":1,"publication_status":"published","date_updated":"2025-05-28T11:42:51Z","publication_identifier":{"issn":["00143820"]},"month":"04","oa_version":"Submitted Version","publist_id":"6327","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","department":[{"_id":"NiBa"}],"doi":"10.1111/evo.13191","external_id":{"isi":["000398545200003"]},"page":"845 - 858","_id":"1063","intvolume":" 71","title":"Evolutionary rescue in randomly mating, selfing, and clonal populations","type":"journal_article","status":"public","article_processing_charge":"No","citation":{"ama":"Uecker H. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 2017;71(4):845-858. doi:10.1111/evo.13191","short":"H. Uecker, Evolution 71 (2017) 845–858.","chicago":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13191.","apa":"Uecker, H. (2017). Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13191","mla":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” Evolution, vol. 71, no. 4, Wiley-Blackwell, 2017, pp. 845–58, doi:10.1111/evo.13191.","ieee":"H. Uecker, “Evolutionary rescue in randomly mating, selfing, and clonal populations,” Evolution, vol. 71, no. 4. Wiley-Blackwell, pp. 845–858, 2017.","ista":"Uecker H. 2017. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 71(4), 845–858."},"isi":1},{"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Georg F","last_name":"Osang","orcid":"0000-0002-8882-5116","full_name":"Osang, Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2017-06-01T00:00:00Z","volume":122,"abstract":[{"lang":"eng","text":"We consider the problem of reachability in pushdown graphs. We study the problem for pushdown graphs with constant treewidth. Even for pushdown graphs with treewidth 1, for the reachability problem we establish the following: (i) the problem is PTIME-complete, and (ii) any subcubic algorithm for the problem would contradict the k-clique conjecture and imply faster combinatorial algorithms for cliques in graphs."}],"file_date_updated":"2019-10-15T07:44:51Z","ec_funded":1,"publication":"Information Processing Letters","year":"2017","language":[{"iso":"eng"}],"day":"01","scopus_import":"1","file":[{"file_name":"IST-2018-991-v1+2_2018_Chatterjee_Pushdown_PREPRINT.pdf","file_size":247657,"access_level":"open_access","date_updated":"2019-10-15T07:44:51Z","content_type":"application/pdf","creator":"system","date_created":"2018-12-12T10:13:17Z","relation":"main_file","file_id":"4998"}],"publisher":"Elsevier","date_created":"2018-12-11T11:49:57Z","project":[{"grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7"}],"has_accepted_license":"1","oa":1,"publication_status":"published","publication_identifier":{"issn":["00200190"]},"ddc":["000"],"date_updated":"2023-09-20T12:08:18Z","oa_version":"Submitted Version","month":"06","publist_id":"6323","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Pushdown reachability with constant treewidth","pubrep_id":"991","status":"public","type":"journal_article","citation":{"ieee":"K. Chatterjee and G. F. Osang, “Pushdown reachability with constant treewidth,” Information Processing Letters, vol. 122. Elsevier, pp. 25–29, 2017.","ista":"Chatterjee K, Osang GF. 2017. Pushdown reachability with constant treewidth. Information Processing Letters. 122, 25–29.","chicago":"Chatterjee, Krishnendu, and Georg F Osang. “Pushdown Reachability with Constant Treewidth.” Information Processing Letters. Elsevier, 2017. https://doi.org/10.1016/j.ipl.2017.02.003.","short":"K. Chatterjee, G.F. Osang, Information Processing Letters 122 (2017) 25–29.","ama":"Chatterjee K, Osang GF. Pushdown reachability with constant treewidth. Information Processing Letters. 2017;122:25-29. doi:10.1016/j.ipl.2017.02.003","mla":"Chatterjee, Krishnendu, and Georg F. Osang. “Pushdown Reachability with Constant Treewidth.” Information Processing Letters, vol. 122, Elsevier, 2017, pp. 25–29, doi:10.1016/j.ipl.2017.02.003.","apa":"Chatterjee, K., & Osang, G. F. (2017). Pushdown reachability with constant treewidth. Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2017.02.003"},"article_processing_charge":"No","isi":1,"quality_controlled":"1","department":[{"_id":"KrCh"},{"_id":"HeEd"}],"external_id":{"isi":["000399506600005"]},"doi":"10.1016/j.ipl.2017.02.003","intvolume":" 122","page":"25 - 29","_id":"1065"}]