Superresolution Fluorescence Microscopy (nanoscopy)

Nuclear Organisation

Publication list Christoph Cremer (1972 – 2016)

D. Żurek-Biesiada, A. T. Szczurek, K. Prakash, G. K. Mohanab, H.-K. Lee, J.-Y. Roignant, U. Birk, J. W. Dobrucki, C. Cremer (2015) Localization microscopy of DNA in situ using Vybrant® DyeCycle™ Violet Fluorescent Probe: a new approach to study nuclear nanostructure at single molecule resolution. Exp. Cell Res. 343: 97-106.


D. Żurek-Biesiada , A. T. Szczurek, K. Prakash, G. Best, G. K. Mohana, H.-K. Lee, J. -Y. Roignant, J. W. Dobrucki, C. Cremer, U. Birk (2016) Quantitative Super Resolution Localization microscopy of DNA in situ using Vybrant® DyeCycle™ Violet Fluorescent Probe. Data in Brief 7:157-171. doi: 10.1016/j.dib.2016.01.041.


R. Lopez Perez,G. Best,N. H. Nicolay,C. Greubel, S.Rossberger,J. Reindl, G. Dollinger, K.-J. Weber, C. Cremer, P. E. Huber (2016) Superresolution light microscopy shows nanostructure of carbon ion radiation-induced DNA double-strand

break repair foci. The FASEB Journal 30:2767-2776.


A.Szczurek, U. Birk, C.Cremer (2016) Light Microscopy of Chromatin Texture in normal and Cancer Cells on the Nanoscale. Frontiers in Genetics 7:Article 114, pp. 1-7 (June 2016). doi:10.3389/fgene.2016.00114


T. Cremer, M. Cremer, B. Hübner, H. Strickfaden,  D. Smeets, J. Popken, M. Sterr, Y. Markaki,  K. Rippe, C. Cremer (2015) The 4D nucleome: Evidence for a dynamic nuclear landscape based on coaligned active and inactive nuclear compartments. FEBS Letters  589: 2931–2943.


K. Prakash, D. Fournier, S. Redl, G. Best, M. Borsos, R. Ketting, K. Tachibana-Konwalski, C. Cremer, U. Birk (2015) Super-resolution imaging reveals structurally distinct periodic patterns of chromatin along pachytene chromosomes, Proc. Natl. Acad. Sci. USA 112 (47):14635–14640.


T. Cremer, C. Cremer, P. Lichter (2014) Recollections of a scientific journey published in Human Genetics: from chromosome territories to interphase cytogenetics and comparative genome hybridization. Hum Genet (2014) 133:403–416.


A.T. Szczurek, K. Prakash, H. K. Lee, D. J. Żurek-Biesiada, G. Best, M. Hagmann, J. W. Dobrucki, C. Cremer, U. Birk (2014) Single molecule localization microscopy of the distribution of chromatin using Hoechst and DAPI fluorescent probes. Nucleus 5 (4)1-10.

First report on the use of standard DNA dyes in photoswitching based single molecule superresolution microscopy, featuring a structural resolution of few tens of nm.


R. Kaufmann, C. Cremer, J. G. Gall (2012) Superresolution imaging of transcription units on newt lampbrush chromosomes, Chromosome Research, DOI 10.1007/s10577-012-9306-z-

First report on the use of standard fluorophores in photoswitching based single molecule dual color superresolution microscopy of the spatial distribution of splicing factors as a function of the length of the transcribed DNA.


T. Cremer T, Y. Markaki Y, B. Hübner B, A. Zunhammer A,  H. Strickfaden H, S. Beichmanis S, M. Heß M, L. Schermelleh L, M. Cremer, C.Cremer C (2012) Chromosome Territory Organization within the Nucleus. Encyclopedia of Molecular Cell Biology and Molecular Medicine, DOI: 10.1002/3527600906.mcb.200300046.pub2.


Y. Weiland, P. Lemmer, C. Cremer  (2011) Combining FISH with Localisation Microscopy, Superresolution Imaging of Nuclear Genome Nanostructures, Chromosome Research  19: 5 – 23.

First detailed report to use single molecule superresolution microscopy based on photoswitching of standard fluorophores to perform light microscopy at the nanoscale of a specific chromatin domain in 3D intact nuclei.


C. Grossmann, J. Schwarz-Finsterle, E. Schmitt, U. Birk, G. Hildenbrand, C. Cremer, L. Trakhtenbrot, and M. Hausmann Variations of the spatial fluorescence distribution in ABL gene chromatin domains measured in blood cell nuclei by SMI microscopy after COMBO – FISH labelling . In: Microscopy: Science, Technology, Applications and Education (Ed. Mendez-Vilas A, Diaz J), Formatex Research Center, pp. 688-695.

