[{"date_created":"2018-12-11T11:56:38Z","doi":"10.1093/nar/gkt1290","date_published":"2014-03-05T00:00:00Z","publication":"Nucleic Acids Research","day":"05","year":"2014","has_accepted_license":"1","oa":1,"publisher":"Oxford University Press","quality_controlled":"1","acknowledgement":"California Institute for Regenerative Medicine [RT2-01880 and TR2-01756]. Funding for open access charge: California Institute for Regenerative Medicine [RT2-01880 and TR2-01756]\r\nCC BY 3,0","title":"DICE, an efficient system for iterative genomic editing in human pluripotent stem cells","publist_id":"4684","author":[{"first_name":"Fangfang","last_name":"Zhu","full_name":"Zhu, Fangfang"},{"first_name":"Matthew","full_name":"Gamboa, Matthew","last_name":"Gamboa"},{"first_name":"Alfonso","full_name":"Farruggio, Alfonso","last_name":"Farruggio"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Bosiljka","full_name":"Tasic, Bosiljka","last_name":"Tasic"},{"last_name":"Schüle","full_name":"Schüle, Birgitt","first_name":"Birgitt"},{"full_name":"Chen Tsai, Yanru","last_name":"Chen Tsai","first_name":"Yanru"},{"full_name":"Calos, Michele","last_name":"Calos","first_name":"Michele"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Zhu F, Gamboa M, Farruggio A, Hippenmeyer S, Tasic B, Schüle B, Chen Tsai Y, Calos M. 2014. DICE, an efficient system for iterative genomic editing in human pluripotent stem cells. Nucleic Acids Research. 42(5), e34.","chicago":"Zhu, Fangfang, Matthew Gamboa, Alfonso Farruggio, Simon Hippenmeyer, Bosiljka Tasic, Birgitt Schüle, Yanru Chen Tsai, and Michele Calos. “DICE, an Efficient System for Iterative Genomic Editing in Human Pluripotent Stem Cells.” Nucleic Acids Research. Oxford University Press, 2014. https://doi.org/10.1093/nar/gkt1290.","apa":"Zhu, F., Gamboa, M., Farruggio, A., Hippenmeyer, S., Tasic, B., Schüle, B., … Calos, M. (2014). DICE, an efficient system for iterative genomic editing in human pluripotent stem cells. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkt1290","ama":"Zhu F, Gamboa M, Farruggio A, et al. DICE, an efficient system for iterative genomic editing in human pluripotent stem cells. Nucleic Acids Research. 2014;42(5). doi:10.1093/nar/gkt1290","ieee":"F. Zhu et al., “DICE, an efficient system for iterative genomic editing in human pluripotent stem cells,” Nucleic Acids Research, vol. 42, no. 5. Oxford University Press, 2014.","short":"F. Zhu, M. Gamboa, A. Farruggio, S. Hippenmeyer, B. Tasic, B. Schüle, Y. Chen Tsai, M. Calos, Nucleic Acids Research 42 (2014).","mla":"Zhu, Fangfang, et al. “DICE, an Efficient System for Iterative Genomic Editing in Human Pluripotent Stem Cells.” Nucleic Acids Research, vol. 42, no. 5, e34, Oxford University Press, 2014, doi:10.1093/nar/gkt1290."},"article_number":"e34","issue":"5","volume":42,"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"e9268f5f96a820f04d7ebbf85927c3cb","file_id":"4738","creator":"system","file_size":11044478,"date_updated":"2020-07-14T12:45:35Z","file_name":"IST-2018-961-v1+1_2014_Hippenmeyer_DICE.pdf","date_created":"2018-12-12T10:09:15Z"}],"publication_status":"published","intvolume":" 42","month":"03","scopus_import":1,"oa_version":"Preprint","abstract":[{"text":"To reveal the full potential of human pluripotent stem cells, new methods for rapid, site-specific genomic engineering are needed. Here, we describe a system for precise genetic modification of human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). We identified a novel human locus, H11, located in a safe, intergenic, transcriptionally active region of chromosome 22, as the recipient site, to provide robust, ubiquitous expression of inserted genes. Recipient cell lines were established by site-specific placement of a ‘landing pad’ cassette carrying attP sites for phiC31 and Bxb1 integrases at the H11 locus by spontaneous or TALEN-assisted homologous recombination. Dual integrase cassette exchange (DICE) mediated by phiC31 and Bxb1 integrases was used to insert genes of interest flanked by phiC31 