Publications
Peer-reviewed original research articles:
(for an up-to-date list, see my profile on google scholar)
Publications before 2020:
H. Schneckenburger, V. Richter, M. Gelleri, S. Ritz, R. Vaz Pandolfo, F. Schock, J. v. Hase, U. Birk, C. Cremer: "High-resolution deep view microscopy of cells and tissues", Quantum Electronics, doi:10.1070/QEL17204 (2020) [pdf]
U. Birk: "Super-Resolution Microscopy of Chromatin", Genes, doi:10.3390/genes10070493 (2019) [pdf]
U. Birk, Ph. Roebrock: "User-position aware adaptive display of 3D data without additional stereoscopic hardware" SPIE Digital Library, Proc. SPIE 11041, Machine Vision Applications, doi:10.1117/12.2522678 (2019) [pdf]
J. Neumann, K. Ziegler, M. Gelléri, J. Fröhlich-Nowoisky, F. Liu, I. Bellinghausen, D. Schuppan, U. Birk, U. Pöschl, C. Cremer, K. Lucas: "Nanoscale distribution of TLR4 on primary human macrophages stimulated with LPS and ATI." Nanoscale, doi:10.1039/c9nr00943d (2019) [pdf]
C. Cremer, A. Szczurek, H. Strickfaden, U. Birk, M. Cremer, T. Cremer: "Der Zellkern–eine Stadt in der Zelle, Teil 2: Chromatin‐Nanoarchitektur und Genregulation." Biologie in unserer Zeit, doi:10.1002/biuz.201810640 (2018) [pdf]
A. Szczurek, U. Birk, H. Knecht, J. Dobrucki, C. Cremer: "Super-resolution binding activated localization microscopy through reversible change of DNA conformation." doi:10.1080/19491034.2017.1419846 (2018) [pdf]
U. Birk, J. v. Hase, C. Cremer: "Super-resolution microscopy with very large working distance by means of distributed aperture illumination." Sci.Rep., doi:10.1038/s41598-017-03743-4 (2017) [pdf]
A.T. Szczurek, L. Klewes, J. Xing, A. Gourram, U. Birk, H. Knecht, J.W. Dobrucki, S. Mai, C. Cremer: "Imaging chromatin nanostructure with binding-activated localisation microscopy based on DNA structure fluctuations." Nucleic Acids Research, doi:10.1093/nar/gkw1301 (2017) [pdf]
A.T. Szczurek, J. Xing, U. Birk, C. Cremer: "Single Molecule Localization Microscopy of Mammalian Cell Nuclei on the Nanoscale." Front. Genet. 4:11, doi:10.3389/fgene.2016.00114 (2016). [pdf]
C. Cremer, U. Birk: "Perspectives in Super-resolved Fluorescence Microscopy: What comes next?" Front. Phys. 4:11, doi:10.3389/fphy.2016.00011 (2016). [pdf]
I. Kirmes, A. Szczurek, K. Prakash, I. Charapitsa, C. Heiser, M. Musheev, F. Schock, K. Fornalczyk, D. Ma, U. Birk, C. Cremer, G. Reid: "A transient ischemic environment induces reversible compaction of chromatin." Genome Biology doi:10.1186/s13059-015-0802-2 (2015). [biorxiv pdf]
K. Prakash, D. Fournier, S. Redl, G. Best, M. Borsos, V. Tiwari, K. Tachibana-Konwalski, R. Ketting, S. Parekh, C. Cremer, U. Birk: "Super-resolution imaging reveals structurally distinct periodic patterns of chromatin along pachytene chromosomes." PNAS (2015). [biorxiv pdf]
S. Zhu, D. Dong, U.J. Birk, M. Rieckher, N. Tavernarakis, X. Qu, J. Liang, J. Tian, J. Ripoll: "Automated motion correction for in vivo optical projection tomography." IEEE Trans Med Imaging 31(7): 1358-71, doi:10.1109/TMI.2012.2188836 (2012), PMID 22374352. [pdf]
M. Rieckher, U. Birk (co-first author), H. Meyer, J. Ripoll, N. Tavernarakis: "Microscopic optical projection tomography in vivo." PLoS ONE 6(4)e18963 (2011). [pdf]