First report on the nanoscale analysis of a specific cancer related nuclear gene domain using ‘oligo-paints’ and axially structured illumination based superresolution microscopy


C. Cremer, R. Kaufmann, M. Gunkel, S. Pres, Y. Weiland, P. Müller, T. Ruckelshausen, P. Lemmer, F. Geiger, S. Degenhard, C. Wege, N. A. W. Lemmermann, R. Holtappels, H. Strickfaden, M. Hausmann (2011) Superresolution Imaging of Biological Nanostructures by Spectral Precision Distance Microscopy (SPDM), Biotechnology Journal 6: 1037 – 1051.

Contains first report on photoswitching based single molecule superresolution microscopy of the nucleus of a live cell with histones labelled with a standard Green Fluorescent Protein.


Y. Markaki, M. Gunkel, L. Schermelleh, S. Beichmanis, J. Neumann,M. Heidemann, H. Leonhardt, D. Eick, C. Cremer, T. Cremer, Functional nuclear organization of transcription and DNA replication: a topographical marriage between chromatin domains and the interchromatin compartment (2010) Cold Spring Harbor Symposia on Quantitative Biology 75:475 – 492.

First report to combine laterally structured illumination microscopy and photoswitching based single molecule dual color superresolution microscopy in the analysis of nuclear organization.


M. Bohn, P.  Diesinger, R.  Kaufmann , Y. Weiland, P. Müller, M. Gunkel, A. von Ketteler, P. Lemmer , M. Hausmann, C. Cremer (2010) Localization microscopy reveals expression dependent parameters of chromatin nanostructure. Biophys. J. 99: 1358 – 1367.

First report to combine photoswitching based single molecule superresolution microscopy and approaches of theoretical polymer physics in the analysis of nuclear organization.


L.-O. Tykocinski,  A. Sinemus, E. Rezavandy, Y. Weiland, D. Baddeley, C. Cremer, S. Sonntag, K. Willeke, J. Derbinski,  B. Kyewski (2010) Epigenetic regulation of promiscuous gene expression in thymic medullary epithelial cells. Proc. Natl. Acad. Sci. USA  107 (45): 19426–19431.

First report on the use of localization microscopy based superresolution with photostable dyes to study nanostructure changes in a specific gene domain upon epigenetic regulation, featuring an optical resolution in the 50 nm range.


D. Hübschmann, N. Kepper, C. Cremer, G. Kreth (2010) Quantitative Approaches to Nuclear Architecture Analysis and Modelling, in: N.M. Adams and P.S. Freemont (eds.), Advances in Nuclear Architecture, 87 – 129. DOI 10.1007/978-90-481-9899-3_3, Springer Inc.


D. Baddeley, V.O. Chagin, L. Schermelleh, S. Martin, A. Pombo, P.M. Carlton, A. Gahl, P. Domaing, U. Birk, H. Leonhardt, C. Cremer, M.C. Cardoso (2010) Measurement of replication structures at the nanometer scale using super-resolution light microscopy. Nucleic Acids Res 38: e8 1-11. doi:10.1093/nar/gkp901.

First report to use axially structured illumination based superresolution microscopy for the quantitative nanoscale analysis of replication structures.


M. Lang, T. Jegou, I. Chung, K. Richter, S. Münch, A. Udvarhelyi, C. Cremer, P. Hemmerich, J. Engelhardt, S. Hell, K. Rippe (2010). On the three-dimensional organization of promyelocytic leukemia nuclear bodies”, J. of Cell Science 123: 392 – 412.

First report to apply 4Pi-microscopy based superresolution to the nanoscale imaging of a cancer related nuclear body.


C. Heride M.Ricou, K.Kieu, J.von Hase, V. Guillemot,  C. Cremer, K. Dubrana, L. Sabatier (2010)  Distance between homologous  chromosomes results from chromosome positioning constraints, J. of  Cell Science 123: 4063-4075.


J. Rouquette, C. Cremer, T. Cremer, S. Fakan, Functional nuclear architecture studied by microscopy (2010) International Review of Cell and Molecular Biology 282: 1 – 90.


P. Müller, E. Schmitt, A. Jacob, J. Hoheisel, R. Kaufmann, C. Cremer, M. Hausmann (2010) COMBO-FISH Enables High Precision Localization Microscopy as a Prerequisite for Nanostructure Analysis of Genome Loci, Int. J. Mol. Sci. 11: 4094-4105.

First report to use ‘oligo-paints’ in combination with photoswitching based single molecule based superresolution microscopy to analyse nuclear genome structures on the nanoscale


M. Gunkel, F. Erdel, K. Rippe, P. Lemmer, R. Kaufmann, C. Hörmann, R. Amberger, C. Cremer (2009) Dual color localization microscopy of cellular nanostructures. Biotechnology J. 4: 927 – 938.

First report on  single molecule based dual color superresolution microscopy using standard green fluorescent proteins in the photoswitching mode, and its application to quantitatively analyse the distribution of individual histones and chromatin remodeling proteins in 3D intact nuclei on the nanoscale.


