Research articles
Hu, B., Lelek, S., Spanjaard, B., El-Sammak, H., Simoes, M., Mintcheva, J., Aliee, H., Schäfer, R., Meyer, A.M., Theis, F., Stainier, D.Y.R., Panáková, D., Junker, J.P. Origin and function of activated fibroblast states during zebrafish heart regeneration. Nat Genet doi:10.1038/s41588-022-01129-5, 2022.
Boogerd, C.J., Lacraz, G.P.A, Vértesy, A., van Kampen, S.J., Perini, I., de Ruiter, H., Versteeg, D., Brodehl, A., van der Kraak, P., Giacca, M.,de Jonge, N., Junker, J.P., van Oudenaarden, A., Vink, A., van Rooij, E. Spatial transcriptomics unveils ZBTB11 as a regulator of cardiomyocyte degeneration in arrhythmogenic cardiomyopathy. Cardiovasc Res doi:10.1093/cvr/cvac072, 2022.
McGarvey, A.C., Kopp, W., Vučićević, D., Kempfer, R., Mattonet, K., Hirsekorn, A., Bilić, I., Trinks, A., Merks, A.M., Panáková, D., Pombo, A., Akalin, A., Junker, J.P., Stainier, D.Y.R., Garfield, D., Ohler, U., Lacadie, S.A. Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in wildtype and cloche/npas4l mutant zebrafish embryos. Cell Genomics 2(1): 100083, 2022.
Singh, S.P., Chawla, P., Hnatiuk, A., Kamel, M., Silva, L.D., Spanjaard, B., Eski, S.E., Janjuha, S., Olivares-Chauvet, P., Kayisoglu, O., Rost, F., Bläsche, J., Kränkel, A., Petzold, A., Kurth, T., Reinhardt, S., Junker, J.P., Ninov, N.. A single-cell atlas of de novo β-cell regeneration reveals the contribution of hybrid β/δ-cells to diabetes recovery in zebrafish. Development 149, dev199853, 2022.
Holler, K., Neuschulz, A., Drewe-Boß, P., Mintcheva, J., Spanjaard, B., Arsiè, R., Ohler, U., Landthaler, M., Junker, J.P. Spatio-temporal mRNA tracking in the early zebrafish embryo. Nat Commun 12: 3358, 2021.
Buchumenski, I., Holler, K., Appelbaum, L., Eisenberg, E., Junker, J.P., Levanon, E.Y. Systematic identification of A-to-I RNA editing in zebrafish development and adult organs. Nucleic Acids Res 49(8): 4325-4337, 2021.
Moreno-Ayala, R., Olivares-Chauvet, P., Schäfer, R., Junker, J.P. Variability of an early developmental cell population underlies stochastic laterality defects. Cell Rep 34(2): 108606, 2021.
Schwabe, D., Formichetti, S., Junker, J.P., Falcke, M., Rajewsky, N. The transcriptome dynamics of single cells during the cell cycle. Mol Syst Biol 16(11): e9946, 2020.
Yvernogeau, L., Klaus, A., Maas, J., Morin-Poulard, I., Weijts, B., Schulte-Merker, S., Berezikov, E., Junker, J.P., Robin, C. Multispecies RNA tomography reveals regulators of hematopoietic stem cell birth in the embryonic aorta. Blood 136(7): 831-844, 2020.
Ebbing, A., Vértesy, Á., Betist, M.C., Spanjaard, B., Junker, J.P., Berezikov, E., van Oudenaarden, A., Korswagen, H.C. (2018). Spatial transcriptomics of C. elegans males and hermaphrodites identifies sex-specific differences in gene expression patterns. Dev Cell 47, 801-813.
Spanjaard, B., Hu, B., Mitic, N., Olivares-Chauvet, P., Janjuha, S., Ninov, N., Junker, J.P. (2018). Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars. Nat Biotechnol 36, 469-473.
Adolphe, C., Junker, J.P., Lyubimova, A., van Oudenaarden, A., Wainwright, B. (2017). Patched receptors sense, interpret and establish an epidermal Hedgehog signalling gradient. J Invest Dermatol 137, 179-186.
Lacraz, G.P.A., Junker, J.P., Gladka, M.M., Molenaar, B., Scholman, K.T., Vigil-Garcia, M., Versteeg, D., de Ruiter, H., Vermunt, M.W., Creyghton, M.P., Huibers, M.M.H., de Jonge, N., van Oudenaarden, A., van Rooij, E. (2017). Tomo-seq identifies SOX9 as a key regulator of cardiac fibrosis during ischemic injury. Circulation 136, 1396-1409.
Wu, C.C., Kruse, F., Vasudevarao, M.D., Junker, J.P., Zebrowski, D.C., Fischer, K., Noel, E.S., Gruen, D., Berezikov, E., Engel, F.B., van Oudenaarden, A., Weidinger, G., Bakkers, J. (2016). Spatially resolved genome-wide transcriptional profiling identifies BMP signaling as essential regulator of zebrafish cardiomyocyte regeneration. Dev Cell 36, 36-49.
Hu, Y.C., Nicholls, P.K., Soh, Y.Q.S., Daniele, J.R., Junker, J.P., van Oudenaarden, A., Page, D.C. (2015). Licensing of primordial germ cells for gametogenesis depends on genital ridge signaling. PLoS Genet 11, e1005019.
Schuijers, J., Junker, J.P., Mokry, M., Hatzis, P., Koo, B.K., Sasselli, V., van der Flier, L.G., Cuppen, E., van Oudenaarden, A., Clevers, H. (2015). Ascl2 acts as an R-spondin/Wnt- responsive switch to control stemness in intestinal crypts. Cell Stem Cell 16, 158-170.