U.J. Birk, M. Rieckher, N. Konstantinides, A. Darrell, A. Sarasa-Renedo, H. Meyer, N. Tavernarakis, J. Ripoll: "Correction for specimen movement and rotation errors for in-vivo Optical Projection Tomography." J Biomed Opt Expr 1(1): 87-96, doi:10.1364/BOE.1.000087 (2010). [pdf]
A. Sarasa-Renedo, R. Favicchio, U. Birk, G. Zacharakis, C. Mamalaki, J. Ripoll: "Source intensity profile in noncontact optical tomography." Opt Lett 35: 34-36, doi:10.1364/OL.35.000034 (2010). [pdf]
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: "Measurement of replication structures at the nanometer scale using super-resolution light microscopy." Nucleic Acids Research doi:10.1093/nar/gkp901: 1-11 (2009). [pdf]
J. Reymann, D. Baddeley, M. Gunkel, P. Lemmer, W. Stadter, T. Jegou, K. Rippe, C. Cremer, U. Birk: "High-precision Structural Analysis of Subnuclear Complexes in Fixed and Live Cells via Spatially Modulated Illumination (SMI) Microscopy." Chrom Res 16: 367-382, doi:10.1007/s10577-008-1238-2 (2008). [pdf]
D. Baddeley, C. Batram, Y. Weiland, C. Cremer, U. Birk: "Nanostructure Analysis Using Spatially Modulated Illumination Microscopy." Nat. Protocols 2: 2640-2646, doi:10.1038/nprot.2007.399 (2007). [pdf]
H. Mathée, D. Baddeley, C. Wotzlaw, J. Fandrey, C. Cremer, U. Birk: "Nanostructure of Specific Chromatin Regions and Nuclear Complexes." Histochem Cell Biol 125(1-2): 75-82, doi:10.1007/s00418-005-0096-7 (2006). [pdf]
S. Martin, A. V. Failla, U. Spöri (U. Birk), C. Cremer, A. Pombo: "Measuring the Size of Biological Nanostructures with Spatially Modulated Illumination Microscopy." Mol Biol Cell 15(5): 2449-2455, doi:10.1091/mbc.e04-01-0045 (2004). [pdf]
Monographs:
Editorship:
Chapters in books:
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 4, vol. 1 (A. Méndez-Vilas & J. Díaz, eds.), 688-695 (FORMATEX, Badajoz, 2010). [pdf]
U.J. Birk, I. Upmann, D. Toomre, C. Wagner, C. Cremer: "Size Estimation of Protein Clusters in the Nanometer Range by Using Spatially Modulated Illumination Microscopy." In: Modern Research and Educational Topics in Microscopy 1 (A. Méndez-Vilas & J. Díaz, eds.), 272-279 (FORMATEX, Badajoz, 2007). [pdf]
Other:
Conference proceedings:
Additionally, I have published a number of conference papers. Below is a short selection:
U. Birk, Ph. Roebrock: "User-position aware adaptive display of 3D data without additional stereoscopic hardware." Proceedings of SPIE, doi:10.1117/12.2522678 (2019) [pdf]
U. Birk: "Benutzerpositionsabhängige adaptive Anzeige von 3D-Daten ohne zusätzliche stereoskopische Hardware." DGaO Proceedins, ISSN: 1614-8436 - urn:nbn:de:0287-2018-P029-9 (2018) [pdf]
S. Fenz, H. Mathée, G. Kreth, D. Baddeley, Y. Weiland, J. Schwarz-Finsterle, C. Cremer, U. J. Birk: "Two-color intranuclear distance measurements of gene regions in human lymphocytes." Proc. SPIE 6630; doi:10.1117/12.727506 (2007). [pdf]
U. J. Birk, D. Baddeley, C. Cremer: "Local protein/gene density measurements using SMI microscopy with interferometric illumination: Measurement of nuclear protein concentration." Proc. SPIE 6188; doi:10.1117/12.668023 (2006). [pdf]