[{"citation":{"ista":"Field D, Fraisse C. 2019. Breaking down barriers in morning glories. Molecular ecology. 28(7), 1579–1581.","ama":"Field D, Fraisse C. Breaking down barriers in morning glories. <i>Molecular ecology</i>. 2019;28(7):1579-1581. doi:<a href=\"https://doi.org/10.1111/mec.15048\">10.1111/mec.15048</a>","ieee":"D. Field and C. Fraisse, “Breaking down barriers in morning glories,” <i>Molecular ecology</i>, vol. 28, no. 7. Wiley, pp. 1579–1581, 2019.","short":"D. Field, C. Fraisse, Molecular Ecology 28 (2019) 1579–1581.","mla":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” <i>Molecular Ecology</i>, vol. 28, no. 7, Wiley, 2019, pp. 1579–81, doi:<a href=\"https://doi.org/10.1111/mec.15048\">10.1111/mec.15048</a>.","apa":"Field, D., &#38; Fraisse, C. (2019). Breaking down barriers in morning glories. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.15048\">https://doi.org/10.1111/mec.15048</a>","chicago":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” <i>Molecular Ecology</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/mec.15048\">https://doi.org/10.1111/mec.15048</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","day":"01","isi":1,"file_date_updated":"2020-07-14T12:47:31Z","oa":1,"date_published":"2019-04-01T00:00:00Z","language":[{"iso":"eng"}],"month":"04","date_updated":"2026-04-16T08:33:17Z","publisher":"Wiley","department":[{"_id":"NiBa"}],"intvolume":"        28","oa_version":"Published Version","type":"journal_article","scopus_import":"1","_id":"6466","quality_controlled":"1","file":[{"file_id":"6472","date_updated":"2020-07-14T12:47:31Z","file_size":367711,"access_level":"open_access","relation":"main_file","checksum":"521e3aff3e9263ddf2ffbfe0b6157715","content_type":"application/pdf","file_name":"2019_MolecularEcology_Field.pdf","date_created":"2019-05-20T11:49:06Z","creator":"dernst"}],"has_accepted_license":"1","ddc":["580","576"],"date_created":"2019-05-19T21:59:15Z","year":"2019","doi":"10.1111/mec.15048","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"issue":"7","publication":"Molecular ecology","article_processing_charge":"No","page":"1579-1581","external_id":{"isi":["000474808300001"]},"publication_status":"published","abstract":[{"lang":"eng","text":"One of the most striking and consistent results in speciation genomics is the heterogeneous divergence observed across the genomes of closely related species. This pattern was initially attributed to different levels of gene exchange—with divergence preserved at loci generating a barrier to gene flow but homogenized at unlinked neutral loci. Although there is evidence to support this model, it is now recognized that interpreting patterns of divergence across genomes is not so straightforward. One \r\nproblem is that heterogenous divergence between populations can also be generated by other processes (e.g. recurrent selective sweeps or background selection) without any involvement of differential gene flow. Thus, integrated studies that identify which loci are likely subject to divergent selection are required to shed light on the interplay between selection and gene flow during the early phases of speciation. In this issue of Molecular Ecology, Rifkin et al. (2019) confront this challenge using a pair of sister morning glory species. They wisely design their sampling to take the geographic context of individuals into account, including geographically isolated (allopatric) and co‐occurring (sympatric) populations. This enabled them to show that individuals are phenotypically less differentiated in sympatry. They also found that the loci that resist introgression are enriched for those most differentiated in allopatry and loci that exhibit signals of divergent selection. One great strength of the \r\nstudy is the combination of methods from population genetics and molecular evolution, including the development of a model to simultaneously infer admixture proportions and selfing rates."}],"title":"Breaking down barriers in morning glories","author":[{"last_name":"Field","first_name":"David","full_name":"Field, David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","volume":28},{"article_type":"original","intvolume":"        15","oa_version":"Published Version","type":"journal_article","_id":"6467","scopus_import":"1","isi":1,"oa":1,"month":"04","language":[{"iso":"eng"}],"date_published":"2019-04-03T00:00:00Z","publisher":"Royal Society of London","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"date_updated":"2026-06-18T19:05:03Z","ec_funded":1,"day":"03","status":"public","citation":{"ama":"Fraisse C, Welch JJ. The distribution of epistasis on simple fitness landscapes. <i>Biology Letters</i>. 2019;15(4). doi:<a href=\"https://doi.org/10.1098/rsbl.2018.0881\">10.1098/rsbl.2018.0881</a>","ista":"Fraisse C, Welch JJ. 2019. The distribution of epistasis on simple fitness landscapes. Biology Letters. 15(4), 0881.","short":"C. Fraisse, J.J. Welch, Biology Letters 15 (2019).","ieee":"C. Fraisse and J. J. Welch, “The distribution of epistasis on simple fitness landscapes,” <i>Biology Letters</i>, vol. 15, no. 4. Royal Society of London, 2019.","mla":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” <i>Biology Letters</i>, vol. 15, no. 4, 0881, Royal Society of London, 2019, doi:<a href=\"https://doi.org/10.1098/rsbl.2018.0881\">10.1098/rsbl.2018.0881</a>.","chicago":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” <i>Biology Letters</i>. Royal Society of London, 2019. <a href=\"https://doi.org/10.1098/rsbl.2018.0881\">https://doi.org/10.1098/rsbl.2018.0881</a>.","apa":"Fraisse, C., &#38; Welch, J. J. (2019). The distribution of epistasis on simple fitness landscapes. <i>Biology Letters</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rsbl.2018.0881\">https://doi.org/10.1098/rsbl.2018.0881</a>"},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Christelle","last_name":"Fraisse","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"},{"full_name":"Welch, John J.","last_name":"Welch","first_name":"John J."}],"volume":15,"related_material":{"link":[{"url":"https://dx.doi.org/10.6084/m9.figshare.c.4461008","relation":"supplementary_material"}],"record":[{"status":"public","id":"9799","relation":"research_data"},{"status":"public","id":"9798","relation":"research_data"}]},"pmid":1,"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA (small nucleolar RNA). Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations."}],"publication_status":"published","external_id":{"isi":["000465405300010"],"pmid":["31014191"]},"title":"The distribution of epistasis on simple fitness landscapes","year":"2019","date_created":"2019-05-19T21:59:15Z","article_number":"0881","issue":"4","publication_identifier":{"issn":["1744-9561"],"eissn":["1744-957X"]},"doi":"10.1098/rsbl.2018.0881","publication":"Biology Letters","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rsbl.2018.0881"}],"ddc":["570"]},{"year":"2019","date_created":"2019-05-19T21:59:17Z","issue":"11","doi":"10.1113/JP277681","publication_identifier":{"issn":["0022-3751"],"eissn":["1469-7793"]},"publication":"Journal of Physiology","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1113/JP277681","open_access":"1"}],"ddc":["570"],"author":[{"last_name":"Éltes","first_name":"Tímea","full_name":"Éltes, Tímea"},{"last_name":"Szoboszlay","first_name":"Miklos","full_name":"Szoboszlay, Miklos"},{"full_name":"Szigeti, Margit Katalin","orcid":"0000-0001-9500-8758","id":"44F4BDC0-F248-11E8-B48F-1D18A9856A87","first_name":"Margit Katalin","last_name":"Szigeti"},{"full_name":"Nusser, Zoltan","first_name":"Zoltan","last_name":"Nusser"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":597,"pmid":1,"page":"2925–2947","article_processing_charge":"No","abstract":[{"text":"Investigating neuronal activity using genetically encoded Ca2+ indicators in behaving animals is hampered by inaccuracies in spike inference from fluorescent tracers. Here we combine two‐photon [Ca2+] imaging with cell‐attached recordings, followed by post hoc determination of the expression level of GCaMP6f, to explore how it affects the amplitude, kinetics and temporal summation of somatic [Ca2+] transients in mouse hippocampal pyramidal cells (PCs). The amplitude of unitary [Ca2+] transients (evoked by a single action potential) negatively correlates with GCaMP6f expression, but displays large variability even among PCs with similarly low expression levels. The summation of fluorescence signals is frequency‐dependent, supralinear and also shows remarkable cell‐to‐cell variability. We performed experimental data‐based simulations and found that spike inference error rates using MLspike depend strongly on unitary peak amplitudes and GCaMP6f expression levels. We provide simple methods for estimating the unitary [Ca2+] transients in individual weakly GCaMP6f‐expressing PCs, with which we achieve spike inference error rates of ∼5%. ","lang":"eng"}],"external_id":{"pmid":["31006863"],"isi":["000470780400013"]},"publication_status":"published","title":"Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells","status":"public","day":"01","citation":{"chicago":"Éltes, Tímea, Miklos Szoboszlay, Margit Katalin Szigeti, and Zoltan Nusser. “Improved Spike Inference Accuracy by Estimating the Peak Amplitude of Unitary [Ca2+] Transients in Weakly GCaMP6f-Expressing Hippocampal Pyramidal Cells.” <i>Journal of Physiology</i>. Wiley, 2019. <a href=\"https://doi.org/10.1113/JP277681\">https://doi.org/10.1113/JP277681</a>.","apa":"Éltes, T., Szoboszlay, M., Szigeti, M. K., &#38; Nusser, Z. (2019). Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. <i>Journal of Physiology</i>. Wiley. <a href=\"https://doi.org/10.1113/JP277681\">https://doi.org/10.1113/JP277681</a>","mla":"Éltes, Tímea, et al. “Improved Spike Inference Accuracy by Estimating the Peak Amplitude of Unitary [Ca2+] Transients in Weakly GCaMP6f-Expressing Hippocampal Pyramidal Cells.” <i>Journal of Physiology</i>, vol. 597, no. 11, Wiley, 2019, pp. 2925–2947, doi:<a href=\"https://doi.org/10.1113/JP277681\">10.1113/JP277681</a>.","ieee":"T. Éltes, M. Szoboszlay, M. K. Szigeti, and Z. Nusser, “Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells,” <i>Journal of Physiology</i>, vol. 597, no. 11. Wiley, pp. 2925–2947, 2019.","short":"T. Éltes, M. Szoboszlay, M.K. Szigeti, Z. Nusser, Journal of Physiology 597 (2019) 2925–2947.","ama":"Éltes T, Szoboszlay M, Szigeti MK, Nusser Z. Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. <i>Journal of Physiology</i>. 