[{"type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"When electron microscopy (EM) was introduced in the 1930s it gave scientists their first look into the nanoworld of cells. Over the last 80 years EM has vastly increased our understanding of the complex cellular structures that underlie the diverse functions that cells need to maintain life. One drawback that has been difficult to overcome was the inherent lack of volume information, mainly due to the limit on the thickness of sections that could be viewed in a transmission electron microscope (TEM). For many years scientists struggled to achieve three-dimensional (3D) EM using serial section reconstructions, TEM tomography, and scanning EM (SEM) techniques such as freeze-fracture. Although each technique yielded some special information, they required a significant amount of time and specialist expertise to obtain even a very small 3D EM dataset. Almost 20 years ago scientists began to exploit SEMs to image blocks of embedded tissues and perform serial sectioning of these tissues inside the SEM chamber. Using first focused ion beams (FIB) and subsequently robotic ultramicrotomes (serial block-face, SBF-SEM) microscopists were able to collect large volumes of 3D EM information at resolutions that could address many important biological questions, and do so in an efficient manner. We present here some examples of 3D EM taken from the many diverse specimens that have been imaged in our core facility. We propose that the next major step forward will be to efficiently correlate functional information obtained using light microscopy (LM) with 3D EM datasets to more completely investigate the important links between cell structures and their functions."}],"_id":"1879","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 259","ddc":["570"],"status":"public","title":"Developing 3D SEM in a broad biological context","pubrep_id":"459","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":2899898,"creator":"system","access_level":"open_access","file_name":"IST-2016-459-v1+1_KREMER_et_al-2015-Journal_of_Microscopy.pdf","checksum":"3649c5372d1644062d728ea9287e367f","date_created":"2018-12-12T10:11:19Z","date_updated":"2020-07-14T12:45:19Z","relation":"main_file","file_id":"4872"}],"scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"short":"A. Kremer, S. Lippens, S. Bartunkova, B. Asselbergh, C. Blanpain, M. Fendrych, A. Goossens, M. Holt, S. Janssens, M. Krols, J. Larsimont, C. Mc Guire, M. Nowack, X. Saelens, A. Schertel, B. Schepens, M. Slezak, V. Timmerman, C. Theunis, R. Van Brempt, Y. Visser, C. Guérin, Journal of Microscopy 259 (2015) 80–96.","mla":"Kremer, A., et al. “Developing 3D SEM in a Broad Biological Context.” Journal of Microscopy, vol. 259, no. 2, Wiley-Blackwell, 2015, pp. 80–96, doi:10.1111/jmi.12211.","chicago":"Kremer, A, Stefaan Lippens, Sonia Bartunkova, Bob Asselbergh, Cendric Blanpain, Matyas Fendrych, A Goossens, et al. “Developing 3D SEM in a Broad Biological Context.” Journal of Microscopy. Wiley-Blackwell, 2015. https://doi.org/10.1111/jmi.12211.","ama":"Kremer A, Lippens S, Bartunkova S, et al. Developing 3D SEM in a broad biological context. Journal of Microscopy. 2015;259(2):80-96. doi:10.1111/jmi.12211","apa":"Kremer, A., Lippens, S., Bartunkova, S., Asselbergh, B., Blanpain, C., Fendrych, M., … Guérin, C. (2015). Developing 3D SEM in a broad biological context. Journal of Microscopy. Wiley-Blackwell. https://doi.org/10.1111/jmi.12211","ieee":"A. Kremer et al., “Developing 3D SEM in a broad biological context,” Journal of Microscopy, vol. 259, no. 2. Wiley-Blackwell, pp. 80–96, 2015.","ista":"Kremer A, Lippens S, Bartunkova S, Asselbergh B, Blanpain C, Fendrych M, Goossens A, Holt M, Janssens S, Krols M, Larsimont J, Mc Guire C, Nowack M, Saelens X, Schertel A, Schepens B, Slezak M, Timmerman V, Theunis C, Van Brempt R, Visser Y, Guérin C. 2015. Developing 3D SEM in a broad biological context. Journal of Microscopy. 259(2), 80–96."