Publications about analyses with Simi BioCell
Goolam, M., Scialdone, A., Graham, S.J.L., Macaulay, I.C., Jedrusik, A., Hupalowska, A., Voet, T., Marioni, J.C., Zernicka-Goetz, M. (2016). Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos. Cell, Vol. 165 (1), p.61-74. [WWW]
Stach, T., Anselmi, C. (2015). High-precision morphology: bifocal 4D-microscopy enables the comparison of detailed cell lineages of two chordate species separated for more than 525 million years. BMC Biology 2015, 13 (113). [WWW]
Schiffer, P.H., Nsah, N.A., Grothehumann, H., Kroiher, M., Loer, C., Schierenberg, E. (2014). Developmental variations among Panagrolaimid nematodes indicate developmental system drift within a small taxonomic unit. Development Genes and Evolution, Vol. 224 (3), 183-188. [WWW]
Fischer, A.H.L, Arendt, D. (2013). Mesoteloblast-Like Mesodermal Stem Cells in the Polychaete Annelid Platynereis dumerilii (Nereididae). Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, Vol. 320 (2), 94–104. [WWW]
Bashar, M.K., Fujimori, T., Komatsu, K., Kobayashi, T.J. (2012). Adaptive cell nuclei detection from fluorescence images by optimizing object sizes. Conference paper: Conference on Biomedical Engineering and Sciences (IECBES 2012). [WWW]
Bashar, M.K., Fujimori, T., Komatsu, K., Kobayashi, T.J. (2012). Automatic Extraction of Nuclei Centroids of Mouse Embryonic Cells from Fluorescence Microscopy Images. PLoS ONE, 7(5). [WWW]
Bashar, M.K., Fujimori, T., Komatsu, K., Kobayashi, T.J. (2012). Improving the detection of cell centroids from fluorescence images by adaptive filtering. Conference paper: 7th International Conference on Electrical & Computer Engineering (ICECE 2012). [WWW]
Bischoff, M. (2012). Lamellipodia-based migrations of larval epithelial cells are required for normal closure of the adult epidermis of Drosophila. Developmental Biology, Vol. 363 (1), 179-190. [WWW]
Claudiu A. Giurumescu, Sukryool Kang, Thomas A. Planchon, Eric Betzig, Joshua Bloomekatz, Deborah Yelon, Pamela Cosman, Andrew D. Chisholm (2012). Quantitative semi-automated analysis of morphogenesis with single-cell resolution in complex embryos. Development 2012 (139), 4271-4279. [WWW]
Pennerstorfer, M., Scholtz, G. (2012). Early cleavage in Phoronis muelleri (Phoronida) displays spiral features. Evolution & Development, Vol. 14 (6), 484–500. [WWW]
Alwes, F., Hinchen, B., Extavour, C.G. (2011). Patterns of cell lineage, movement, and migration from germ layer specification to gastrulation in the amphipod crustacean Parhyale hawaiensis. Developmental Biology, Vol. 359 (1), 110-123. [WWW]
Viveiros, R., Hutter, H., Moerman, D.G. (2011). Membrane extensions are associated with proper anterior migration of muscle cells during Caenorhabditis elegans embryogenesis. Developmental Biology, Vol. 358 (1), 189-200. [WWW]
Schnabel, R. (2010). Quantitative 4D-Mikroskopie: Bioinformatische zelluläre Verhaltensbiologie. BIOspektrum, 6-2010, 644-647. [WWW]
Cabello, J., Neukomm, L.J., Günesdogan, U., Burkart, K., Charette, S.J., Lochnit, G., Hengartner, M.O. & Schnabel, R. (2010). The Wnt Pathway Controls Cell Death Engulfment, Spindle Orientation, and Migration through CED-10/Rac. PLoS Biology, 8 (2) e1000297.
Jedrusik, A., Bruce, A.W., Tan, M.H., Leong, D.E., Skamagki, M., Yao, M. & Zernicka-Goetz, M. (2010). Maternally and zygotically provided Cdx2 have novel and critical roles for early development of the mouse embryo. Developmental Biology, 344 (1) 66-78.