2019;597(11):2925–2947. doi:<a href=\"https://doi.org/10.1113/JP277681\">10.1113/JP277681</a>","ista":"Éltes T, Szoboszlay M, Szigeti MK, Nusser Z. 2019. Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. 597(11), 2925–2947."},"article_type":"original","oa_version":"Published Version","intvolume":"       597","type":"journal_article","_id":"6470","scopus_import":"1","isi":1,"oa":1,"month":"06","language":[{"iso":"eng"}],"date_published":"2019-06-01T00:00:00Z","publisher":"Wiley","department":[{"_id":"GaNo"}],"date_updated":"2026-06-18T19:05:34Z"},{"citation":{"short":"S.A. Cepeda Humerez, Estimating Information Flow in Single Cells, Institute of Science and Technology Austria, 2019.","ieee":"S. A. Cepeda Humerez, “Estimating information flow in single cells,” Institute of Science and Technology Austria, 2019.","ista":"Cepeda Humerez SA. 2019. Estimating information flow in single cells. Institute of Science and Technology Austria.","ama":"Cepeda Humerez SA. Estimating information flow in single cells. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6473\">10.15479/AT:ISTA:6473</a>","chicago":"Cepeda Humerez, Sarah A. “Estimating Information Flow in Single Cells.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6473\">https://doi.org/10.15479/AT:ISTA:6473</a>.","apa":"Cepeda Humerez, S. A. (2019). <i>Estimating information flow in single cells</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6473\">https://doi.org/10.15479/AT:ISTA:6473</a>","mla":"Cepeda Humerez, Sarah A. <i>Estimating Information Flow in Single Cells</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6473\">10.15479/AT:ISTA:6473</a>."},"alternative_title":["ISTA Thesis"],"status":"public","day":"23","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"month":"05","date_published":"2019-05-23T00:00:00Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"}],"date_updated":"2026-04-16T08:37:38Z","oa":1,"file_date_updated":"2020-07-14T12:47:31Z","_id":"6473","oa_version":"Published Version","type":"dissertation","has_accepted_license":"1","ddc":["004"],"corr_author":"1","file":[{"content_type":"application/zip","file_name":"Thesis_Cepeda.zip","date_created":"2019-05-23T11:18:16Z","creator":"scepeda","file_id":"6480","date_updated":"2020-07-14T12:47:31Z","file_size":23937464,"access_level":"closed","checksum":"75f9184c1346e10a5de5f9cc7338309a","relation":"source_file"},{"date_created":"2019-05-23T11:18:13Z","content_type":"application/pdf","file_name":"CepedaThesis.pdf","creator":"scepeda","file_id":"6481","relation":"main_file","checksum":"afdc0633ddbd71d5b13550d7fb4f4454","access_level":"open_access","date_updated":"2020-07-14T12:47:31Z","file_size":16646985}],"publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:6473","year":"2019","date_created":"2019-05-21T00:11:23Z","degree_awarded":"PhD","title":"Estimating information flow in single cells","keyword":["Information estimation","Time-series","data analysis"],"supervisor":[{"last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"page":"135","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Single cells are constantly interacting with their environment and each other, more importantly, the accurate perception of environmental cues is crucial for growth, survival, and reproduction. This communication between cells and their environment can be formalized in mathematical terms and be quantified as the information flow between them, as prescribed by information theory. \r\nThe recent availability of real–time dynamical patterns of signaling molecules in single cells has allowed us to identify encoding about the identity of the environment in the time–series. However, efficient estimation of the information transmitted by these signals has been a data–analysis challenge due to the high dimensionality of the trajectories and the limited number of samples. In the first part of this thesis, we develop and evaluate decoding–based estimation methods to lower bound the mutual information and derive model–based precise information estimates for biological reaction networks governed by the chemical master equation. This is followed by applying the decoding-based methods to study the intracellular representation of extracellular changes in budding yeast, by observing the transient dynamics of nuclear translocation of 10 transcription factors in response to 3 stress conditions. Additionally, we apply these estimators to previously published data on ERK and Ca2+ signaling and yeast stress response. We argue that this single cell decoding-based measure of information provides an unbiased, quantitative and interpretable measure for the fidelity of biological signaling processes. \r\nFinally, in the last section, we deal with gene regulation which is primarily controlled by transcription factors (TFs) that bind to the DNA to activate gene expression. The possibility that non-cognate TFs activate transcription diminishes the accuracy of regulation with potentially disastrous effects for the cell. This ’crosstalk’ acts as a previously unexplored source of noise in biochemical networks and puts a strong constraint on their performance. To mitigate erroneous initiation we propose an out of equilibrium scheme that implements kinetic proofreading. We show that such architectures are favored  over their equilibrium counterparts for complex organisms despite introducing noise in gene expression. "}],"publication_status":"published","related_material":{"record":[{"status":"public","id":"2016","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"281","status":"public"},{"id":"1576","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"6900"}]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"full_name":"Cepeda Humerez, Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","last_name":"Cepeda Humerez","first_name":"Sarah A"}],"OA_place":"publisher"},{"_id":"6477","scopus_import":"1","type":"journal_article","article_type":"original","oa_version":"Published Version","intvolume":"        91","arxiv":1,"department":[{"_id":"MaSe"}],"publisher":"American Physical Society","date_updated":"2023-08-25T10:37:56Z","language":[{"iso":"eng"}],"month":"05","date_published":"2019-05-22T00:00:00Z","oa":1,"file_date_updated":"2020-07-14T12:47:31Z","isi":1,"day":"22","status":"public","citation":{"apa":"Abanin, D. A., Altman, E., Bloch, I., &#38; Serbyn, M. (2019). Colloquium: Many-body localization, thermalization, and entanglement. <i>Reviews of Modern Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/revmodphys.91.021001\">https://doi.org/10.1103/revmodphys.91.021001</a>","chicago":"Abanin, Dmitry A., Ehud Altman, Immanuel Bloch, and Maksym Serbyn. “Colloquium: Many-Body Localization, Thermalization, and Entanglement.” <i>Reviews of Modern Physics</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/revmodphys.91.021001\">https://doi.org/10.1103/revmodphys.91.021001</a>.","mla":"Abanin, Dmitry A., et al. “Colloquium: Many-Body Localization, Thermalization, and Entanglement.” <i>Reviews of Modern Physics</i>, vol. 91, no. 2, 021001, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/revmodphys.91.021001\">10.1103/revmodphys.91.021001</a>.","ieee":"D. A. Abanin, E. Altman, I. Bloch, and M. Serbyn, “Colloquium: Many-body localization, thermalization, and entanglement,” <i>Reviews of Modern Physics</i>, vol. 91, no. 2. American Physical Society, 2019.","short":"D.A. Abanin, E. Altman, I. Bloch, M. Serbyn, Reviews of Modern Physics 91 (2019).","ama":"Abanin DA, Altman E, Bloch I, Serbyn M. Colloquium: Many-body localization, thermalization, and entanglement. <i>Reviews of Modern Physics</i>. 2019;91(2). doi:<a href=\"https://doi.org/10.1103/revmodphys.91.021001\">10.1103/revmodphys.91.021001</a>","ista":"Abanin DA, Altman E, Bloch I, Serbyn M. 2019. Colloquium: Many-body localization, thermalization, and entanglement. Reviews of Modern Physics. 91(2), 021001."},"volume":91,"author":[{"full_name":"Abanin, Dmitry A.","first_name":"Dmitry A.","last_name":"Abanin"},{"full_name":"Altman, Ehud","last_name":"Altman","first_name":"Ehud"},{"last_name":"Bloch","first_name":"Immanuel","full_name":"Bloch, Immanuel"},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","last_name":"Serbyn"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Colloquium: Many-body localization, thermalization, and entanglement","abstract":[{"text":"Thermalizing quantum systems are conventionallydescribed by statistical mechanics at equilib-rium. However, not all systems fall into this category, with many-body localization providinga generic mechanism for thermalization to fail in strongly disordered systems. Many-bodylocalized (MBL) systems remain perfect insulators at nonzero temperature, which do notthermalize and therefore cannot be describedusing statistical mechanics. This Colloquiumreviews recent theoretical and experimental advances in studies of MBL systems, focusing onthe new perspective provided by entanglement and nonequilibrium experimental probes suchas quantum quenches. Theoretically, MBL systems exhibit a new kind of robust integrability: anextensive set of quasilocal integrals of motion emerges, which provides an intuitive explanationof the breakdown of thermalization. A description based on quasilocal integrals of motion isused to predict dynamical properties of MBL systems, such as the spreading of quantumentanglement, the behavior of local observables, and the response to external dissipativeprocesses. Furthermore, MBL systems can exhibit eigenstate transitions and quantum ordersforbidden in thermodynamic equilibrium. An outline isgiven of the current theoretical under-standing of the quantum-to-classical transitionbetween many-body localized and ergodic phasesand anomalous transport in the vicinity of that transition. Experimentally, synthetic quantumsystems, which are well isolated from an external thermal reservoir, provide natural platforms forrealizing the MBL phase. Recent experiments with ultracold atoms, trapped ions, superconductingqubits, and quantum materials, in which different signatures of many-body localization have beenobserved, are reviewed. This Colloquium concludes by listing outstanding challenges andpromising future research directions.","lang":"eng"}],"publication_status":"published","external_id":{"isi":["000469046900001"],"arxiv":["1804.11065"]},"article_processing_charge":"No","publication":"Reviews of Modern Physics","issue":"2","publication_identifier":{"issn":["1539-0756"],"eissn":["0034-6861"]},"doi":"10.1103/revmodphys.91.021001","article_number":"021001","year":"2019","date_created":"2019-05-23T07:38:43Z","ddc":["530"],"has_accepted_license":"1","file":[{"creator":"mserbyn","content_type":"application/pdf","file_name":"RevModPhys.91.021001.pdf","date_created":"2019-05-23T07:39:05Z","date_updated":"2020-07-14T12:47:31Z","file_size":1695677,"access_level":"open_access","checksum":"4aec0e6662b09f6e0f828cd30ff2c3a6","relation":"main_file","file_id":"6478"}],"quality_controlled":"1"},{"oa":1,"publisher":"Springer Nature","arxiv":1,"department":[{"_id":"ChLa"}],"date_updated":"2025-04-15T07:10:25Z","month":"02","language":[{"iso":"eng"}],"date_published":"2019-02-14T00:00:00Z","type":"conference","intvolume":"     11269","oa_version":"Preprint","_id":"6482","scopus_import":"1","project":[{"grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7"}],"citation":{"chicago":"Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a ConvNet Operates Outside of Its Specifications,” 11269:244–59. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-12939-2_18\">https://doi.org/10.1007/978-3-030-12939-2_18</a>.","apa":"Sun, R., &#38; Lampert, C. (2019). KS(conf): A light-weight test if a ConvNet operates outside of Its specifications (Vol. 11269, pp. 244–259). Presented at the GCPR: Conference on Pattern Recognition, Stuttgart, Germany: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-12939-2_18\">https://doi.org/10.1007/978-3-030-12939-2_18</a>","mla":"Sun, Rémy, and Christoph Lampert. <i>KS(Conf): A Light-Weight Test If a ConvNet Operates Outside of Its Specifications</i>. Vol. 11269, Springer Nature, 2019, pp. 244–59, doi:<a href=\"https://doi.org/10.1007/978-3-030-12939-2_18\">10.1007/978-3-030-12939-2_18</a>.","short":"R. Sun, C. Lampert, in:, Springer Nature, 2019, pp. 244–259.","ieee":"R. Sun and C. Lampert, “KS(conf): A light-weight test if a ConvNet operates outside of Its specifications,” presented at the GCPR: Conference on Pattern Recognition, Stuttgart, Germany, 2019, vol. 11269, pp. 244–259.","ista":"Sun R, Lampert C. 2019. KS(conf): A light-weight test if a ConvNet operates outside of Its specifications. GCPR: Conference on Pattern Recognition, LNCS, vol. 11269, 244–259.","ama":"Sun R, Lampert C. KS(conf): A light-weight test if a ConvNet operates outside of Its specifications. In: Vol 11269. Springer Nature; 2019:244-259. doi:<a href=\"https://doi.org/10.1007/978-3-030-12939-2_18\">10.1007/978-3-030-12939-2_18</a>"},"ec_funded":1,"status":"public","day":"14","alternative_title":["LNCS"],"abstract":[{"text":"Computer vision systems for automatic image categorization have become accurate and reliable enough that they can run continuously for days or even years as components of real-world commercial applications. A major open problem in this context, however, is quality control. Good classification performance can only be expected if systems run under the specific conditions, in particular data distributions, that they were trained for. Surprisingly, none of the currently used deep network architectures have a built-in functionality that could detect if a network operates on data from a distribution it was not trained for, such that potentially a warning to the human users could be triggered. In this work, we describe KS(conf), a procedure for detecting such outside of specifications (out-of-specs) operation, based on statistical testing of the network outputs. We show by extensive experiments using the ImageNet, AwA2 and DAVIS datasets on a variety of ConvNets architectures that KS(conf) reliably detects out-of-specs situations. It furthermore has a number of properties that make it a promising candidate for practical deployment: it is easy to implement, adds almost no overhead to the system, works with all networks, including pretrained ones, and requires no a priori knowledge of how the data distribution could change. ","lang":"eng"}],"publication_status":"published","external_id":{"arxiv":["1804.04171"]},"page":"244-259","article_processing_charge":"No","title":"KS(conf): A light-weight test if a ConvNet operates outside of Its specifications","volume":11269,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Rémy","last_name":"Sun","full_name":"Sun, Rémy"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert"}],"related_material":{"record":[{"status":"public","id":"6944","relation":"later_version"}]},"quality_controlled":"1","conference":{"location":"Stuttgart, Germany","end_date":"2018-10-12","name":"GCPR: Conference on Pattern Recognition","start_date":"2018-10-09"},"main_file_link":[{"url":"https://arxiv.org/abs/1804.04171","open_access":"1"}],"year":"2019","date_created":"2019-05-24T09:48:36Z","doi":"10.1007/978-3-030-12939-2_18","publication_identifier":{"isbn":["9783030129385","9783030129392"],"issn":["0302-9743"],"eissn":["1611-3349"]}},{"date_created":"2019-05-24T10:09:12Z","year":"2019","status":"public","publication":"Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming","day":"01","doi":"10.1145/3293883.3297000","publication_identifier":{"isbn":["9781450362252"]},"quality_controlled":"1","citation":{"chicago":"Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. <i>Lock-Free Channels for Programming via Communicating Sequential Processes</i>. <i>Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3293883.3297000\">https://doi.org/10.1145/3293883.3297000</a>.","apa":"Koval, N., Alistarh, D.-A., &#38; Elizarov, R. (2019). <i>Lock-free channels for programming via communicating sequential processes</i>. <i>Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming</i> (pp. 417–418). Washington, NY, United States: ACM. <a href=\"https://doi.org/10.1145/3293883.3297000\">https://doi.org/10.1145/3293883.3297000</a>","mla":"Koval, Nikita, et al. “Lock-Free Channels for Programming via Communicating Sequential Processes.” <i>Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming</i>, ACM, 2019, pp. 417–18, doi:<a href=\"https://doi.org/10.1145/3293883.3297000\">10.1145/3293883.3297000</a>.","ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, <i>Lock-free channels for programming via communicating sequential processes</i>. ACM, 2019, pp. 417–418.","short":"N. Koval, D.-A. Alistarh, R. Elizarov, Lock-Free Channels for Programming via Communicating Sequential Processes, ACM, 2019.","ista":"Koval N, Alistarh D-A, Elizarov R. 2019. Lock-free channels for programming via communicating sequential processes, ACM,p.","ama":"Koval N, Alistarh D-A, Elizarov R. <i>Lock-Free Channels for Programming via Communicating Sequential Processes</i>. ACM; 2019:417-418. doi:<a href=\"https://doi.org/10.1145/3293883.3297000\">10.1145/3293883.3297000</a>"},"conference":{"end_date":"2019-02-20","location":"Washington, NY, United States","start_date":"2019-02-16","name":"PPoPP: Principles and Practice of Parallel Programming"},"type":"conference_poster","author":[{"first_name":"Nikita","last_name":"Koval","full_name":"Koval, Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Roman","last_name":"Elizarov","full_name":"Elizarov, Roman"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","_id":"6485","publication_status":"published","external_id":{"isi":["000587604600044"]},"abstract":[{"lang":"eng","text":"Traditional concurrent programming involves manipulating shared mutable state. Alternatives to this programming style are communicating sequential processes (CSP) [1] and actor [2] models, which share data via explicit communication. Rendezvous channelis the common abstraction for communication between several processes, where senders and receivers perform a rendezvous handshake as a part of their protocol (senders wait for receivers and vice versa). Additionally to this, channels support the select expression. In this work, we present the first efficient lock-free channel algorithm, and compare it against Go [3] and Kotlin [4] baseline implementations."}],"article_processing_charge":"No","isi":1,"page":"417-418","date_updated":"2024-12-11T11:42:22Z","department":[{"_id":"DaAl"}],"publisher":"ACM","date_published":"2019-02-01T00:00:00Z","title":"Lock-free channels for programming via communicating sequential processes","language":[{"iso":"eng"}],"month":"02"},{"volume":11561,"author":[{"last_name":"Garcia Soto","first_name":"Miriam","full_name":"Garcia Soto, Miriam","orcid":"0000−0003−2936−5719","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Schilling, Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065","first_name":"Christian","last_name":"Schilling"},{"full_name":"Zeleznik, Luka","id":"3ADCA2E4-F248-11E8-B48F-1D18A9856A87","first_name":"Luka","last_name":"Zeleznik"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","external_id":{"isi":["000491468000016"]},"abstract":[{"text":"We present two algorithmic approaches for synthesizing linear hybrid automata from experimental data. Unlike previous approaches, our algorithms work without a template and generate an automaton with nondeterministic guards and invariants, and with an arbitrary number and topology of modes. They thus construct a succinct model from the data and provide formal guarantees. In particular, (1) the generated automaton can reproduce the data up to a specified tolerance and (2) the automaton is tight, given the first guarantee. Our first approach encodes the synthesis problem as a logical formula in the theory of linear arithmetic, which can then be solved by an SMT solver. This approach minimizes the number of modes in the resulting model but is only feasible for limited data sets. To address scalability, we propose a second approach that does not enforce to find a minimal model. The algorithm constructs an initial automaton and then iteratively extends the automaton based on processing new data. Therefore the algorithm is well-suited for online and synthesis-in-the-loop applications. The core of the algorithm is a membership query that checks whether, within the specified tolerance, a given data set can result from the execution of a given automaton. We solve this membership problem for linear hybrid automata by repeated reachability computations. We demonstrate the effectiveness of the algorithm on synthetic data sets and on cardiac-cell measurements.","lang":"eng"}],"article_processing_charge":"No","page":"297-314","keyword":["Synthesis","Linear hybrid automaton","Membership"],"title":"Membership-based synthesis of linear hybrid