[{"OA_place":"publisher","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"research_data","id":"9719"}]},"pubrep_id":"587","publication_status":"published","scopus_import":"1","issue":"3","publication":"Molecular Biology and Evolution","ddc":["576"],"day":"01","abstract":[{"lang":"eng","text":"Parasitism creates selection for resistance mechanisms in host populations and is hypothesized to promote increased host evolvability. However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance."}],"oa_version":"Published Version","author":[{"first_name":"Sébastien","last_name":"Wielgoss","full_name":"Wielgoss, Sébastien"},{"last_name":"Bergmiller","first_name":"Tobias","full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346"},{"last_name":"Bischofberger","full_name":"Bischofberger, Anna M.","first_name":"Anna M."},{"last_name":"Hall","first_name":"Alex R.","full_name":"Hall, Alex R."}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","external_id":{"isi":["000371219500015"],"pmid":["26609077"]},"file":[{"content_type":"application/pdf","file_size":634037,"file_name":"2016_MolBiolEvol_Wielgoss.pdf","file_id":"5750","creator":"dernst","checksum":"47d9010690b6c5c17f2ac830cc63ac5c","date_updated":"2020-07-14T12:47:10Z","access_level":"open_access","relation":"main_file","date_created":"2018-12-18T13:21:45Z"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"department":[{"_id":"CaGu"}],"title":"Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria","doi":"10.1093/molbev/msv270","acknowledgement":"The authors thank three anonymous reviewers and the editor for helpful comments on the manuscript, as well as Dominique Schneider for feedback on an earlier draft, Jenna Gallie for lytic λ and Julien Capelle for T5 and T6. This work was supported by the Swiss National Science Foundation (PZ00P3_148255 to A.H.) and an EU Marie Curie PEOPLE Postdoctoral Fellowship for Career Development (FP7-PEOPLE-2012-IEF-331824 to S.W.).","date_updated":"2026-04-29T05:57:02Z","status":"public","publisher":"Oxford University Press","type":"journal_article","intvolume":"        33","isi":1,"OA_type":"gold","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5749","page":"770-782","year":"2016","pmid":1,"language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"date_created":"2018-12-18T13:18:10Z","oa":1,"article_processing_charge":"No","volume":33,"month":"03","citation":{"ista":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. 2016. Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. Molecular Biology and Evolution. 33(3), 770–782.","short":"S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, Molecular Biology and Evolution 33 (2016) 770–782.","ama":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. <i>Molecular Biology and Evolution</i>. 2016;33(3):770-782. doi:<a href=\"https://doi.org/10.1093/molbev/msv270\">10.1093/molbev/msv270</a>","chicago":"Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex R. Hall. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/molbev/msv270\">https://doi.org/10.1093/molbev/msv270</a>.","apa":"Wielgoss, S., Bergmiller, T., Bischofberger, A. M., &#38; Hall, A. R. (2016). Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msv270\">https://doi.org/10.1093/molbev/msv270</a>","ieee":"S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. Hall, “Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria,” <i>Molecular Biology and Evolution</i>, vol. 33, no. 3. Oxford University Press, pp. 770–782, 2016.","mla":"Wielgoss, Sébastien, et al. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.” <i>Molecular Biology and Evolution</i>, vol. 33, no. 3, Oxford University Press, 2016, pp. 770–82, doi:<a href=\"https://doi.org/10.1093/molbev/msv270\">10.1093/molbev/msv270</a>."},"file_date_updated":"2020-07-14T12:47:10Z","DOAJ_listed":"1","date_published":"2016-03-01T00:00:00Z"},{"status":"public","type":"journal_article","publisher":"Nature Publishing Group","date_updated":"2026-05-12T22:30:10Z","intvolume":"        18","doi":"10.1038/ncb3426","acknowledgement":"This work was supported by the German Research Foundation (DFG) Priority Program SP 1464 to T.E.B.S. and M.S., and European Research Council (ERC GA 281556) and Human Frontiers Program grants to M.S.\r\nService Units of IST Austria for excellent technical support.","publist_id":"5949","page":"1253 - 1259","acknowledged_ssus":[{"_id":"SSU"}],"_id":"1321","year":"2016","article_type":"original","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:51:21Z","language":[{"iso":"eng"}],"quality_controlled":"1","file_date_updated":"2020-07-14T12:44:43Z","date_published":"2016-10-24T00:00:00Z","volume":18,"article_processing_charge":"No","month":"10","oa":1,"citation":{"ama":"Leithner AF, Eichner A, Müller J, et al. Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. <i>Nature Cell Biology</i>. 2016;18:1253-1259. doi:<a href=\"https://doi.org/10.1038/ncb3426\">10.1038/ncb3426</a>","chicago":"Leithner, Alexander F, Alexander Eichner, Jan Müller, Anne Reversat, Markus Brown, Jan Schwarz, Jack Merrin, et al. “Diversified Actin Protrusions Promote Environmental Exploration but Are Dispensable for Locomotion of Leukocytes.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncb3426\">https://doi.org/10.1038/ncb3426</a>.","ieee":"A. F. Leithner <i>et al.</i>, “Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes,” <i>Nature Cell Biology</i>, vol. 18. Nature Publishing Group, pp. 1253–1259, 2016.","mla":"Leithner, Alexander F., et al. “Diversified Actin Protrusions Promote Environmental Exploration but Are Dispensable for Locomotion of Leukocytes.” <i>Nature Cell Biology</i>, vol. 18, Nature Publishing Group, 2016, pp. 1253–59, doi:<a href=\"https://doi.org/10.1038/ncb3426\">10.1038/ncb3426</a>.","apa":"Leithner, A. F., Eichner, A., Müller, J., Reversat, A., Brown, M., Schwarz, J., … Sixt, M. K. (2016). Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb3426\">https://doi.org/10.1038/ncb3426</a>","short":"A.F. Leithner, A. Eichner, J. Müller, A. Reversat, M. Brown, J. Schwarz, J. Merrin, D. De Gorter, F.K. Schur, J. Bayerl, I. de Vries, S. Wieser, R. Hauschild, F. Lai, M. Moser, D. Kerjaschki, K. Rottner, V. Small, T. Stradal, M.K. Sixt, Nature Cell Biology 18 (2016) 1253–1259.","ista":"Leithner AF, Eichner A, Müller J, Reversat A, Brown M, Schwarz J, Merrin J, De Gorter D, Schur FK, Bayerl J, de Vries I, Wieser S, Hauschild R, Lai F, Moser M, Kerjaschki D, Rottner K, Small V, Stradal T, Sixt MK. 2016. Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. Nature Cell Biology. 18, 1253–1259."},"corr_author":"1","publication_status":"published","scopus_import":"1","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"323"}]},"ec_funded":1,"oa_version":"Submitted Version","publication":"Nature Cell Biology","project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","call_identifier":"FP7","grant_number":"281556"}],"abstract":[{"lang":"eng","text":"Most migrating cells extrude their front by the force of actin polymerization. Polymerization requires an initial nucleation step, which is mediated by factors establishing either parallel filaments in the case of filopodia or branched filaments that form the branched lamellipodial network. Branches are considered essential for regular cell motility and are initiated by the Arp2/3 complex, which in turn is activated by nucleation-promoting factors of the WASP and WAVE families. Here we employed rapid amoeboid crawling leukocytes and found that deletion of the WAVE complex eliminated actin branching and thus lamellipodia formation. The cells were left with parallel filaments at the leading edge, which translated, depending on the differentiation status of the cell, into a unipolar pointed cell shape or cells with multiple filopodia. Remarkably, unipolar cells migrated with increased speed and enormous directional persistence, while they were unable to turn towards chemotactic gradients. Cells with multiple filopodia retained chemotactic activity but their migration was progressively impaired with increasing geometrical complexity of the extracellular environment. These findings establish that diversified leading edge protrusions serve as explorative structures while they slow down actual locomotion."}],"day":"24","ddc":["570"],"external_id":{"isi":["000387165600018"]},"author":[{"orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F","last_name":"Leithner","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F"},{"last_name":"Eichner","first_name":"Alexander","full_name":"Eichner, Alexander","id":"4DFA52AE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Müller, Jan","first_name":"Jan","last_name":"Müller","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D"},{"orcid":"0000-0003-0666-8928","full_name":"Reversat, Anne","id":"35B76592-F248-11E8-B48F-1D18A9856A87","first_name":"Anne","last_name":"Reversat"},{"first_name":"Markus","last_name":"Brown","full_name":"Brown, Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schwarz, Jan","first_name":"Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz"},{"full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","last_name":"Merrin","orcid":"0000-0001-5145-4609"},{"first_name":"David","full_name":"De Gorter, David","last_name":"De Gorter"},{"first_name":"Florian","full_name":"Schur, Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","orcid":"0000-0003-4790-8078"},{"first_name":"Jonathan","last_name":"Bayerl","full_name":"Bayerl, Jonathan"},{"full_name":"De Vries, Ingrid","last_name":"De Vries","first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87"},{"id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","full_name":"Wieser, Stefan","last_name":"Wieser","first_name":"Stefan","orcid":"0000-0002-2670-2217"},{"first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522"},{"first_name":"Frank","full_name":"Lai, Frank","last_name":"Lai"},{"first_name":"Markus","full_name":"Moser, Markus","last_name":"Moser"},{"first_name":"Dontscho","last_name":"Kerjaschki","full_name":"Kerjaschki, Dontscho"},{"first_name":"Klemens","last_name":"Rottner","full_name":"Rottner, Klemens"},{"last_name":"Small","full_name":"Small, Victor","first_name":"Victor"},{"full_name":"Stradal, Theresia","first_name":"Theresia","last_name":"Stradal"},{"orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","title":"Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes","file":[{"file_size":4433280,"content_type":"application/pdf","file_name":"2018_NatureCell_Leithner.pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:43Z","relation":"main_file","date_created":"2020-05-14T16:33:46Z","creator":"dernst","file_id":"7844","checksum":"e1411cb7c99a2d9089c178a6abef25e7"}],"tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"}]},{"quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:50:35Z","citation":{"short":"D.