[{"file_date_updated":"2023-02-03T10:56:39Z","page":"183-205","series_title":"MIMB","quality_controlled":"1","publisher":"Springer Nature","editor":[{"full_name":"Margadant, Coert","last_name":"Margadant","first_name":"Coert"}],"author":[{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"full_name":"Scheele, Colinda L.G.J.","last_name":"Scheele","first_name":"Colinda L.G.J."}],"_id":"12428","pmid":1,"scopus_import":"1","license":"https://creativecommons.org/licenses/by/4.0/","title":"A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland","alternative_title":["Methods in Molecular Biology"],"intvolume":"      2608","publication_status":"published","department":[{"_id":"EdHa"}],"date_created":"2023-01-29T23:00:58Z","article_processing_charge":"No","ddc":["570"],"volume":2608,"external_id":{"pmid":["36653709"]},"date_updated":"2023-02-03T10:58:56Z","citation":{"short":"E.B. Hannezo, C.L.G.J. Scheele, in:, C. Margadant (Ed.), Cell Migration in Three Dimensions, Springer Nature, 2023, pp. 183–205.","mla":"Hannezo, Edouard B., and Colinda L. G. J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” <i>Cell Migration in Three Dimensions</i>, edited by Coert Margadant, vol. 2608, Springer Nature, 2023, pp. 183–205, doi:<a href=\"https://doi.org/10.1007/978-1-0716-2887-4_12\">10.1007/978-1-0716-2887-4_12</a>.","ista":"Hannezo EB, Scheele CLGJ. 2023.A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Cell Migration in Three Dimensions. Methods in Molecular Biology, vol. 2608, 183–205.","ama":"Hannezo EB, Scheele CLGJ. A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Margadant C, ed. <i>Cell Migration in Three Dimensions</i>. Vol 2608. MIMB. Springer Nature; 2023:183-205. doi:<a href=\"https://doi.org/10.1007/978-1-0716-2887-4_12\">10.1007/978-1-0716-2887-4_12</a>","apa":"Hannezo, E. B., &#38; Scheele, C. L. G. J. (2023). A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In C. Margadant (Ed.), <i>Cell Migration in Three Dimensions</i> (Vol. 2608, pp. 183–205). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-2887-4_12\">https://doi.org/10.1007/978-1-0716-2887-4_12</a>","chicago":"Hannezo, Edouard B, and Colinda L.G.J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” In <i>Cell Migration in Three Dimensions</i>, edited by Coert Margadant, 2608:183–205. MIMB. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-1-0716-2887-4_12\">https://doi.org/10.1007/978-1-0716-2887-4_12</a>.","ieee":"E. B. Hannezo and C. L. G. J. Scheele, “A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland,” in <i>Cell Migration in Three Dimensions</i>, vol. 2608, C. Margadant, Ed. Springer Nature, 2023, pp. 183–205."},"year":"2023","abstract":[{"lang":"eng","text":"The mammary gland consists of a bilayered epithelial structure with an extensively branched morphology. The majority of this epithelial tree is laid down during puberty, during which actively proliferating terminal end buds repeatedly elongate and bifurcate to form the basic structure of the ductal tree. Mammary ducts consist of a basal and luminal cell layer with a multitude of identified sub-lineages within both layers. The understanding of how these different cell lineages are cooperatively driving branching morphogenesis is a problem of crossing multiple scales, as this requires information on the macroscopic branched structure of the gland, as well as data on single-cell dynamics driving the morphogenic program. Here we describe a method to combine genetic lineage tracing with whole-gland branching analysis. Quantitative data on the global organ structure can be used to derive a model for mammary gland branching morphogenesis and provide a backbone on which the dynamics of individual cell lineages can be simulated and compared to lineage-tracing approaches. Eventually, these quantitative models and experiments allow to understand the couplings between the macroscopic shape of the mammary gland and the underlying single-cell dynamics driving branching morphogenesis."