Publications

	Dual spindle formation in zygotes keeps parental genomes apart in early mammalian embryos Judith Reichmann, Bianca Nijmeijer, M. Julius Hossain, Manuel Eguren, Isabell Schneider, Antonio Z. Politi, M. Julia Roberti, Lars Hufnagel, Takashi Hiiragi, Jan Ellenberg, doi: https://doi.org/10.1101/198275;
	Inverted light-sheet microscope for imaging mouse pre-implantation development Strnad P., Gunther S., Reichmann J.,et al. (2016). Inverted light-sheet microscope for imaging mouse pre-implantation development. Nature Methods 13, 139–142;
	Confocal multiview light-sheet microscopy de Medeiros, G. et al. Confocal multiview light-sheet microscopy. Nat. Commun. 6:8881 doi: 10.1038/ncomms9881 (2015).;
	Lattice light-sheet microscopy- Imaging molecules to embryos at high spatiotemporal resolution Chen, B.-C., Legant, W. R., Wang, K., Shao, L., Milkie, D. E., Davidson, M. W.…Betzig, E. (2014). Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution. Science, 346, 1257998;
	Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy Keller, P. J., Schmidt, A. D., Wittbrodt, J., & Stelzer, E. H. K. (2008). Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science, 322, 1065-1069;
	Optical Sectioning Deep Inside Live Embryos by Selective Plane Illumination Microscopy Huisken, J., Swoger, J., Del Bene, F., Wittbrodt, J., & Stelzer, E. H. K. (2004). Optical sectioning deep inside live embryos by selective plane illumination microscopy. Science, 305, 1007-1009;

Re-scan confocal microscopy: scanning twice for better resolution

De Luca G. M. R., Breedijk R. M. P., Brandt R., Zeelenberg C. H. C., de Jong B. E., Timmermans W., Azar L. N., Hoebe R., Stallinga S., Manders E. M. M., “Re-scan confocal microscopy: scanning twice for better resolution,” Biomed. Opt. Express 4, 2644–2656 (2013).10.1364/BOE.4.002644

Configurations of the Re-scan Confocal Microscope (RCM) for biomedical applications.

DE Luca G.M., Desclos E, Breedijk R.M., Dolz-Edo L, Smits G.J., Bielefeld P, Picavet L, Fitzsimons C.P., Hoebe R, Manders E.M. “Configurations of the Re-scan Confocal Microscope (RCM) for biomedical applications.” Journal of Microscopy. 2017 Mar 3.

	The Tetraodon nigroviridis reference transcriptome-developmental transition length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome Basu S, Hadzhiev Y, Petrosino G, Nepal C, Gehrig J, Armant O, Ferg M, Strahle U, Sanges R, Müller F. “The Tetraodon nigroviridis reference transcriptome: developmental transition, length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome.” Sci Rep. 2016; 6: 33210. Published online 2016 Sep 15. doi: 10.1038/srep33210;
	Two independent transcription initiation codes overlap on vertebrate core promoters Haberle V, Li N, Hadzhiev Y, Plessy C, Previti C, Nepal C, Gehrig J, Dong X, Akalin A, Suzuki AM, van Ijcken WF, Armant O, Ferg M, Strähle U, Carninci P, Müller F, Lenhard B. “Two independent transcription initiation codes overlap on vertebrate core promoters.” Nature. 2014 Feb 16. doi:10.1038/nature12974. [Epub ahead of print] PubMed PMID: 24531765.
	Genetic oscillations. A Doppler effect in embryonic pattern formation. Soroldoni D, Jörg DJ, Morelli LG, Richmond DL, Schindelin J, Jülicher F, Oates AC.”Genetic oscillations. A Doppler effect in embryonic pattern formation.” Science. 2014 Jul 11;345(6193):222-5. doi: 10.1126/science.1253089.
	Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis Nepal C, Hadzhiev Y, Previti C, Haberle V, Li N, Takahashi H, Suzuki AM, Sheng Y, Abdelhamid RF, Anand S, Gehrig J, Akalin A, Kockx CE, van der Sloot AA, van Ijcken WF, Armant O, Rastegar S, Watson C, Strähle U, Stupka E, Carninci P, Lenhard B, Müller F.”Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis.” Genome Res. 2013 Nov;23(11):1938-50. doi: 10.1101/gr.153692.112. Epub 2013 Sep 3. PMID: 24002785.