R. Kaufmann, P. Lemmer, M. Gunkel, Y. Weiland, P. Müller, M. Hausmann, D. Baddeley, R. Amberger, C. Cremer (2009)  SPDM – Single Molecule Superresolution of Cellular Nanostructures. Invited paper, Proc. SPIE 7185 :71850J-1 – 71850J-19. 

First report on single molecule based superresolution microscopy using standard green fluorescent proteins in the photoswitching mode, and its application to analyse the histone distribution in 3D intact nuclei with an optical resolution in the few tens of nm range.


J. Reymann, D. Baddeley, P. Lemmer, W. Stadter, T. Jegou, K. Rippe, C. Cremer, U. Birk (2008) High precision structural analysis of subnuclear complexes in fixed and live cells via Spatially Modulated Illumination (SMI) microscopy. Chromosome Research 16: 367 –382.

First report on an effective single molecule based superresolution microscopy method with individual standard fluorophores in the photoswitching mode (published prior to dSTORM) and its application to analyse the distribution of nuclear pore complexes in 3D intact nuclei with an optical resolution in the few tens of nm range.


O. Ronneberger, D. Baddeley, F. Scheipl, P. J. Verveer, H. Burkhardt, C. Cremer, L. Fahrmeir,  T. Cremer, B. Joffe (2008) Spatial quantitative analysis of fluorescently labeled nuclear structures: Problems, methods, pitfalls. Chromosome Research 16: 523–562.


J. Rauch, T.A. Knoch, I. Solovei, K. Teller, S. Stein, K. Buiting, B. Horsthemke, J. Langowski, T. Cremer, M. Hausmann, C. Cremer (2008) Lightoptical precision measurements of the active and inactive Prader-Willi Syndrome imprinted regions in human cell nuclei. Differentiation 76: 66 – 83.

First detailed report on the use of localization based superresolution microscopy with photostable fluorophores to study quantitatively in 3D intact nuclei a specific genome region in the active and silenced state.


C. Batram, D. Baddeley, G. Kreth, C. Cremer (2008) High precision measurements of centromere 8 and the 8q24/c-myc gene region in metaphase and interphase human  fibroblasts indicate differential condensation. J. of Structural Biology 164: 293 – 303.


W. Friedland, H. G. Paretzke, F. Ballerini, A. Ottolenghi, G. Kreth, C. Cremer (2008) First Steps towards systems radiation biology studies concerned with DNA and chromosome structure within living cells. Radiat. Environ. Biophys. 47: 49 – 61.


U.J. Birk, D. Baddeley, C. Cremer (2008) Nanosizing by spatially modulated illumination (SMI) microscopy and applications to the nucleus. In R. Hancock (ed) The Nucleus, Vol. 2: Chromatin, Transcription, Envelope, Proteins, Dynamics, and Imaging. DOI 10.1007/978-1-60327-461-6_21.


L.Brianna Caddle, J.L. Grant, J. Szatkiewicz, J. von Hase, B.J. Shirley, J. Bewersdorf, C. Cremer, A. Arneodo, A. Khalil, K.D. Mills (2007) Chromosome neighborhood composition determines translocation outcomes after exposure to high-dose radiation in primary cells. Chromosome Res. 15: 1061 – 1073.


G. Kreth, S.K. Pazhanisamy, M. Hausmann, C. Cremer (2007) Cell type-specific quantitative predictions of radiation-induced chromosome aberrations: A computer model approach. Radiat. Res. 167: 515 – 525.


J. Schwarz-Finsterle, S. Stein, C. Großmann, E. Schmitt, L. Trakhtenbrot, G. Rechavi, N. Amariglio, C. Cremer, M. Hausmann (2007) Comparison of triple helical COMBO-FISH and standard FISH by means of quantitative microscopic image analysis of abl/bcr positions in cell nuclei. J. Biochem. Biophys. Methods 70:397 – 406.

First report on the use of ‘oligo-paints’ to analyse the nuclear distribution of a specific, cancer related gene.


S. Fenz, H. Mathee, G. Kreth, D. Baddeley, Y. Weiland, J. Schwarz-Finsterle, C.G. Cremer, U.J. Birk (2007) Two-color intranuclear distance measurements of gene regions in human lymphocytes. Proc. SPIE 6630: 663002-1 – 663002-10.


G. Kreth and C. Cremer (2007) Chromatin Structure and the Formation of Chromosomal Alterations in Chromosomal Alterations: Methods, Results and Importance in Human Health, Ed. Günter Obe, Springer Verlag Heidelberg.


L. S. Shopland, C. R. Lynch, K. A. Peterson, K. Thornton, N. Kepper, J. von Hase, S. Stein, S. Vincent, K. R. Molloy, G. Kreth, C. Cremer, C. J. Bult, T. P. O’Brien (2006) Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence. J. Cell Biology 174: 27–38.


H. Mathée, D. Baddeley, C. Wotzlaw, J. Fandrey, C. Cremer, U. Birk (2006) Nanostructure of specific chromatin regions and nuclear complexes. Histochem. Cell Biology 125: 75-82.