},"publication":"Journal of Microscopy","page":"80 - 96","date_published":"2015-08-01T00:00:00Z","publist_id":"5218","file_date_updated":"2020-07-14T12:45:19Z","acknowledgement":"The Zeiss Merlin with Gatan 3View2XP and Zeiss Auriga were acquired through a CLEM grant from Minister Ingrid Lieten to the VIB Bio-Imaging-Core. Michiel Krols and Saskia Lippens are the recipients of a fellowship from the FWO (Fonds Wetenschappelijk Onderzoek) of Flanders.","year":"2015","publisher":"Wiley-Blackwell","department":[{"_id":"JiFr"}],"publication_status":"published","author":[{"last_name":"Kremer","first_name":"A","full_name":"Kremer, A"},{"last_name":"Lippens","first_name":"Stefaan","full_name":"Lippens, Stefaan"},{"last_name":"Bartunkova","first_name":"Sonia","full_name":"Bartunkova, Sonia"},{"last_name":"Asselbergh","first_name":"Bob","full_name":"Asselbergh, Bob"},{"last_name":"Blanpain","first_name":"Cendric","full_name":"Blanpain, Cendric"},{"full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","first_name":"Matyas"},{"last_name":"Goossens","first_name":"A","full_name":"Goossens, A"},{"full_name":"Holt, Matthew","first_name":"Matthew","last_name":"Holt"},{"full_name":"Janssens, Sophie","first_name":"Sophie","last_name":"Janssens"},{"last_name":"Krols","first_name":"Michiel","full_name":"Krols, Michiel"},{"full_name":"Larsimont, Jean","last_name":"Larsimont","first_name":"Jean"},{"last_name":"Mc Guire","first_name":"Conor","full_name":"Mc Guire, Conor"},{"last_name":"Nowack","first_name":"Moritz","full_name":"Nowack, Moritz"},{"first_name":"Xavier","last_name":"Saelens","full_name":"Saelens, Xavier"},{"full_name":"Schertel, Andreas","last_name":"Schertel","first_name":"Andreas"},{"last_name":"Schepens","first_name":"B","full_name":"Schepens, B"},{"full_name":"Slezak, M","last_name":"Slezak","first_name":"M"},{"first_name":"Vincent","last_name":"Timmerman","full_name":"Timmerman, Vincent"},{"last_name":"Theunis","first_name":"Clara","full_name":"Theunis, Clara"},{"full_name":"Van Brempt, Ronald","first_name":"Ronald","last_name":"Van Brempt"},{"first_name":"Y","last_name":"Visser","full_name":"Visser, Y"},{"full_name":"Guérin, Christophe","first_name":"Christophe","last_name":"Guérin"}],"volume":259,"date_created":"2018-12-11T11:54:30Z","date_updated":"2021-01-12T06:53:48Z","month":"08","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1111/jmi.12211","language":[{"iso":"eng"}]},{"date_published":"2015-01-15T00:00:00Z","publication":"New Journal of Physics","citation":{"ista":"Könenberg M, Moser T, Seiringer R, Yngvason J. 2015. Superfluid behavior of a Bose-Einstein condensate in a random potential. New Journal of Physics. 17, 013022.","apa":"Könenberg, M., Moser, T., Seiringer, R., & Yngvason, J. (2015). Superfluid behavior of a Bose-Einstein condensate in a random potential. New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/17/1/013022","ieee":"M. Könenberg, T. Moser, R. Seiringer, and J. Yngvason, “Superfluid behavior of a Bose-Einstein condensate in a random potential,” New Journal of Physics, vol. 17. IOP Publishing Ltd., 2015.","ama":"Könenberg M, Moser T, Seiringer R, Yngvason J. Superfluid behavior of a Bose-Einstein condensate in a random potential. New Journal of Physics. 2015;17. doi:10.1088/1367-2630/17/1/013022","chicago":"Könenberg, Martin, Thomas Moser, Robert Seiringer, and Jakob Yngvason. “Superfluid Behavior of a Bose-Einstein Condensate in a Random Potential.” New Journal of Physics. IOP Publishing Ltd., 2015. https://doi.org/10.1088/1367-2630/17/1/013022.","mla":"Könenberg, Martin, et al. “Superfluid Behavior of a Bose-Einstein Condensate in a Random Potential.” New Journal of Physics, vol. 17, 013022, IOP Publishing Ltd., 2015, doi:10.1088/1367-2630/17/1/013022.","short":"M. Könenberg, T. Moser, R. Seiringer, J. Yngvason, New Journal of Physics 17 (2015)."},"day":"15","has_accepted_license":"1","scopus_import":1,"pubrep_id":"447","file":[{"date_created":"2018-12-12T10:12:44Z","date_updated":"2020-07-14T12:45:20Z","checksum":"38fdf2b5ac30445e26a5d613abd84b16","file_id":"4963","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":768108,"file_name":"IST-2016-447-v1+1_document_1_.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1880","status":"public","title":"Superfluid behavior of a Bose-Einstein condensate in a random potential","ddc":["530"],"intvolume":" 17","abstract":[{"lang":"eng","text":"We investigate the relation between Bose-Einstein condensation (BEC) and superfluidity in the ground state of a one-dimensional model of interacting bosons in a strong random potential. We prove rigorously that in a certain parameter regime the superfluid fraction can be arbitrarily small while complete BEC prevails. In another regime there is both complete BEC and complete superfluidity, despite the strong disorder"}],"type":"journal_article","doi":"10.1088/1367-2630/17/1/013022","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"_id":"26450934-B435-11E9-9278-68D0E5697425","name":"NSERC Postdoctoral