-C. Tarlungeanu, E. Deliu, C. Dotter, M. Kara, P. Janiesch, M. Scalise, M. Galluccio, M. Tesulov, E. Morelli, F. Sönmez, K. Bilgüvar, R. Ohgaki, Y. Kanai, A. Johansen, S. Esharif, T. Ben Omran, M. Topcu, A. Schlessinger, C. Indiveri, K. Duncan, A. Caglayan, M. Günel, J. Gleeson, G. Novarino, Cell 167 (2016) 1481–1494.","ista":"Tarlungeanu D-C, Deliu E, Dotter C, Kara M, Janiesch P, Scalise M, Galluccio M, Tesulov M, Morelli E, Sönmez F, Bilgüvar K, Ohgaki R, Kanai Y, Johansen A, Esharif S, Ben Omran T, Topcu M, Schlessinger A, Indiveri C, Duncan K, Caglayan A, Günel M, Gleeson J, Novarino G. 2016. Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. Cell. 167(6), 1481–1494.","ama":"Tarlungeanu D-C, Deliu E, Dotter C, et al. Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. <i>Cell</i>. 2016;167(6):1481-1494. doi:<a href=\"https://doi.org/10.1016/j.cell.2016.11.013\">10.1016/j.cell.2016.11.013</a>","chicago":"Tarlungeanu, Dora-Clara, Elena Deliu, Christoph Dotter, Majdi Kara, Philipp Janiesch, Mariafrancesca Scalise, Michele Galluccio, et al. “Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.” <i>Cell</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.cell.2016.11.013\">https://doi.org/10.1016/j.cell.2016.11.013</a>.","mla":"Tarlungeanu, Dora-Clara, et al. “Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.” <i>Cell</i>, vol. 167, no. 6, Cell Press, 2016, pp. 1481–94, doi:<a href=\"https://doi.org/10.1016/j.cell.2016.11.013\">10.1016/j.cell.2016.11.013</a>.","ieee":"D.-C. Tarlungeanu <i>et al.</i>, “Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder,” <i>Cell</i>, vol. 167, no. 6. Cell Press, pp. 1481–1494, 2016.","apa":"Tarlungeanu, D.-C., Deliu, E., Dotter, C., Kara, M., Janiesch, P., Scalise, M., … Novarino, G. (2016). Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2016.11.013\">https://doi.org/10.1016/j.cell.2016.11.013</a>"},"month":"12","volume":167,"article_processing_charge":"No","oa":1,"date_published":"2016-12-01T00:00:00Z","file_date_updated":"2020-07-14T12:44:37Z","publist_id":"6170","acknowledgement":"This work was supported by NICHD (P01HD070494) and SFARI (grant 275275) to J.G.G., and FWF (SFB35_3523) to G.N.\r\nWe thank A.C. Manzano, Mike Liu, and F. Marr for technical assistance, and R. Shigemoto and the IST Austria Electron Microscopy (EM) Facility for assistance. We acknowledge support from CIDR for genome-wide SNP analysis (X01HG008823) and Broad Institute Center for Mendelian Disorders (UM1HG008900 to D. MacArthur), the Yale Center for Mendelian Disorders (U54HG006504 to M.G.), the Gregory M. Kiez and Mehmet Kutman Foundation (M.G.), Italian Ministry of Instruction University and Research (PON01_00937 to C.I.), and NIH (R01-GM108911 to A.S.). This work was supported by NICHD (P01HD070494) and SFARI (grant 275275) to J.G.G., and FWF (SFB35_3523) to G.N.\r\n\r\n#EMFacility","doi":"10.1016/j.cell.2016.11.013","intvolume":"       167","type":"journal_article","status":"public","publisher":"Cell Press","date_updated":"2026-05-12T22:31:06Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","isi":1,"year":"2016","page":"1481 - 1494","_id":"1183","author":[{"first_name":"Dora-Clara","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","last_name":"Tarlungeanu","full_name":"Tarlungeanu, Dora-Clara"},{"orcid":"0000-0002-7370-5293","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","full_name":"Deliu, Elena","last_name":"Deliu","first_name":"Elena"},{"orcid":"0000-0002-9033-9096","full_name":"Dotter, Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Dotter"},{"last_name":"Kara","first_name":"Majdi","full_name":"Kara, Majdi"},{"last_name":"Janiesch","full_name":"Janiesch, Philipp","first_name":"Philipp"},{"last_name":"Scalise","full_name":"Scalise, Mariafrancesca","first_name":"Mariafrancesca"},{"last_name":"Galluccio","first_name":"Michele","full_name":"Galluccio, Michele"},{"last_name":"Tesulov","full_name":"Tesulov, Mateja","first_name":"Mateja"},{"id":"3F4D1282-F248-11E8-B48F-1D18A9856A87","last_name":"Morelli","full_name":"Morelli, Emanuela","first_name":"Emanuela"},{"first_name":"Fatma","full_name":"Sönmez, Fatma","last_name":"Sönmez"},{"last_name":"Bilgüvar","full_name":"Bilgüvar, Kaya","first_name":"Kaya"},{"full_name":"Ohgaki, Ryuichi","first_name":"Ryuichi","last_name":"Ohgaki"},{"full_name":"Kanai, Yoshikatsu","last_name":"Kanai","first_name":"Yoshikatsu"},{"full_name":"Johansen, Anide","last_name":"Johansen","first_name":"Anide"},{"first_name":"Seham","full_name":"Esharif, Seham","last_name":"Esharif"},{"full_name":"Ben Omran, Tawfeg","last_name":"Ben Omran","first_name":"Tawfeg"},{"first_name":"Meral","last_name":"Topcu","full_name":"Topcu, Meral"},{"full_name":"Schlessinger, Avner","last_name":"Schlessinger","first_name":"Avner"},{"full_name":"Indiveri, Cesare","first_name":"Cesare","last_name":"Indiveri"},{"first_name":"Kent","last_name":"Duncan","full_name":"Duncan, Kent"},{"full_name":"Caglayan, Ahmet","last_name":"Caglayan","first_name":"Ahmet"},{"first_name":"Murat","last_name":"Günel","full_name":"Günel, Murat"},{"last_name":"Gleeson","first_name":"Joseph","full_name":"Gleeson, Joseph"},{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000389470500012"]},"department":[{"_id":"GaNo"}],"file":[{"content_type":"application/pdf","file_size":73907957,"file_name":"IST-2017-771-v1+1_Tarlungeanu_et_al._Final_edited.pdf","creator":"system","checksum":"7fe01ab12a6610d3db421e0136db2f77","file_id":"5030","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:44:37Z","date_created":"2018-12-12T10:13:44Z"}],"title":"Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder","pubrep_id":"771","has_accepted_license":"1","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"395"}]},"scopus_import":"1","publication_status":"published","project":[{"_id":"25473368-B435-11E9-9278-68D0E5697425","name":"Transmembrane Transporters in Health and Disease","call_identifier":"FWF","grant_number":"F03523"}],"day":"01","ddc":["576","616"],"abstract":[{"lang":"eng","text":"Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. We previously described abnormalities in the branched-chain amino acid (BCAA) catabolic pathway as a cause of ASD. Here, we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation, and severe neurological abnormalities. Furthermore, we identified several patients with autistic traits and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. Finally, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for the BCAA in human brain function."}],"publication":"Cell","issue":"6","oa_version":"Submitted Version"},{"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"866 - 877","acknowledged_ssus":[{"_id":"SSU"}],"_id":"1100","year":"2016","doi":"10.1016/j.celrep.2016.06.036","acknowledgement":"We are grateful to members of the C.-P.H. and H.J. labs for discussions, R. Hauschild and the different Scientific Service Units at IST Austria for technical help, M. Dravecka for performing initial experiments, A. Schier for reading an earlier version of the manuscript, K.W. Rogers for technical help, and C. Hill, A. Bruce, and L. Solnica-Krezel for sending plasmids. This work was supported by grants from the Austrian Science Foundation (FWF): (T560-B17) and (I 812-B12) to V.R. and C.-P.H., and from the European Union (EU FP7): (6275) to H.J. A.I.-P. is supported by a Ramon Areces fellowship.","publist_id":"6275","status":"public","publisher":"Cell Press","type":"journal_article","date_updated":"2026-05-12T22:31:15Z","intvolume":"        16","month":"07","volume":16,"article_processing_charge":"No","oa":1,"citation":{"apa":"Sako, K., Pradhan, S., Barone, V., Inglés Prieto, Á., Mueller, P., Ruprecht, V., … Heisenberg, C.-P. J. (2016). Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2016.06.036\">https://doi.org/10.1016/j.celrep.2016.06.036</a>","mla":"Sako, Keisuke, et al. “Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.” <i>Cell Reports</i>, vol. 16, no. 3, Cell Press, 2016, pp. 866–77, doi:<a href=\"https://doi.org/10.1016/j.celrep.2016.06.036\">10.1016/j.celrep.2016.06.036</a>.","ieee":"K. Sako <i>et al.</i>, “Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation,” <i>Cell Reports</i>, vol. 16, no. 3. Cell Press, pp. 866–877, 2016.","ama":"Sako K, Pradhan S, Barone V, et al. Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. <i>Cell Reports</i>. 2016;16(3):866-877. doi:<a href=\"https://doi.org/10.1016/j.celrep.2016.06.036\">10.1016/j.celrep.2016.06.036</a>","chicago":"Sako, Keisuke, Saurabh Pradhan, Vanessa Barone, Álvaro Inglés Prieto, Patrick Mueller, Verena Ruprecht, Daniel Capek, Sanjeev Galande, Harald L Janovjak, and Carl-Philipp J Heisenberg. “Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.” <i>Cell Reports</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.celrep.2016.06.036\">https://doi.org/10.1016/j.celrep.2016.06.036</a>.","ista":"Sako K, Pradhan S, Barone V, Inglés Prieto Á, Mueller P, Ruprecht V, Capek D, Galande S, Janovjak HL, Heisenberg C-PJ. 2016. Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. Cell Reports. 16(3), 866–877.","short":"K. Sako, S. Pradhan, V. Barone, Á. Inglés Prieto, P. Mueller, V. Ruprecht, D. Capek, S. Galande, H.L. Janovjak, C.-P.J. Heisenberg, Cell Reports 16 (2016) 866–877."},"file_date_updated":"2018-12-12T10:11:04Z","date_published":"2016-07-19T00:00:00Z","language":[{"iso":"eng"}],"quality_controlled":"1","date_created":"2018-12-11T11:50:08Z","issue":"3","publication":"Cell Reports","project":[{"grant_number":"T 560-B17","name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation","call_identifier":"FWF","_id":"2529486C-B435-11E9-9278-68D0E5697425"},{"name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","call_identifier":"FWF","_id":"2527D5CC-B435-11E9-9278-68D0E5697425","grant_number":"I812-B12"},{"name":"Microbial Ion Channels for Synthetic Neurobiology","call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564"}],"day":"19","abstract":[{"text":"During metazoan development, the temporal pattern of morphogen signaling is critical for organizing cell fates in space and time. Yet, tools for temporally controlling morphogen signaling within the embryo are still scarce. Here, we developed a photoactivatable Nodal receptor to determine how the temporal pattern of Nodal signaling affects cell fate specification during zebrafish gastrulation. By using this receptor to manipulate the duration of Nodal signaling in vivo by light, we show that extended Nodal signaling within the organizer promotes prechordal plate specification and suppresses endoderm differentiation. Endoderm differentiation is suppressed by extended Nodal signaling inducing expression of the transcriptional repressor goosecoid (gsc) in prechordal plate progenitors, which in turn restrains Nodal signaling from upregulating the endoderm differentiation gene sox17 within these cells. Thus, optogenetic manipulation of Nodal signaling identifies a critical role of Nodal signaling duration for organizer cell fate