T. Cremer and C. Cremer (2006) Rise, fall and resurrection of chromosome territories: a historical perspective. Part I. The rise of chromosome territories. European Journal of Histochemistry 50:161-176.


T. Cremer and C. Cremer (2006) Rise, fall and resurrection of chromosome territories: a historical perspective Part II. Fall and resurrection of CTs during the 1950th to 1980th. Part III. Chromosome territories and the functional nuclear architecture: experiments and models from the 1990th to the present. European Journal of Histochemistry 50 :223-272.


H. Albiez, M. Cremer, C. Tiberi, L. Vecchio, L. Schermelleh, S. Dittrich, K. Küpper, B. Joffe, T. Thormeyer, J. von Hase, S. Yang, K. Rohr, H. Leonhardt, I. Solovei, C. Cremer, S. Fakan, T. Cremer (2006) Chromatin domains and the interchromatin compartment form structurally defined and functionally interacting nuclear networks. Chromosome Research 14:707–733.


G. Hildenbrand, A. Rapp, U. Spöri, C. Wagner, C. Cremer, M. Hausmann (2005) Nano-Sizing of Specific Gene Domains in Intact Human Cell Nuclei by Spatially Modulated Illumination Light Microscopy. Biophysical Journal 88: 4312–4318.

First report to measure the size of a specific chromatin domain in intac t humen cell nuclei by axially structured illumination based superresolution microscopy.


A.Bolzer, G. Kreth, I. Solovei, D. Koehler, K. Saracoglu, C. Fauth, S. Müller, R. Eils, C. Cremer, M. R. Speicher, T. Cremer (2005) Three-Dimensional Maps of All Chromosomes in Human Male Fibroblast Nuclei and Prometaphase Rosettes. Public Library of Science (PloS) 3: 826-842.

First positional map of all chromosome territories in an individual human cell nucleus.


Jutta Schwarz-Finsterle, Stefan Stein, Constance Großmann, Eberhard Schmitt, Helmut Schneider, Luba Trakhtenbrot, Gideon Rechavi, Ninette Amariglio, Christoph Cremer, Michael Hausmann (2005) COMBO-FISH for focussed fluorescence labelling of gene domains: 3D-analysis of the genome architecture of abl and bcr in human blood cells, Cell Biology International 29: 1038 – 1046.


M. Hausmann, G. Hildenbrand, J. Schwarz-Finsterle, U. Birk, H. Schneider, C. Cremer, E. Schmitt (2005) New Technologies Measure Genome Domains. Biophotonics International October 2005: 34 - 36.


S. Martin, A. V. Failla, U. Spoeri, C. Cremer and A. Pombo (2004) Measuring the Size of Biological Nanostructures with Spatially Modulated Illumination Microscopy. Molecular Biology of the Cell 15: 2449–2455.

First measurements of the size of a specific nuclear protein complex in 3D intact nuclei in the < 100 nm range by axially structured illumination microscopy.


G. Kreth, J. Finsterle, J. von Hase, M. Cremer, C. Cremer (2004) Radial Arrangement of Chromosome Territories in Human Cell Nuclei: A Computer Model Approach Based on Gene Density Indicates a Probabilistic Global Positioning Code, Biophysical Journal 86: 2803 –2812.


W. G. Müller, D. Rieder, G. Kreth, C. Cremer, Z. Trajanoski,  J. G. McNally (2004) Generic Features of Tertiary Chromatin Structure as Detected in Natural Chromosomes. Molecular and Cellular Biology 24: 9359–9370.


G. Kreth, J. Finsterle, C. Cremer (2004) Virtual radiation biophysics: implications of nuclear structure. Cytogenet. Genome Res 104:157 –161.


S. Stadler, V. Schnapp, R. Mayer, Stein, C. Cremer, C. Bonifer, T. Cremer, S. Dietzel (2004) The architecture of chicken chromosome territories changes during differentiation. BMC Cell Biology 5:44.


I. Solovei, L. Schermelleh, K. Düring, A. Engelhardt, S. Stein, C. Cremer, T. Cremer (2004) Differences in centromere positioning of cycling and postmitotic human cell types. Chromosoma 112: 410-423.


M. Cremer, R. Zinner, S. Stein, H. Albiez, B. Wagler, C. Cremer, T. Cremer (2004) Three dimensional analysis of histone methylation patterns in normal and tumor cell nuclei. European Journal of Histochemistry  48 :11- 23.


T. Cremer, C. Cremer (2003) Chromatin in the cell nucleus: Higher order organization. In Nature Encyclopedia of the Human Genome. DOI: 10.1038/npg.els.0005768.


Cl. Weierich, A. Brero, S. Stein, J. von Hase, C. Cremer, T. Cremer, I. Solovei (2003) Three-dimensional arrangements of centromeres and telomeres in nuclei of human and murine lymphocytes. Chromosome Research 11: 485-502.