Morris, S.A., Teo, R.T.Y., Li, H., Robson, P., Glover, D.M. & Zernicka-Goetz, M. (2010). Origin and formation of the first two distinct cell types of the inner cell mass in the mouse embryo, PNAS, 107 (14) 6364-6369.
Biscoff, M. & Cseresnyes, Z. (2009). Cell rearrangements, cell divisions and cell death in a migrating epithelial sheet in the abdomen of Drosophila. Development, 136, 2403-2411.
Schulze, J. & Schierenberg, E. (2009). Embryogenesis of Romanomermis culicivorax: an alternative way to construct a nematode. Dev Biology, 334, 10-21.
Willems, M., Egger, B., Wolff, C., Mouton, S., Houthoofd, W., Fonderie, P., Couvreur, M., Artois, T. & Borgonie, G. (2009). Embryonic origins of hull cells in the flatworm Macrostomum lignano through cell lineage analysis: developmental and phylogenetic implications. Dev Genes Evol, 219, 409-417.
Biscoff, M., Parfitt, D-E. & Zemicka-Goetz, M. (2008). Formation of the embryonic-abembryonic axis of the mouse blastocyst: relationships between orientation of early cleavage divisions and pattern of symmetric/asymmetric divisions. Development, 135, 953-962.
Houthoofd, W., Willems, M., Jacobsen, K., Coomans, A. & Borgonie, G. (2008). The embryonic cell lineage of the nematode Rhabditophanes sp. Int J Dev Biol, 52, 963-967.
Jedrusik, A., Parfitt, D.-E., Guo, G., Skamagki, M., Grabarek, J.B., Johnson, M.H., Robson, P. & Zernicka-Goetz, M. (2008). Role of Cdx2 and cell polarity in cell allocation and specification of trophectoderm and inner cell mass in the mouse embryo. Genes & Development. 22, 2692–2706.
Ninkovic, J., Stigloher, C., Lillesaar, C. & Bally-Cuif, L. (2008). Gsk3β/PKA and Gli1 regulate the maintenance of neural progenitors at the midbrain-hindbrain boundary in concert with E(Spl) factor activity. Development, 135, 3137-3148.
Ravin, R., Hoeppner, D., Munno, D., Carmel, L., Sullivan, J., Levitt, D., Miller, J., Athaide, C., Panchision, D. & McKay, R. (2008). Potency and Fate Specification in CNS Stem Cell Populations In Vitro. Cell Stem Cell, 3 (6) 670-680.
Schulze, J. & Schierenberg, E. (2008). Cellular pattern formation, establishment of polarity and segregation of colored cytoplasm in embryos of the nematode Romanomermis culicivorax. Developmental Biology, 315, 426-436.
Stach, T., Winter, J., Bouquet, J.-M., Chourrout, D. & Schnabel, R. (2008). Embryology of a planktonic tunicate reveals traces of sessility. PNAS, 105 (20) 7229-7234.
Von Hilchen, C.M., Beckervordersandforth, R.M., Rickert, C., Technau, G.M. & Altenhein, B. (2008). Identity, origin, and migration of peripheral glial cells in the Drosophila embryo. Mechanisms of Development, 125, 337-352.
Hejnol, A., Schnabel, R. & Scholtz, G. (2006). A 4D-microscopic analysis of the germ band in the isopod crustacean Porcellio scaber (Malacostraca, Peracarida)—developmental and phylogenetic implications. Dev Genes Evol, 216, 755-767.
Houthoofd, W., Willems, M., Vangestel, S., Mertens, C., Bert, W. & Borgonie, G. (2006). Different roads to form the same gut in nematodes. Evol. Dev. 8 (4) 362-369.
Wolff, C. & Scholtz, G. (2006). Cell lineage analysis of the mandibular segment of the amphipod Orchestia cavimana reveals that the crustacean paragnaths are sternal outgrowths and not limbs. Frontiers in Zoology, 3 (19) DOI; 10.1038/cdd.2010.3
Hejnol, A. & Schnabel, R. (2005). The eutardigrade Thulinia stephaniae has an indeterminate development and the potential to regulate early blastomere ablations. Development, 132, 1349-1361.