automata","date_created":"2019-05-27T07:09:53Z","year":"2019","publication":"31st International Conference on Computer-Aided Verification","doi":"10.1007/978-3-030-25540-4_16","publication_identifier":{"isbn":["9783030255398"],"issn":["0302-9743"]},"file":[{"creator":"dernst","date_created":"2019-08-14T11:05:30Z","file_name":"2019_CAV_GarciaSoto.pdf","content_type":"application/pdf","checksum":"1f1d61b83a151031745ef70a501da3d6","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:47:32Z","file_size":674795,"file_id":"6817"}],"quality_controlled":"1","corr_author":"1","conference":{"location":"New York City, NY, USA","end_date":"2019-07-18","start_date":"2019-07-15","name":"CAV: Computer-Aided Verification"},"ddc":["000"],"has_accepted_license":"1","type":"conference","intvolume":"     11561","oa_version":"Published Version","scopus_import":"1","_id":"6493","file_date_updated":"2020-07-14T12:47:32Z","oa":1,"isi":1,"date_updated":"2025-04-15T06:26:13Z","publisher":"Springer","department":[{"_id":"ToHe"}],"date_published":"2019-07-12T00:00:00Z","month":"07","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"day":"12","status":"public","alternative_title":["LNCS"],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems"}],"citation":{"apa":"Garcia Soto, M., Henzinger, T. A., Schilling, C., &#38; Zeleznik, L. (2019). Membership-based synthesis of linear hybrid automata. In <i>31st International Conference on Computer-Aided Verification</i> (Vol. 11561, pp. 297–314). New York City, NY, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-030-25540-4_16\">https://doi.org/10.1007/978-3-030-25540-4_16</a>","chicago":"Garcia Soto, Miriam, Thomas A Henzinger, Christian Schilling, and Luka Zeleznik. “Membership-Based Synthesis of Linear Hybrid Automata.” In <i>31st International Conference on Computer-Aided Verification</i>, 11561:297–314. Springer, 2019. <a href=\"https://doi.org/10.1007/978-3-030-25540-4_16\">https://doi.org/10.1007/978-3-030-25540-4_16</a>.","mla":"Garcia Soto, Miriam, et al. “Membership-Based Synthesis of Linear Hybrid Automata.” <i>31st International Conference on Computer-Aided Verification</i>, vol. 11561, Springer, 2019, pp. 297–314, doi:<a href=\"https://doi.org/10.1007/978-3-030-25540-4_16\">10.1007/978-3-030-25540-4_16</a>.","short":"M. Garcia Soto, T.A. Henzinger, C. Schilling, L. Zeleznik, in:, 31st International Conference on Computer-Aided Verification, Springer, 2019, pp. 297–314.","ieee":"M. Garcia Soto, T. A. Henzinger, C. Schilling, and L. Zeleznik, “Membership-based synthesis of linear hybrid automata,” in <i>31st International Conference on Computer-Aided Verification</i>, New York City, NY, USA, 2019, vol. 11561, pp. 297–314.","ama":"Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. Membership-based synthesis of linear hybrid automata. In: <i>31st International Conference on Computer-Aided Verification</i>. Vol 11561. Springer; 2019:297-314. doi:<a href=\"https://doi.org/10.1007/978-3-030-25540-4_16\">10.1007/978-3-030-25540-4_16</a>","ista":"Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. 2019. Membership-based synthesis of linear hybrid automata. 31st International Conference on Computer-Aided Verification. CAV: Computer-Aided Verification, LNCS, vol. 11561, 297–314."}},{"oa":1,"isi":1,"date_updated":"2025-04-22T13:48:09Z","publisher":"Elsevier","arxiv":1,"department":[{"_id":"JaMa"}],"date_published":"2019-03-05T00:00:00Z","language":[{"iso":"eng"}],"month":"03","type":"journal_article","intvolume":"       266","oa_version":"Preprint","article_type":"original","scopus_import":"1","_id":"65","publist_id":"7989","citation":{"mla":"Dareiotis, Konstantinos, et al. “Entropy Solutions for Stochastic Porous Media Equations.” <i>Journal of Differential Equations</i>, vol. 266, no. 6, Elsevier, 2019, pp. 3732–63, doi:<a href=\"https://doi.org/10.1016/j.jde.2018.09.012\">10.1016/j.jde.2018.09.012</a>.","apa":"Dareiotis, K., Gerencser, M., &#38; Gess, B. (2019). Entropy solutions for stochastic porous media equations. <i>Journal of Differential Equations</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jde.2018.09.012\">https://doi.org/10.1016/j.jde.2018.09.012</a>","chicago":"Dareiotis, Konstantinos, Mate Gerencser, and Benjamin Gess. “Entropy Solutions for Stochastic Porous Media Equations.” <i>Journal of Differential Equations</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.jde.2018.09.012\">https://doi.org/10.1016/j.jde.2018.09.012</a>.","ista":"Dareiotis K, Gerencser M, Gess B. 2019. Entropy solutions for stochastic porous media equations. Journal of Differential Equations. 266(6), 3732–3763.","ama":"Dareiotis K, Gerencser M, Gess B. Entropy solutions for stochastic porous media equations. <i>Journal of Differential Equations</i>. 2019;266(6):3732-3763. doi:<a href=\"https://doi.org/10.1016/j.jde.2018.09.012\">10.1016/j.jde.2018.09.012</a>","ieee":"K. Dareiotis, M. Gerencser, and B. Gess, “Entropy solutions for stochastic porous media equations,” <i>Journal of Differential Equations</i>, vol. 266, no. 6. Elsevier, pp. 3732–3763, 2019.","short":"K. Dareiotis, M. Gerencser, B. Gess, Journal of Differential Equations 266 (2019) 3732–3763."},"day":"05","status":"public","external_id":{"arxiv":["1803.06953"],"isi":["000456332500026"]},"publication_status":"published","abstract":[{"lang":"eng","text":"We provide an entropy formulation for porous medium-type equations with a stochastic, non-linear, spatially inhomogeneous forcing. Well-posedness and L1-contraction is obtained in the class of entropy solutions. Our scope allows for porous medium operators Δ(|u|m−1u) for all m∈(1,∞), and Hölder continuous diffusion nonlinearity with exponent 1/2."}],"article_processing_charge":"No","page":"3732-3763","title":"Entropy solutions for stochastic porous media equations","volume":266,"author":[{"last_name":"Dareiotis","first_name":"Konstantinos","full_name":"Dareiotis, Konstantinos"},{"last_name":"Gerencser","first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Gerencser, Mate"},{"last_name":"Gess","first_name":"Benjamin","full_name":"Gess, Benjamin"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1803.06953"}],"date_created":"2018-12-11T11:44:26Z","year":"2019","publication":"Journal of Differential Equations","doi":"10.1016/j.jde.2018.09.012","issue":"6"},{"oa":1,"file_date_updated":"2020-10-14T08:59:33Z","isi":1,"publisher":"Wiley","department":[{"_id":"JiFr"}],"date_updated":"2023-08-28T08:40:13Z","language":[{"iso":"eng"}],"month":"10","date_published":"2019-10-01T00:00:00Z","type":"journal_article","article_type":"original","intvolume":"       224","oa_version":"Submitted Version","_id":"6504","scopus_import":"1","citation":{"ista":"Zhang Y, He P, Ma X, Yang Z, Pang C, Yu J, Wang G, Friml J, Xiao G. 2019. Auxin-mediated statolith production for root gravitropism. New Phytologist. 224(2), 761–774.","ama":"Zhang Y, He P, Ma X, et al. Auxin-mediated statolith production for root gravitropism. <i>New Phytologist</i>. 2019;224(2):761-774. doi:<a href=\"https://doi.org/10.1111/nph.15932\">10.1111/nph.15932</a>","ieee":"Y. Zhang <i>et al.</i>, “Auxin-mediated statolith production for root gravitropism,” <i>New Phytologist</i>, vol. 224, no. 2. Wiley, pp. 761–774, 2019.","short":"Y. Zhang, P. He, X. Ma, Z. Yang, C. Pang, J. Yu, G. Wang, J. Friml, G. Xiao, New Phytologist 224 (2019) 761–774.","mla":"Zhang, Yuzhou, et al. “Auxin-Mediated Statolith Production for Root Gravitropism.” <i>New Phytologist</i>, vol. 224, no. 2, Wiley, 2019, pp. 761–74, doi:<a href=\"https://doi.org/10.1111/nph.15932\">10.1111/nph.15932</a>.","chicago":"Zhang, Yuzhou, P He, X Ma, Z Yang, C Pang, J Yu, G Wang, Jiří Friml, and G Xiao. “Auxin-Mediated Statolith Production for Root Gravitropism.” <i>New Phytologist</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/nph.15932\">https://doi.org/10.1111/nph.15932</a>.","apa":"Zhang, Y., He, P., Ma, X., Yang, Z., Pang, C., Yu, J., … Xiao, G. (2019). Auxin-mediated statolith production for root gravitropism. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.15932\">https://doi.org/10.1111/nph.15932</a>"},"day":"01","status":"public","abstract":[{"lang":"eng","text":"Root gravitropism is one of the most important processes allowing plant adaptation to the land environment. Auxin plays a central role in mediating root gravitropism, but how auxin contributes to gravitational perception and the subsequent response is still unclear.\r\n\r\nHere, we showed that the local auxin maximum/gradient within the root apex, which is generated by the PIN directional auxin transporters, regulates the expression of three key starch granule synthesis genes, SS4, PGM and ADG1, which in turn influence the accumulation of starch granules that serve as a statolith perceiving gravity.\r\n\r\nMoreover, using the cvxIAA‐ccvTIR1 system, we also showed that TIR1‐mediated auxin signaling is required for starch granule formation and gravitropic response within root tips. In addition, axr3 mutants showed reduced auxin‐mediated starch granule accumulation and disruption of gravitropism within the root apex.\r\n\r\nOur results indicate that auxin‐mediated statolith production relies on the TIR1/AFB‐AXR3‐mediated auxin signaling pathway. In summary, we propose a dual role for auxin in gravitropism: the regulation of both gravity perception and response."