fellowship"}],"month":"01","author":[{"last_name":"Könenberg","first_name":"Martin","full_name":"Könenberg, Martin"},{"id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Moser","full_name":"Moser, Thomas"},{"full_name":"Seiringer, Robert","first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"},{"last_name":"Yngvason","first_name":"Jakob","full_name":"Yngvason, Jakob"}],"date_updated":"2021-01-12T06:53:48Z","date_created":"2018-12-11T11:54:30Z","volume":17,"year":"2015","acknowledgement":"Support from the Natural Sciences and Engineering Research Council of Canada NSERC (MK and RS) and from the Austrian Science Fund FWF (JY, under project P 22929-N16) is gratefully acknowledged","publication_status":"published","publisher":"IOP Publishing Ltd.","department":[{"_id":"RoSe"}],"file_date_updated":"2020-07-14T12:45:20Z","publist_id":"5214","article_number":"013022"},{"oa_version":"Preprint","_id":"1882","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 8997","title":"Compositionality for quantitative specifications","status":"public","abstract":[{"lang":"eng","text":"We provide a framework for compositional and iterative design and verification of systems with quantitative information, such as rewards, time or energy. It is based on disjunctive modal transition systems where we allow actions to bear various types of quantitative information. Throughout the design process the actions can be further refined and the information made more precise. We show how to compute the results of standard operations on the systems, including the quotient (residual), which has not been previously considered for quantitative non-deterministic systems. Our quantitative framework has close connections to the modal nu-calculus and is compositional with respect to general notions of distances between systems and the standard operations."}],"type":"conference","alternative_title":["LNCS"],"date_published":"2015-01-30T00:00:00Z","citation":{"chicago":"Fahrenberg, Uli, Jan Kretinsky, Axel Legay, and Louis Traonouez. “Compositionality for Quantitative Specifications,” 8997:306–24. Springer, 2015. https://doi.org/10.1007/978-3-319-15317-9_19.","mla":"Fahrenberg, Uli, et al. Compositionality for Quantitative Specifications. Vol. 8997, Springer, 2015, pp. 306–24, doi:10.1007/978-3-319-15317-9_19.","short":"U. Fahrenberg, J. Kretinsky, A. Legay, L. Traonouez, in:, Springer, 2015, pp. 306–324.","ista":"Fahrenberg U, Kretinsky J, Legay A, Traonouez L. 2015. Compositionality for quantitative specifications. FACS: Formal Aspects of Component Software, LNCS, vol. 8997, 306–324.","ieee":"U. Fahrenberg, J. Kretinsky, A. Legay, and L. Traonouez, “Compositionality for quantitative specifications,” presented at the FACS: Formal Aspects of Component Software, Bertinoro, Italy, 2015, vol. 8997, pp. 306–324.","apa":"Fahrenberg, U., Kretinsky, J., Legay, A., & Traonouez, L. (2015). Compositionality for quantitative specifications (Vol. 8997, pp. 306–324). Presented at the FACS: Formal Aspects of Component Software, Bertinoro, Italy: Springer. https://doi.org/10.1007/978-3-319-15317-9_19","ama":"Fahrenberg U, Kretinsky J, Legay A, Traonouez L. Compositionality for quantitative specifications. In: Vol 8997. Springer; 2015:306-324. doi:10.1007/978-3-319-15317-9_19"},"page":"306 - 324","day":"30","scopus_import":1,"author":[{"full_name":"Fahrenberg, Uli","last_name":"Fahrenberg","first_name":"Uli"},{"full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","first_name":"Jan","last_name":"Kretinsky"},{"first_name":"Axel","last_name":"Legay","full_name":"Legay, Axel"},{"last_name":"Traonouez","first_name":"Louis","full_name":"Traonouez, Louis"}],"volume":8997,"date_updated":"2021-01-12T06:53:49Z","date_created":"2018-12-11T11:54:31Z","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) project S11402-N23 (RiSE), and by the Czech Science Foundation, grant No. P202/12/G061.","year":"2015","publisher":"Springer","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publication_status":"published","publist_id":"5216","ec_funded":1,"doi":"10.1007/978-3-319-15317-9_19","conference":{"end_date":"2014-09-12","start_date":"2014-09-10","location":"Bertinoro, Italy","name":"FACS: Formal Aspects of Component Software"},"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1408.1256"}],"project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"quality_controlled":"1","month":"01"},{"date_published":"2015-02-02T00:00:00Z","article_type":"original","citation":{"ieee":"S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, and K. Klemm, “Anomalous scaling in an age-dependent branching model,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 2. American Institute of Physics, 2015.","apa":"Keller-Schmidt, S., Tugrul, M., Eguíluz, V., Hernandez Garcia, E., & Klemm, K. (2015). Anomalous scaling in an age-dependent branching model. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.91.022803","ista":"Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. 2015. Anomalous scaling in an age-dependent branching model. Physical Review E Statistical Nonlinear and Soft Matter Physics. 91(2), 022803.","ama":"Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. Anomalous scaling in an age-dependent branching model. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2015;91(2). doi:10.1103/PhysRevE.91.022803","chicago":"Keller-Schmidt, Stephanie, Murat Tugrul, Víctor Eguíluz, Emilio Hernandez Garcia, and Konstantin Klemm. “Anomalous Scaling in an Age-Dependent Branching Model.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2015. https://doi.org/10.1103/PhysRevE.91.022803.","short":"S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, K. Klemm, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).","mla":"Keller-Schmidt, Stephanie, et al. “Anomalous Scaling in an Age-Dependent Branching Model.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 2, 022803, American Institute of Physics, 2015, doi:10.1103/PhysRevE.91.022803."},"publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","article_processing_charge":"No","day":"02","scopus_import":1,"oa_version":"Preprint","intvolume":" 91","title":"Anomalous scaling in an age-dependent branching model","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1883","issue":"2","abstract":[{"lang":"eng","text":"We introduce a one-parametric family of tree growth models, in which branching probabilities decrease with branch age τ as τ-α. Depending on the exponent α, the scaling of tree depth with tree size n displays a transition between the logarithmic scaling of random trees and an algebraic growth. At the transition (α=1) tree depth grows as (logn)2. This anomalous scaling is in good agreement with the trend observed in evolution of biological species, thus providing a theoretical support for age-dependent speciation and associating it to the occurrence of a critical point.\r\n"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.91.022803","quality_controlled":"1","external_id":{"arxiv":["1012.3298"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1012.3298"}],"month":"02","volume":91,"date_updated":"2021-01-12T06:53:49Z","date_created":"2018-12-11T11:54:31Z","author":[{"full_name":"Keller-Schmidt, Stephanie","last_name":"Keller-Schmidt","first_name":"Stephanie"},{"full_name":"Tugrul, Murat","first_name":"Murat","last_name":"Tugrul","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8523-0758"},{"full_name":"Eguíluz, Víctor","first_name":"Víctor","last_name":"Eguíluz"},{"full_name":"Hernandez Garcia, Emilio","last_name":"Hernandez Garcia","first_name":"Emilio"},{"last_name":"Klemm","first_name":"Konstantin","full_name":"Klemm, Konstantin"}],"publisher":"American Institute of Physics","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2015","publist_id":"5213","article_number":"022803"},{"date_created":"2018-12-11T11:54:30Z","date_updated":"2021-01-12T06:53:47Z","oa_version":"None","volume":128,"author":[{"last_name":"Cires Rodriguez","first_name":"Eduardo","id":"2AD56A7A-F248-11E8-B48F-1D18A9856A87","full_name":"Cires Rodriguez, Eduardo"},{"first_name":"José","last_name":"Prieto","full_name":"Prieto, José"}],"status":"public","publication_status":"published","title":"Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula","intvolume":" 128","department":[{"_id":"JiFr"}],"publisher":"Springer","_id":"1878","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2015","abstract":[{"lang":"eng","text":"Petrocoptis is a small genus of chasmophytic plants endemic to the Iberian Peninsula, with some localized populations in the French Pyrenees. Within the genus, a dozen species have been recognized based on morphological diversity, most of them with limited distribution area, in small populations and frequently with potential threats to their survival. To date, however, a molecular evaluation of the current systematic treatments has not been carried out. The aim of the present study is to infer phylogenetic relationships among its subordinate taxa by using plastidial rps16 intron and nuclear internal transcribed spacer (ITS) DNA sequences; and evaluate the phylogenetic placement of the genus Petrocoptis within the family Caryophyllaceae. The monophyly of Petrocoptis is supported by both ITS and rps16 intron sequence analyses. Furthermore, time estimates using BEAST analyses indicate a Middle to Late Miocene diversification (10.59 Myr, 6.44–15.26 Myr highest posterior densities [HPD], for ITS; 14.30 Myr, 8.61–21.00 Myr HPD, for rps16 intron)."