and Bxb1 attB sites at the H11 locus, replacing the landing pad. This system provided complete control over content, direction and copy number of inserted genes, with a specificity of 100%. A series of genes, including mCherry and various combinations of the neural transcription factors LMX1a, FOXA2 and OTX2, were inserted in recipient cell lines derived from H9 ESC, as well as iPSC lines derived from a Parkinson’s disease patient and a normal sibling control. The DICE system offers rapid, efficient and precise gene insertion in ESC and iPSC and is particularly well suited for repeated modifications of the same locus.","lang":"eng"}],"file_date_updated":"2020-07-14T12:45:35Z","department":[{"_id":"SiHi"}],"ddc":["571","610"],"date_updated":"2021-01-12T06:56:22Z","pubrep_id":"961","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)"},"type":"journal_article","_id":"2261"},{"date_published":"2014-01-01T00:00:00Z","volume":800,"doi":"10.1007/978-94-007-7687-6_1","date_created":"2018-12-11T11:56:39Z","page":"1 - 24","day":"01","language":[{"iso":"eng"}],"publication":" Cellular and Molecular Control of Neuronal Migration","publication_status":"published","year":"2014","month":"01","intvolume":" 800","publisher":"Springer","scopus_import":1,"alternative_title":["Advances in Experimental Medicine and Biology"],"quality_controlled":"1","oa_version":"None","abstract":[{"text":"Coordinated migration of newly-born neurons to their target territories is essential for correct neuronal circuit assembly in the developing brain. Although a cohort of signaling pathways has been implicated in the regulation of cortical projection neuron migration, the precise molecular mechanisms and how a balanced interplay of cell-autonomous and non-autonomous functions of candidate signaling molecules controls the discrete steps in the migration process, are just being revealed. In this chapter, I will focally review recent advances that improved our understanding of the cell-autonomous and possible cell-nonautonomous functions of the evolutionarily conserved LIS1/NDEL1-complex in regulating the sequential steps of cortical projection neuron migration. I will then elaborate on the emerging concept that the Reelin signaling pathway, acts exactly at precise stages in the course of cortical projection neuron migration. Lastly, I will discuss how finely tuned transcriptional programs and downstream effectors govern particular aspects in driving radial migration at discrete stages and how they regulate the precise positioning of cortical projection neurons in the developing cerebral cortex.","lang":"eng"}],"title":"Molecular pathways controlling the sequential steps of cortical projection neuron migration","department":[{"_id":"SiHi"}],"editor":[{"first_name":"Laurent","full_name":"Nguyen, Laurent","last_name":"Nguyen"}],"publist_id":"4679","author":[{"last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:56:23Z","citation":{"mla":"Hippenmeyer, Simon. “Molecular Pathways Controlling the Sequential Steps of Cortical Projection Neuron Migration.” Cellular and Molecular Control of Neuronal Migration, edited by Laurent Nguyen, vol. 800, Springer, 2014, pp. 1–24, doi:10.1007/978-94-007-7687-6_1.","ieee":"S. Hippenmeyer, “Molecular pathways controlling the sequential steps of cortical projection neuron migration,” in Cellular and Molecular Control of Neuronal Migration, vol. 800, L. Nguyen, Ed. Springer, 2014, pp. 1–24.","short":"S. Hippenmeyer, in:, L. Nguyen (Ed.), Cellular and Molecular Control of Neuronal Migration, Springer, 2014, pp. 1–24.","ama":"Hippenmeyer S. Molecular pathways controlling the sequential steps of cortical projection neuron migration. In: Nguyen L, ed. Cellular and Molecular Control of Neuronal Migration. Vol 800. Springer; 2014:1-24. doi:10.1007/978-94-007-7687-6_1","apa":"Hippenmeyer, S. (2014). Molecular pathways controlling the sequential steps of cortical projection neuron migration. In L. Nguyen (Ed.), Cellular and Molecular Control of Neuronal Migration (Vol. 800, pp. 1–24). Springer. https://doi.org/10.1007/978-94-007-7687-6_1","chicago":"Hippenmeyer, Simon. “Molecular Pathways Controlling the Sequential Steps of Cortical Projection Neuron Migration.” In Cellular and Molecular Control of Neuronal Migration, edited by Laurent Nguyen, 800:1–24. Springer, 2014. https://doi.org/10.1007/978-94-007-7687-6_1.","ista":"Hippenmeyer S. 2014.Molecular pathways controlling the sequential steps of cortical projection neuron migration. In: Cellular and Molecular Control of Neuronal Migration. Advances in Experimental Medicine and Biology, vol. 800, 1–24."