}],"publication_status":"published","external_id":{"isi":["000487184200024"],"pmid":["31111487"]},"page":"761-774","article_processing_charge":"No","title":"Auxin-mediated statolith production for root gravitropism","volume":224,"author":[{"last_name":"Zhang","first_name":"Yuzhou","full_name":"Zhang, Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2627-6956"},{"last_name":"He","first_name":"P","full_name":"He, P"},{"last_name":"Ma","first_name":"X","full_name":"Ma, X"},{"first_name":"Z","last_name":"Yang","full_name":"Yang, Z"},{"full_name":"Pang, C","first_name":"C","last_name":"Pang"},{"full_name":"Yu, J","first_name":"J","last_name":"Yu"},{"full_name":"Wang, G","last_name":"Wang","first_name":"G"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"},{"last_name":"Xiao","first_name":"G","full_name":"Xiao, G"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"file":[{"success":1,"creator":"dernst","file_name":"2019_NewPhytologist_Zhang_accepted.pdf","content_type":"application/pdf","date_created":"2020-10-14T08:59:33Z","file_size":1099061,"date_updated":"2020-10-14T08:59:33Z","access_level":"open_access","relation":"main_file","checksum":"6488243334538f5c39099a701cbf76b9","file_id":"8661"}],"quality_controlled":"1","ddc":["580"],"has_accepted_license":"1","year":"2019","date_created":"2019-05-28T14:33:26Z","publication":"New Phytologist","issue":"2","doi":"10.1111/nph.15932","publication_identifier":{"issn":["0028-646x"],"eissn":["1469-8137"]}},{"scopus_import":"1","_id":"6506","oa_version":"Preprint","intvolume":"         4","article_type":"original","type":"journal_article","date_published":"2019-07-01T00:00:00Z","month":"07","language":[{"iso":"eng"}],"date_updated":"2023-08-28T08:39:47Z","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","isi":1,"oa":1,"status":"public","day":"01","citation":{"mla":"Noda-García, Lianet, et al. “Chance and Pleiotropy Dominate Genetic Diversity in Complex Bacterial Environments.” <i>Nature Microbiology</i>, vol. 4, no. 7, Springer Nature, 2019, pp. 1221–1230, doi:<a href=\"https://doi.org/10.1038/s41564-019-0412-y\">10.1038/s41564-019-0412-y</a>.","apa":"Noda-García, L., Davidi, D., Korenblum, E., Elazar, A., Putintseva, E., Aharoni, A., &#38; Tawfik, D. S. (2019). Chance and pleiotropy dominate genetic diversity in complex bacterial environments. <i>Nature Microbiology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41564-019-0412-y\">https://doi.org/10.1038/s41564-019-0412-y</a>","chicago":"Noda-García, Lianet, Dan Davidi, Elisa Korenblum, Assaf Elazar, Ekaterina Putintseva, Asaph Aharoni, and Dan S. Tawfik. “Chance and Pleiotropy Dominate Genetic Diversity in Complex Bacterial Environments.” <i>Nature Microbiology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41564-019-0412-y\">https://doi.org/10.1038/s41564-019-0412-y</a>.","ama":"Noda-García L, Davidi D, Korenblum E, et al. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. <i>Nature Microbiology</i>. 2019;4(7):1221–1230. doi:<a href=\"https://doi.org/10.1038/s41564-019-0412-y\">10.1038/s41564-019-0412-y</a>","ista":"Noda-García L, Davidi D, Korenblum E, Elazar A, Putintseva E, Aharoni A, Tawfik DS. 2019. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. 4(7), 1221–1230.","ieee":"L. Noda-García <i>et al.</i>, “Chance and pleiotropy dominate genetic diversity in complex bacterial environments,” <i>Nature Microbiology</i>, vol. 4, no. 7. Springer Nature, pp. 1221–1230, 2019.","short":"L. Noda-García, D. Davidi, E. Korenblum, A. Elazar, E. Putintseva, A. Aharoni, D.S. Tawfik, Nature Microbiology 4 (2019) 1221–1230."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Noda-García","first_name":"Lianet","full_name":"Noda-García, Lianet"},{"full_name":"Davidi, Dan","last_name":"Davidi","first_name":"Dan"},{"first_name":"Elisa","last_name":"Korenblum","full_name":"Korenblum, Elisa"},{"full_name":"Elazar, Assaf","first_name":"Assaf","last_name":"Elazar"},{"first_name":"Ekaterina","last_name":"Putintseva","full_name":"Putintseva, Ekaterina","id":"2EF67C84-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Asaph","last_name":"Aharoni","full_name":"Aharoni, Asaph"},{"full_name":"Tawfik, Dan S.","last_name":"Tawfik","first_name":"Dan S."}],"volume":4,"title":"Chance and pleiotropy dominate genetic diversity in complex bacterial environments","article_processing_charge":"No","page":"1221–1230","external_id":{"isi":["000480348200017"]},"publication_status":"published","abstract":[{"text":"How does environmental complexity affect the evolution of single genes? Here, we measured the effects of a set of Bacillus subtilis glutamate dehydrogenase mutants across 19 different environments—from phenotypically homogeneous single-cell populations in liquid media to heterogeneous biofilms, plant roots and soil populations. The effects of individual gene mutations on organismal fitness were highly reproducible in liquid cultures. However, 84% of the tested alleles showed opposing fitness effects under different growth conditions (sign environmental pleiotropy). In colony biofilms and soil samples, different alleles dominated in parallel replica experiments. Accordingly, we found that in these heterogeneous cell populations the fate of mutations was dictated by a combination of selection and drift. The latter relates to programmed prophage excisions that occurred during biofilm development. Overall, for each condition, a wide range of glutamate dehydrogenase mutations persisted and sometimes fixated as a result of the combined action of selection, pleiotropy and chance. However, over longer periods and in multiple environments, nearly all of this diversity would be lost—across all the environments and conditions that we tested, the wild type was the fittest allele.","lang":"eng"}],"doi":"10.1038/s41564-019-0412-y","publication_identifier":{"issn":["2058-5276"]},"issue":"7","publication":"Nature Microbiology","date_created":"2019-05-29T13:03:30Z","year":"2019","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/340828v2","open_access":"1"}],"quality_controlled":"1"},{"volume":47,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3036-1475","full_name":"Bao, Zhigang","last_name":"Bao","first_name":"Zhigang"},{"first_name":"László","last_name":"Erdös","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"first_name":"Kevin","last_name":"Schnelli","orcid":"0000-0003-0954-3231","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","full_name":"Schnelli, Kevin"}],"publication_status":"published","external_id":{"arxiv":["1612.05920"],"isi":["000466616100003"]},"abstract":[{"lang":"eng","text":"Let U and V be two independent N by N random matrices that are distributed according to Haar measure on U(N). Let Σ be a nonnegative deterministic N by N matrix. The single ring theorem [Ann. of Math. (2) 174 (2011) 1189–1217] asserts that the empirical eigenvalue distribution of the matrix X:=UΣV∗ converges weakly, in the limit of large N, to a deterministic measure which is supported on a single ring centered at the origin in ℂ. Within the bulk regime, that is, in the interior of the single ring, we establish the convergence of the empirical eigenvalue distribution on the optimal local scale of order N−1/2+ε and establish the optimal convergence rate. The same results hold true when U and V are Haar distributed on O(N)."}],"article_processing_charge":"No","page":"1270-1334","title":"Local single ring theorem on optimal scale","date_created":"2019-06-02T21:59:13Z","year":"2019","publication":"Annals of Probability","doi":"10.1214/18-AOP1284","publication_identifier":{"issn":["0091-1798"]},"issue":"3","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1612.05920"}],"type":"journal_article","oa_version":"Preprint","intvolume":"        47","scopus_import":"1","_id":"6511","oa":1,"isi":1,"date_updated":"2025-07-10T11:53:28Z","department":[{"_id":"LaEr"}],"publisher":"Institute of Mathematical Statistics","arxiv":1,"date_published":"2019-05-01T00:00:00Z","month":"05","language":[{"iso":"eng"}],"ec_funded":1,"day":"01","status":"public","project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Single Ring Theorem on Optimal Scale.” <i>Annals of Probability</i>. Institute of Mathematical Statistics, 2019. <a href=\"https://doi.org/10.1214/18-AOP1284\">https://doi.org/10.1214/18-AOP1284</a>.","apa":"Bao, Z., Erdös, L., &#38; Schnelli, K. (2019). Local single ring theorem on optimal scale. <i>Annals of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/18-AOP1284\">https://doi.org/10.1214/18-AOP1284</a>","mla":"Bao, Zhigang, et al. “Local Single Ring Theorem on Optimal Scale.” <i>Annals of Probability</i>, vol. 47, no. 3, Institute of Mathematical Statistics, 2019, pp. 1270–334, doi:<a href=\"https://doi.org/10.1214/18-AOP1284\">10.1214/18-AOP1284</a>.","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Local single ring theorem on optimal scale,” <i>Annals of Probability</i>, vol. 47, no. 3. Institute of Mathematical Statistics, pp. 1270–1334, 2019.","short":"Z. Bao, L. Erdös, K. Schnelli, Annals of Probability 47 (2019) 1270–1334.","ista":"Bao Z, Erdös L, Schnelli K. 2019. Local single ring theorem on optimal scale. Annals of Probability. 47(3), 1270–1334.","ama":"Bao Z, Erdös L, Schnelli K. Local single ring theorem on optimal scale. <i>Annals of Probability</i>. 2019;47(3):1270-1334. doi:<a href=\"https://doi.org/10.1214/18-AOP1284\">10.1214/18-AOP1284</a>"}},{"oa":1,"isi":1,"date_updated":"2025-07-10T11:53:29Z","publisher":"Springer Nature","department":[{"_id":"EdHa"}],"date_published":"2019-06-06T00:00:00Z","month":"06","language":[{"iso":"eng"}],"type":"journal_article","intvolume":"       570","oa_version":"Submitted Version","article_type":"original","scopus_import":"1","_id":"6513","citation":{"apa":"Guiu, J., Hannezo, E. B., Yui, S., Demharter, S., Ulyanchenko, S., Maimets, M., … Jensen, K. B. (2019). Tracing the origin of adult intestinal stem cells. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-019-1212-5\">https://doi.org/10.1038/s41586-019-1212-5</a>","chicago":"Guiu, Jordi, Edouard B Hannezo, Shiro Yui, Samuel Demharter, Svetlana Ulyanchenko, Martti Maimets, Anne Jørgensen, et al. “Tracing the Origin of Adult Intestinal Stem Cells.” <i>Nature</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41586-019-1212-5\">https://doi.org/10.1038/s41586-019-1212-5</a>.","mla":"Guiu, Jordi, et al. “Tracing the Origin of Adult Intestinal Stem Cells.” <i>Nature</i>, vol. 570, Springer Nature, 2019, pp. 107–11, doi:<a href=\"https://doi.org/10.1038/s41586-019-1212-5\">10.1038/s41586-019-1212-5</a>.","ieee":"J. Guiu <i>et al.</i>, “Tracing the origin of adult intestinal stem cells,” <i>Nature</i>, vol. 570. Springer Nature, pp. 107–111, 2019.","short":"J. Guiu, E.B. Hannezo, S. Yui, S. Demharter, S. Ulyanchenko, M. Maimets, A. Jørgensen, S. Perlman, L. Lundvall, L.S. Mamsen, A. Larsen, R.H. Olesen, C.Y. Andersen, L.L. Thuesen, K.J. Hare, T.H. Pers, K. Khodosevich, B.D. Simons, K.B. Jensen, Nature 570 (2019) 107–111.","ama":"Guiu J, Hannezo EB, Yui S, et al. Tracing the origin of adult intestinal stem cells. <i>Nature</i>. 2019;570:107-111. doi:<a href=\"https://doi.org/10.1038/s41586-019-1212-5\">10.1038/s41586-019-1212-5</a>","ista":"Guiu J, Hannezo EB, Yui S, Demharter S, Ulyanchenko S, Maimets M, Jørgensen A, Perlman S, Lundvall L, Mamsen LS, Larsen A, Olesen RH, Andersen CY, Thuesen LL, Hare KJ, Pers TH, Khodosevich K, Simons BD, Jensen KB. 2019. Tracing the origin of adult intestinal stem cells. Nature. 570, 107–111."