}],"publist_id":"5217","issue":"2","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2015-01-24T00:00:00Z","doi":"10.1007/s10265-014-0691-6","quality_controlled":"1","page":"223 - 238","publication":"Journal of Plant Research","citation":{"ama":"Cires Rodriguez E, Prieto J. Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula. Journal of Plant Research. 2015;128(2):223-238. doi:10.1007/s10265-014-0691-6","apa":"Cires Rodriguez, E., & Prieto, J. (2015). Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula. Journal of Plant Research. Springer. https://doi.org/10.1007/s10265-014-0691-6","ieee":"E. Cires Rodriguez and J. Prieto, “Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula,” Journal of Plant Research, vol. 128, no. 2. Springer, pp. 223–238, 2015.","ista":"Cires Rodriguez E, Prieto J. 2015. Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula. Journal of Plant Research. 128(2), 223–238.","short":"E. Cires Rodriguez, J. Prieto, Journal of Plant Research 128 (2015) 223–238.","mla":"Cires Rodriguez, Eduardo, and José Prieto. “Phylogenetic Relationships of Petrocoptis A. Braun Ex Endl. (Caryophyllaceae), a Discussed Genus from the Iberian Peninsula.” Journal of Plant Research, vol. 128, no. 2, Springer, 2015, pp. 223–38, doi:10.1007/s10265-014-0691-6.","chicago":"Cires Rodriguez, Eduardo, and José Prieto. “Phylogenetic Relationships of Petrocoptis A. Braun Ex Endl. (Caryophyllaceae), a Discussed Genus from the Iberian Peninsula.” Journal of Plant Research. Springer, 2015. https://doi.org/10.1007/s10265-014-0691-6."},"day":"24","month":"01","scopus_import":1},{"date_created":"2018-12-11T11:54:32Z","date_updated":"2021-01-12T06:53:50Z","oa_version":"Preprint","volume":199,"author":[{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik"},{"full_name":"Dubuis, Julien","last_name":"Dubuis","first_name":"Julien"},{"first_name":"Mariela","last_name":"Petkova","full_name":"Petkova, Mariela"},{"last_name":"Gregor","first_name":"Thomas","full_name":"Gregor, Thomas"}],"title":"Positional information, positional error, and readout precision in morphogenesis: A mathematical framework","status":"public","publication_status":"published","department":[{"_id":"GaTk"}],"intvolume":" 199","publisher":"Genetics Society of America","_id":"1885","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","abstract":[{"text":"The concept of positional information is central to our understanding of how cells determine their location in a multicellular structure and thereby their developmental fates. Nevertheless, positional information has neither been defined mathematically nor quantified in a principled way. Here we provide an information-theoretic definition in the context of developmental gene expression patterns and examine the features of expression patterns that affect positional information quantitatively. We connect positional information with the concept of positional error and develop tools to directly measure information and error from experimental data. We illustrate our framework for the case of gap gene expression patterns in the early Drosophila embryo and show how information that is distributed among only four genes is sufficient to determine developmental fates with nearly single-cell resolution. Our approach can be generalized to a variety of different model systems; procedures and examples are discussed in detail. ","lang":"eng"}],"publist_id":"5210","issue":"1","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1534/genetics.114.171850","date_published":"2015-01-01T00:00:00Z","quality_controlled":"1","page":"39 - 59","publication":"Genetics","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.5599"}],"citation":{"chicago":"Tkačik, Gašper, Julien Dubuis, Mariela Petkova, and Thomas Gregor. “Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework.” Genetics. Genetics Society of America, 2015. https://doi.org/10.1534/genetics.114.171850.","short":"G. Tkačik, J. Dubuis, M. Petkova, T. Gregor, Genetics 199 (2015) 39–59.","mla":"Tkačik, Gašper, et al. “Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework.” Genetics, vol. 199, no. 1, Genetics Society of America, 2015, pp. 39–59, doi:10.1534/genetics.114.171850.","apa":"Tkačik, G., Dubuis, J., Petkova, M., & Gregor, T. (2015). Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.114.171850","ieee":"G. Tkačik, J. Dubuis, M. Petkova, and T. Gregor, “Positional information, positional error, and readout precision in morphogenesis: A mathematical framework,” Genetics, vol. 199, no. 1. Genetics Society of America, pp. 39–59, 2015.","ista":"Tkačik G, Dubuis J, Petkova M, Gregor T. 2015. Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. Genetics. 199(1), 39–59.","ama":"Tkačik G, Dubuis J, Petkova M, Gregor T. Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. Genetics. 2015;199(1):39-59. doi:10.1534/genetics.114.171850"},"month":"01","day":"01","scopus_import":1},{"scopus_import":1,"month":"06","day":"15","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","citation":{"apa":"Sokolowski, T. R., & Tkačik, G. (2015). Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.91.062710","ieee":"T. R. Sokolowski and G. Tkačik, “Optimizing information flow in small genetic networks. IV. Spatial coupling,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 6. American Institute of Physics, 2015.","ista":"Sokolowski TR, Tkačik G. 2015. Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. 91(6), 062710.","ama":"Sokolowski TR, Tkačik G. Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2015;91(6). doi:10.1103/PhysRevE.91.062710","chicago":"Sokolowski, Thomas R, and Gašper Tkačik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2015. https://doi.org/10.1103/PhysRevE.91.062710.","short":"T.R. Sokolowski, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).","mla":"Sokolowski, Thomas R., and Gašper Tkačik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 6, 062710, American Institute of Physics, 2015, doi:10.1103/PhysRevE.91.062710."},"main_file_link":[{"url":"http://arxiv.org/abs/1501.04015","open_access":"1"}],"oa":1,"quality_controlled":"1","doi":"10.1103/PhysRevE.91.062710","date_published":"2015-06-15T00:00:00Z","language":[{"iso":"eng"}],"article_number":"062710","type":"journal_article","abstract":[{"lang":"eng","text":"We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying signals subject to gene regulatory noise? Here we extend our information-theoretic framework for gene regulation to spatially extended systems. As an example, we consider a lattice of nuclei responding to a concentration field of a transcriptional regulator (the "input") by expressing a single diffusible target gene. When input concentrations are low, diffusive coupling markedly improves information transmission; optimal gene activation functions also systematically change. A qualitatively new regulatory strategy emerges where individual cells respond to the input in a nearly step-like fashion that is subsequently averaged out by strong diffusion. While motivated by early patterning events in the Drosophila embryo, our framework is generically applicable to spatially coupled stochastic gene expression models."}],"publist_id":"5145","issue":"6","year":"2015","_id":"1940","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"Optimizing information flow in small genetic networks. IV. Spatial coupling","department":[{"_id":"GaTk"}],"intvolume":" 91","publisher":"American Institute of Physics","author":[{"orcid":"0000-0002-1287-3779","id":"3E999752-F248-11E8-B48F-1D18A9856A87","last_name":"Sokolowski","first_name":"Thomas R","full_name":"Sokolowski, Thomas R"},{"first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"}],"date_created":"2018-12-11T11:54:49Z","date_updated":"2021-01-12T06:54:13Z","volume":91,"oa_version":"Preprint"},{"title":"On the distribution of local extrema in quantum chaos","publication_status":"published","status":"public","intvolume":" 379","department":[{"_id":"HeEd"}],"publisher":"Elsevier","year":"2015","_id":"1938","acknowledgement":"F.P. was supported by the Graduate School of IST Austria. S.S. was partially supported by CRC1060 of the DFG\r\nThe authors thank Olga Symonova and Michael Kerber for sharing their implementation of the persistence algorithm. ","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:54:49Z","date_updated":"2021-01-12T06:54:12Z","volume":379,"oa_version":"None","author":[{"orcid":"0000-0002-8379-3768","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","last_name":"Pausinger","first_name":"Florian","full_name":"Pausinger, Florian"},{"full_name":"Steinerberger, Stefan","last_name":"Steinerberger","first_name":"Stefan"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We numerically investigate the distribution of extrema of 'chaotic' Laplacian eigenfunctions on two-dimensional manifolds. Our contribution is two-fold: (a) we count extrema on grid graphs with a small number of randomly added edges and show the behavior to coincide with the 1957 prediction of Longuet-Higgins for the continuous case and (b) we compute the regularity of their spatial distribution using discrepancy, which is a classical measure from the theory of Monte Carlo integration. The first part suggests that grid graphs with randomly added edges should behave like two-dimensional surfaces with ergodic geodesic flow; in the second part we show that the extrema are more regularly distributed in space than the grid Z2."