Braun, V., Azevedo, R.B.R., Gumbel, M., Agapow, P.-M., Leroi, A.M. & Meinzer, H.-P. (2003). ALES: cell lineage analysis and mapping of developmental events. Bioinformatics, 19 (7) 851-858.
Houthoofd, W., Jacobsen, K., Mertens, C., Vangestel, S., Coomans, A. & Borgonie, G. (2003). Embryonic cell lineage of the marine nematode Pellioditis marina. Developmental Biology, 258, 57-69.
Urbach, R., Schnabel, R. & Technau, G.M. (2003). The pattern of neuroblast formation, mitotic domains and proneural gene expression during early brain development in Drosophila. Development. 130, 3589-3606.
Braun, V., Gumbel, M., Leroi, A.M. & Meinzer, H.-P. (2002). Proceedings of the 1st Computational Embryology Workshop. German Cancer Research Center, Heidelberg.
Borgonie, G., Jacobsen, K. & Coomans, A. (2000). Embryonic lineage evolution in nematodes. Nematology, 2, 1, 65-69.
Schnabel, R. (1999). Biology in pictures: a question of fate. Curr. Biol, 12, R543.
Dolinski, C., Borgonie, G., Schnabel, R. & Baldwin, J.G. (1998). Buccal capsule development as a consideration for phylogenetic analysis of Rhabditida (Nemata)*. Dev Genes Evol. 208, 495-503.
Schnabel, R. & Schnabel. H. (1997). Hox genes misled by local environments. Nature, 385, 588-589.
Publications about analyses of Caenorhabditis elegans with Simi BioCell
Ertl, I., Porta-de-la-Riva, M., Gómez-Orte, E., Rubio,K. Aristizábal-Corrales, D., Cornes, E., Fontrodona, L., Osteikietxea, X., Ayuso, C., Askjaer, P., Cabello, J., Cerón, J. (2016). Functional Interplay of Two Paralogs Encoding SWI/SNF Chromatin-Remodeling Accessory Subunits During Caenorhabditis elegans Development. GENETICS, Vol. 203 (1). [WWW]
Pinto, S.M., Almendinger, J., Cabello, J., Hengartner, M.O. (2016). Loss of Acetylcholine Signaling Reduces Cell Clearance Deficiencies in Caenorhabditis elegans. PLoS One, 2016, 11(2). [WWW]
Müller, A., Winkler , J., Fiedler, F., Sastradihardja, T., Binder, C., Schnabel, R., Kungel, J., Rothemund, S., Hennig, C., Schöneberg, T., Prömel, S. (2015). Oriented Cell Division in the C. elegans Embryo Is Coordinated by G-Protein Signaling Dependent on the Adhesion GPCR LAT-1. PLoS Genet 11(10). [WWW]
Vidal, B., Santella, A., Serrano-Saiz, E., Zhirong Bao, Chiou-Fen Chuang, Hobert, O. (2015). C. elegans SoxB genes are dispensable for embryonic neurogenesis but required for terminal differentiation of specific neuron types. Development 2015 (142), 2464-2477. [WWW]
Giurumescu, C.A., Chisholm, A.D. (2011). Cell Identification and Cell Lineage Analysis. Methods in Cell Biology, Vol. 106 (2011), 323-341. [WWW]
González-Cabo, P., Bolinches-Amorós, A., Cabello, J., Ros, S., Moreno, S., Baylis, H.A., Palau, F., Vázquez-Manrique, R.P. (2011). Disruption of the ATP-binding Cassette B7 (ABTM-1/ABCB7) Induces Oxidative Stress and Premature Cell Death in Caenorhabditis elegans. The Journal of Biological Chemistry (286), 21304-21314. [WWW]
Nehme, R., Grote, P., Tomasi, T, Löser, S., Holzkamp, H., Schnabel, R. & Conradt, B. (2010). Transcriptional upregulation of both egl-1 BH3-only and ced-3 caspase is required for the death of the male-specific CEM neurons. Cell death regulation in C. elegans. Cell Death and Differentiation, 17 (8) 1266-1276.