}],"doi":"10.1007/978-1-0716-2887-4_12","day":"19","language":[{"iso":"eng"}],"publication":"Cell Migration in Three Dimensions","has_accepted_license":"1","month":"01","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","file":[{"date_updated":"2023-02-03T10:56:39Z","content_type":"application/pdf","file_name":"2023_MIMB_Hannezo.pdf","date_created":"2023-02-03T10:56:39Z","file_size":826598,"checksum":"aec1b8d3ba938ddf9d8fcb777f3c38ee","file_id":"12500","creator":"dernst","success":1,"access_level":"open_access","relation":"main_file"}],"date_published":"2023-01-19T00:00:00Z","type":"book_chapter","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"eisbn":["9781071628874"],"eissn":["1940-6029"],"isbn":["9781071628867"]}},{"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","place":"New York, NY, United States","publication_identifier":{"eissn":["1940-6029"],"issn":["1064-3745"],"eisbn":["978-1-0716-3004-4"],"isbn":["978-1-0716-3003-7"]},"date_published":"2023-03-01T00:00:00Z","type":"book_chapter","language":[{"iso":"eng"}],"month":"03","oa_version":"None","publication":"DNA Manipulation and Analysis","volume":2633,"abstract":[{"lang":"eng","text":"Here we describe the in vivo DNA assembly approach, where molecular cloning procedures are performed using an E. coli recA-independent recombination pathway, which assembles linear fragments of DNA with short homologous termini. This pathway is present in all standard laboratory E. coli strains and, by bypassing the need for in vitro DNA assembly, allows simplified molecular cloning to be performed without the plasmid instability issues associated with specialized recombination-cloning bacterial strains. The methodology requires specific primer design and can perform all standard plasmid modifications (insertions, deletions, mutagenesis, and sub-cloning) in a rapid, simple, and cost-efficient manner, as it does not require commercial kits or specialized bacterial strains. Additionally, this approach can be used to perform complex procedures such as multiple modifications to a plasmid, as up to 6 linear fragments can be assembled in vivo by this recombination pathway. Procedures generally require less than 3 h, involving PCR amplification, DpnI digestion of template DNA, and transformation, upon which circular plasmids are assembled. In this chapter we describe the requirements, procedure, and potential pitfalls when using this technique, as well as protocol variations to overcome the most common issues."}],"doi":"10.1007/978-1-0716-3004-4_3","day":"01","external_id":{"pmid":["36853454"]},"date_updated":"2023-03-16T08:34:24Z","citation":{"short":"S. Arroyo-Urea, J. Watson, J. García-Nafría, in:, G. Scarlett (Ed.), DNA Manipulation and Analysis, Springer Nature, New York, NY, United States, 2023, pp. 33–44.","mla":"Arroyo-Urea, Sandra, et al. “Molecular Cloning Using In Vivo DNA Assembly.” <i>DNA Manipulation and Analysis</i>, edited by Garry Scarlett, vol. 2633, Springer Nature, 2023, pp. 33–44, doi:<a href=\"https://doi.org/10.1007/978-1-0716-3004-4_3\">10.1007/978-1-0716-3004-4_3</a>.","ista":"Arroyo-Urea S, Watson J, García-Nafría J. 2023.Molecular Cloning Using In Vivo DNA Assembly. In: DNA Manipulation and Analysis. Methods in Molecular Biology, vol. 2633, 33–44.","apa":"Arroyo-Urea, S., Watson, J., &#38; García-Nafría, J. (2023). Molecular Cloning Using In Vivo DNA Assembly. In G. Scarlett (Ed.), <i>DNA Manipulation and Analysis</i> (Vol. 2633, pp. 33–44). New York, NY, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-3004-4_3\">https://doi.org/10.1007/978-1-0716-3004-4_3</a>","ama":"Arroyo-Urea S, Watson J, García-Nafría J. Molecular Cloning Using In Vivo DNA Assembly. In: Scarlett G, ed. <i>DNA Manipulation and Analysis</i>. Vol 2633. MIMB. New York, NY, United States: Springer Nature; 2023:33-44. doi:<a href=\"https://doi.org/10.1007/978-1-0716-3004-4_3\">10.1007/978-1-0716-3004-4_3</a>","chicago":"Arroyo-Urea, Sandra, Jake Watson, and Javier García-Nafría. “Molecular Cloning Using In Vivo DNA Assembly.” In <i>DNA Manipulation and Analysis</i>, edited by Garry Scarlett, 2633:33–44. MIMB. New York, NY, United States: Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-1-0716-3004-4_3\">https://doi.org/10.1007/978-1-0716-3004-4_3</a>.","ieee":"S. Arroyo-Urea, J. Watson, and J. García-Nafría, “Molecular Cloning Using In Vivo DNA Assembly,” in <i>DNA Manipulation and Analysis</i>, vol. 2633, G. Scarlett, Ed. New York, NY, United States: Springer Nature, 2023, pp. 33–44."