}],"publist_id":"5152","issue":"6","quality_controlled":"1","page":"535 - 541","publication":"Physics Letters, Section A","citation":{"chicago":"Pausinger, Florian, and Stefan Steinerberger. “On the Distribution of Local Extrema in Quantum Chaos.” Physics Letters, Section A. Elsevier, 2015. https://doi.org/10.1016/j.physleta.2014.12.010.","mla":"Pausinger, Florian, and Stefan Steinerberger. “On the Distribution of Local Extrema in Quantum Chaos.” Physics Letters, Section A, vol. 379, no. 6, Elsevier, 2015, pp. 535–41, doi:10.1016/j.physleta.2014.12.010.","short":"F. Pausinger, S. Steinerberger, Physics Letters, Section A 379 (2015) 535–541.","ista":"Pausinger F, Steinerberger S. 2015. On the distribution of local extrema in quantum chaos. Physics Letters, Section A. 379(6), 535–541.","apa":"Pausinger, F., & Steinerberger, S. (2015). On the distribution of local extrema in quantum chaos. Physics Letters, Section A. Elsevier. https://doi.org/10.1016/j.physleta.2014.12.010","ieee":"F. Pausinger and S. Steinerberger, “On the distribution of local extrema in quantum chaos,” Physics Letters, Section A, vol. 379, no. 6. Elsevier, pp. 535–541, 2015.","ama":"Pausinger F, Steinerberger S. On the distribution of local extrema in quantum chaos. Physics Letters, Section A. 2015;379(6):535-541. doi:10.1016/j.physleta.2014.12.010"},"language":[{"iso":"eng"}],"doi":"10.1016/j.physleta.2014.12.010","date_published":"2015-03-06T00:00:00Z","scopus_import":1,"day":"06","month":"03"},{"citation":{"short":"H. Rakusová, M. Fendrych, J. Friml, Current Opinion in Plant Biology 23 (2015) 116–123.","mla":"Rakusová, Hana, et al. “Intracellular Trafficking and PIN-Mediated Cell Polarity during Tropic Responses in Plants.” Current Opinion in Plant Biology, vol. 23, no. 2, Elsevier, 2015, pp. 116–23, doi:10.1016/j.pbi.2014.12.002.","chicago":"Rakusová, Hana, Matyas Fendrych, and Jiří Friml. “Intracellular Trafficking and PIN-Mediated Cell Polarity during Tropic Responses in Plants.” Current Opinion in Plant Biology. Elsevier, 2015. https://doi.org/10.1016/j.pbi.2014.12.002.","ama":"Rakusová H, Fendrych M, Friml J. Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants. Current Opinion in Plant Biology. 2015;23(2):116-123. doi:10.1016/j.pbi.2014.12.002","ieee":"H. Rakusová, M. Fendrych, and J. Friml, “Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants,” Current Opinion in Plant Biology, vol. 23, no. 2. Elsevier, pp. 116–123, 2015.","apa":"Rakusová, H., Fendrych, M., & Friml, J. (2015). Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2014.12.002","ista":"Rakusová H, Fendrych M, Friml J. 2015. Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants. Current Opinion in Plant Biology. 23(2), 116–123."},"publication":"Current Opinion in Plant Biology","page":"116 - 123","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","date_published":"2015-02-01T00:00:00Z","doi":"10.1016/j.pbi.2014.12.002","language":[{"iso":"eng"}],"scopus_import":1,"month":"02","day":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1944","year":"2015","acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP); the Agency for Innovation by Science and Technology (IWT) (predoctoral fellowship to H.R.); and the People Programme (Marie Curie Actions) of the European Union","intvolume":" 23","department":[{"_id":"JiFr"}],"publisher":"Elsevier","publication_status":"published","status":"public","title":"Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants","author":[{"full_name":"Rakusová, Hana","first_name":"Hana","last_name":"Rakusová"},{"full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","first_name":"Matyas","last_name":"Fendrych"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"}],"volume":23,"oa_version":"None","date_created":"2018-12-11T11:54:51Z","date_updated":"2021-01-12T06:54:15Z","type":"journal_article","publist_id":"5140","ec_funded":1,"issue":"2"},{"scopus_import":1,"has_accepted_license":"1","day":"15","page":"433 - 444","citation":{"ama":"Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. Succinct representation of concurrent trace sets. In: ACM; 2015:433-444. doi:10.1145/2676726.2677008","ieee":"A. Gupta, T. A. Henzinger, A. Radhakrishna, R. Samanta, and T. Tarrach, “Succinct representation of concurrent trace sets,” presented at the POPL: Principles of Programming Languages, Mumbai, India, 2015, pp. 433–444.","apa":"Gupta, A., Henzinger, T. A., Radhakrishna, A., Samanta, R., & Tarrach, T. (2015). Succinct representation of concurrent trace sets (pp. 433–444). Presented at the POPL: Principles of Programming Languages, Mumbai, India: ACM. https://doi.org/10.1145/2676726.2677008","ista":"Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. 