specification during gastrulation.","lang":"eng"}],"ddc":["570","576"],"ec_funded":1,"oa_version":"Published Version","pubrep_id":"754","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"961"},{"id":"50","relation":"dissertation_contains","status":"public"}]},"publication_status":"published","scopus_import":"1","file":[{"date_created":"2018-12-12T10:11:04Z","access_level":"open_access","relation":"main_file","date_updated":"2018-12-12T10:11:04Z","creator":"system","file_id":"4857","file_name":"IST-2017-754-v1+1_1-s2.0-S2211124716307768-main.pdf","file_size":3921947,"content_type":"application/pdf"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"CaHe"},{"_id":"HaJa"}],"title":"Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation","license":"https://creativecommons.org/licenses/by/4.0/","author":[{"first_name":"Keisuke","full_name":"Sako, Keisuke","last_name":"Sako","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6453-8075"},{"last_name":"Pradhan","first_name":"Saurabh","full_name":"Pradhan, Saurabh"},{"orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa","last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa"},{"orcid":"0000-0002-5409-8571","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","full_name":"Inglés Prieto, Álvaro","first_name":"Álvaro","last_name":"Inglés Prieto"},{"full_name":"Mueller, Patrick","last_name":"Mueller","first_name":"Patrick"},{"full_name":"Ruprecht, Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","last_name":"Ruprecht","first_name":"Verena","orcid":"0000-0003-4088-8633"},{"orcid":"0000-0001-5199-9940","last_name":"Capek","id":"31C42484-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","full_name":"Capek, Daniel"},{"full_name":"Galande, Sanjeev","first_name":"Sanjeev","last_name":"Galande"},{"orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L","full_name":"Janovjak, Harald L"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"external_id":{"isi":["000380264200024"]}},{"language":[{"iso":"eng"}],"quality_controlled":"1","arxiv":1,"date_created":"2018-12-11T11:52:01Z","conference":{"end_date":"2016-01-22","name":"POPL: Principles of Programming Languages","start_date":"2016-01-20","location":"St. Petersburg, FL, USA"},"oa":1,"volume":"20-22","month":"01","citation":{"mla":"Chatterjee, Krishnendu, et al. <i>Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components</i>. Vol. 20–22, ACM, 2016, pp. 733–47, doi:<a href=\"https://doi.org/10.1145/2837614.2837624\">10.1145/2837614.2837624</a>.","ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Algorithms for algebraic path properties in concurrent systems of constant treewidth components,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 733–747.","apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2016). Algorithms for algebraic path properties in concurrent systems of constant treewidth components (Vol. 20–22, pp. 733–747). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. <a href=\"https://doi.org/10.1145/2837614.2837624\">https://doi.org/10.1145/2837614.2837624</a>","ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. In: Vol 20-22. ACM; 2016:733-747. doi:<a href=\"https://doi.org/10.1145/2837614.2837624\">10.1145/2837614.2837624</a>","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components,” 20–22:733–47. ACM, 2016. <a href=\"https://doi.org/10.1145/2837614.2837624\">https://doi.org/10.1145/2837614.2837624</a>.","short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, ACM, 2016, pp. 733–747.","ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2016. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. POPL: Principles of Programming Languages, POPL, vol. 20–22, 733–747."},"date_published":"2016-01-11T00:00:00Z","doi":"10.1145/2837614.2837624","publist_id":"5761","date_updated":"2026-05-12T22:31:18Z","type":"conference","status":"public","publisher":"ACM","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1437","page":"733 - 747","year":"2016","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0003-1702-6584","first_name":"Amir","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir"},{"orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus"},{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"}],"external_id":{"arxiv":["1510.07565"]},"main_file_link":[{"url":"http://arxiv.org/abs/1510.07565","open_access":"1"}],"department":[{"_id":"KrCh"}],"title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","alternative_title":["POPL"],"related_material":{"record":[{"id":"5441","status":"public","relation":"earlier_version"},{"relation":"earlier_version","status":"public","id":"5442"},{"id":"6009","status":"public","relation":"later_version"},{"status":"public","relation":"dissertation_contains","id":"821"},{"relation":"dissertation_contains","status":"public","id":"8934"}]},"corr_author":"1","publication_status":"published","scopus_import":1,"abstract":[{"lang":"eng","text":"We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time. Our main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks."}],"day":"11","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"ec_funded":1,"oa_version":"Preprint"},{"citation":{"ista":"Chatterjee K, Fu H, Goharshady AK. 2016. Termination analysis of probabilistic programs through Positivstellensatz’s. CAV: Computer Aided Verification, LNCS, vol. 9779, 3–22.","short":"K. Chatterjee, H. Fu, A.K. Goharshady, in:, Springer, 2016, pp. 3–22.","chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Termination Analysis of Probabilistic Programs through Positivstellensatz’s,” 9779:3–22. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-41528-4_1\">https://doi.org/10.1007/978-3-319-41528-4_1</a>.","ama":"Chatterjee K, Fu H, Goharshady AK. Termination analysis of probabilistic programs through Positivstellensatz’s. In: Vol 9779. Springer; 2016:3-22. doi:<a href=\"https://doi.org/10.1007/978-3-319-41528-4_1\">10.1007/978-3-319-41528-4_1</a>","apa":"Chatterjee, K., Fu, H., &#38; Goharshady, A. K. (2016). Termination analysis of probabilistic programs through Positivstellensatz’s (Vol. 9779, pp. 3–22). Presented at the CAV: Computer Aided Verification, Toronto, Canada: Springer. <a href=\"https://doi.org/10.1007/978-3-319-41528-4_1\">https://doi.org/10.1007/978-3-319-41528-4_1</a>","ieee":"K. Chatterjee, H. Fu, and A. K. Goharshady, “Termination analysis of probabilistic programs through Positivstellensatz’s,” presented at the CAV: Computer Aided Verification, Toronto, Canada, 2016, vol. 9779, pp. 3–22.","mla":"Chatterjee, Krishnendu, et al. <i>Termination Analysis of Probabilistic Programs through Positivstellensatz’s</i>. Vol. 9779, Springer, 2016, pp. 3–22, doi:<a href=\"https://doi.org/10.1007/978-3-319-41528-4_1\">10.1007/978-3-319-41528-4_1</a>."},"oa":1,"month":"07","volume":9779,"article_processing_charge":"No","date_published":"2016-07-01T00:00:00Z","quality_controlled":"1","language":[{"iso":"eng"}],"conference":{"location":"Toronto, Canada","start_date":"2016-07-17","end_date":"2016-07-23","name":"CAV: Computer Aided Verification"},"arxiv":1,"date_created":"2018-12-11T11:51:43Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"year":"2016","_id":"1386","page":"3 - 22","publist_id":"5824","doi":"10.1007/978-3-319-41528-4_1","intvolume":"      9779","date_updated":"2026-05-12T22:31:19Z","publisher":"Springer","type":"conference","status":"public","department":[{"_id":"KrCh"}],"main_file_link":[{"url":"http://arxiv.org/abs/1604.07169","open_access":"1"}],"title":"Termination analysis of probabilistic programs through Positivstellensatz's","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Fu, Hongfei","first_name":"Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","last_name":"Fu"},{"orcid":"0000-0003-1702-6584","last_name":"Goharshady","full_name":"Goharshady, Amir","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir"}],"external_id":{"isi":["000387731200001"],"arxiv":["1604.07169"]},"abstract":[{"text":"We consider nondeterministic probabilistic programs with the most basic liveness property of termination. We present efficient methods for termination analysis of nondeterministic probabilistic programs with polynomial guards and assignments. Our approach is through synthesis of polynomial ranking supermartingales, that on one hand significantly generalizes linear ranking supermartingales and on the other hand is a counterpart of polynomial ranking-functions for proving termination of nonprobabilistic programs. The approach synthesizes polynomial ranking-supermartingales through Positivstellensatz's, yielding an efficient method which is not only sound, but also semi-complete over a large subclass of programs. We show experimental results to demonstrate that our approach can handle several classical programs with complex polynomial guards and assignments, and can synthesize efficient quadratic ranking-supermartingales when a linear one does not exist even for simple affine programs.","lang":"eng"}],"day":"01","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"},{"grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"oa_version":"Preprint","ec_funded":1,"related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"alternative_title":["LNCS"],"scopus_import":"1","corr_author":"1","publication_status":"published"},{"publication_status":"published","scopus_import":"1","article_number":"15094","oa_version":"Submitted Version","publication":"Nature Plants","issue":"7","abstract":[{"lang":"eng","text":"In plants, vacuolar H+-ATPase (V-ATPase) activity acidifies both the trans-Golgi network/early endosome (TGN/EE) and the vacuole. This dual V-ATPase function has impeded our understanding of how the pH homeostasis within the plant TGN/EE controls exo- and endocytosis. Here, we show that the weak V-ATPase mutant deetiolated3 (det3) displayed a pH increase in the TGN/EE, but not in the vacuole, strongly impairing secretion and recycling of the brassinosteroid receptor and the cellulose synthase complexes to the plasma membrane, in contrast to mutants lacking tonoplast-localized V-ATPase activity only. The brassinosteroid insensitivity and the cellulose deficiency defects in det3 were tightly correlated with reduced Golgi and TGN/EE motility. Thus, our results provide strong evidence that acidification of the TGN/EE, but not of the vacuole, is indispensable for functional secretion and recycling in plants."