},"year":"2023","publisher":"Springer Nature","editor":[{"full_name":"Scarlett, Garry","first_name":"Garry","last_name":"Scarlett"}],"page":"33-44","series_title":"MIMB","quality_controlled":"1","alternative_title":["Methods in Molecular Biology"],"title":"Molecular Cloning Using In Vivo DNA Assembly","intvolume":"      2633","publication_status":"published","department":[{"_id":"PeJo"}],"article_processing_charge":"No","date_created":"2023-03-12T23:01:02Z","author":[{"full_name":"Arroyo-Urea, Sandra","last_name":"Arroyo-Urea","first_name":"Sandra"},{"last_name":"Watson","first_name":"Jake","full_name":"Watson, Jake","orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"first_name":"Javier","last_name":"García-Nafría","full_name":"García-Nafría, Javier"}],"_id":"12720","pmid":1,"scopus_import":"1"},{"language":[{"iso":"eng"}],"oa_version":"None","acknowledged_ssus":[{"_id":"Bio"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"project":[{"grant_number":"724373","name":"Cellular navigation along spatial gradients","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425"}],"month":"04","publication":"The Immune Synapse","place":"New York, NY","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_identifier":{"eisbn":["9781071631355"],"eissn":["1940-6029"],"issn":["1064-3745"],"isbn":["9781071631348"]},"date_published":"2023-04-28T00:00:00Z","type":"book_chapter","publisher":"Springer Nature","editor":[{"full_name":"Baldari, Cosima","last_name":"Baldari","first_name":"Cosima"},{"full_name":"Dustin, Michael","last_name":"Dustin","first_name":"Michael"}],"page":"137-147","ec_funded":1,"quality_controlled":"1","series_title":"MIMB","publication_status":"published","date_created":"2023-05-22T08:41:48Z","department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"article_processing_charge":"No","title":"En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses","alternative_title":["Methods in Molecular Biology"],"intvolume":"      2654","pmid":1,"_id":"13052","scopus_import":"1","author":[{"id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","first_name":"Alexander F","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin","first_name":"Jack"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"acknowledgement":"A.L. was funded by an Erwin Schrödinger postdoctoral fellowship of the Austrian Science Fund (FWF, project number: J4542-B) and is an EMBO non-stipendiary postdoctoral fellow. This work was supported by a European Research Council grant ERC-CoG-72437 to M.S. We thank the Imaging & Optics facility, the Nanofabrication facility, and the Miba Machine Shop of ISTA for their excellent support.","volume":2654,"doi":"10.1007/978-1-0716-3135-5_9","day":"28","abstract":[{"lang":"eng","text":"Imaging of the immunological synapse (IS) between dendritic cells (DCs) and T cells in suspension is hampered by suboptimal alignment of cell-cell contacts along the vertical imaging plane. This requires optical sectioning that often results in unsatisfactory resolution in time and space. Here, we present a workflow where DCs and T cells are confined between a layer of glass and polydimethylsiloxane (PDMS) that orients the cells along one, horizontal imaging plane, allowing for fast en-face-imaging of the DC-T cell IS."}],"date_updated":"2023-10-17T08:44:53Z","citation":{"mla":"Leithner, Alexander F., et al. “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses.” <i>The Immune Synapse</i>, edited by Cosima Baldari and Michael Dustin, vol. 2654, Springer Nature, 2023, pp. 137–47, doi:<a href=\"https://doi.org/10.1007/978-1-0716-3135-5_9\">10.1007/978-1-0716-3135-5_9</a>.","short":"A.F. Leithner, J. Merrin, M.K. Sixt, in:, C. Baldari, M. Dustin (Eds.), The Immune Synapse, Springer Nature, New York, NY, 2023, pp. 137–147.","ista":"Leithner AF, Merrin J, Sixt MK. 2023.En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In: The Immune Synapse. Methods in Molecular Biology, vol. 2654, 137–147.","ama":"Leithner AF, Merrin J, Sixt MK. En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In: Baldari C, Dustin M, eds. <i>The Immune Synapse</i>. Vol 2654. MIMB. New York, NY: Springer Nature; 2023:137-147. doi:<a href=\"https://doi.org/10.1007/978-1-0716-3135-5_9\">10.1007/978-1-0716-3135-5_9</a>","apa":"Leithner, A. F., Merrin, J., &#38; Sixt, M. K. (2023). En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In C. Baldari &#38; M. Dustin (Eds.), <i>The Immune Synapse</i> (Vol. 2654, pp. 137–147). New York, NY: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-3135-5_9\">https://doi.org/10.1007/978-1-0716-3135-5_9</a>","ieee":"A. F. Leithner, J. Merrin, and M. K. Sixt, “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses,” in <i>The Immune Synapse</i>, vol. 2654, C. Baldari and M. Dustin, Eds. New York, NY: Springer Nature, 2023, pp. 137–147.","chicago":"Leithner, Alexander F, Jack Merrin, and Michael K Sixt. “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses.” In <i>The Immune Synapse</i>, edited by Cosima Baldari and Michael Dustin, 2654:137–47. MIMB. New York, NY: Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-1-0716-3135-5_9\">https://doi.org/10.1007/978-1-0716-3135-5_9</a>."},"year":"2023","external_id":{"pmid":["37106180"]}},{"publication":"Germline Development in the Zebrafish","month":"02","oa_version":"None","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"language":[{"iso":"eng"}],"keyword":["Tissue tension","Morphogenesis","Laser ablation","Zebrafish folliculogenesis","Granulosa cells"],"date_published":"2021-02-20T00:00:00Z","type":"book_chapter","publication_identifier":{"eisbn":["978-1-0716-0970-5"],"eissn":["1940-6029"],"issn":["1064-3745"],"isbn":["978-1-0716-0969-9"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","author":[{"id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","last_name":"Xia","first_name":"Peng","full_name":"Xia, Peng","orcid":"0000-0002-5419-7756"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"_id":"9245","pmid":1,"scopus_import":"1","alternative_title":["Methods in Molecular Biology"],"title":"Quantifying tissue tension in the granulosa layer after laser surgery","intvolume":"      2218","publication_status":"published","department":[{"_id":"CaHe"}],"article_processing_charge":"No","date_created":"2021-03-14T23:01:34Z","page":"117-128","ec_funded":1,"quality_controlled":"1","publisher":"Humana","editor":[{"full_name":"Dosch, Roland","first_name":"Roland","last_name":"Dosch"}],"external_id":{"pmid":["33606227"]},"date_updated":"2022-06-03T10:57:55Z","year":"2021","citation":{"chicago":"Xia, Peng, and Carl-Philipp J Heisenberg. “Quantifying Tissue Tension in the Granulosa Layer after Laser Surgery.” In <i>Germline Development in the Zebrafish</i>, edited by Roland Dosch, 2218:117–28. Humana, 2021. <a href=\"https://doi.org/10.1007/978-1-0716-0970-5_10\">https://doi.org/10.1007/978-1-0716-0970-5_10</a>.","ieee":"P. Xia and C.-P. J. Heisenberg, “Quantifying tissue tension in the granulosa layer after laser surgery,” in <i>Germline Development in the Zebrafish</i>, vol. 2218, R. Dosch, Ed. Humana, 2021, pp. 117–128.","ama":"Xia P, Heisenberg C-PJ. Quantifying tissue tension in the granulosa layer after laser surgery. In: Dosch R, ed. <i>Germline Development in the Zebrafish</i>. Vol 2218. Humana; 2021:117-128. doi:<a href=\"https://doi.org/10.1007/978-1-0716-0970-5_10\">10.1007/978-1-0716-0970-5_10</a>","apa":"Xia, P., &#38; Heisenberg, C.-P. J. (2021). Quantifying tissue tension in the granulosa layer after laser surgery. In R. Dosch (Ed.), <i>Germline Development in the Zebrafish</i> (Vol. 2218, pp. 117–128). Humana. <a href=\"https://doi.org/10.1007/978-1-0716-0970-5_10\">https://doi.org/10.1007/978-1-0716-0970-5_10</a>","ista":"Xia P, Heisenberg C-PJ. 2021.Quantifying tissue tension in the granulosa layer after laser surgery. In: Germline Development in the Zebrafish. Methods in Molecular Biology, vol. 2218, 117–128.","short":"P. Xia, C.-P.J. Heisenberg, in:, R. Dosch (Ed.), Germline Development in the Zebrafish, Humana, 2021, pp. 117–128.","mla":"Xia, Peng, and Carl-Philipp J. Heisenberg. “Quantifying Tissue Tension in the Granulosa Layer after Laser Surgery.” <i>Germline Development in the Zebrafish</i>, edited by Roland Dosch, vol. 2218, Humana, 2021, pp. 117–28, doi:<a href=\"https://doi.org/10.1007/978-1-0716-0970-5_10\">10.1007/978-1-0716-0970-5_10</a>."