The Tetraodon nigroviridis reference transcriptome-developmental transition length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome

Basu S, Hadzhiev Y, Petrosino G, Nepal C, Gehrig J, Armant O, Ferg M, Strahle U, Sanges R, Müller F. “The Tetraodon nigroviridis reference transcriptome: developmental transition, length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome.” Sci Rep. 2016; 6: 33210. Published online 2016 Sep 15. doi: 10.1038/srep33210;

Two independent transcription initiation codes overlap on vertebrate core promoters

Haberle V, Li N, Hadzhiev Y, Plessy C, Previti C, Nepal C, Gehrig J, Dong X, Akalin A, Suzuki AM, van Ijcken WF, Armant O, Ferg M, Strähle U, Carninci P, Müller F, Lenhard B. “Two independent transcription initiation codes overlap on vertebrate core promoters.” Nature. 2014 Feb 16. doi:10.1038/nature12974. [Epub ahead of print] PubMed PMID: 24531765.

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

Nepal C, Hadzhiev Y, Previti C, Haberle V, Li N, Takahashi H, Suzuki AM, Sheng Y, Abdelhamid RF, Anand S, Gehrig J, Akalin A, Kockx CE, van der Sloot AA, van Ijcken WF, Armant O, Rastegar S, Watson C, Strähle U, Stupka E, Carninci P, Lenhard B, Müller F. “Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis.” Genome Res. 2013 Nov;23(11):1938-50. doi: 10.1101/gr.153692.112. Epub 2013 Sep 3. PMID: 24002785.

	Degradation of Methylammonium Lead Iodide Perovskite Structures through Light and Electron Beam Driven Ion Migration Yuan, Haifeng, et al. “Degradation of Methylammonium Lead Iodide Perovskite Structures through Light and Electron Beam Driven Ion Migration.” The Journal of Physical Chemistry Letters 7 (2016): 561-566.
	Correlated light and electron microscopy: ultrastructure lights up! de Boer, Pascal, Jacob P. Hoogenboom, and Ben NG Giepmans. “Correlated light and electron microscopy: ultrastructure lights up!” Nature methods 12.6 (2015): 503-513.
	Standard fluorescent proteins as dual-modality probes for correlative experiments in an integrated light and electron microscope Brama, Elisabeth, et al. “Standard fluorescent proteins as dual-modality probes for correlative experiments in an integrated light and electron microscope.” Journal of Chemical Biology 8.4 (2015): 179-188.
	Fixation-resistant photoactivatable fluorescent proteins for CLEM. Paez-Segala, Maria G., et al. “Fixation-resistant photoactivatable fluorescent proteins for CLEM.” Nature methods 12.3 (2015): 215-218.
	Integrated light and scanning electron microscopy of GFP-expressing cells Peddie, Christopher J., et al. “Integrated light and scanning electron microscopy of GFP-expressing cells.” Methods in cell biology 124 (2014): 363-389.
	Correlated cryogenic photoactivated localization microscopy and cryo-electron tomography. Chang, Yi-Wei, et al. “Correlated cryogenic photoactivated localization microscopy and cryo-electron tomography.” Nature methods 11.7 (2014): 737-739.
	Correlative photoactivated localization and scanning electron microscopy. Kopek, Benjamin G., et al. “Correlative photoactivated localization and scanning electron microscopy.” PLoS One 8.10 (2013): e77209.
	Fixation-resistant photoactivatable fluorescent proteins for CLEM. Paez-Segala, Maria G., et al. “Fixation-resistant photoactivatable fluorescent proteins for CLEM.” Nature methods 12.3 (2015): 215-218.