T.P. O’Brien, C.J. Bult, C. Cremer, M. Grunze, B.B. Knowles, J. Langowski, J. McNally, Th. Pederson, J. C. Politz, A. Pombo, G. Schmahl, J.P. Spatz, R. van Driel (2003) Genome function and nuclear architecture: From gene expression to nanoscience. Genome Research, 13: 1029-1041.


M. Hausmann, R. Winkler, G. Hildenbrand, J. Finsterle, A. Weisel, A. Rapp, S. Janz, C.Cremer (2003) COMBO-FISH: A new approach for specific labeling of non-denatured chromatin targets by computer selected DNA oligo-probe combinations. BioTechniques 35:564-577.

First report on the concept of oligonucleotide based Fluorescence in situ Hybridization (‘oligo-painting’) based microscopy and its experimental application to visualize a cancer related, specific  nuclear gene domain.


H. Tanabe, S. Müller, M. Neusser, J.v. Hase, E, Calcagno, M. Cremer, I. Solovei, C. Cremer, T. Cremer (2002) Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates. Proc.Natl. Acad. Sci. USA 99: 4424 – 4429.

First quantitative analysis of  the evolutionary conservation of chromosome territory distribution


Solovei, A. Cavallo, L. Schermelleh, F. Jaunin, C. Scasselati, D. Cmarko, C. Cremer, S. Fakan, T. Cremer (2002) Spatial preservation of nuclear chromatin  architecture during three-dimensional fluorescence in situ hybridization (3D-FISH). Exp. Cell Res. 276: 10 – 23.


G. Kreth, P. Edelmann, Ch. Münkel, J. Langowski, C. Cremer (2002) Translocation frequencies for X and Y chromosomes predicted by computer simulations of nuclear structure, Some Aspects of Chromosome Structure and Functions (Edits. R.C. Sobti, G. Obe, R.S. Athwal) pp. 57 – 71. Narosa Publ. House, New Delhi.


T. Cremer & C. Cremer (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nature Reviews Genetics 2: 292 – 301.

One of the most cited reviews  on nuclear organization.


M. Cremer, J. von Hase, T. Volm, A. Brero, G. Kreth, J. Walter, C. Fischer, I. Solovei, C. Cremer, T. Cremer (2001) Non-random radial higher order chromatin arrangements in nuclei of diploid human cells. Chromosome Research 9: 541 - 567.


A.Esa, A. E. Coleman, P. Edelmann, S. Silva, C. Cremer, S. Janz (2001) Conformational differences in the 3D-nanostructure of the immunoglobulin heavy-chain locus, a hotspot of chromosomal translocations in B lymphocytes. Cancer Genetics and Cytogenetics 127: 168 – 173.

The first report on the use of localization microscopy based superresolution microscopy to study conformational differences of  a cancer related hotspot region.


P. Edelmann, H. Bornfleth, D. Zink, T. Cremer, C. Cremer (2001) Morphology and dynamics of chromosome territories in living cells, Bioch. Biophys. Acta 1551: 29 – 40.

First quantitative analysis of the dynamics of chromosome territories in living cells.


A. L. Kovalchuk, A. Esa, A. E. Coleman, S. S. Park, T. Ried, C. Cremer, S. Janz (2001) Translocation Remodeling in the Primary BALB/c Plasmacytoma TEPC 3610. Genes Chromosomes Cancer  30: 283-291.


F.A. Habermann, M. Cremer, J. Walter, G. Kreth, J. von Hase, K. Bauer, J. Wienberg, C. Cremer, T. Cremer, I. Solovei (2001) Arrangements of macro- and microchromosomes in chicken cells. Chromosome Research 9: 569 – 584.


G. Kreth, P. Edelmann, C. Cremer (2001): Towards a dynamical approach for the simulation of large scale, cancer correlated chromatin structures. It. J. Anat. Embryol. 106:21 – 30.


T. Cremer, G. Kreth, H. Koester, R.H.A. Fink, R. Heintzmann, M. Cremer, I. Solovei, D. Zink, C. Cremer (2000) Chromosome territories, interchromatin domain compartment  and nuclear matrix: An integrated view of the functional nuclear architecture. Critical Reviews in Eukaryotic Gene Expression 10: 179 – 212.


A.Esa, P. Edelmann, L. Trakthenbrot, N. Amariglio, G. Rechavi, M. Hausmann, C. Cremer (2000) 3D-spectral precision distance microscopy (SPDM) of chromatin nanostructures after triple-colour labeling: a study of the BCR region on chromosome 22 and the Philadelphia chromosome. J. Microscopy 199: 96 – 105.

First detailed experimental report on the application of a localization based superresolution microscopy approach to the analysis of a cancer related nuclear breakpoint region.