},"status":"public","type":"book_chapter","_id":"2265"},{"year":"2014","has_accepted_license":"1","day":"03","page":"2936 - 2943","date_created":"2018-12-11T11:56:42Z","doi":"10.1109/ICCV.2013.365","date_published":"2014-03-03T00:00:00Z","oa":1,"publisher":"IEEE","quality_controlled":"1","citation":{"ista":"Olsson C, Ulen J, Boykov Y, Kolmogorov V. 2014. Partial enumeration and curvature regularization. ICCV: International Conference on Computer Vision, 2936–2943.","chicago":"Olsson, Carl, Johannes Ulen, Yuri Boykov, and Vladimir Kolmogorov. “Partial Enumeration and Curvature Regularization,” 2936–43. IEEE, 2014. https://doi.org/10.1109/ICCV.2013.365.","apa":"Olsson, C., Ulen, J., Boykov, Y., & Kolmogorov, V. (2014). Partial enumeration and curvature regularization (pp. 2936–2943). Presented at the ICCV: International Conference on Computer Vision, Sydney, Australia: IEEE. https://doi.org/10.1109/ICCV.2013.365","ama":"Olsson C, Ulen J, Boykov Y, Kolmogorov V. Partial enumeration and curvature regularization. In: IEEE; 2014:2936-2943. doi:10.1109/ICCV.2013.365","ieee":"C. Olsson, J. Ulen, Y. Boykov, and V. Kolmogorov, “Partial enumeration and curvature regularization,” presented at the ICCV: International Conference on Computer Vision, Sydney, Australia, 2014, pp. 2936–2943.","short":"C. Olsson, J. Ulen, Y. Boykov, V. Kolmogorov, in:, IEEE, 2014, pp. 2936–2943.","mla":"Olsson, Carl, et al. Partial Enumeration and Curvature Regularization. IEEE, 2014, pp. 2936–43, doi:10.1109/ICCV.2013.365."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Olsson","full_name":"Olsson, Carl","first_name":"Carl"},{"last_name":"Ulen","full_name":"Ulen, Johannes","first_name":"Johannes"},{"last_name":"Boykov","full_name":"Boykov, Yuri","first_name":"Yuri"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir"}],"publist_id":"4669","title":"Partial enumeration and curvature regularization","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"IST-2016-566-v1+1_iccv13_part_enumeration.pdf","date_created":"2018-12-12T10:09:30Z","creator":"system","file_size":378601,"date_updated":"2020-07-14T12:45:36Z","file_id":"4754","checksum":"4a74b5c92d6dcd2348c2c10ec8dd18bf","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"abstract":[{"text":"Energies with high-order non-submodular interactions have been shown to be very useful in vision due to their high modeling power. Optimization of such energies, however, is generally NP-hard. A naive approach that works for small problem instances is exhaustive search, that is, enumeration of all possible labelings of the underlying graph. We propose a general minimization approach for large graphs based on enumeration of labelings of certain small patches. \r\nThis partial enumeration technique reduces complex high-order energy formulations to pairwise Constraint Satisfaction Problems with unary costs (uCSP), which can be efficiently solved using standard methods like TRW-S. Our approach outperforms a number of existing state-of-the-art algorithms on well known difficult problems (e.g. curvature regularization, stereo, deconvolution); it gives near global minimum and better speed. \r\nOur main application of interest is curvature regularization. In the context of segmentation, our partial enumeration technique allows to evaluate curvature directly on small patches using a novel integral geometry approach.