2015. Succinct representation of concurrent trace sets. POPL: Principles of Programming Languages, 433–444.","short":"A. Gupta, T.A. Henzinger, A. Radhakrishna, R. Samanta, T. Tarrach, in:, ACM, 2015, pp. 433–444.","mla":"Gupta, Ashutosh, et al. Succinct Representation of Concurrent Trace Sets. ACM, 2015, pp. 433–44, doi:10.1145/2676726.2677008.","chicago":"Gupta, Ashutosh, Thomas A Henzinger, Arjun Radhakrishna, Roopsha Samanta, and Thorsten Tarrach. “Succinct Representation of Concurrent Trace Sets,” 433–44. ACM, 2015. https://doi.org/10.1145/2676726.2677008."},"date_published":"2015-01-15T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"We present a method and a tool for generating succinct representations of sets of concurrent traces. We focus on trace sets that contain all correct or all incorrect permutations of events from a given trace. We represent trace sets as HB-Formulas that are Boolean combinations of happens-before constraints between events. To generate a representation of incorrect interleavings, our method iteratively explores interleavings that violate the specification and gathers generalizations of the discovered interleavings into an HB-Formula; its complement yields a representation of correct interleavings.\r\n\r\nWe claim that our trace set representations can drive diverse verification, fault localization, repair, and synthesis techniques for concurrent programs. We demonstrate this by using our tool in three case studies involving synchronization synthesis, bug summarization, and abstraction refinement based verification. In each case study, our initial experimental results have been promising.\r\n\r\nIn the first case study, we present an algorithm for inferring missing synchronization from an HB-Formula representing correct interleavings of a given trace. The algorithm applies rules to rewrite specific patterns in the HB-Formula into locks, barriers, and wait-notify constructs. In the second case study, we use an HB-Formula representing incorrect interleavings for bug summarization. While the HB-Formula itself is a concise counterexample summary, we present additional inference rules to help identify specific concurrency bugs such as data races, define-use order violations, and two-stage access bugs. In the final case study, we present a novel predicate learning procedure that uses HB-Formulas representing abstract counterexamples to accelerate counterexample-guided abstraction refinement (CEGAR). In each iteration of the CEGAR loop, the procedure refines the abstraction to eliminate multiple spurious abstract counterexamples drawn from the HB-Formula."}],"ddc":["005"],"status":"public","title":"Succinct representation of concurrent trace sets","_id":"1992","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2018-12-12T10:17:56Z","date_updated":"2020-07-14T12:45:22Z","checksum":"f0d4395b600f410a191256ac0b73af32","relation":"main_file","file_id":"5314","file_size":399462,"content_type":"application/pdf","creator":"system","file_name":"IST-2015-317-v1+1_author_version.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","pubrep_id":"317","publication_identifier":{"isbn":["978-1-4503-3300-9"]},"month":"01","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1145/2676726.2677008","conference":{"name":"POPL: Principles of Programming Languages","end_date":"2015-01-17","start_date":"2015-01-15","location":"Mumbai, India"},"publist_id":"5091","file_date_updated":"2020-07-14T12:45:22Z","department":[{"_id":"ToHe"}],"publisher":"ACM","publication_status":"published","year":"2015","date_updated":"2021-01-12T06:54:33Z","date_created":"2018-12-11T11:55:05Z","author":[{"full_name":"Gupta, Ashutosh","first_name":"Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"first_name":"Arjun","last_name":"Radhakrishna","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun"},{"first_name":"Roopsha","last_name":"Samanta","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","full_name":"Samanta, Roopsha"},{"first_name":"Thorsten","last_name":"Tarrach","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4409-8487","full_name":"Tarrach, Thorsten"}]}]