}],"day":"06","external_id":{"pmid":["27250258"],"isi":["000364407200001"]},"author":[{"first_name":"Luo","full_name":"Yu, Luo","last_name":"Yu"},{"full_name":"Scholl, Stefan","first_name":"Stefan","last_name":"Scholl"},{"last_name":"Doering","first_name":"Anett","full_name":"Doering, Anett"},{"last_name":"Yi","full_name":"Yi, Zhang","first_name":"Zhang"},{"first_name":"Niloufer","last_name":"Irani","full_name":"Irani, Niloufer"},{"first_name":"Simone","last_name":"Di Rubbo","full_name":"Di Rubbo, Simone"},{"full_name":"Neumetzler, Lutz","last_name":"Neumetzler","first_name":"Lutz"},{"full_name":"Krishnamoorthy, Praveen","last_name":"Krishnamoorthy","first_name":"Praveen"},{"last_name":"Van Houtte","full_name":"Van Houtte, Isabelle","first_name":"Isabelle"},{"full_name":"Mylle, Evelien","first_name":"Evelien","last_name":"Mylle"},{"full_name":"Bischoff, Volker","first_name":"Volker","last_name":"Bischoff"},{"last_name":"Vernhettes","first_name":"Samantha","full_name":"Vernhettes, Samantha"},{"full_name":"Winne, Johan","last_name":"Winne","first_name":"Johan"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí"},{"full_name":"Stierhof, York","first_name":"York","last_name":"Stierhof"},{"first_name":"Karin","full_name":"Schumacher, Karin","last_name":"Schumacher"},{"full_name":"Persson, Staffan","last_name":"Persson","first_name":"Staffan"},{"last_name":"Russinova","first_name":"Eugenia","full_name":"Russinova, Eugenia"}],"title":"V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4905525/"}],"department":[{"_id":"JiFr"}],"type":"journal_article","status":"public","publisher":"Nature Publishing Group","date_updated":"2025-09-29T11:04:05Z","intvolume":"         1","doi":"10.1038/nplants.2015.94","publist_id":"5827","_id":"1383","year":"2015","pmid":1,"article_type":"original","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:51:42Z","language":[{"iso":"eng"}],"quality_controlled":"1","date_published":"2015-07-06T00:00:00Z","article_processing_charge":"No","volume":1,"month":"07","oa":1,"citation":{"apa":"Yu, L., Scholl, S., Doering, A., Yi, Z., Irani, N., Di Rubbo, S., … Russinova, E. (2015). V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. <i>Nature Plants</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nplants.2015.94\">https://doi.org/10.1038/nplants.2015.94</a>","ieee":"L. Yu <i>et al.</i>, “V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis,” <i>Nature Plants</i>, vol. 1, no. 7. Nature Publishing Group, 2015.","mla":"Yu, Luo, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis and Recycling in Arabidopsis.” <i>Nature Plants</i>, vol. 1, no. 7, 15094, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/nplants.2015.94\">10.1038/nplants.2015.94</a>.","ama":"Yu L, Scholl S, Doering A, et al. V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. <i>Nature Plants</i>. 2015;1(7). doi:<a href=\"https://doi.org/10.1038/nplants.2015.94\">10.1038/nplants.2015.94</a>","chicago":"Yu, Luo, Stefan Scholl, Anett Doering, Zhang Yi, Niloufer Irani, Simone Di Rubbo, Lutz Neumetzler, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis and Recycling in Arabidopsis.” <i>Nature Plants</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/nplants.2015.94\">https://doi.org/10.1038/nplants.2015.94</a>.","ista":"Yu L, Scholl S, Doering A, Yi Z, Irani N, Di Rubbo S, Neumetzler L, Krishnamoorthy P, Van Houtte I, Mylle E, Bischoff V, Vernhettes S, Winne J, Friml J, Stierhof Y, Schumacher K, Persson S, Russinova E. 2015. V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. 1(7), 15094.","short":"L. Yu, S. Scholl, A. Doering, Z. Yi, N. Irani, S. Di Rubbo, L. Neumetzler, P. Krishnamoorthy, I. Van Houtte, E. Mylle, V. Bischoff, S. Vernhettes, J. Winne, J. Friml, Y. Stierhof, K. Schumacher, S. Persson, E. Russinova, Nature Plants 1 (2015)."}},{"conference":{"name":"NIPS: Neural Information Processing Systems","end_date":"2015-12-12","location":"Montreal, Canada","start_date":"2015-12-07"},"date_created":"2018-12-11T11:51:56Z","quality_controlled":"1","author":[{"first_name":"Roland","last_name":"Kwitt","full_name":"Kwitt, Roland"},{"last_name":"Huber","full_name":"Huber, Stefan","first_name":"Stefan","id":"4700A070-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8871-5814"},{"first_name":"Marc","last_name":"Niethammer","full_name":"Niethammer, Marc"},{"last_name":"Lin","full_name":"Lin, Weili","first_name":"Weili"},{"full_name":"Bauer, Ulrich","first_name":"Ulrich","last_name":"Bauer","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9683-0724"}],"language":[{"iso":"eng"}],"title":"Statistical topological data analysis-A kernel perspective","date_published":"2015-12-01T00:00:00Z","citation":{"short":"R. Kwitt, S. Huber, M. Niethammer, W. Lin, U. Bauer, in:, Neural Information Processing Systems Foundation, 2015, pp. 3070–3078.","ista":"Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. 2015. Statistical topological data analysis-A kernel perspective. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 28, 3070–3078.","ieee":"R. Kwitt, S. Huber, M. Niethammer, W. Lin, and U. Bauer, “Statistical topological data analysis-A kernel perspective,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2015, vol. 28, pp. 3070–3078.","mla":"Kwitt, Roland, et al. <i>Statistical Topological Data Analysis-A Kernel Perspective</i>. Vol. 28, Neural Information Processing Systems Foundation, 2015, pp. 3070–78.","apa":"Kwitt, R., Huber, S., Niethammer, M., Lin, W., &#38; Bauer, U. (2015). Statistical topological data analysis-A kernel perspective (Vol. 28, pp. 3070–3078). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems Foundation.","chicago":"Kwitt, Roland, Stefan Huber, Marc Niethammer, Weili Lin, and Ulrich Bauer. “Statistical Topological Data Analysis-A Kernel Perspective,” 28:3070–78. Neural Information Processing Systems Foundation, 2015.","ama":"Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. Statistical topological data analysis-A kernel perspective. In: Vol 28. Neural Information Processing Systems Foundation; 2015:3070-3078."},"department":[{"_id":"HeEd"}],"oa":1,"main_file_link":[{"url":"https://papers.nips.cc/paper/5887-statistical-topological-data-analysis-a-kernel-perspective","open_access":"1"}],"month":"12","volume":28,"article_processing_charge":"No","intvolume":"        28","date_updated":"2025-06-03T11:41:36Z","status":"public","type":"conference","publisher":"Neural Information Processing Systems Foundation","publication_status":"published","publist_id":"5782","alternative_title":["Advances in Neural Information Processing Systems"],"acknowledgement":"This work was partially supported by the Austrian Science FUnd, project no. KLI 00012.","oa_version":"Submitted Version","year":"2015","_id":"1424","page":"3070 - 3078","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","abstract":[{"lang":"eng","text":"We consider the problem of statistical computations with persistence diagrams, a summary representation of topological features in data. These diagrams encode persistent homology, a widely used invariant in topological data analysis. While several avenues towards a statistical treatment of the diagrams have been explored recently, we follow an alternative route that is motivated by the success of methods based on the embedding of probability measures into reproducing kernel Hilbert spaces. In fact, a positive definite kernel on persistence diagrams has recently been proposed, connecting persistent homology to popular kernel-based learning techniques such as support vector machines. However, important properties of that kernel enabling a principled use in the context of probability measure embeddings remain to be explored. Our contribution is to close this gap by proving universality of a variant of the original kernel, and to demonstrate its effective use in twosample hypothesis testing on synthetic as well as real-world data."}]},{"main_file_link":[{"url":"http://papers.nips.cc/paper/6007-lifelong-learning-with-non-iid-tasks","open_access":"1"}],"department":[{"_id":"ChLa"}],"title":"Lifelong learning with non-i.i.d. tasks","author":[{"full_name":"Pentina, Anastasia","last_name":"Pentina","id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","first_name":"Anastasia"},{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert"}],"day":"01","abstract":[{"lang":"eng","text":"In this work we aim at extending the theoretical foundations of lifelong learning. Previous work analyzing this scenario is based on the assumption that learning tasks are sampled i.i.d. from a task environment or limited to strongly constrained data distributions. Instead, we study two scenarios when lifelong learning is possible, even though the observed tasks do not form an i.i.d. sample: first, when they are sampled from the same environment, but possibly with dependencies, and second, when the task environment is allowed to change over time in a consistent way. In the first case we prove a PAC-Bayesian theorem that can be seen as a direct generalization of the analogous previous result for the i.i.d. case. For the second scenario we propose to learn an inductive bias in form of a transfer procedure. We present a generalization bound and show on a toy example how it can be used to identify a beneficial transfer algorithm."}],"project":[{"grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding"}],"ec_funded":1,"oa_version":"None","alternative_title":["Advances in Neural Information Processing Systems"],"publication_status":"published","scopus_import":"1","oa":1,"month":"01","article_processing_charge":"No","volume":2015,"citation":{"ista":"Pentina A, Lampert C. 2015. Lifelong learning with non-i.i.d. tasks. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 2015, 1540–1548.","short":"A. Pentina, C. Lampert, in:, Neural Information Processing Systems Foundation, 2015, pp. 1540–1548.","chicago":"Pentina, Anastasia, and Christoph Lampert. “Lifelong Learning with Non-i.i.d. Tasks,” 2015:1540–48. Neural Information Processing Systems Foundation, 2015.","ama":"Pentina A, Lampert C. Lifelong learning with non-i.i.d. tasks. In: Vol 2015. Neural Information Processing Systems Foundation; 2015:1540-1548.","apa":"Pentina, A., &#38; Lampert, C. (2015). Lifelong learning with non-i.i.d. tasks (Vol. 2015, pp. 1540–1548). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems Foundation.","ieee":"A. Pentina and C. Lampert, “Lifelong learning with non-i.i.d. tasks,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2015, vol. 2015, pp. 1540–1548.","mla":"Pentina, Anastasia, and Christoph Lampert. <i>Lifelong Learning with Non-i.i.d. Tasks</i>. Vol. 2015, Neural Information Processing Systems Foundation, 2015, pp. 1540–48."},"date_published":"2015-01-01T00:00:00Z","language":[{"iso":"eng"}],"quality_controlled":"1","date_created":"2018-12-11T11:51:57Z","conference":{"location":"Montreal, Canada","start_date":"2015-12-07","name":"NIPS: Neural Information Processing Systems","end_date":"2015-12-12"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1425","page":"1540 - 1548","year":"2015","publist_id":"5781","date_updated":"2025-06-03T11:41:45Z","type":"conference","publisher":"Neural Information Processing Systems Foundation","status":"public","intvolume":"      2015"},{"language":[{"iso":"eng"}],"quality_controlled":"1","date_created":"2018-12-11T11:51:58Z","arxiv":1,"conference":{"location":"Madrid, Spain","start_date":"2015-07-11","name":"GECCO: Genetic and evolutionary computation conference","end_date":"2015-07-15"},"article_processing_charge":"No","month":"07","oa":1,"citation":{"ista":"Paixao T, Sudholt D, Heredia J, Trubenova B. 2015. First steps towards a runtime comparison of natural and artificial evolution. Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. GECCO: Genetic and evolutionary computation conference, 1455–1462.","short":"T. Paixao, D. Sudholt, J. Heredia, B. Trubenova, in:, Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–1462.","chicago":"Paixao, Tiago, Dirk Sudholt, Jorge Heredia, and Barbora Trubenova. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” In <i>Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation</i>, 1455–62. ACM, 2015. <a href=\"https://doi.org/10.1145/2739480.2754758\">https://doi.org/10.1145/2739480.2754758</a>.","ama":"Paixao T, Sudholt D, Heredia J, Trubenova B. First steps towards a runtime comparison of natural and artificial evolution. In: <i>Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation</i>. ACM; 2015:1455-1462. doi:<a href=\"https://doi.org/10.1145/2739480.2754758\">10.1145/2739480.2754758</a>","apa":"Paixao, T., Sudholt, D., Heredia, J., &#38; Trubenova, B. (2015). First steps towards a runtime comparison of natural and artificial evolution. In <i>Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation</i> (pp. 1455–1462). Madrid, Spain: ACM. <a href=\"https://doi.org/10.1145/2739480.2754758\">https://doi.org/10.1145/2739480.2754758</a>","mla":"Paixao, Tiago, et al. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” <i>Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation</i>, ACM, 2015, pp. 1455–62, doi:<a href=\"https://doi.org/10.1145/2739480.2754758\">10.1145/2739480.2754758</a>.","ieee":"T. Paixao, D. Sudholt, J. Heredia, and B. Trubenova, “First steps towards a runtime comparison of natural and artificial evolution,” in <i>Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation</i>, Madrid, Spain, 2015, pp. 1455–1462."},"date_published":"2015-07-11T00:00:00Z","doi":"10.1145/2739480.2754758","publist_id":"5768","type":"conference","publisher":"ACM","status":"public","date_updated":"2025-09-23T08:50:33Z","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"1455 - 1462","_id":"1430","year":"2015","author":[{"orcid":"0000-0003-2361-3953","last_name":"Paixao","full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago"},{"first_name":"Dirk","last_name":"Sudholt","full_name":"Sudholt, Dirk"},{"full_name":"Heredia, Jorge","last_name":"Heredia","first_name":"Jorge"},{"last_name":"Trubenova","first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967"}],"external_id":{"arxiv":["1504.06260"],"isi":["000358795700182"]},"main_file_link":[{"url":"http://arxiv.org/abs/1504.06260","open_access":"1"}],"department":[{"_id":"NiBa"},{"_id":"CaGu"}],"title":"First steps towards a runtime comparison of natural and artificial evolution","publication_status":"published","scopus_import":"1","publication":"Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation","project":[{"grant_number":"618091","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"day":"11","abstract":[{"text":"Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse their runtime on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrence of new mutations is much longer than the time it takes for a new beneficial mutation to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a (1+1)-type process where the probability of accepting a new genotype (improvements or worsenings) depends on the change in fitness. We present an initial runtime analysis of SSWM, quantifying its performance for various parameters and investigating differences to the (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient.","lang":"eng"}],"ec_funded":1,"oa_version":"Preprint"},{"ec_funded":1,"oa_version":"Submitted Version","project":[{"grant_number":"259668","name":"Provable Security for Physical Cryptography","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"day":"04","abstract":[{"lang":"eng","text":"Cryptographic access control offers selective access to encrypted data via a combination of key management and functionality-rich cryptographic schemes, such as attribute-based encryption. Using this approach, publicly available meta-data may inadvertently leak information on the access policy that is enforced by cryptography, which renders cryptographic access control unusable in settings where this information is highly sensitive. We begin to address this problem by presenting rigorous definitions for policy privacy in cryptographic access control. For concreteness we set our results in the model of Role-Based Access Control (RBAC), where we identify and formalize several different flavors of privacy, however, our framework should serve as inspiration for other models of access control. Based on our insights we propose a new system which significantly improves on the privacy properties of state-of-the-art constructions. Our design is based on a novel type of privacy-preserving attribute-based encryption, which we introduce and show how to instantiate. We present our results in the context of a cryptographic RBAC system by Ferrara et al. (CSF'13), which uses cryptography to control read access to files, while write access is still delegated to trusted monitors. We give an extension of the construction that permits cryptographic control over write access. Our construction assumes that key management uses out-of-band channels between the policy enforcer and the users but eliminates completely the need for monitoring read/write access to the data."}],"publication_status":"published","scopus_import":"1","title":"Policy privacy in cryptographic access control","main_file_link":[{"url":"http://epubs.surrey.ac.uk/808055/","open_access":"1"}],"department":[{"_id":"KrPi"}],"external_id":{"isi":["000380428500004"]},"author":[{"full_name":"Ferrara, Anna","last_name":"Ferrara","first_name":"Anna"},{"first_name":"Georg","last_name":"Fuchsbauer","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","full_name":"Fuchsbauer, Georg"},{"first_name":"Bin","full_name":"Liu, Bin","last_name":"Liu"},{"first_name":"Bogdan","full_name":"Warinschi, Bogdan","last_name":"Warinschi"}],"page":"46-60","_id":"1474","year":"2015","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","type":"conference","publisher":"IEEE","date_updated":"2025-09-23T09:50:52Z","doi":"10.1109/CSF.2015.11","publist_id":"5722","date_published":"2015-09-04T00:00:00Z","month":"09","article_processing_charge":"No","oa":1,"citation":{"mla":"Ferrara, Anna, et al. <i>Policy Privacy in Cryptographic Access Control</i>. IEEE, 2015, pp. 46–60, doi:<a href=\"https://doi.org/10.1109/CSF.2015.11\">10.1109/CSF.2015.11</a>.","ieee":"A. Ferrara, G. Fuchsbauer, B. Liu, and B. Warinschi, “Policy privacy in cryptographic access control,” presented at the CSF: Computer Security Foundations, Verona, Italy, 2015, pp. 46–60.","apa":"Ferrara, A., Fuchsbauer, G., Liu, B., &#38; Warinschi, B. (2015). Policy privacy in cryptographic access control (pp. 46–60). Presented at the CSF: Computer Security Foundations, Verona, Italy: IEEE. <a href=\"https://doi.org/10.1109/CSF.2015.11\">https://doi.org/10.1109/CSF.2015.11</a>","chicago":"Ferrara, Anna, Georg Fuchsbauer, Bin Liu, and Bogdan Warinschi. “Policy Privacy in Cryptographic Access Control,” 46–60. IEEE, 2015. <a href=\"https://doi.org/10.1109/CSF.2015.11\">https://doi.org/10.1109/CSF.2015.11</a>.","ama":"Ferrara A, Fuchsbauer G, Liu B, Warinschi B. Policy privacy in cryptographic access control. In: IEEE; 2015:46-60. doi:<a href=\"https://doi.org/10.1109/CSF.2015.11\">10.1109/CSF.2015.11</a>","short":"A. Ferrara, G. Fuchsbauer, B. Liu, B. Warinschi, in:, IEEE, 2015, pp. 46–60.","ista":"Ferrara A, Fuchsbauer G, Liu B, Warinschi B. 2015. Policy privacy in cryptographic access control. CSF: Computer Security Foundations, 46–60."},"date_created":"2018-12-11T11:52:14Z","conference":{"start_date":"2015-07-13","location":"Verona, Italy","name":"CSF: Computer Security Foundations","end_date":"2015-07-17"},"language":[{"iso":"eng"}],"quality_controlled":"1"},{"external_id":{"pmid":["25138099"],"isi":["000354474600013"]},"author":[{"full_name":"Kuechler, Alma","last_name":"Kuechler","first_name":"Alma"},{"last_name":"Zink","full_name":"Zink, Alexander","first_name":"Alexander"},{"last_name":"Wieland","first_name":"Thomas","full_name":"Wieland, Thomas"},{"last_name":"Lüdecke","full_name":"Lüdecke, Hermann","first_name":"Hermann"},{"first_name":"Kirsten","full_name":"Cremer, Kirsten","last_name":"Cremer"},{"full_name":"Salviati, Leonardo","last_name":"Salviati","first_name":"Leonardo"},{"full_name":"Magini, Pamela","last_name":"Magini","first_name":"Pamela"},{"last_name":"Najafi","first_name":"Kimia","full_name":"Najafi, Kimia"},{"first_name":"Christiane","full_name":"Zweier, Christiane","last_name":"Zweier"},{"last_name":"Czeschik","first_name":"Johanna","full_name":"Czeschik, Johanna"},{"last_name":"Aretz","first_name":"Stefan","full_name":"Aretz, Stefan"},{"full_name":"Endele, Sabine","last_name":"Endele","first_name":"Sabine"},{"first_name":"Federica","last_name":"Tamburrino","full_name":"Tamburrino, Federica"},{"first_name":"Claudia","full_name":"Pinato, Claudia","last_name":"Pinato"},{"last_name":"Clementi","full_name":"Clementi, Maurizio","first_name":"Maurizio"},{"first_name":"Jasmin","full_name":"Gundlach, Jasmin","last_name":"Gundlach"},{"full_name":"Maylahn, Carina","first_name":"Carina","last_name":"Maylahn"},{"full_name":"Mazzanti, Laura","last_name":"Mazzanti","first_name":"Laura"},{"last_name":"Wohlleber","full_name":"Wohlleber, Eva","first_name":"Eva"},{"last_name":"Schwarzmayr","full_name":"Schwarzmayr, Thomas","first_name":"Thomas"},{"last_name":"Kariminejad","first_name":"Roxana","full_name":"Kariminejad, Roxana"},{"last_name":"Schlessinger","full_name":"Schlessinger, Avner","first_name":"Avner"},{"last_name":"Wieczorek","first_name":"Dagmar","full_name":"Wieczorek, Dagmar"},{"last_name":"Strom","first_name":"Tim","full_name":"Strom, Tim"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178"},{"first_name":"Hartmut","full_name":"Engels, Hartmut","last_name":"Engels"}],"title":"Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4795044/","open_access":"1"}],"department":[{"_id":"GaNo"}],"publication_status":"published","oa_version":"Submitted Version","issue":"6","publication":"European Journal of Human Genetics","day":"15","abstract":[{"text":"Intellectual disability (ID) has an estimated prevalence of 2-3%. Due to its extreme heterogeneity, the genetic basis of ID remains elusive in many cases. Recently, whole exome sequencing (WES) studies revealed that a large proportion of sporadic cases are caused by de novo gene variants. To identify further genes involved in ID, we performed WES in 250 patients with unexplained ID and their unaffected parents and included exomes of 51 previously sequenced