J. Tajbakhsh, H. Luz, H. Bornfleth, S. Lampel, C. Cremer, P. Lichter (2000) Spatial distribution of GC- and AT-rich DNA sequences within human chromosome territories. Exp. Cell Res. 255: 229 – 237


J. Rauch, D. Wolf, J.M. Craig, M. Hausmann, C. Cremer (2000): Quantitative microscopy after fluorescence in situ hybridization – a comparison between repeat-depleted and non-depleted DNA probes, J. Biochem. Biophys. Methods 44: 59 – 72.


I. Solovei, D. Kienle, G. Little, R.Eils, L.Salelyeva, M. Schwab, W. Jäger, C. Cremer, T. Cremer (2000) Topology of double minutes (dmins) and homogeneously staining regions (HSRs) in nuclei of human neuroblastoma cell lines. Genes Chromosomes and Cancer 29: 297 – 308.


J. Rauch, M. Hausmann, I. Solovei, B. Horsthemke, T. Cremer, C. Cremer (2000): Measurement of local chromatin compaction by Spectral Precision Distance microscopy. In: Laser Microscopy (Edits. H.J. Tanke, H. Schneckenburger), Proc. SPIE 4164: 1 – 9.

First report on the use of localization based superresolution microscopy to study conformational changes in  an imprinted genome region


H. Bornfleth, P. Edelmann, D. Zink, T. Cremer, C. Cremer (1999): Quantitative motion analysis of sub-chromosomal foci in vivo in four-dimensional microscopic images. Biophys. J. 77: 2871 – 2886.


C. Cremer, P. Edelmann, H. Bornfleth, G. Kreth, H. Muench, H. Luz, M. Hausmann (1999) Principles of Spectral Precision Distance confocal microscopy for the analysis of molecular nuclear structure. In: Handbook of Computer Vision and Applications (ed. B. Jähne, H. Haußecker, P. Geißler), Ch. 41., Vol. 3, Academic Press San Diego, New York: 839-857.

First full description of the principles of localization based superresolution fluorescence microscopy using  optical  isolation


D. Zink, H. Bornfleth, A. Visser, C. Cremer, T. Cremer (1999): Organization of early and late replicating DNA in human chromosome territories. Exp. Cell Res. 247: 176-188.


S. Dietzel, K. Schiebel, G. Little, P. Edelmann, G. A. Rappold, R. Eils, C. Cremer & T. Cremer (1999): The 3D Positioning of ANT2 and ANT3 genes within female X-chromosome territories correlates with gene activity. Exp. Cell Res. 252: 363 – 375.


M. Hausmann, A. Esa, P. Edelmann, L. Trakhtenbrot, H. Bornfleth, B. Schneider, J. Bradl, I. Ben-Bassat, G. Rechavi, C. Cremer (1999): Advanced precision light microscopy for the analysis of 3D-nanostructures of chromatin breakpoint regions: Towards a structure-function relationship of the BCR-ABL region. NATO ASI Series (Editor: G. Horneck, Kluwer Academic Publ., Dordrecht) 55: 219-230.


H. Bornfleth, P. Edelmann, D. Zink, C. Cremer (1999): Three-dimensional analysis of genome topology. In: Handbook of Computer Vision and Applications, Vol. III (ed. B. Jähne, H. Haußecker, P. Geißler), Academic Press, 859-878.


T. Cremer, S. Dietzel, I. Solovei, D. Zink, R. Eils, G. Little, W. Jäger, C. Münkel, J. Langowski, E.H.K. Stelzer, H. Bornfleth, G. Kreth, P. Edelmann, C. Cremer (1999) New approaches for the analysis of chromosomes in human cell nuclei. Verh. Dtsch. Ges. Zyt. 21: 25 - 29.


C. Cremer, P. Edelmann, A. Esa, H. Bornfleth, B. Schneider, J. Bradl, B. Rinke, L. Trakhtenbrot, S. Dietzel, M. Hausmann, T. Cremer (1999) Spektrale Präzisionsdistanzmikroskopie in der Genomforschung (Spectral Precision Distance Microscopy in Genome Research). Z. Med. Physik 9: 14-20.

First concept on the application of superresolution microscopy with photostable fluorophors to nuclear structure analysis.


S. Dietzel, R. Eils, K. Sätzler, H. Bornfleth, A. Jauch, C. Cremer, T. Cremer (1998) Evidence against a looped structure of the inactive human X-chromosome territory. Exp. Cell Res. 240: 187-196.


G. Kreth, Ch. Münkel, J. Langowski, T. Cremer, C. Cremer (1998) Chromatin structure and chromatin aberrations: Modelling of damage induced by isotropic and localized irradiation. Mutat. Research 404: 77-88.


C. Cremer, H. Bornfleth, J. Bradl, A. Esa, G. Kreth, B. Rinke, R. Eils, C. Münkel, S. Dietzel, M. Granzow, A. Jauch, X.-Y. Guan, P. S. Meltzer, J. M. Trent, L. Trakhtenbrot, D. Zink, J. Langowski, M. Hausmann, T. Cremer (1997) Nuclear architecture and the formation of chromosome aberrations. Radiat. Res. 148: 513-515.