},"abstract":[{"text":"Tissue morphogenesis is driven by mechanical forces triggering cell movements and shape changes. Quantitatively measuring tension within tissues is of great importance for understanding the role of mechanical signals acting on the cell and tissue level during morphogenesis. Here we introduce laser ablation as a useful tool to probe tissue tension within the granulosa layer, an epithelial monolayer of somatic cells that surround the zebrafish female gamete during folliculogenesis. We describe in detail how to isolate follicles, mount samples, perform laser surgery, and analyze the data.","lang":"eng"}],"doi":"10.1007/978-1-0716-0970-5_10","day":"20","volume":2218,"acknowledgement":"We thank Prof. Masazumi Tada and Roland Dosch for providing transgenic zebrafish lines, the Heisenberg lab for technical assistance and feedback on the manuscript, and the Bioimaging and Fish facilities of IST Austria for continuous support. This work was funded by an ERC advanced grant (MECSPEC to C.-P.H.)."},{"language":[{"iso":"eng"}],"oa_version":"None","acknowledged_ssus":[{"_id":"Bio"}],"month":"10","publication":"Plant Cell Division","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eisbn":["978-1-0716-1744-1"],"issn":["1064-3745"],"eissn":["1940-6029"],"isbn":["978-1-0716-1743-4"]},"date_published":"2021-10-28T00:00:00Z","type":"book_chapter","publisher":"Humana Press","page":"105-114","quality_controlled":"1","series_title":"MIMB","publication_status":"published","article_processing_charge":"No","department":[{"_id":"JiFr"}],"date_created":"2021-11-11T10:03:30Z","title":"Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy","alternative_title":["Methods in Molecular Biology"],"intvolume":"      2382","_id":"10268","pmid":1,"scopus_import":"1","author":[{"id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer","first_name":"Lukas","full_name":"Hörmayer, Lukas"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","last_name":"Glanc","first_name":"Matous"}],"acknowledgement":"We thank B. De Rybel for allowing M.G. to work on this manuscript during a postdoc in his laboratory, and EMBO for supporting M.G. with a Long-Term fellowship (ALTF 1005-2019) during this time. We acknowledge the service and support by the Bioimaging Facility at IST Austria, and finally, we thank A. Mally for proofreading and correcting the manuscript.","volume":2382,"doi":"10.1007/978-1-0716-1744-1_6","day":"28","abstract":[{"text":"The analysis of dynamic cellular processes such as plant cytokinesis stands and falls with live-cell time-lapse confocal imaging. Conventional approaches to time-lapse imaging of cell division in Arabidopsis root tips are tedious and have low throughput. Here, we describe a protocol for long-term time-lapse simultaneous imaging of multiple root tips on a vertical-stage confocal microscope with automated root tracking. We also provide modifications of the basic protocol to implement this imaging method in the analysis of genetic, pharmacological or laser ablation wounding-mediated experimental manipulations. Our method dramatically improves the efficiency of cell division time-lapse imaging by increasing the throughput, while reducing the person-hour requirements of such experiments.","lang":"eng"}],"date_updated":"2022-06-03T06:47:06Z","citation":{"ieee":"L. Hörmayer, J. Friml, and M. Glanc, “Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy,” in <i>Plant Cell Division</i>, vol. 2382, Humana Press, 2021, pp. 105–114.","chicago":"Hörmayer, Lukas, Jiří Friml, and Matous Glanc. “Automated Time-Lapse Imaging and Manipulation of Cell Divisions in Arabidopsis Roots by Vertical-Stage Confocal Microscopy.” In <i>Plant Cell Division</i>, 2382:105–14. MIMB. Humana Press, 2021. <a href=\"https://doi.org/10.1007/978-1-0716-1744-1_6\">https://doi.org/10.1007/978-1-0716-1744-1_6</a>.","ama":"Hörmayer L, Friml J, Glanc M. Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy. In: <i>Plant Cell Division</i>. Vol 2382. MIMB. Humana Press; 2021:105-114. doi:<a href=\"https://doi.org/10.1007/978-1-0716-1744-1_6\">10.1007/978-1-0716-1744-1_6</a>","apa":"Hörmayer, L., Friml, J., &#38; Glanc, M. (2021). Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy. In <i>Plant Cell Division</i> (Vol. 2382, pp. 105–114). Humana Press. <a href=\"https://doi.org/10.1007/978-1-0716-1744-1_6\">https://doi.org/10.1007/978-1-0716-1744-1_6</a>","ista":"Hörmayer L, Friml J, Glanc M. 2021.Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy. In: Plant Cell Division. Methods in Molecular Biology, vol. 2382, 105–114.","mla":"Hörmayer, Lukas, et al. “Automated Time-Lapse Imaging and Manipulation of Cell Divisions in Arabidopsis Roots by Vertical-Stage Confocal Microscopy.” <i>Plant Cell Division</i>, vol. 2382, Humana Press, 2021, pp. 105–14, doi:<a href=\"https://doi.org/10.1007/978-1-0716-1744-1_6\">10.1007/978-1-0716-1744-1_6</a>.","short":"L. Hörmayer, J. Friml, M. Glanc, in:, Plant Cell Division, Humana Press, 2021, pp. 105–114."},"year":"2021","external_id":{"pmid":["34705235"]}},{"abstract":[{"text":"This paper serves as a user guide to the Vienna graph clustering framework. We review our general memetic algorithm, VieClus, to tackle the graph clustering problem. A key component of our contribution are natural recombine operators that employ ensemble clusterings as well as multi-level techniques. Lastly, we combine these techniques with a scalable communication protocol, producing a system that is able to compute high-quality solutions in a short amount of time. After giving a description of the algorithms employed, we establish the connection of the graph clustering problem to protein–protein interaction networks and moreover give a description on how the software can be used, what file formats are expected, and how this can be used to find functional groups in protein–protein interaction networks.","lang":"eng"}],"day":"04","doi":"10.1007/978-1-4939-9873-9_16","external_id":{"pmid":["31583641"]},"year":"2019","citation":{"ista":"Biedermann S, Henzinger MH, Schulz C, Schuster B. 2019.Vienna Graph Clustering. In: Protein-Protein Interaction Networks. Methods in Molecular Biology, vol. 2074, 215–231.","mla":"Biedermann, Sonja, et al. “Vienna Graph Clustering.” <i>Protein-Protein Interaction Networks</i>, edited by Stefan Canzar and Francisca Rojas Ringeling, vol. 2074, Springer Nature, 2019, pp. 215–231, doi:<a href=\"https://doi.org/10.1007/978-1-4939-9873-9_16\">10.1007/978-1-4939-9873-9_16</a>.","short":"S. Biedermann, M.H. Henzinger, C. Schulz, B. Schuster, in:, S. Canzar, F. Rojas Ringeling (Eds.), Protein-Protein Interaction Networks, Springer Nature, 2019, pp. 215–231.","ieee":"S. Biedermann, M. H. Henzinger, C. Schulz, and B. Schuster, “Vienna Graph Clustering,” in <i>Protein-Protein Interaction Networks</i>, vol. 2074, S. Canzar and F. Rojas Ringeling, Eds. Springer Nature, 2019, pp. 215–231.","chicago":"Biedermann, Sonja, Monika H Henzinger, Christian Schulz, and Bernhard Schuster. “Vienna Graph Clustering.” In <i>Protein-Protein Interaction Networks</i>, edited by Stefan Canzar and Francisca Rojas Ringeling, 2074:215–231. MIMB. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-1-4939-9873-9_16\">https://doi.org/10.1007/978-1-4939-9873-9_16</a>.","ama":"Biedermann S, Henzinger MH, Schulz C, Schuster B. Vienna Graph Clustering. In: Canzar S, Rojas Ringeling F, eds. <i>Protein-Protein Interaction Networks</i>. Vol 2074. MIMB. Springer Nature; 2019:215–231. doi:<a href=\"https://doi.org/10.1007/978-1-4939-9873-9_16\">10.1007/978-1-4939-9873-9_16</a>","apa":"Biedermann, S., Henzinger, M. H., Schulz, C., &#38; Schuster, B. (2019). Vienna Graph Clustering. In S. Canzar &#38; F. Rojas Ringeling (Eds.), <i>Protein-Protein Interaction Networks</i> (Vol. 2074, pp. 215–231). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-4939-9873-9_16\">https://doi.org/10.1007/978-1-4939-9873-9_16</a>"},"date_updated":"2023-02-17T09:34:26Z","extern":"1","volume":2074,"intvolume":"      2074","alternative_title":["Methods in Molecular Biology"],"title":"Vienna Graph Clustering","article_processing_charge":"No","date_created":"2022-08-16T06:54:48Z","publication_status":"published","author":[{"last_name":"Biedermann","first_name":"Sonja","full_name":"Biedermann, Sonja"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"first_name":"Christian","last_name":"Schulz","full_name":"Schulz, Christian"},{"last_name":"Schuster","first_name":"Bernhard","full_name":"Schuster, Bernhard"}],"scopus_import":"1","pmid":1,"_id":"11847","editor":[{"first_name":"Stefan","last_name":"Canzar","full_name":"Canzar, Stefan"},{"full_name":"Rojas Ringeling, Francisca","first_name":"Francisca","last_name":"Rojas Ringeling"}],"publisher":"Springer Nature","series_title":"MIMB","quality_controlled":"1","page":"215–231","publication_identifier":{"eisbn":["9781493998739"],"issn":["1064-3745"],"eissn":["1940-6029"],"isbn":["9781493998722"]},"type":"book_chapter","date_published":"2019-10-04T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"10","oa_version":"None","publication":"Protein-Protein