child-parents trios in the analysis. Exome analysis revealed de novo intragenic variants in SET domain-containing 5 (SETD5) in two patients. One patient carried a nonsense variant, and the other an 81 bp deletion located across a splice-donor site. Chromosomal microarray diagnostics further identified four de novo non-recurrent microdeletions encompassing SETD5. CRISPR/Cas9 mutation modelling of the two intragenic variants demonstrated nonsense-mediated decay of the resulting transcripts, pointing to a loss-of-function (LoF) and haploinsufficiency as the common disease-causing mechanism of intragenic SETD5 sequence variants and SETD5-containing microdeletions. In silico domain prediction of SETD5, a predicted SET domain-containing histone methyltransferase (HMT), substantiated the presence of a SET domain and identified a novel putative PHD domain, strengthening a functional link to well-known histone-modifying ID genes. All six patients presented with ID and certain facial dysmorphisms, suggesting that SETD5 sequence variants contribute substantially to the microdeletion 3p25.3 phenotype. The present report of two SETD5 LoF variants in 301 patients demonstrates a prevalence of 0.7% and thus SETD5 variants as a relatively frequent cause of ID.","lang":"eng"}],"date_created":"2018-12-11T11:54:01Z","language":[{"iso":"eng"}],"quality_controlled":"1","date_published":"2015-06-15T00:00:00Z","oa":1,"article_processing_charge":"No","volume":23,"month":"06","citation":{"chicago":"Kuechler, Alma, Alexander Zink, Thomas Wieland, Hermann Lüdecke, Kirsten Cremer, Leonardo Salviati, Pamela Magini, et al. “Loss-of-Function Variants of SETD5 Cause Intellectual Disability and the Core Phenotype of Microdeletion 3p25.3 Syndrome.” <i>European Journal of Human Genetics</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/ejhg.2014.165\">https://doi.org/10.1038/ejhg.2014.165</a>.","ama":"Kuechler A, Zink A, Wieland T, et al. Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. <i>European Journal of Human Genetics</i>. 2015;23(6):753-760. doi:<a href=\"https://doi.org/10.1038/ejhg.2014.165\">10.1038/ejhg.2014.165</a>","apa":"Kuechler, A., Zink, A., Wieland, T., Lüdecke, H., Cremer, K., Salviati, L., … Engels, H. (2015). Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. <i>European Journal of Human Genetics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ejhg.2014.165\">https://doi.org/10.1038/ejhg.2014.165</a>","mla":"Kuechler, Alma, et al. “Loss-of-Function Variants of SETD5 Cause Intellectual Disability and the Core Phenotype of Microdeletion 3p25.3 Syndrome.” <i>European Journal of Human Genetics</i>, vol. 23, no. 6, Nature Publishing Group, 2015, pp. 753–60, doi:<a href=\"https://doi.org/10.1038/ejhg.2014.165\">10.1038/ejhg.2014.165</a>.","ieee":"A. Kuechler <i>et al.</i>, “Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome,” <i>European Journal of Human Genetics</i>, vol. 23, no. 6. Nature Publishing Group, pp. 753–760, 2015.","ista":"Kuechler A, Zink A, Wieland T, Lüdecke H, Cremer K, Salviati L, Magini P, Najafi K, Zweier C, Czeschik J, Aretz S, Endele S, Tamburrino F, Pinato C, Clementi M, Gundlach J, Maylahn C, Mazzanti L, Wohlleber E, Schwarzmayr T, Kariminejad R, Schlessinger A, Wieczorek D, Strom T, Novarino G, Engels H. 2015. Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. European Journal of Human Genetics. 23(6), 753–760.","short":"A. Kuechler, A. Zink, T. Wieland, H. Lüdecke, K. Cremer, L. Salviati, P. Magini, K. Najafi, C. Zweier, J. Czeschik, S. Aretz, S. Endele, F. Tamburrino, C. Pinato, M. Clementi, J. Gundlach, C. Maylahn, L. Mazzanti, E. Wohlleber, T. Schwarzmayr, R. Kariminejad, A. Schlessinger, D. Wieczorek, T. Strom, G. Novarino, H. Engels, European Journal of Human Genetics 23 (2015) 753–760."},"date_updated":"2025-09-23T09:30:27Z","publisher":"Nature Publishing Group","status":"public","type":"journal_article","intvolume":"        23","doi":"10.1038/ejhg.2014.165","publist_id":"5324","_id":"1789","page":"753 - 760","year":"2015","pmid":1,"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"date_created":"2018-12-11T11:54:02Z","language":[{"iso":"eng"}],"quality_controlled":"1","file_date_updated":"2020-07-14T12:45:16Z","date_published":"2015-06-01T00:00:00Z","oa":1,"article_processing_charge":"No","volume":10,"month":"06","citation":{"ama":"Symonova O, Topp C, Edelsbrunner H. DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. <i>PLoS One</i>. 2015;10(6). doi:<a href=\"https://doi.org/10.1371/journal.pone.0127657\">10.1371/journal.pone.0127657</a>","chicago":"Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.” <i>PLoS One</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0127657\">https://doi.org/10.1371/journal.pone.0127657</a>.","ieee":"O. Symonova, C. Topp, and H. Edelsbrunner, “DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots,” <i>PLoS One</i>, vol. 10, no. 6. Public Library of Science, 2015.","mla":"Symonova, Olga, et al. “DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.” <i>PLoS One</i>, vol. 10, no. 6, e0127657, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0127657\">10.1371/journal.pone.0127657</a>.","apa":"Symonova, O., Topp, C., &#38; Edelsbrunner, H. (2015). DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0127657\">https://doi.org/10.1371/journal.pone.0127657</a>","short":"O. Symonova, C. Topp, H. Edelsbrunner, PLoS One 10 (2015).","ista":"Symonova O, Topp C, Edelsbrunner H. 2015. DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. PLoS One. 10(6), e0127657."},"date_updated":"2025-09-23T08:30:43Z","publisher":"Public Library of Science","type":"journal_article","status":"public","intvolume":"        10","doi":"10.1371/journal.pone.0127657","publist_id":"5318","_id":"1793","year":"2015","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000356630900069"]},"author":[{"full_name":"Symonova, Olga","first_name":"Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","last_name":"Symonova","orcid":"0000-0003-2012-9947"},{"full_name":"Topp, Christopher","last_name":"Topp","first_name":"Christopher"},{"first_name":"Herbert","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"}],"title":"DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots","file":[{"creator":"system","file_id":"5150","checksum":"d20f26461ca575276ad3ed9ce4bfc787","date_updated":"2020-07-14T12:45:16Z","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:15:30Z","file_name":"IST-2016-454-v1+1_journal.pone.0127657.pdf","content_type":"application/pdf","file_size":1850825}],"department":[{"_id":"MaJö"},{"_id":"HeEd"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","corr_author":"1","scopus_import":"1","article_number":"e0127657","has_accepted_license":"1","related_material":{"record":[{"relation":"research_data","status":"public","id":"9737"}]},"pubrep_id":"454","oa_version":"Published Version","issue":"6","publication":"PLoS One","day":"01","ddc":["000"],"abstract":[{"text":"We present a software platform for reconstructing and analyzing the growth of a plant root system from a time-series of 3D voxelized shapes. It aligns the shapes with each other, constructs a geometric graph representation together with the function that records the time of growth, and organizes the branches into a hierarchy that reflects the order of creation. The software includes the automatic computation of structural and dynamic traits for each root in the system enabling the quantification of growth on fine-scale. These are important advances in plant phenotyping with applications to the study of genetic and environmental influences on growth.","lang":"eng"}]},{"has_accepted_license":"1","pubrep_id":"450","article_number":"10781","scopus_import":"1","corr_author":"1","publication_status":"published","ddc":["530"],"abstract":[{"text":"It is known that in classical fluids turbulence typically occurs at high Reynolds numbers. But can turbulence occur at low Reynolds numbers? Here we investigate the transition to turbulence in the classic Taylor-Couette system in which the rotating fluids are manufactured ferrofluids with magnetized nanoparticles embedded in liquid carriers. We find that, in the presence of a magnetic field transverse to the symmetry axis of the system, turbulence can occur at Reynolds numbers that are at least one order of magnitude smaller than those in conventional fluids. This is established by extensive computational ferrohydrodynamics through a detailed investigation of transitions in the flow structure, and characterization of behaviors of physical quantities such as the energy, the wave number, and the angular momentum through the bifurcations. A finding is that, as the magnetic field is increased, onset of turbulence can be determined accurately and reliably. Our results imply that experimental investigation of turbulence may be feasible by using ferrofluids. Our study of transition to and evolution of turbulence in the Taylor-Couette ferrofluidic flow system provides insights into the challenging problem of turbulence control.","lang":"eng"}],"day":"12","publication":"Scientific Reports","oa_version":"Published Version","author":[{"orcid":"0000-0001-5964-0203","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","full_name":"Altmeyer, Sebastian","last_name":"Altmeyer"},{"first_name":"Younghae","full_name":"Do, Younghae","last_name":"Do"},{"last_name":"Lai","full_name":"Lai, Ying","first_name":"Ying"}],"external_id":{"isi":["000356150200001"]},"department":[{"_id":"BjHo"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file":[{"content_type":"application/pdf","file_size":2449723,"checksum":"7716f582f8c9d82d8f2bf80bf896b440","creator":"system","file_id":"5280","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:45:16Z","date_created":"2018-12-12T10:17:26Z","file_name":"IST-2016-450-v1+1_srep10781.pdf"}],"title":"Transition to turbulence in Taylor-Couette ferrofluidic flow","publist_id":"5306","doi":"10.1038/srep10781","intvolume":"         5","date_updated":"2025-09-29T10:58:13Z","publisher":"Nature Publishing Group","status":"public","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"year":"2015","_id":"1804","quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:54:06Z","citation":{"ista":"Altmeyer S, Do Y, Lai Y. 2015. Transition to turbulence in Taylor-Couette ferrofluidic flow. Scientific Reports. 5, 10781.","short":"S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 5 (2015).","apa":"Altmeyer, S., Do, Y., &#38; Lai, Y. (2015). Transition to turbulence in Taylor-Couette ferrofluidic flow. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep10781\">https://doi.org/10.1038/srep10781</a>","ieee":"S. Altmeyer, Y. Do, and Y. Lai, “Transition to turbulence in Taylor-Couette ferrofluidic flow,” <i>Scientific Reports</i>, vol. 5. Nature Publishing Group, 2015.","mla":"Altmeyer, Sebastian, et al. “Transition to Turbulence in Taylor-Couette Ferrofluidic Flow.” <i>Scientific Reports</i>, vol. 5, 10781, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/srep10781\">10.1038/srep10781</a>.","ama":"Altmeyer S, Do Y, Lai Y. Transition to turbulence in Taylor-Couette ferrofluidic flow. <i>Scientific Reports</i>. 