R. Eils, S. Dietzel, E. Bertin, M. Granzow, E. Schröck, M. R. Speicher, T. Ried, M. Robert-Nicoud, C. Cremer, T. Cremer (1996) Three-dimensional reconstruction of painted human interphase chromosomes: Active and inactive X chromosome territories have similar volumes but differ in shape and surface structure. J. Cell Biology 135: 1427-1440.


Harald Bornfleth, Daniele Zink, Kurt Sätzler, Roland Eils, and Christoph Cremer. Modellgestützte Segmentierung von Replikationsdomänen in dreidimensionalen konfokalen Mikroskopiebildern [Model based Segmentation of Replication Domains in three dimensional Microscopy Images] (1996) In: Mustererkennung 1996, pp. 408-419. Jähne B., Geissler P., Haussecker H., Hering F. (eds.), Springer Heidelberg New York Tokio (1996).


C. Cremer, Ch. Münkel, M. Granzow, A. Jauch, S. Dietzel, R. Eils, L. Y. Guan, P. S. Meltzer, J. M. Trent, J. Langowski, T. Cremer (1996) Nuclear architecture and the induction of chromosomal aberrations. Mutation Res 366: 97-116.


B. Rinke, A. Bischoff, M.-C. Meffert, R. Scharschmidt, M. Hausmann, E. H. K. Stelzer, T. Cremer, C. Cremer (1995): Volume ratios of painted chromosome territories 5, 7 and X in female human cell nuclei studied with laser confocal microscopy and the Cavalieri estimator. Bioimaging 3: 1-11.


C. Münkel, R. Eils, J. Imhoff, S. Dietzel, C. Cremer, T. Cremer (1995): Simulation of the distribution of chromosome territories in interphase under geometrical contraints. Bioimaging 3: 108-120.


S. Dietzel, E. Weilandt, R. Eils, C. Münkel, C. Cremer, T. Cremer (1995): Three-dimensional distribution of centromeric or paracentromeric heterochromatin of chromosomes 1, 7, 15, and 17 in human lymphocyte nuclei studied with light microscopic axial tomography. Bioimaging 3: 121-133.

First publication with enhanced  3D topology resolution of nuclear structure obtained by axial tomography.


T. Cremer, S. Dietzel, R. Eils, P. Lichter, C. Cremer (1995): Chromosome territories, nuclear matrix filaments and interchromatin channels: a topological view on nuclear architecture and function. Kew Chromosome Conference IV (P.E. Brandham, and M.D. Benett, eds. Royal Botanic Gardens, Kew.: 63-81.


T. Cremer, A. Kurz, R. Zirbel, S. Dietzel, B. Rinke, E. Schröck, M.R. Speicher, U. Mathieu, A. Jauch, P. Emmerich, H. Scherthan, T. Ried, C. Cremer, P. Lichter (1993): The role of chromosome territories in the functional compartmentalization of the cell nucleus. Cold Spring Harb. Symp. Quant. Biol. 58: 777 - 792.


A.Bischoff, J. Albers, I. Kharboush, E. Stelzer, T. Cremer, C. Cremer (1992): Differences of size and shape of active and inactive X-chromosome domains in human amniotic fluid cell nuclei. Microscopy Res. and Technique 25:68-77.


B. Geiger, D. Komitowski, A. Jauch, M. Hausmann, C. Cremer (1991): Optical sectioning and 3d-image reconstruction to determine the volumes of specific chromosome regions in human interphase cell nuclei. Optik  86: 113-119.


T. Cremer, B. Remm, I. Kharboush, A. Jauch, J. Wienberg, E. Stelzer, C. Cremer (1991): Non-iosotopic in situ hybridization and digital image analysis of chromosomes in mitotic and interphase cells. Rev. Eur. Technol. Biomed. 13: 50 - 54.


T. Cremer, S. Popp, P. Emmerich, P. Lichter, C. Cremer (1990): Rapid metaphase and interphase detection of radiation-induced chromosome aberrations in human lymphocytes by chromosomal suppression in situ hybridization. Cytometry 11: 110-118.


S. Popp, H.P. Scholl, P. Loos, A Jauch, E. Stelzer, C. Cremer, T. Cremer (1990): Distribution of chromosome 18 and X centric heterochromatin in the interphase nucleus of cultured human cells. Exp. Cell. Res. 189: 1 - 12.


P. Emmerich, P. Loos, A Jauch, A.H.N. Hopman, J. Wiegant, M. Higgins, B.N. White, M. van der Ploeg, C. Cremer, T. Cremer (1989): Double in situ hybridization in combination with digitized image analysis: A new approach to study interphase chromosome topography. Exp. Cell Res. 181: 126 - 140.


P. Loos, T. Cremer, M. Hausmann, A. Jauch, P. Emmerich, W. Schlegel, C. Cremer (1987): Distances between two chromosomes in interphase nuclei as determined with digital image analysis. In: Clinical Cytometry (Eds. G. Burger, J.S. Ploem and K. Goerttler), pp. 285 - 287. Academic Press, London.