Soh, Y.Q.S., Junker, J.P., Gill, M.E., Mueller, J.L., van Oudenaarden, A., Page, D.C. (2015). A gene regulatory program for meiotic prophase in the fetal ovary. PLoS Genet 11, (9): e1005531.
Welling, M., Chen, H.H., Muñoz, J., Musheev, M.U., Kester, L., Junker, J.P., Mischerikow, N., Arbab, M., Kuijk, E., Silberstein, L., Kharchenko, P.V., Geens, M., Niehrs, C., van de Velde, H., van Oudenaarden, A., Heck, A.J., Geijsen, N. (2015). DAZL regulates Tet1 translation in murine embryonic stem cells. EMBO Rep 16, 791-802.
Junker, J.P., Noël, E.S., Guryev, V., Peterson, K.A., Shah, G., Huisken, J., McMahon, A.P., Berezikov, E., Bakkers, J., van Oudenaarden, A. (2014). Genome-wide RNA tomography in the zebrafish embryo. Cell 159, 662-675.
Junker, J.P., Peterson, K.A., Nishi, Y., Mao, J., McMahon, A.P., van Oudenaarden, A. (2014). A predictive model of bifunctional transcription factor signaling during embryonic tissue patterning. Dev Cell 31, 448-460.
Lyubimova, A., Itzkovitz, S., Junker, J.P., Fan, Z.P., Wu, X., van Oudenaarden, A. (2013). Single-molecule mRNA detection and counting in mammalian tissue. Nat Protoc 8, 1743- 1758.
Peterson, K.A., Nishi, Y., Ma, W., Vedenko, A., Shokri, L., Zhang, X., McFarlane, M., Baizabal, J.M., Junker, J.P., van Oudenaarden, A., Mikkelsen, T., Bernstein, B.E., Bailey, T.L., Bulyk, M.L., Wong, W.H., McMahon, A.P. (2012). Neural-specific Sox2 input and differential Gli- binding affinity provide context and positional information in Shh-directed neural patterning. Genes Dev 26, 2802-2816.
Yu, J., Valerius, M.T., Duah, M., Staser, K., Hansard, J.K., Guo, J.J., McMahon, J., Vaughan, J., Faria, D., Georgas, K., Rumballe, B., Ren, Q., Krautzberger, A.M., Junker, J.P., Thiagarajan, R.D., Machanick, P., Gray, P.A., van Oudenaarden, A., Rowitch, D.H., Stiles, C.D., Ma, Q., Grimmond, S.M., Bailey, T.L., Little, M.H., McMahon, A.P. (2012). Identification of molecular compartments and genetic circuitry in the developing mammalian kidney. Development 139, 1863-1873.
Junker, J.P., Rief, M. (2010). Evidence for a broad transition-state ensemble in calmodulin folding from single-molecule force spectroscopy. Angew Chem Int Ed 49, 3306-3309.
Junker, J.P., Rief, M. (2009). Single-molecule force spectroscopy distinguishes target binding modes of calmodulin. Proc Natl Acad Sci USA 106(34), 14361-14366.
Junker, J.P., Ziegler, F., Rief, M. (2009). Ligand-dependent equilibrium fluctuations of single calmodulin molecules. Science 323(5914), 633-637.
Dietz, H., Bertz, M., Schlierf, M., Berkemeier, F., Bornschloegl, T., Junker, J.P., Rief, M. (2006). Cysteine engineering of polyproteins for single-molecule force spectroscopy. Nat Protoc 1(1), 80-84.
Junker, J.P., Hell, K., Schlierf, M., Neupert, W., Rief, M. (2005). Influence of substrate binding on the mechanical stability of mouse dihydrofolate reductase. Biophys J 89(5), L46-L48.
Reviews, Book Chapters
Hu, B., Junker, J.P. (2021). Mit Einzelzell-Genomik die Entscheidungen von Zellen verfolgen. Biospektrum 27, 25–27.
Moreno-Ayala R, Junker J.P. (2021). Single-cell genomics to study developmental cell fate decisions in zebrafish. Brief Funct Genomics, elab018.
Olivares-Chauvet, P., Junker, J.P. Inclusion of temporal information in single cell transcriptomics. Int J Biochem Cell Biol 122: 105745, 2020.
Holler, K., Junker, J.P. (2019). RNA tomography for spatially resolved transcriptomics (Tomo- seq). Methods Mol Biol 1920, 129-141.
Spanjaard, B., Junker, J.P. (2017). Methods for lineage tracing on the organism-wide level. Curr Opin Cell Biol 49, 16-21.
Kruse, F., Junker, J.P., van Oudenaarden, A., Bakkers, J. (2016). Tomo-seq: A method to obtain genome-wide expression data with spatial resolution. Methods Cell Biol 135, 299-307.
Junker, J.P., van Oudenaarden, A. (2014). Every cell is special: genome-wide studies add a new dimension to single-cell biology. Cell 157, 8-11.
Editorials
Rajewsky, N., Almouzni, G., Gorski, S.A. et al. LifeTime and improving European healthcare through cell-based interceptive medicine. Nature 587, 377–386 (2020). https://doi.org/10.1038/s41586-020-2715-9
Junker, J.P. (2019). Detouring the roadblocks in gene expression. Nat Rev Mol Cell Biol 20, 197.
Junker, J.P., van Oudenaarden, A. (2015). Single-cell transcriptomics enters the age of mass production. Mol Cell 58, 563-564.
Junker, J.P., van Oudenaarden, A. (2012). When noisy neighbors are a blessing: analysis of gene expression noise identifies coregulated genes. Mol Cell 45, 437-438.
Rief, M., Junker, J.P., Schlierf, M, Hell, K., Neupert, W. (2006). Response to the Comment by Ainavarapu et al. Biophysical Journal 91 (5), 2011-2012.
Junker Lab Berlin 