Bertrand, V. & Hobert, O. (2009). Linking asymmetric cell division to the terminal differentiation program of postmitotic neurons in C. elegans. Dev Cell, 16 (4) 563-575.
Lahl, V., Schulze, J. & Schierenberg, E. (2009). Differences in embryonic pattern formation between Caenorhabditis elegans and its close parthenogenetic relative Diploscapter coronatus. Int J Dev Biol, 53, 507-515.
Langenhan, T., Prömel, S., Mestek, L., Esmaeili, B., Waller-Evans, H., Hennig, C., Kohara, Y., Avery, L., Vakonakis, I., Schnabel, R. & Russ, A.P. (2009). Latrophilin signaling links anterior-posterior tissue polarity and oriented cell divisions in the C. elegans embryo. Dev Cell, 17 (4) 494-504.
Meyvis, Y., Houthoofd, W., Visser, A., Borgonie, G., Gevaert, K., Vercruysse, J., Claerebout, E. & Geldhof, P. (2009). Analysis of the translationally controlled tumour protein in the nematodes Ostertagia ostertagi and Caenorhabditis elegans suggests a pivotal role in egg production. Int J Parasitol, 39 (11) 1205-1213.
Moser, S.C., von Elsner, S., Büssing, I., Alpi, A., Schnabel, R. & Gartner, A. (2009). Functional Dissection of Caenorhabditis elegans CLK-2/ TEL2 Cell Cycle Defects during Embryogenesis and Germline Development. PloS Genetics, 5, (4): e1000451.
Sarin, S., Antionio, C., Tursun, B. & Hobert, O. (2009). The C. elegans Tailless/TLX transcription factor nhr-67 controls neuronal identity and left/right asymmetric fate diversification. Development, 136, 2933-2944.
Asencio, C., Navas, P., Cabello, J., Schnabel, R., Cypser, J.R., Johnson, T.E. & Rodríguez-Aguilera, J.C. (2008). Coenzyme Q supports distinct developmental processes in Caenorhabditis elegans . Mechanisms of Ageing and Development, 130, 145-153.
Ray, P., Schnabel, R. & Okkema, P.G. (2008). Behavioral and synaptic defects in C. elegans lacking the NK-2 homeobox gene ceh-28. Developmental Neurobiology, 68, 421-433.
Smit, R.B., Schnabel, R. & Gaudet, J. (2008). The HLH-6 Transcription Factor Regulates C. elegans Pharyngeal Gland Development and Function. PloS Genetics, 4 (10).
Hamahashi, S., Kitano, H. & Onami, S. (2007). A system for measuring cell division patterns of early Caenorhabditis elegans embryos by using image processing and object tracking. Syst Comp Jpn, 38, (11) 12-24.
Hunt-Newbury, R. et al. (2007). High-Throughput In Vivo Analysis of Gene Expression in Caenorhabditis elegans. PLoS Biology, 5 (9) e237.
Tiraihi, A. & Tiraihi, T. (2007). Early onset of regionalization in EMS lineage of C. elegans embryo: A quantitative study. Biosystems, 90 (3) 676-686.
Asencio, C., Rodríguez-Aguilera, J.C., Vázquez, R., Baylis, H., Cabello, J., Schnabel, R., Gavilána. Á. & Navas, P. (2006). Differential expression pattern of coq-8 gene during development in Caenorhabditis elegans. Gene Expr. Patterns, 6, 433-439.
Biscoff, M., & Schnabel, R. (2006). A Posterior Centre Establishes and Maintains Polarity of the Caenorhabditis elegans Embryo by a Wnt-Dependent Relay Mechanism. PLoS Biology, 4 (12) e396.
Biscoff, M., & Schnabel, R. (2006). Global cell sorting is mediated by local cell–cell interactions in the C. elegans embryo. Developmental Biology, 294, 432-444.
Boyle, T.J., Bao, Z., Murray, J.I., Araya, C.L. & Waterson, R.H. (2006). AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis. BMC Bioinformatics, 7, 275.
Murray, J.I., Bao, Z., Boyle, T.J. & Waterson, R.H. (2006). The lineaging of fluorescently-labeled Caenorhabditis elegans embryos with StarryNite and AceTree. Nature Protocols, 1, 1468-1476.