Interaction Networks","language":[{"iso":"eng"}]},{"volume":1189,"abstract":[{"text":"Mechanically coupled cells can generate forces driving cell and tissue morphogenesis during development. Visualization and measuring of these forces is of major importance to better understand the complexity of the biomechanic processes that shape cells and tissues. Here, we describe how UV laser ablation can be utilized to quantitatively assess mechanical tension in different tissues of the developing zebrafish and in cultures of primary germ layer progenitor cells ex vivo.","lang":"eng"}],"day":"22","doi":"10.1007/978-1-4939-1164-6_15","external_id":{"pmid":["25245697"]},"citation":{"short":"M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, C.-P.J. Heisenberg, in:, C. Nelson (Ed.), Tissue Morphogenesis, Springer, New York, NY, 2014, pp. 219–235.","mla":"Smutny, Michael, et al. “UV Laser Ablation to Measure Cell and Tissue-Generated Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” <i>Tissue Morphogenesis</i>, edited by Celeste Nelson, vol. 1189, Springer, 2014, pp. 219–35, doi:<a href=\"https://doi.org/10.1007/978-1-4939-1164-6_15\">10.1007/978-1-4939-1164-6_15</a>.","ista":"Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. 2014.UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In: Tissue Morphogenesis. vol. 1189, 219–235.","apa":"Smutny, M., Behrndt, M., Campinho, P., Ruprecht, V., &#38; Heisenberg, C.-P. J. (2014). UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In C. Nelson (Ed.), <i>Tissue Morphogenesis</i> (Vol. 1189, pp. 219–235). New York, NY: Springer. <a href=\"https://doi.org/10.1007/978-1-4939-1164-6_15\">https://doi.org/10.1007/978-1-4939-1164-6_15</a>","ama":"Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In: Nelson C, ed. <i>Tissue Morphogenesis</i>. Vol 1189. Methods in Molecular Biology. New York, NY: Springer; 2014:219-235. doi:<a href=\"https://doi.org/10.1007/978-1-4939-1164-6_15\">10.1007/978-1-4939-1164-6_15</a>","ieee":"M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, and C.-P. J. Heisenberg, “UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo,” in <i>Tissue Morphogenesis</i>, vol. 1189, C. Nelson, Ed. New York, NY: Springer, 2014, pp. 219–235.","chicago":"Smutny, Michael, Martin Behrndt, Pedro Campinho, Verena Ruprecht, and Carl-Philipp J Heisenberg. “UV Laser Ablation to Measure Cell and Tissue-Generated Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” In <i>Tissue Morphogenesis</i>, edited by Celeste Nelson, 1189:219–35. Methods in Molecular Biology. New York, NY: Springer, 2014. <a href=\"https://doi.org/10.1007/978-1-4939-1164-6_15\">https://doi.org/10.1007/978-1-4939-1164-6_15</a>."},"year":"2014","date_updated":"2023-09-05T14:12:00Z","editor":[{"last_name":"Nelson","first_name":"Celeste","full_name":"Nelson, Celeste"}],"publisher":"Springer","quality_controlled":"1","series_title":"Methods in Molecular Biology","page":"219-235","intvolume":"      1189","title":"UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo","article_processing_charge":"No","department":[{"_id":"CaHe"}],"date_created":"2019-03-26T08:55:59Z","publication_status":"published","author":[{"id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","full_name":"Smutny, Michael","orcid":"0000-0002-5920-9090","last_name":"Smutny","first_name":"Michael"},{"last_name":"Behrndt","first_name":"Martin","full_name":"Behrndt, Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Campinho, Pedro","orcid":"0000-0002-8526-5416","last_name":"Campinho","first_name":"Pedro","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Verena","last_name":"Ruprecht","orcid":"0000-0003-4088-8633","full_name":"Ruprecht, Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"pmid":1,"_id":"6178","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","place":"New York, NY","publication_identifier":{"eissn":["1940-6029"],"issn":["1064-3745"],"isbn":["9781493911639","9781493911646"]},"type":"book_chapter","date_published":"2014-08-22T00:00:00Z","language":[{"iso":"eng"}],"month":"08","oa_version":"None","publication":"Tissue