\r\n","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"month":"03","date_updated":"2021-01-12T06:56:28Z","ddc":["000"],"file_date_updated":"2020-07-14T12:45:36Z","department":[{"_id":"VlKo"}],"_id":"2275","conference":{"end_date":"2013-12-08","location":"Sydney, Australia","start_date":"2013-12-01","name":"ICCV: International Conference on Computer Vision"},"type":"conference","pubrep_id":"566","status":"public"},{"page":"189 - 203","date_published":"2014-02-01T00:00:00Z","doi":"10.1002/hipo.22214","date_created":"2018-12-11T11:56:46Z","has_accepted_license":"1","year":"2014","day":"01","publication":"Hippocampus","publisher":"Wiley-Blackwell","quality_controlled":"1","oa":1,"acknowledgement":"Funded by Deutsche Forschungsgemeinschaft. Grant Numbers: SFB 505, SFB 780, BA1582/2-1 Excellence Initiative of the German Research Foundation (Spemann Graduate School). Grant Number: GSC-4 Lichtenberg Professorship-Award (VW-Foundation); Schram-Foundation; Excellence Initiative Brain Links-Brain Tools. The authors thank Drs. Jonas-Frederic Sauer and Claudio Elgueta for critically reading the manuscript. They also thank Karin Winterhalter, Margit Northemann and Ulrich Nöller for technical assistance.","author":[{"full_name":"Hosp, Jonas","last_name":"Hosp","first_name":"Jonas"},{"first_name":"Michael","full_name":"Strüber, Michael","last_name":"Strüber"},{"full_name":"Yanagawa, Yuchio","last_name":"Yanagawa","first_name":"Yuchio"},{"first_name":"Kunihiko","full_name":"Obata, Kunihiko","last_name":"Obata"},{"first_name":"Imre","full_name":"Vida, Imre","last_name":"Vida"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"},{"first_name":"Marlene","last_name":"Bartos","full_name":"Bartos, Marlene"}],"publist_id":"4646","title":"Morpho-physiological criteria divide dentate gyrus interneurons into classes","citation":{"ama":"Hosp J, Strüber M, Yanagawa Y, et al. Morpho-physiological criteria divide dentate gyrus interneurons into classes. Hippocampus. 2014;23(2):189-203. doi:10.1002/hipo.22214","apa":"Hosp, J., Strüber, M., Yanagawa, Y., Obata, K., Vida, I., Jonas, P. M., & Bartos, M. (2014). Morpho-physiological criteria divide dentate gyrus interneurons into classes. Hippocampus. Wiley-Blackwell. https://doi.org/10.1002/hipo.22214","ieee":"J. Hosp et al., “Morpho-physiological criteria divide dentate gyrus interneurons into classes,” Hippocampus, vol. 23, no. 2. Wiley-Blackwell, pp. 189–203, 2014.","short":"J. Hosp, M. Strüber, Y. Yanagawa, K. Obata, I. Vida, P.M. Jonas, M. Bartos, Hippocampus 23 (2014) 189–203.","mla":"Hosp, Jonas, et al. “Morpho-Physiological Criteria Divide Dentate Gyrus Interneurons into Classes.” Hippocampus, vol. 23, no. 2, Wiley-Blackwell, 2014, pp. 189–203, doi:10.1002/hipo.22214.","ista":"Hosp J, Strüber M, Yanagawa Y, Obata K, Vida I, Jonas PM, Bartos M. 2014. Morpho-physiological criteria divide dentate gyrus interneurons into classes. Hippocampus. 23(2), 189–203.","chicago":"Hosp, Jonas, Michael Strüber, Yuchio Yanagawa, Kunihiko Obata, Imre Vida, Peter M Jonas, and Marlene Bartos. “Morpho-Physiological Criteria Divide Dentate Gyrus Interneurons into Classes.” Hippocampus. Wiley-Blackwell, 2014. https://doi.org/10.1002/hipo.22214."},"user_id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","volume":23,"issue":"2","license":"https://creativecommons.org/licenses/by-nc/4.0/","publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5178","checksum":"ff6bc75a79dbc985a2e31b79253e6444","file_size":801589,"date_updated":"2020-07-14T12:45:37Z","creator":"system","file_name":"IST-2016-461-v1+1_Hosp_et_al-2014-Hippocampus.pdf","date_created":"2018-12-12T10:15:54Z"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"02","intvolume":" 23","abstract":[{"lang":"eng","text":"GABAergic inhibitory interneurons control fundamental aspects of neuronal network function. Their functional roles are assumed to be defined by the identity of their input synapses, the architecture of their dendritic tree, the passive and active membrane properties and finally the nature of their postsynaptic targets. Indeed, interneurons display a high