C. Cremer, T. Cremer (1986): Induction of chromosome shattering by ultraviolet light and caffeine: The influence of different distributions of photolesions. Mutat. Res. 163: 33 - 40.


T. Cremer, C. Cremer (1985): Chromosomenspezifische DNA-Bibliotheken in der Humangenetik (Chromosome specific DNA-Libraries in Human Genetics). In: Molekular- und Zellbiologie [Herausgeber: N. Blin, M.F. Trendelenburg, E. R. Schmidt]. Springer-Verlag, Berlin-Heidelberg-New York.

First concept how to use chromosome specific DNA libraries in molecular cytogenetics.


G. A. Rappold, T. Cremer, C. Cremer, W. Back, J. Bogenberger, H.J. Cooke (1984): Chromosome assignment of two cloned DNA probes hybridizing predominantly to human sex chromosomes. Hum. Genet. 65: 257 - 261.


C. Cremer, G. Rappold, J.W. Gray, C.R. Müller, H.H. Ropers (1984): Preparative dual beam sorting of the human Y chromosome and in situ hybridization of cloned DNA probes. Cytometry 5: 572 - 579.

First detailed report on the establishment of an effective DNA library of a specific human chromosome to study nuclear architecture by chromosome painting


T. Cremer, H. Baumann, K. Nakanishi, C. Cremer (1984): Correlation between interphase and metaphase chromosome arrangements as studied by laser-uv-microbeam experiments. In: Chromosomes Today 8: 203 - 212.


M. Raith, T. Cremer, C. Cremer, G. Speith (1984): Sister chromatid exchange (SCE) induced by laser-uv-microirradiation: Correlation between the distribution of photolesions and the distribution of SCEs. In: Sister Chromatid Exchanges (Herausgeber: R.R. Tice, A. Hollaender). Plenum Publishing Corporation, New York, pp. 181 – 197.


C. Cremer, T. Cremer, L. Hens, H. Baumann, J.J. Cornelis, K. Nakanishi (1983): UV-microirradiation of the Chinese hamster cell nucleus and caffeine posttreatment: immunochemical localization of DNA photolesions in cells with partial and generalized chromosome shattering. Mutat. Res. 107: 465 - 475.


L. Hens, H. Baumann, T. Cremer, A. Sutter, J.J. Cornelis, C. Cremer (1983): Immunocytochemical localization of chromatin regions uv-microirradiated in S phase or anaphase. Exp. Cell Res. 149: 257 - 269.


T. Cremer, C. Cremer, H. Baumann, E.-K. Luedtke, K. Sperling, V. Teuber, C. Zorn (1982): Rabl's model of the interphase chromosome arrangement tested in Chinese hamster cells by premature chromosome condensation and laser-uv-microbeam experiments. Hum. Genet. 60: 46 - 56.


T. Cremer, S.P. Peterson, C. Cremer, M.W. Berns (1981): Microirradiation of Chinese hamster cells at wavelength 365 nm: Effects of psoralen and caffeine. Radiat. Res. 85: 529 - 543.


C. Cremer, T. Cremer, G. Jabbur (1981): Laser-uv-microirradiation of Chinese hamster cells: The influence of the distribution of photolesions on unscheduled DNA synthesis. Photochem. Photobiol. 33: 925 - 928.


C. Cremer, T. Cremer, C. Zorn, J. Zimmer (1981): Induction of chromosome shattering by ultraviolet light and caffeine: Comparison of whole cell and partial cell irradiation. Mutat. Res. 84: 331 - 348.


C. Cremer, T. Cremer, M. Fukuda, K. Nakanishi (1980): Detection of Laser-uv-microirradiation induced DNA photolesions by immunofluorescent staining. Hum. Genet. 54: 107 - 110.


T. Cremer, C. Cremer, J. Zimmer, C. Zorn (1980): UV-microirradiation of Chinese hamster cells and posttreatment with caffeine: Indication for clastogenic effects remote from the irradiation site. In: DNA Repair and Late Effects (H. Altmann, E. Riklis, H. Slor, Eds.) pp. 53 - 62. Nuclear Research Center, Negev, Israel.


C. Zorn, C. Cremer, T. Cremer, J. Zimmer (1979): Unscheduled DNA synthesis after partial uv irradiation of the cell nucleus. Distribution in interphase and metaphase. Exp. Cell Res. 124: 111 - 119.

First direct evidence for the existence of chromosome territories in the nucleus of live mammalian cells.


C. Zorn, T. Cremer, C. Cremer, J. Zimmer (1976): Laser-uv-micro-irradiation of interphase nuclei and posttreatment with caffeine: A new approach to establish the arrangement of interphase chromosomes. Hum. Genet. 35: 83 – 89.

First report to probe basic principles of nuclear organization by a focused laser beam.