Schnabel, R., Bischoff, M., Hintze, A., Schulz, A.K., Hejnol, A., Meinhardt, H. & Hutter, H. (2006), Fate dependent global cell sorting in the C. elegans embryo defines a new mechanism for pattern formation. Developmental Biology, 294, 418-431.
Bao, Z., Murray, J.I., Boyle, T., Ooi, S.L., Sandel, M.J. & Waterston, R.H. (2005). Automated cell lineage tracing in Caenorhabditis elegans. PNAS, 103 (8) 2707-2712.
Gavilán, A., Asencio, C., Cabello, J., Rodríguez-Aguilera, J.C., Schnabel, R. & Navas, P. (2005). C. elegans knockouts in ubiquinone biosynthesis genes result in different phenotypes during larval development. Biofactors, 25, 21-29.
Hamahashi, S., Onami, S. & Kitano, H. (2005). Detection of nuclei in 4D Nomarski DIC microscope images of early Caenorhabditis elegans embryos using local image entropy and object tracking. BMC Bioinformatics. 24 (6) 125.
Kinchen, J.M, Cabello, J., Klingele, D., Wong, K., Feichtinger, R., Schnabel, H., Schnabel, R. & Hengartner, M.O. (2005). Two pathways converge at CED-10 to mediate actin rearrangement and corpse removal in C. elegans. Nature, 434, 93-99.
Karabinos, A., Büssing, I., Schulz, E., Wan, J., Weber, K. & Schnabel, R. (2003). Functional analysis of the single calmodulin gene in the nematode C. elegans by RNA interference and 4-D microscopy. European J. Cell Biology, 82, 557-583.
Mohadessi, S. (2003). Design and implementation of a MovieComponent for extension of ALES based on the existing CellO-Framework. mbi Technical report.
Clucas, C., Cabello, J., Büssing, I., Schnabel, R. & Johnstone, I.L. (2002). Oncogenic potential of a C.elegans cdc25 gene is demonstrated by a gain-offunction allele. EMBO J., 21, 665-674.
Ginzburg, V.E., Roy, P.J. & Culotti, J.G. (2002). Semaphorin 1a and semaphorin 1b are required for correct epidermal cell positioning and adhesion during morphogenesis in C. elegans. Development, 129, 2065-2078.
Hope, I.A., Mounsey, A., Bauer, P. & Aslam, S. (2002). The forkhead gene family of Caenorhabditis elegans. Gene, 30 (304) 43-55.
Hoeppner, D.J., Hengartner, M.O. & Schnabel, R. (2001). Engulfment genes cooperate with ced-3 to promote cell death in Caenorhabditis elegans. Nature, 412, 202-206.
Dantonel, J.-C., Quintin, S., Lakatos, L., Labouesse, M. & Tora, L. (2000). TBP-like Factor Is Required for Embryonic RNA Polymerase II Transcription in C. elegans. Molecular Cell, 6, 715-722.
Brunschwig, K., Wittmann, C., Schnabel, R., Bürglin, T.R., Tobler, H. & Müller, F. (1999). Anterior organization of the Caenorhabditis elegans embryo by the labial-like Hox gene ceh-13. Development, 128, 1537-1546.
Schnabel, R. (1999). Microscopy in C. elegans. A Practical Approach. I.A. Hope, ed. 119-141.
Horner, M.A., Quintin, S., Domeier, M.E, Kimble, J., Labouesse, M. & Mango, S.E. (1998). pha-4, an HNF-3 homolog, specifies pharyngeal organ identity in Caenorhabditis elegans. Genes & Development, 12, 1947-1952.
Kaletta, T., Schnabel, H. & Schnabel, R. (1997). Binary specification of the embryonic lineage in Caenorhabditis elegans. Nature, 390, 294-298.
Schnabel, R., Hutter, H.,Moerman, D. & Schnabel, H. (1997). Assessing Normal Embryogenesis in Caenorhabditis elegans Using a 4D Microscope: Variability of Development and Regional Specification. Development Biology, 184, 234-265.