},"day":"06","status":"public","external_id":{"pmid":["31092921"],"isi":["000470149000048"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Adult intestinal stem cells are located at the bottom of crypts of Lieberkühn, where they express markers such as LGR5 1,2 and fuel the constant replenishment of the intestinal epithelium1. Although fetal LGR5-expressing cells can give rise to adult intestinal stem cells3,4, it remains unclear whether this population in the patterned epithelium represents unique intestinal stem-cell precursors. Here we show, using unbiased quantitative lineage-tracing approaches, biophysical modelling and intestinal transplantation, that all cells of the mouse intestinal epithelium—irrespective of their location and pattern of LGR5 expression in the fetal gut tube—contribute actively to the adult intestinal stem cell pool. Using 3D imaging, we find that during fetal development the villus undergoes gross remodelling and fission. This brings epithelial cells from the non-proliferative villus into the proliferative intervillus region, which enables them to contribute to the adult stem-cell niche. Our results demonstrate that large-scale remodelling of the intestinal wall and cell-fate specification are closely linked. Moreover, these findings provide a direct link between the observed plasticity and cellular reprogramming of differentiating cells in adult tissues following damage5,6,7,8,9, revealing that stem-cell identity is an induced rather than a hardwired property."}],"article_processing_charge":"No","page":"107-111","title":"Tracing the origin of adult intestinal stem cells","volume":570,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Guiu","first_name":"Jordi","full_name":"Guiu, Jordi"},{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo"},{"full_name":"Yui, Shiro","last_name":"Yui","first_name":"Shiro"},{"full_name":"Demharter, Samuel","first_name":"Samuel","last_name":"Demharter"},{"last_name":"Ulyanchenko","first_name":"Svetlana","full_name":"Ulyanchenko, Svetlana"},{"first_name":"Martti","last_name":"Maimets","full_name":"Maimets, Martti"},{"last_name":"Jørgensen","first_name":"Anne","full_name":"Jørgensen, Anne"},{"full_name":"Perlman, Signe","last_name":"Perlman","first_name":"Signe"},{"first_name":"Lene","last_name":"Lundvall","full_name":"Lundvall, Lene"},{"last_name":"Mamsen","first_name":"Linn Salto","full_name":"Mamsen, Linn Salto"},{"first_name":"Agnete","last_name":"Larsen","full_name":"Larsen, Agnete"},{"first_name":"Rasmus H.","last_name":"Olesen","full_name":"Olesen, Rasmus H."},{"full_name":"Andersen, Claus Yding","last_name":"Andersen","first_name":"Claus Yding"},{"full_name":"Thuesen, Lea Langhoff","last_name":"Thuesen","first_name":"Lea Langhoff"},{"full_name":"Hare, Kristine Juul","last_name":"Hare","first_name":"Kristine Juul"},{"full_name":"Pers, Tune H.","last_name":"Pers","first_name":"Tune H."},{"last_name":"Khodosevich","first_name":"Konstantin","full_name":"Khodosevich, Konstantin"},{"full_name":"Simons, Benjamin D.","last_name":"Simons","first_name":"Benjamin D."},{"last_name":"Jensen","first_name":"Kim B.","full_name":"Jensen, Kim B."}],"pmid":1,"quality_controlled":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986928","open_access":"1"}],"date_created":"2019-06-02T21:59:14Z","year":"2019","publication":"Nature","doi":"10.1038/s41586-019-1212-5","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]}},{"oa":1,"file_date_updated":"2020-07-14T12:47:32Z","language":[{"iso":"eng"}],"month":"07","date_published":"2019-07-01T00:00:00Z","department":[{"_id":"HeEd"}],"publisher":"Carleton University","date_updated":"2021-01-12T08:07:50Z","oa_version":"Published Version","intvolume":"        10","type":"journal_article","_id":"6515","scopus_import":1,"citation":{"ieee":"R. Dyer, G. Vegter, and M. Wintraecken, “Simplices modelled on spaces of constant curvature,” <i>Journal of Computational Geometry </i>, vol. 10, no. 1. Carleton University, pp. 223–256, 2019.","short":"R. Dyer, G. Vegter, M. Wintraecken, Journal of Computational Geometry  10 (2019) 223–256.","ista":"Dyer R, Vegter G, Wintraecken M. 2019. Simplices modelled on spaces of constant curvature. Journal of Computational Geometry . 10(1), 223–256.","ama":"Dyer R, Vegter G, Wintraecken M. Simplices modelled on spaces of constant curvature. <i>Journal of Computational Geometry </i>. 2019;10(1):223–256. doi:<a href=\"https://doi.org/10.20382/jocg.v10i1a9\">10.20382/jocg.v10i1a9</a>","apa":"Dyer, R., Vegter, G., &#38; Wintraecken, M. (2019). Simplices modelled on spaces of constant curvature. <i>Journal of Computational Geometry </i>. Carleton University. <a href=\"https://doi.org/10.20382/jocg.v10i1a9\">https://doi.org/10.20382/jocg.v10i1a9</a>","chicago":"Dyer, Ramsay, Gert Vegter, and Mathijs Wintraecken. “Simplices Modelled on Spaces of Constant Curvature.” <i>Journal of Computational Geometry </i>. Carleton University, 2019. <a href=\"https://doi.org/10.20382/jocg.v10i1a9\">https://doi.org/10.20382/jocg.v10i1a9</a>.","mla":"Dyer, Ramsay, et al. “Simplices Modelled on Spaces of Constant Curvature.” <i>Journal of Computational Geometry </i>, vol. 10, no. 1, Carleton University, 2019, pp. 223–256, doi:<a href=\"https://doi.org/10.20382/jocg.v10i1a9\">10.20382/jocg.v10i1a9</a>."},"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","day":"01","page":"223–256","abstract":[{"lang":"eng","text":"We give non-degeneracy criteria for Riemannian simplices based on simplices in spaces of constant sectional curvature. It extends previous work on Riemannian simplices, where we developed Riemannian simplices with respect to Euclidean reference simplices. The criteria we give in this article are in terms of quality measures for spaces of constant curvature that we develop here. We see that simplices in spaces that have nearly constant curvature, are already non-degenerate under very weak quality demands. This is of importance because it allows for sampling of Riemannian manifolds based on anisotropy of the manifold and not (absolute) curvature."}],"publication_status":"published","title":"Simplices modelled on spaces of constant curvature","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Dyer, Ramsay","last_name":"Dyer","first_name":"Ramsay"},{"first_name":"Gert","last_name":"Vegter","full_name":"Vegter, Gert"},{"id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken","first_name":"Mathijs"}],"volume":10,"quality_controlled":"1","file":[{"creator":"mwintrae","content_type":"application/pdf","file_name":"mainJournalFinal.pdf","date_created":"2019-06-03T09:30:01Z","file_size":2170882,"date_updated":"2020-07-14T12:47:32Z","access_level":"open_access","relation":"main_file","checksum":"57b4df2f16a74eb499734ec8ee240178","file_id":"6516"}],"has_accepted_license":"1","ddc":["510"],"year":"2019","date_created":"2019-06-03T09:35:33Z","issue":"1","publication_identifier":{"issn":["1920-180X"]},"doi":"10.20382/jocg.v10i1a9","publication":"Journal of Computational Geometry "},{"quality_controlled":"1","file":[{"date_created":"2019-06-08T11:44:20Z","file_name":"2019_Neuroscience_Maes.pdf","content_type":"application/pdf","creator":"dernst","file_id":"6551","relation":"main_file","checksum":"553c9dbd39727fbed55ee991c51ca4d1","access_level":"open_access","file_size":1779287,"date_updated":"2020-07-14T12:47:33Z"}],"corr_author":"1","ddc":["570"],"has_accepted_license":"1","article_number":"134310","date_created":"2019-06-05T13:16:24Z","year":"2019","publication":"Neuroscience Letters","publication_identifier":{"issn":["0304-3940"]},"doi":"10.1016/j.neulet.2019.134310","external_id":{"isi":["000486094600037"],"pmid":["31158432"]},"publication_status":"published","abstract":[{"text":"Microglia have emerged as a critical component of neurodegenerative diseases. Genetic manipulation of microglia can elucidate their functional impact in disease. In neuroscience, recombinant viruses such as lentiviruses and adeno-associated viruses (AAVs) have been successfully used to target various cell types in the brain, although effective transduction of microglia is rare. In this review, we provide a short background of lentiviruses and AAVs, and strategies for designing recombinant viral vectors. Then, we will summarize recent literature on successful microglial transductions in vitro and in vivo, and discuss the current challenges. Finally, we provide guidelines for reporting the efficiency and specificity of viral targeting in microglia, which will enable the microglial research community to assess and improve methodologies for future studies.","lang":"eng"}],"article_processing_charge":"No","title":"Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges","volume":707,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Maes, Margaret E","orcid":"0000-0001-9642-1085","id":"3838F452-F248-11E8-B48F-1D18A9856A87","last_name":"Maes","first_name":"Margaret E"},{"orcid":"0000-0001-9434-8902","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","full_name":"Colombo, Gloria","last_name":"Colombo","first_name":"Gloria"},{"full_name":"Schulz, Rouven","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5297-733X","first_name":"Rouven","last_name":"Schulz"},{"full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","first_name":"Sandra"}],"pmid":1,"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"Microglia action towards neuronal circuit formation and function in health and disease","call_identifier":"H2020","grant_number":"715571","_id":"25D4A630-B435-11E9-9278-68D0E5697425"},{"_id":"267F75D8-B435-11E9-9278-68D0E5697425","name":"Modulating microglia through G protein-coupled receptor (GPCR) signaling"}],"citation":{"chicago":"Maes, Margaret E, Gloria Colombo, Rouven Schulz, and Sandra Siegert. “Targeting Microglia with Lentivirus and AAV: Recent Advances and Remaining Challenges.” <i>Neuroscience Letters</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.neulet.2019.134310\">https://doi.org/10.1016/j.neulet.2019.134310</a>.","apa":"Maes, M. E., Colombo, G., Schulz, R., &#38; Siegert, S. (2019). Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. <i>Neuroscience Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neulet.2019.134310\">https://doi.org/10.1016/j.neulet.2019.134310</a>","mla":"Maes, Margaret E., et al. “Targeting Microglia with Lentivirus and AAV: Recent Advances and Remaining Challenges.” <i>Neuroscience Letters</i>, vol. 707, 134310, Elsevier, 2019, doi:<a href=\"https://doi.org/10.1016/j.neulet.2019.134310\">10.1016/j.neulet.2019.134310</a>.","short":"M.E. Maes, G. Colombo, R. Schulz, S. Siegert, Neuroscience Letters 707 (2019).","ieee":"M. E. Maes, G. Colombo, R. Schulz, and S. Siegert, “Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges,” <i>Neuroscience Letters</i>, vol. 707. Elsevier, 2019.","ista":"Maes ME, Colombo G, Schulz R, Siegert S. 2019. Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience Letters. 707, 134310.","ama":"Maes ME, Colombo G, Schulz R, Siegert S. Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. <i>Neuroscience Letters</i>. 2019;707. doi:<a href=\"https://doi.org/10.1016/j.neulet.2019.134310\">10.1016/j.neulet.2019.134310</a>"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"day":"10","status":"public","file_date_updated":"2020-07-14T12:47:33Z","oa":1,"isi":1,"date_updated":"2025-03-31T16:01:17Z","department":[{"_id":"SaSi"}],"publisher":"Elsevier","date_published":"2019-08-10T00:00:00Z","month":"08","language":[{"iso":"eng"}],"type":"journal_article","oa_version":"Published Version","intvolume":"       707","article_type":"original","scopus_import":"1","_id":"6521"},{"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2019.03.035"}],"ddc":["570"],"date_created":"2019-06-09T21:59:10Z","year":"2019","publication_identifier":{"issn":["09609822"]},"doi":"10.1016/j.cub.2019.03.035","issue":"11","publication":"Current Biology","article_processing_charge":"No","page":"R458-R463","external_id":{"isi":["000470902000023"],"pmid":["31163158"]},"publication_status":"published","abstract":[{"lang":"eng","text":"When animals become sick, infected cells and an armada of activated immune cells attempt to eliminate the pathogen from the body. Once infectious particles have breached the body's physical barriers of the skin or gut lining, an initially local response quickly escalates into a systemic response, attracting mobile immune cells to the site of infection. These cells complement the initial, unspecific defense with a more specialized, targeted response. This can also provide long-term immune memory and protection against future infection. The cell-autonomous defenses of the infected cells are thus aided by the actions of recruited immune cells. These specialized cells are the most mobile cells in the body, constantly patrolling through the otherwise static tissue to detect incoming pathogens. Such constant immune surveillance means infections are noticed immediately and can be rapidly cleared from the body. Some immune cells also remove infected cells that have succumbed to infection. All this prevents pathogen replication and spread to healthy tissues. Although this may involve the sacrifice of some somatic tissue, this is typically replaced quickly. Particular care is, however, given to the reproductive organs, which should always remain disease free (immune privilege). "}],"title":"Social immunity in insects","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"}],"volume":29,"pmid":1,"citation":{"apa":"Cremer, S. (2019). Social immunity in insects. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2019.03.035\">https://doi.org/10.1016/j.cub.2019.03.035</a>","chicago":"Cremer, Sylvia. “Social Immunity in Insects.” <i>Current Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cub.2019.03.035\">https://doi.org/10.1016/j.cub.2019.03.035</a>.","mla":"Cremer, Sylvia. “Social Immunity in Insects.” <i>Current Biology</i>, vol. 29, no. 11, Elsevier, 2019, pp. R458–63, doi:<a href=\"https://doi.org/10.1016/j.cub.2019.03.035\">10.1016/j.cub.2019.03.035</a>.","ieee":"S. Cremer, “Social immunity in insects,” <i>Current Biology</i>, vol. 29, no. 11. Elsevier, pp. R458–R463, 2019.","short":"S. Cremer, Current Biology 29 (2019) R458–R463.","ista":"Cremer S. 2019. Social immunity in insects. Current Biology. 29(11), R458–R463.","ama":"Cremer S. Social immunity in insects. <i>Current Biology</i>. 2019;29(11):R458-R463. doi:<a href=\"https://doi.org/10.1016/j.cub.2019.03.035\">10.1016/j.cub.2019.03.035</a>"},"status":"public","day":"03","isi":1,"oa":1,"date_published":"2019-06-03T00:00:00Z","language":[{"iso":"eng"}],"month":"06","date_updated":"2026-06-18T19:07:39Z","publisher":"Elsevier","department":[{"_id":"SyCr"}],"oa_version":"Published Version","intvolume":"        29","article_type":"original","type":"journal_article","scopus_import":"1","_id":"6552"},{"title":"3-manifold triangulations with small treewidth","keyword":["computational 3-manifold topology","fixed-parameter tractability","layered triangulations","structural graph theory","treewidth","cutwidth","Heegaard genus"],"page":"44:1-44:20","article_processing_charge":"No","abstract":[{"text":"Motivated by fixed-parameter tractable (FPT) problems in computational topology, we consider the treewidth tw(M) of a compact, connected 3-manifold M, defined to be the minimum treewidth of the face pairing graph of any triangulation T of M. In this setting the relationship between the topology of a 3-manifold and its treewidth is of particular interest. First, as a corollary of work of Jaco and Rubinstein, we prove that for any closed, orientable 3-manifold M the treewidth tw(M) is at most 4g(M)-2, where g(M) denotes Heegaard genus of M. In combination with our earlier work with Wagner, this yields that for non-Haken manifolds the Heegaard genus and the treewidth are within a constant factor. Second, we characterize all 3-manifolds of treewidth one: These are precisely the lens spaces and a single other Seifert fibered space. Furthermore, we show that all remaining orientable Seifert fibered spaces over the 2-sphere or a non-orientable surface have treewidth two. In particular, for every spherical 3-manifold we exhibit a triangulation of treewidth at most two. Our results further validate the parameter of treewidth (and other related parameters such as cutwidth or congestion) to be useful for topological computing, and also shed more light on the scope of existing FPT-algorithms in the field.","lang":"eng"}],"external_id":{"arxiv":["1812.05528"]},"publication_status":"published","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8032"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Huszár","first_name":"Kristóf","full_name":"Huszár, Kristóf","id":"33C26278-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5445-5057"},{"full_name":"Spreer, Jonathan","last_name":"Spreer","first_name":"Jonathan"}],"volume":129,"has_accepted_license":"1","conference":{"name":"SoCG: Symposium on Computational Geometry","start_date":"2019-06-18","end_date":"2019-06-21","location":"Portland, Oregon, United States"},"ddc":["516"],"corr_author":"1","file":[{"file_size":905885,"date_updated":"2020-07-14T12:47:33Z","checksum":"29d18c435368468aa85823dabb157e43","relation":"main_file","access_level":"open_access","file_id":"6557","creator":"kschuh","file_name":"2019_LIPIcs-Huszar.pdf","content_type":"application/pdf","date_created":"2019-06-12T06:45:33Z"}],"quality_controlled":"1","doi":"10.4230/LIPIcs.SoCG.2019.44","publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-95977-104-7"]},"publication":"35th International Symposium on Computational Geometry","year":"2019","date_created":"2019-06-11T20:09:57Z","month":"06","language":[{"iso":"eng"}],"date_published":"2019-06-01T00:00:00Z","arxiv":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"UlWa"}],"date_updated":"2026-04-08T07:21:27Z","oa":1,"file_date_updated":"2020-07-14T12:47:33Z","_id":"6556","scopus_import":"1","intvolume":"       129","oa_version":"Published Version","type":"conference","citation":{"mla":"Huszár, Kristóf, and Jonathan Spreer. “3-Manifold Triangulations with Small Treewidth.” <i>35th International Symposium on Computational Geometry</i>, vol. 129, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 44:1-44:20, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2019.44\">10.4230/LIPIcs.SoCG.2019.44</a>.","apa":"Huszár, K., &#38; Spreer, J. (2019). 3-manifold triangulations with small treewidth. In <i>35th International Symposium on Computational Geometry</i> (Vol. 129, p. 44:1-44:20). Portland, Oregon, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2019.44\">https://doi.org/10.4230/LIPIcs.SoCG.2019.44</a>","chicago":"Huszár, Kristóf, and Jonathan Spreer. “3-Manifold Triangulations with Small Treewidth.” In <i>35th International Symposium on Computational Geometry</i>, 129:44:1-44:20. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2019.44\">https://doi.org/10.4230/LIPIcs.SoCG.2019.44</a>.","ama":"Huszár K, Spreer J. 3-manifold triangulations with small treewidth. In: <i>35th International Symposium on Computational Geometry</i>. Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:44:1-44:20. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2019.44\">10.4230/LIPIcs.SoCG.2019.44</a>","ista":"Huszár K, Spreer J. 2019. 3-manifold triangulations with small treewidth. 35th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 129, 44:1-44:20.","ieee":"K. Huszár and J. Spreer, “3-manifold triangulations with small treewidth,” in <i>35th International Symposium on Computational Geometry</i>, Portland, Oregon, United States, 2019, vol. 129, p. 44:1-44:20.","short":"K. Huszár, J. Spreer, in:, 35th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 44:1-44:20."},"alternative_title":["LIPIcs"],"day":"01","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"scopus_import":"1","_id":"6559","type":"journal_article","oa_version":"None","intvolume":"        60","article_type":"original","date_updated":"2026-04-03T09:38:46Z","department":[{"_id":"EdHa"}],"publisher":"Elsevier","date_published":"2019-10-01T00:00:00Z","month":"10","language":[{"iso":"eng"}],"isi":1,"status":"public","day":"01","citation":{"apa":"Hannezo, E. B., &#38; Simons, B. D. (2019). Multiscale dynamics of branching morphogenesis. <i>Current Opinion in Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ceb.2019.04.008\">https://doi.org/10.1016/j.ceb.2019.04.008</a>","chicago":"Hannezo, Edouard B, and Benjamin D. Simons. “Multiscale Dynamics of Branching Morphogenesis.” <i>Current Opinion in Cell Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.ceb.2019.04.008\">https://doi.org/10.1016/j.ceb.2019.04.008</a>.","mla":"Hannezo, Edouard B., and Benjamin D. Simons. “Multiscale Dynamics of Branching Morphogenesis.” <i>Current Opinion in Cell Biology</i>, vol. 60, Elsevier, 2019, pp. 99–105, doi:<a href=\"https://doi.org/10.1016/j.ceb.2019.04.008\">10.1016/j.ceb.2019.04.008</a>.","ieee":"E. B. Hannezo and B. D. Simons, “Multiscale dynamics of branching morphogenesis,” <i>Current Opinion in Cell Biology</i>, vol. 60. Elsevier, pp. 99–105, 2019.","short":"E.B. Hannezo, B.D. Simons, Current Opinion in Cell Biology 60 (2019) 99–105.","ama":"Hannezo EB, Simons BD. Multiscale dynamics of branching morphogenesis. <i>Current Opinion in Cell Biology</i>. 