2015;5. doi:<a href=\"https://doi.org/10.1038/srep10781\">10.1038/srep10781</a>","chicago":"Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Transition to Turbulence in Taylor-Couette Ferrofluidic Flow.” <i>Scientific Reports</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/srep10781\">https://doi.org/10.1038/srep10781</a>."},"oa":1,"month":"06","article_processing_charge":"No","volume":5,"date_published":"2015-06-12T00:00:00Z","file_date_updated":"2020-07-14T12:45:16Z"},{"month":"06","volume":48,"article_processing_charge":"No","oa":1,"citation":{"ista":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. 2015. Homological reconstruction and simplification in R3. Computational Geometry: Theory and Applications. 48(8), 606–621.","short":"D. Attali, U. Bauer, O. Devillers, M. Glisse, A. Lieutier, Computational Geometry: Theory and Applications 48 (2015) 606–621.","apa":"Attali, D., Bauer, U., Devillers, O., Glisse, M., &#38; Lieutier, A. (2015). Homological reconstruction and simplification in R3. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2014.08.010\">https://doi.org/10.1016/j.comgeo.2014.08.010</a>","ieee":"D. Attali, U. Bauer, O. Devillers, M. Glisse, and A. Lieutier, “Homological reconstruction and simplification in R3,” <i>Computational Geometry: Theory and Applications</i>, vol. 48, no. 8. Elsevier, pp. 606–621, 2015.","mla":"Attali, Dominique, et al. “Homological Reconstruction and Simplification in R3.” <i>Computational Geometry: Theory and Applications</i>, vol. 48, no. 8, Elsevier, 2015, pp. 606–21, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2014.08.010\">10.1016/j.comgeo.2014.08.010</a>.","chicago":"Attali, Dominique, Ulrich Bauer, Olivier Devillers, Marc Glisse, and André Lieutier. “Homological Reconstruction and Simplification in R3.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.comgeo.2014.08.010\">https://doi.org/10.1016/j.comgeo.2014.08.010</a>.","ama":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. Homological reconstruction and simplification in R3. <i>Computational Geometry: Theory and Applications</i>. 2015;48(8):606-621. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2014.08.010\">10.1016/j.comgeo.2014.08.010</a>"},"date_published":"2015-06-03T00:00:00Z","language":[{"iso":"eng"}],"quality_controlled":"1","date_created":"2018-12-11T11:54:06Z","OA_type":"free access","article_type":"original","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"606 - 621","_id":"1805","year":"2015","doi":"10.1016/j.comgeo.2014.08.010","publist_id":"5305","type":"journal_article","publisher":"Elsevier","status":"public","date_updated":"2025-09-23T09:18:30Z","intvolume":"        48","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.comgeo.2014.08.010"}],"department":[{"_id":"HeEd"}],"title":"Homological reconstruction and simplification in R3","author":[{"full_name":"Attali, Dominique","last_name":"Attali","first_name":"Dominique"},{"orcid":"0000-0002-9683-0724","first_name":"Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","full_name":"Bauer, Ulrich","last_name":"Bauer"},{"first_name":"Olivier","last_name":"Devillers","full_name":"Devillers, Olivier"},{"last_name":"Glisse","full_name":"Glisse, Marc","first_name":"Marc"},{"full_name":"Lieutier, André","first_name":"André","last_name":"Lieutier"}],"external_id":{"isi":["000357353200006"]},"issue":"8","publication":"Computational Geometry: Theory and Applications","project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Topological Complex Systems","grant_number":"318493"}],"day":"03","abstract":[{"text":"We consider the problem of deciding whether the persistent homology group of a simplicial pair (K,L) can be realized as the homology H∗(X) of some complex X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded in double-struck R3. As a consequence, we show that it is NP-hard to simplify level and sublevel sets of scalar functions on double-struck S3 within a given tolerance constraint. This problem has relevance to the visualization of medical images by isosurfaces. We also show an implication to the theory of well groups of scalar functions: not every well group can be realized by some level set, and deciding whether a well group can be realized is NP-hard.","lang":"eng"}],"ec_funded":1,"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"2812"}]},"OA_place":"publisher","publication_status":"published","corr_author":"1","scopus_import":"1"},{"doi":"10.1051/cocv/2014040","publist_id":"5303","date_updated":"2025-09-23T10:45:09Z","type":"journal_article","status":"public","publisher":"EDP Sciences","intvolume":"        21","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1807","page":"603 - 624","year":"2015","language":[{"iso":"eng"}],"quality_controlled":"1","arxiv":1,"date_created":"2018-12-11T11:54:07Z","oa":1,"volume":21,"article_processing_charge":"No","month":"05","citation":{"ama":"Goldman M, Royo-Letelier J. Sharp interface limit for two components Bose-Einstein condensates. <i>ESAIM - Control, Optimisation and Calculus of Variations</i>. 2015;21(3):603-624. doi:<a href=\"https://doi.org/10.1051/cocv/2014040\">10.1051/cocv/2014040</a>","chicago":"Goldman, Michael, and Jimena Royo-Letelier. “Sharp Interface Limit for Two Components Bose-Einstein Condensates.” <i>ESAIM - Control, Optimisation and Calculus of Variations</i>. EDP Sciences, 2015. <a href=\"https://doi.org/10.1051/cocv/2014040\">https://doi.org/10.1051/cocv/2014040</a>.","ieee":"M. Goldman and J. Royo-Letelier, “Sharp interface limit for two components Bose-Einstein condensates,” <i>ESAIM - Control, Optimisation and Calculus of Variations</i>, vol. 21, no. 3. EDP Sciences, pp. 603–624, 2015.","mla":"Goldman, Michael, and Jimena Royo-Letelier. “Sharp Interface Limit for Two Components Bose-Einstein Condensates.” <i>ESAIM - Control, Optimisation and Calculus of Variations</i>, vol. 21, no. 3, EDP Sciences, 2015, pp. 603–24, doi:<a href=\"https://doi.org/10.1051/cocv/2014040\">10.1051/cocv/2014040</a>.","apa":"Goldman, M., &#38; Royo-Letelier, J. (2015). Sharp interface limit for two components Bose-Einstein condensates. <i>ESAIM - Control, Optimisation and Calculus of Variations</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/cocv/2014040\">https://doi.org/10.1051/cocv/2014040</a>","short":"M. Goldman, J. Royo-Letelier, ESAIM - Control, Optimisation and Calculus of Variations 21 (2015) 603–624.","ista":"Goldman M, Royo-Letelier J. 2015. Sharp interface limit for two components Bose-Einstein condensates. ESAIM - Control, Optimisation and Calculus of Variations. 21(3), 603–624."},"date_published":"2015-05-01T00:00:00Z","publication_status":"published","corr_author":"1","scopus_import":"1","publication":"ESAIM - Control, Optimisation and Calculus of Variations","issue":"3","day":"01","abstract":[{"lang":"eng","text":"We study a double Cahn-Hilliard type functional related to the Gross-Pitaevskii energy of two-components Bose-Einstein condensates. In the case of large but same order intercomponent and intracomponent coupling strengths, we prove Γ-convergence to a perimeter minimisation functional with an inhomogeneous surface tension. We study the asymptotic behavior of the surface tension as the ratio between the intercomponent and intracomponent coupling strengths becomes very small or very large and obtain good agreement with the physical literature. We obtain as a consequence, symmetry breaking of the minimisers for the harmonic potential."}],"oa_version":"Preprint","author":[{"first_name":"Michael","last_name":"Goldman","full_name":"Goldman, Michael"},{"last_name":"Royo-Letelier","first_name":"Jimena","full_name":"Royo-Letelier, Jimena","id":"4D3BED28-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["1401.1727"],"isi":["000356012000001"]},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1401.1727"}],"department":[{"_id":"RoSe"}],"title":"Sharp interface limit for two components Bose-Einstein condensates"},{"citation":{"short":"A. Gupta, T.A. Henzinger, ACM Transactions on Modeling and Computer Simulation 25 (2015).","ista":"Gupta A, Henzinger TA. 2015. Guest editors’ introduction to special issue on computational methods in systems biology. ACM Transactions on Modeling and Computer Simulation. 25(2), 7.","ama":"Gupta A, Henzinger TA. Guest editors’ introduction to special issue on computational methods in systems biology. <i>ACM Transactions on Modeling and Computer Simulation</i>. 2015;25(2). doi:<a href=\"https://doi.org/10.1145/2745799\">10.1145/2745799</a>","chicago":"Gupta, Ashutosh, and Thomas A Henzinger. “Guest Editors’ Introduction to Special Issue on Computational Methods in Systems Biology.” <i>ACM Transactions on Modeling and Computer Simulation</i>. ACM, 2015. <a href=\"https://doi.org/10.1145/2745799\">https://doi.org/10.1145/2745799</a>.","ieee":"A. Gupta and T. A. Henzinger, “Guest editors’ introduction to special issue on computational methods in systems biology,” <i>ACM Transactions on Modeling and Computer Simulation</i>, vol. 25, no. 2. ACM, 2015.","mla":"Gupta, Ashutosh, and Thomas A. Henzinger. “Guest Editors’ Introduction to Special Issue on Computational Methods in Systems Biology.” <i>ACM Transactions on Modeling and Computer Simulation</i>, vol. 25, no. 2, 7, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2745799\">10.1145/2745799</a>.","apa":"Gupta, A., &#38; Henzinger, T. A. (2015). Guest editors’ introduction to special issue on computational methods in systems biology. <i>ACM Transactions on Modeling and Computer Simulation</i>. ACM. <a href=\"https://doi.org/10.1145/2745799\">https://doi.org/10.1145/2745799</a>"},"department":[{"_id":"ToHe"}],"volume":25,"article_processing_charge":"No","month":"05","title":"Guest editors' introduction to special issue on computational methods in systems biology","date_published":"2015-05-01T00:00:00Z","quality_controlled":"1","language":[{"iso":"eng"}],"author":[{"first_name":"Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Ashutosh"},{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"}],"external_id":{"isi":["000354789200001"]},"date_created":"2018-12-11T11:54:07Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","isi":1,"publication":"ACM Transactions on Modeling and Computer Simulation","issue":"2","oa_version":"None","year":"2015","_id":"1808","publist_id":"5302","article_number":"7","doi":"10.1145/2745799","scopus_import":"1","intvolume":"        25","date_updated":"2025-09-23T09:11:51Z","publisher":"ACM","publication_status":"published","type":"journal_article","status":"public"},{"external_id":{"isi":["000354917300064"]},"author":[{"first_name":"Barbora","full_name":"Trubenova, Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967"},{"last_name":"Novak","first_name":"Sebastian","full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-824X"},{"last_name":"Hager","first_name":"Reinmar","full_name":"Hager, Reinmar"}],"title":"Indirect genetic effects and the dynamics of social interactions","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"NiBa"}],"file":[{"content_type":"application/pdf","file_size":2748982,"file_name":"IST-2016-453-v1+1_journal.pone.0126907.pdf","checksum":"d3a4a58ef4bd3b3e2f32b7fd7af4a743","file_id":"4730","creator":"system","relation":"main_file","date_updated":"2020-07-14T12:45:17Z","access_level":"open_access","date_created":"2018-12-12T10:09:07Z"}],"scopus_import":"1","publication_status":"published","corr_author":"1","pubrep_id":"453","related_material":{"record":[{"status":"public","relation":"research_data","id":"9715"},{"status":"public","relation":"research_data","id":"9772"}]},"has_accepted_license":"1","oa_version":"Published Version","day":"18","ddc":["570","576"],"abstract":[{"text":"Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations.","lang":"eng"}],"issue":"5","publication":"PLoS One","date_created":"2018-12-11T11:54:07Z","quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2015-05-18T00:00:00Z","file_date_updated":"2020-07-14T12:45:17Z","citation":{"ista":"Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics of social interactions. PLoS One. 10(5).","short":"B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015).","ama":"Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of social interactions. <i>PLoS One</i>. 