Morphogenesis"},{"place":"Totowa, NJ","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","date_published":"2013-04-03T00:00:00Z","type":"book_chapter","publication_identifier":{"eisbn":["9781627034265"],"eissn":["1940-6029"],"issn":["1064-3745"],"isbn":["9781627034258"]},"language":[{"iso":"eng"}],"publication":"Chemokines","oa_version":"None","month":"04","acknowledgement":"We would like to thank Alexander Eichner and Ingrid de Vries for discussion and critical reading of the manuscript, and Mary Frank for assistance with the recording of videos and images in Fig. 1. M.S. is supported through funding from the German Research Foundation (DFG). M.W. acknowledges the Alexander von Humboldt Foundation for funding.","volume":1013,"date_updated":"2023-09-05T13:15:33Z","year":"2013","citation":{"chicago":"Weber, Michele, and Michael K Sixt. “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations.” In <i>Chemokines</i>, edited by Astrid Cardona and Eroboghene Ubogu, 1013:215–26. MIMB. Totowa, NJ: Humana Press, 2013. <a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">https://doi.org/10.1007/978-1-62703-426-5_14</a>.","ieee":"M. Weber and M. K. Sixt, “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations,” in <i>Chemokines</i>, vol. 1013, A. Cardona and E. Ubogu, Eds. Totowa, NJ: Humana Press, 2013, pp. 215–226.","apa":"Weber, M., &#38; Sixt, M. K. (2013). Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In A. Cardona &#38; E. Ubogu (Eds.), <i>Chemokines</i> (Vol. 1013, pp. 215–226). Totowa, NJ: Humana Press. <a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">https://doi.org/10.1007/978-1-62703-426-5_14</a>","ama":"Weber M, Sixt MK. Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In: Cardona A, Ubogu E, eds. <i>Chemokines</i>. Vol 1013. MIMB. Totowa, NJ: Humana Press; 2013:215-226. doi:<a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">10.1007/978-1-62703-426-5_14</a>","ista":"Weber M, Sixt MK. 2013.Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In: Chemokines. Methods in Molecular Biology, vol. 1013, 215–226.","mla":"Weber, Michele, and Michael K. Sixt. “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations.” <i>Chemokines</i>, edited by Astrid Cardona and Eroboghene Ubogu, vol. 1013, Humana Press, 2013, pp. 215–26, doi:<a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">10.1007/978-1-62703-426-5_14</a>.","short":"M. Weber, M.K. Sixt, in:, A. Cardona, E. Ubogu (Eds.), Chemokines, Humana Press, Totowa, NJ, 2013, pp. 215–226."},"external_id":{"pmid":["23625502"]},"doi":"10.1007/978-1-62703-426-5_14","day":"03","abstract":[{"lang":"eng","text":"Leukocyte migration through the interstitial space is crucial for the maintenance of tolerance and immunity. The main cues for leukocyte trafficking are chemokines thought to directionally guide these cells towards their targets. However, model systems that facilitate quantification of chemokine-guided leukocyte migration in vivo are uncommon. Here we describe an ex vivo crawl-in assay using explanted mouse ears that allows the visualization of chemokine-dependent dendritic cell (DC) motility in the dermal interstitium in real time. We present methods for the preparation of mouse ear sheets and their use in multidimensional confocal imaging experiments to monitor and analyze the directional migration of fluorescently labelled DCs through the dermis and into afferent lymphatic vessels. The assay provides a more physiological approach to study leukocyte migration than in vitro three-dimensional (3D) or 2-dimensional (2D) migration assays such as collagen gels and transwell assays."}],"page":"215-226","series_title":"MIMB","quality_controlled":"1","publisher":"Humana Press","editor":[{"first_name":"Astrid","last_name":"Cardona","full_name":"Cardona, Astrid"},{"full_name":"Ubogu, Eroboghene","last_name":"Ubogu","first_name":"Eroboghene"}],"pmid":1,"_id":"10900","scopus_import":"1","author":[{"id":"3A3FC708-F248-11E8-B48F-1D18A9856A87","last_name":"Weber","first_name":"Michele","full_name":"Weber, Michele"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","date_created":"2022-03-21T07:47:41Z","department":[{"_id":"MiSi"}],"article_processing_charge":"No","title":"Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations","alternative_title":["Methods in Molecular Biology"],"intvolume":"      1013"}]