2019;60:99-105. doi:<a href=\"https://doi.org/10.1016/j.ceb.2019.04.008\">10.1016/j.ceb.2019.04.008</a>","ista":"Hannezo EB, Simons BD. 2019. Multiscale dynamics of branching morphogenesis. Current Opinion in Cell Biology. 60, 99–105."},"pmid":1,"volume":60,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo"},{"full_name":"Simons, Benjamin D.","first_name":"Benjamin D.","last_name":"Simons"}],"title":"Multiscale dynamics of branching morphogenesis","external_id":{"isi":["000486545800014"],"pmid":["31181348"]},"publication_status":"published","abstract":[{"text":"Branching morphogenesis is a prototypical example of complex three-dimensional organ sculpting, required in multiple developmental settings to maximize the area of exchange surfaces. It requires, in particular, the coordinated growth of different cell types together with complex patterning to lead to robust macroscopic outputs. In recent years, novel multiscale quantitative biology approaches, together with biophysical modelling, have begun to shed new light of this topic. Here, we wish to review some of these recent developments, highlighting the generic design principles that can be abstracted across different branched organs, as well as the implications for the broader fields of stem cell, developmental and systems biology.","lang":"eng"}],"article_processing_charge":"No","page":"99-105","publication":"Current Opinion in Cell Biology","doi":"10.1016/j.ceb.2019.04.008","publication_identifier":{"eissn":["1879-0410"],"issn":["0955-0674"]},"date_created":"2019-06-16T21:59:12Z","year":"2019","quality_controlled":"1"},{"citation":{"apa":"Tichy, A.-M., Gerrard, E. J., Legrand, J. M. D., Hobbs, R. M., &#38; Janovjak, H. L. (2019). Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2019.05.033\">https://doi.org/10.1016/j.jmb.2019.05.033</a>","chicago":"Tichy, Alexandra-Madelaine, Elliot J. Gerrard, Julien M.D. Legrand, Robin M. Hobbs, and Harald L Janovjak. “Engineering Strategy and Vector Library for the Rapid Generation of Modular Light-Controlled Protein–Protein Interactions.” <i>Journal of Molecular Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.jmb.2019.05.033\">https://doi.org/10.1016/j.jmb.2019.05.033</a>.","mla":"Tichy, Alexandra-Madelaine, et al. “Engineering Strategy and Vector Library for the Rapid Generation of Modular Light-Controlled Protein–Protein Interactions.” <i>Journal of Molecular Biology</i>, vol. 431, no. 17, Elsevier, 2019, pp. 3046–55, doi:<a href=\"https://doi.org/10.1016/j.jmb.2019.05.033\">10.1016/j.jmb.2019.05.033</a>.","short":"A.-M. Tichy, E.J. Gerrard, J.M.D. Legrand, R.M. Hobbs, H.L. Janovjak, Journal of Molecular Biology 431 (2019) 3046–3055.","ieee":"A.-M. Tichy, E. J. Gerrard, J. M. D. Legrand, R. M. Hobbs, and H. L. Janovjak, “Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions,” <i>Journal of Molecular Biology</i>, vol. 431, no. 17. Elsevier, pp. 3046–3055, 2019.","ama":"Tichy A-M, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak HL. Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. <i>Journal of Molecular Biology</i>. 2019;431(17):3046-3055. doi:<a href=\"https://doi.org/10.1016/j.jmb.2019.05.033\">10.1016/j.jmb.2019.05.033</a>","ista":"Tichy A-M, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak HL. 2019. Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. Journal of Molecular Biology. 431(17), 3046–3055."},"status":"public","day":"09","language":[{"iso":"eng"}],"month":"08","date_published":"2019-08-09T00:00:00Z","publisher":"Elsevier","department":[{"_id":"HaJa"}],"date_updated":"2025-07-10T11:53:33Z","isi":1,"oa":1,"_id":"6564","scopus_import":"1","article_type":"original","intvolume":"       431","oa_version":"Preprint","type":"journal_article","main_file_link":[{"url":"http://www.biorxiv.org/content/10.1101/583369v1","open_access":"1"}],"quality_controlled":"1","issue":"17","doi":"10.1016/j.jmb.2019.05.033","publication_identifier":{"eissn":["1089-8638"],"issn":["0022-2836"]},"publication":"Journal of Molecular Biology","year":"2019","date_created":"2019-06-16T21:59:14Z","title":"Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions","page":"3046-3055","article_processing_charge":"No","abstract":[{"text":"Optogenetics enables the spatio-temporally precise control of cell and animal behavior. Many optogenetic tools are driven by light-controlled protein–protein interactions (PPIs) that are repurposed from natural light-sensitive domains (LSDs). Applying light-controlled PPIs to new target proteins is challenging because it is difficult to predict which of the many available LSDs, if any, will yield robust light regulation. As a consequence, fusion protein libraries need to be prepared and tested, but methods and platforms to facilitate this process are currently not available. Here, we developed a genetic engineering strategy and vector library for the rapid generation of light-controlled PPIs. The strategy permits fusing a target protein to multiple LSDs efficiently and in two orientations. The public and expandable library contains 29 vectors with blue, green or red light-responsive LSDs, many of which have been previously applied ex vivo and in vivo. We demonstrate the versatility of the approach and the necessity for sampling LSDs by generating light-activated caspase-9 (casp9) enzymes. Collectively, this work provides a new resource for optical regulation of a broad range of target proteins in cell and developmental biology.","lang":"eng"}],"publication_status":"published","external_id":{"isi":["000482872100002"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Alexandra-Madelaine","last_name":"Tichy","full_name":"Tichy, Alexandra-Madelaine","id":"29D8BB2C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gerrard, Elliot J.","first_name":"Elliot J.","last_name":"Gerrard"},{"first_name":"Julien M.D.","last_name":"Legrand","full_name":"Legrand, Julien M.D."},{"full_name":"Hobbs, Robin M.","first_name":"Robin M.","last_name":"Hobbs"},{"last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L"}],"volume":431},{"article_processing_charge":"No","abstract":[{"text":"In this paper, we address the problem of synthesizing periodic switching controllers for stabilizing a family of linear systems. Our broad approach consists of constructing a finite game graph based on the family of linear systems such that every winning strategy on the game graph corresponds to a stabilizing switching controller for the family of linear systems. The construction of a (finite) game graph, the synthesis of a winning strategy and the extraction of a stabilizing controller are all computationally feasible. We illustrate our method on an example.","lang":"eng"}],"publication_status":"published","external_id":{"isi":["000470655700087"]},"title":"Formal synthesis of stabilizing controllers for periodically controlled linear switched systems","author":[{"full_name":"Kundu, Atreyee","last_name":"Kundu","first_name":"Atreyee"},{"id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0003−2936−5719","full_name":"Garcia Soto, Miriam","last_name":"Garcia Soto","first_name":"Miriam"},{"first_name":"Pavithra","last_name":"Prabhakar","full_name":"Prabhakar, Pavithra"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"content_type":"application/pdf","file_name":"2019_ICC_Kundu.pdf","date_created":"2020-10-21T13:13:49Z","success":1,"creator":"dernst","file_id":"8687","date_updated":"2020-10-21T13:13:49Z","file_size":396031,"access_level":"open_access","checksum":"d622a91af1e427f6b1e0ba8e18a2b767","relation":"main_file"}],"quality_controlled":"1","has_accepted_license":"1","conference":{"end_date":"2019-01-11","location":"Delhi, India","start_date":"2019-01-09","name":"ICC: Indian Control Conference"},"ddc":["000"],"year":"2019","date_created":"2019-06-17T06:57:33Z","article_number":"8715598","publication_identifier":{"isbn":["978-153866246-5"]},"doi":"10.1109/INDIANCC.2019.8715598","publication":"5th Indian Control Conference Proceedings","isi":1,"oa":1,"file_date_updated":"2020-10-21T13:13:49Z","month":"05","language":[{"iso":"eng"}],"date_published":"2019-05-16T00:00:00Z","department":[{"_id":"ToHe"}],"publisher":"IEEE","date_updated":"2025-09-10T10:36:07Z","oa_version":"Submitted Version","type":"conference","_id":"6565","scopus_import":"1","citation":{"ama":"Kundu A, Garcia Soto M, Prabhakar P. Formal synthesis of stabilizing controllers for periodically controlled linear switched systems. In: <i>5th Indian Control Conference Proceedings</i>. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/INDIANCC.2019.8715598\">10.1109/INDIANCC.2019.8715598</a>","ista":"Kundu A, Garcia Soto M, Prabhakar P. 2019. Formal synthesis of stabilizing controllers for periodically controlled linear switched systems. 5th Indian Control Conference Proceedings. ICC: Indian Control Conference, 8715598.","ieee":"A. Kundu, M. Garcia Soto, and P. Prabhakar, “Formal synthesis of stabilizing controllers for periodically controlled linear switched systems,” in <i>5th Indian Control Conference Proceedings</i>, Delhi, India, 2019.","short":"A. Kundu, M. Garcia Soto, P. Prabhakar, in:, 5th Indian Control Conference Proceedings, IEEE, 2019.","mla":"Kundu, Atreyee, et al. “Formal Synthesis of Stabilizing Controllers for Periodically Controlled Linear Switched Systems.” <i>5th Indian Control Conference Proceedings</i>, 8715598, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/INDIANCC.2019.8715598\">10.1109/INDIANCC.2019.8715598</a>.","apa":"Kundu, A., Garcia Soto, M., &#38; Prabhakar, P. (2019). Formal synthesis of stabilizing controllers for periodically controlled linear switched systems. In <i>5th Indian Control Conference Proceedings</i>. Delhi, India: IEEE. <a href=\"https://doi.org/10.1109/INDIANCC.2019.8715598\">https://doi.org/10.1109/INDIANCC.2019.8715598</a>","chicago":"Kundu, Atreyee, Miriam Garcia Soto, and Pavithra Prabhakar. “Formal Synthesis of Stabilizing Controllers for Periodically Controlled Linear Switched Systems.” In <i>5th Indian Control Conference Proceedings</i>. IEEE, 2019. <a href=\"https://doi.org/10.1109/INDIANCC.2019.8715598\">https://doi.org/10.1109/INDIANCC.2019.8715598</a>."},"project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"status":"public","day":"16"}]