2015;10(5). doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907\">10.1371/journal.pone.0126907</a>","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic Effects and the Dynamics of Social Interactions.” <i>PLoS One</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0126907\">https://doi.org/10.1371/journal.pone.0126907</a>.","apa":"Trubenova, B., Novak, S., &#38; Hager, R. (2015). Indirect genetic effects and the dynamics of social interactions. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0126907\">https://doi.org/10.1371/journal.pone.0126907</a>","ieee":"B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics of social interactions,” <i>PLoS One</i>, vol. 10, no. 5. Public Library of Science, 2015.","mla":"Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social Interactions.” <i>PLoS One</i>, vol. 10, no. 5, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907\">10.1371/journal.pone.0126907</a>."},"article_processing_charge":"No","volume":10,"month":"05","oa":1,"intvolume":"        10","publisher":"Public Library of Science","status":"public","type":"journal_article","date_updated":"2025-09-23T09:21:54Z","publist_id":"5299","doi":"10.1371/journal.pone.0126907","year":"2015","_id":"1809","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1},{"date_published":"2015-06-01T00:00:00Z","file_date_updated":"2020-07-14T12:45:17Z","citation":{"short":"M.T. Bollenbach, Current Opinion in Microbiology 27 (2015) 1–9.","ista":"Bollenbach MT. 2015. Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. Current Opinion in Microbiology. 27, 1–9.","mla":"Bollenbach, Mark Tobias. “Antimicrobial Interactions: Mechanisms and Implications for Drug Discovery and Resistance Evolution.” <i>Current Opinion in Microbiology</i>, vol. 27, Elsevier, 2015, pp. 1–9, doi:<a href=\"https://doi.org/10.1016/j.mib.2015.05.008\">10.1016/j.mib.2015.05.008</a>.","ieee":"M. T. Bollenbach, “Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution,” <i>Current Opinion in Microbiology</i>, vol. 27. Elsevier, pp. 1–9, 2015.","apa":"Bollenbach, M. T. (2015). Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. <i>Current Opinion in Microbiology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mib.2015.05.008\">https://doi.org/10.1016/j.mib.2015.05.008</a>","ama":"Bollenbach MT. Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. <i>Current Opinion in Microbiology</i>. 2015;27:1-9. doi:<a href=\"https://doi.org/10.1016/j.mib.2015.05.008\">10.1016/j.mib.2015.05.008</a>","chicago":"Bollenbach, Mark Tobias. “Antimicrobial Interactions: Mechanisms and Implications for Drug Discovery and Resistance Evolution.” <i>Current Opinion in Microbiology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.mib.2015.05.008\">https://doi.org/10.1016/j.mib.2015.05.008</a>."},"oa":1,"volume":27,"month":"06","article_processing_charge":"No","date_created":"2018-12-11T11:54:08Z","quality_controlled":"1","language":[{"iso":"eng"}],"year":"2015","_id":"1810","page":"1 - 9","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"intvolume":"        27","date_updated":"2025-09-23T07:55:38Z","type":"journal_article","publisher":"Elsevier","status":"public","publist_id":"5298","doi":"10.1016/j.mib.2015.05.008","title":"Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"ToBo"}],"file":[{"creator":"system","checksum":"1683bb0f42ef892a5b3b71a050d65d25","file_id":"5277","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:17:23Z","file_name":"IST-2016-493-v1+1_1-s2.0-S1369527415000594-main.pdf","content_type":"application/pdf","file_size":1047255}],"external_id":{"isi":["000365065400003"]},"author":[{"first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","orcid":"0000-0003-4398-476X"}],"oa_version":"Published Version","ec_funded":1,"day":"01","abstract":[{"text":"Combining antibiotics is a promising strategy for increasing treatment efficacy and for controlling resistance evolution. When drugs are combined, their effects on cells may be amplified or weakened, that is the drugs may show synergistic or antagonistic interactions. Recent work revealed the underlying mechanisms of such drug interactions by elucidating the drugs'; joint effects on cell physiology. Moreover, new treatment strategies that use drug combinations to exploit evolutionary tradeoffs were shown to affect the rate of resistance evolution in predictable ways. High throughput studies have further identified drug candidates based on their interactions with established antibiotics and general principles that enable the prediction of drug interactions were suggested. Overall, the conceptual and technical foundation for the rational design of potent drug combinations is rapidly developing.","lang":"eng"}],"ddc":["570"],"project":[{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF","grant_number":"P27201-B22"},{"_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Optimality principles in responses to antibiotics","grant_number":"303507"},{"name":"Revealing the fundamental limits of cell growth","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013"}],"publication":"Current Opinion in Microbiology","scopus_import":"1","corr_author":"1","publication_status":"published","has_accepted_license":"1","pubrep_id":"493"},{"author":[{"last_name":"Safari","full_name":"Safari, Laleh","first_name":"Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"José","last_name":"Santos","full_name":"Santos, José"},{"last_name":"Amaro","first_name":"Pedro","full_name":"Amaro, Pedro"},{"full_name":"Jänkälä, Kari","last_name":"Jänkälä","first_name":"Kari"},{"last_name":"Fratini","first_name":"Filippo","full_name":"Fratini, Filippo"}],"external_id":{"arxiv":["1409.0110"],"isi":["000355920800016"]},"main_file_link":[{"url":"http://arxiv.org/abs/1409.0110","open_access":"1"}],"department":[{"_id":"MiLe"}],"title":"Analytical evaluation of atomic form factors: Application to Rayleigh scattering","article_number":"052105","corr_author":"1","publication_status":"published","scopus_import":"1","issue":"5","publication":"Journal of Mathematical Physics","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"abstract":[{"lang":"eng","text":"Atomic form factors are widely used for the characterization of targets and specimens, from crystallography to biology. By using recent mathematical results, here we derive an analytical expression for the atomic form factor within the independent particle model constructed from nonrelativistic screened hydrogenic wave functions. The range of validity of this analytical expression is checked by comparing the analytically obtained form factors with the ones obtained within the Hartee-Fock method. As an example, we apply our analytical expression for the atomic form factor to evaluate the differential cross section for Rayleigh scattering off neutral atoms."}],"day":"20","ec_funded":1,"oa_version":"Preprint","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:54:08Z","arxiv":1,"article_processing_charge":"No","volume":56,"month":"05","oa":1,"citation":{"short":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, F. Fratini, Journal of Mathematical Physics 56 (2015).","ista":"Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. 2015. Analytical evaluation of atomic form factors: Application to Rayleigh scattering. Journal of Mathematical Physics. 56(5), 052105.","ieee":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, and F. Fratini, “Analytical evaluation of atomic form factors: Application to Rayleigh scattering,” <i>Journal of Mathematical Physics</i>, vol. 56, no. 5. American Institute of Physics, 2015.","mla":"Safari, Laleh, et al. “Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.” <i>Journal of Mathematical Physics</i>, vol. 56, no. 5, 052105, American Institute of Physics, 2015, doi:<a href=\"https://doi.org/10.1063/1.4921227\">10.1063/1.4921227</a>.","apa":"Safari, L., Santos, J., Amaro, P., Jänkälä, K., &#38; Fratini, F. (2015). Analytical evaluation of atomic form factors: Application to Rayleigh scattering. <i>Journal of Mathematical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4921227\">https://doi.org/10.1063/1.4921227</a>","ama":"Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. Analytical evaluation of atomic form factors: Application to Rayleigh scattering. <i>Journal of Mathematical Physics</i>. 2015;56(5). doi:<a href=\"https://doi.org/10.1063/1.4921227\">10.1063/1.4921227</a>","chicago":"Safari, Laleh, José Santos, Pedro Amaro, Kari Jänkälä, and Filippo Fratini. “Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.” <i>Journal of Mathematical Physics</i>. American Institute of Physics, 2015. <a href=\"https://doi.org/10.1063/1.4921227\">https://doi.org/10.1063/1.4921227</a>."},"date_published":"2015-05-20T00:00:00Z","acknowledgement":"The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n◦ [291734]. F.F. acknowledges support by Fundação de Amparo à Pesquisa do estado de Minas Gerais (FAPEMIG), by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), and by the Austrian Science Fund (FWF) through the START Grant No. Y 591-N16.","doi":"10.1063/1.4921227","publist_id":"5295","publisher":"American Institute of Physics","type":"journal_article","status":"public","date_updated":"2025-09-23T07:53:00Z","intvolume":"        56","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1811","year":"2015"}]