degree of morphological and physiological heterogeneity. However, whether their morphological and physiological characteristics are correlated and whether interneuron diversity can be described by a continuum of GABAergic cell types or by distinct classes has remained unclear. Here we perform a detailed morphological and physiological characterization of GABAergic cells in the dentate gyrus, the input region of the hippocampus. To achieve an unbiased and efficient sampling and classification we used knock-in mice expressing the enhanced green fluorescent protein (eGFP) in glutamate decarboxylase 67 (GAD67)-positive neurons and performed cluster analysis. We identified five interneuron classes, each of them characterized by a distinct set of anatomical and physiological parameters. Cross-correlation analysis further revealed a direct relation between morphological and physiological properties indicating that dentate gyrus interneurons fall into functionally distinct classes which may differentially control neuronal network activity."}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:45:37Z","department":[{"_id":"PeJo"}],"date_updated":"2021-01-12T06:56:32Z","ddc":["570"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","pubrep_id":"461","_id":"2285"},{"type":"journal_article","project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"status":"public","_id":"2407","publist_id":"4519","author":[{"first_name":"Élliott","full_name":"Lieb, Élliott","last_name":"Lieb"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521"}],"title":"Equivalence of two definitions of the effective mass of a polaron","citation":{"ieee":"É. Lieb and R. Seiringer, “Equivalence of two definitions of the effective mass of a polaron,” Journal of Statistical Physics, vol. 154, no. 1–2. Springer, pp. 51–57, 2014.","short":"É. Lieb, R. Seiringer, Journal of Statistical Physics 154 (2014) 51–57.","apa":"Lieb, É., & Seiringer, R. (2014). Equivalence of two definitions of the effective mass of a polaron. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-013-0791-z","ama":"Lieb É, Seiringer R. Equivalence of two definitions of the effective mass of a polaron. Journal of Statistical Physics. 2014;154(1-2):51-57. doi:10.1007/s10955-013-0791-z","mla":"Lieb, Élliott, and Robert Seiringer. “Equivalence of Two Definitions of the Effective Mass of a Polaron.” Journal of Statistical Physics, vol. 154, no. 1–2, Springer, 2014, pp. 51–57, doi:10.1007/s10955-013-0791-z.","ista":"Lieb É, Seiringer R. 2014. Equivalence of two definitions of the effective mass of a polaron. Journal of Statistical Physics. 154(1–2), 51–57.","chicago":"Lieb, Élliott, and Robert Seiringer. “Equivalence of Two Definitions of the Effective Mass of a Polaron.” Journal of Statistical Physics. Springer, 2014. https://doi.org/10.1007/s10955-013-0791-z."},"date_updated":"2021-01-12T06:57:18Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","extern":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1304.1780"}],"publisher":"Springer","quality_controlled":"1","intvolume":" 154","month":"01","abstract":[{"lang":"eng","text":"Two definitions of the effective mass of a particle interacting with a quantum field, such as a polaron, are considered and shown to be equal in models similar to the Fröhlich polaron model. These are: 1. the mass defined by the low momentum energy E(P)≈E(0)+P2/2 M of the translation invariant system constrained to have momentum P and 2. the mass M of a simple particle in an arbitrary slowly varying external potential, V, described by the nonrelativistic Schrödinger equation, whose ground state energy equals that of the combined particle/field system in a bound state in the same V."}],"oa_version":"Submitted Version","page":"51 - 57","date_created":"2018-12-11T11:57:29Z","date_published":"2014-01-01T00:00:00Z","volume":154,"issue":"1-2","doi":"10.1007/s10955-013-0791-z","year":"2014","publication_status":"published","publication":"Journal of Statistical Physics","language":[{"iso":"eng"}],"day":"01"}]