Browse by Research Team

Article

Mapping lineage-traced cells across time points with moslin.
Lange, M., Piran, Z., Klein, M., Spanjaard, B., Klein, D., Junker, J.P., Theis, F.J. and Nitzan, M.
Genome Biology 25 (1): 277. 21 October 2024

In situ Patch-seq analysis of microglia reveals a lack of stress genes as found in FACS-isolated microglia.
Bakina, O., Conrad, T., Mitic, N., Vidal, R.O., Obrusnik, T., Sai, S., Nolte, C., Semtner, M. and Kettenmann, H.
PLoS ONE 19 (7): e0302376. 11 July 2024

Antigen presentation plays positive roles in the regenerative response to cardiac injury in zebrafish.
Cardeira-da-Silva, J., Wang, Q., Sagvekar, P., Mintcheva, J., Latting, S., Günther, S., Ramadass, R., Yekelchyk, M., Preussner, J., Looso, M., Junker, J.P. and Stainier, D.Y.R.
Nature Communications 15 (1): 3637. 29 April 2024

Dissecting the spatiotemporal diversity of adult neural stem cells.
Mitic, N., Neuschulz, A., Spanjaard, B., Schneider, J., Fresmann, N., Novoselc, K.T., Strunk, T., Münster, L., Olivares-Chauvet, P., Ninkovic, J. and Junker, J.P.
Molecular Systems Biology 20 (4): 321-337. 2 April 2024

Inference of differentiation trajectories by transfer learning across biological processes.
Jumde, G., Spanjaard, B. and Junker, J.P.
Cell Systems 15 (1): 75-82.e5. 17 January 2024

Transcription factor induction of vascular blood stem cell niches in vivo.
Hagedorn, E.J., Perlin, J.R., Freeman, R.J., Wattrus, S.J., Han, T., Mao, C., Kim, J.W., Fernández-Maestre, I., Daily, M.L., D'Amato, C., Fairchild, M.J., Riquelme, R., Li, B., Ragoonanan, D.A.V.E., Enkhbayar, K., Henault, E.L., Wang, H.G., Redfield, S.E., Collins, S.H., Lichtig, A., Yang, S., Zhou, Y., Kunar, B., Gomez-Salinero, J.M., Dinh, T.T., Pan, J., Holler, K., Feldman, H.A., Butcher, E.C., van Oudenaarden, A., Rafii, S., Junker, J.P. and Zon, L.I.
Developmental Cell 58 (12): 1037-1051. 19 June 2023

A single-cell RNA labeling strategy for measuring stress response upon tissue dissociation.
Neuschulz, A., Bakina, O., Badillo Lisakowski, V., Olivares-Chauvet, P., Conrad, T., Gotthardt, M., Kettenmann, H. and Junker, J.P.
Molecular Systems Biology 19 (2): e11147. 10 February 2023

Spatial transcriptomics unveils ZBTB11 as a regulator of cardiomyocyte degeneration in arrhythmogenic cardiomyopathy.
Boogerd, C.J., Lacraz, G.P.A., Vértesy, Á., 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. and van Rooij, E.
Cardiovascular Research 119 (2): 477-491. February 2023

MDC1 maintains active elongation complexes of RNA polymerase II.
Pappas, G., Munk, S.H.N., Watanabe, K., Thomas, Q., Gál, Z., Gram, H.H., Lee, M.H., Gómez-Cabello, D., Kanellis, D.C., Olivares-Chauvet, P., Larsen, D.H., Gregersen, L.H., Maya-Mendoza, A., Galanos, P. and Bartek, J.
Cell Reports 42 (1): 111979. 31 January 2023

Long-term imaging reveals behavioral plasticity during C. elegans dauer exit.
Preusser, F., Neuschulz, A., Junker, J.P., Rajewsky, N. and Preibisch, S.
BMC Biology 20 (1): 277. 13 December 2022

Cluster-independent marker feature identification from single-cell omics data using SEMITONES.
Vlot, A.H.C., Maghsudi, S. and Ohler, U.
Nucleic Acids Research 50 (18): e107. 14 October 2022

Origin and function of activated fibroblast states during zebrafish heart regeneration.
Hu, B., Lelek, S., Spanjaard, B., El-Sammak, H., Simões, M.G., Mintcheva, J., Aliee, H., Schäfer, R., Meyer, A.M., Theis, F., Stainier, D.Y.R., Panáková, D. and Junker, J.P.
Nature Genetics 54 (8): 1227-1237. August 2022

Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos.
McGarvey, A.C., Kopp, W., Vučićević, D., Mattonet, K., Kempfer, R., Hirsekorn, A., Bilić, I., Gil, M., Trinks, A., Merks, A.M., Panáková, D., Pombo, A., Akalin, A., Junker, J.P., Stainier, D.Y.R., Garfield, D., Ohler, U. and Lacadie, S.A.
Cell Genomics 2 (1): 100083. 13 January 2022

A single-cell atlas of de novo β-cell regeneration reveals the contribution of hybrid β/δ-cells to diabetes recovery in zebrafish.
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. and Ninov, N.
Development 149 (2): dev199853. January 2022

Single cell biology - a Keystone Symposia report.
Cable, J., Elowitz, M.B., Domingos, A.I., Habib, N., Itzkovitz, S., Hamidzada, H., Balzer, M.S., Yanai, I., Liberali, P., Whited, J., Streets, A., Cai, L., Stergachis, A.B., Hong, C.K.Y., Keren, L., Guilliams, M., Alon, U., Shalek, A.K., Hamel, R., Pfau, S.J., Raj, A., Quake, S.R., Zhang, N.R., Fan, J., Trapnell, C., Wang, B., Greenwald, N.F., Vento-Tormo, R., Santos, S.D.M., Spencer, S.L., Garcia, H.G., Arekatla, G., Gaiti, F., Arbel-Goren, R., Rulands, S., Junker, J.P., Klein, A.M., Morris, S.A., Murray, J.I., Galloway, K.E., Ratz, M. and Romeike, M.
Annals of the New York Academy of Sciences 1506 (1): 74-97. December 2021

Spatio-temporal mRNA tracking in the early zebrafish embryo.
Holler, K., Neuschulz, A., Drewe-Boß, P., Mintcheva, J., Spanjaard, B., Arsiè, R., Ohler, U., Landthaler, M. and Junker, J.P.
Nature Communications 12 : 3358. 7 June 2021

Systematic identification of A-to-I RNA editing in zebrafish development and adult organs.
Buchumenski, I., Holler, K., Appelbaum, L., Eisenberg, E., Junker, J.P. and Levanon, E.Y.
Nucleic Acids Research 49 (8): 4325-4337. 7 May 2021

Variability of an early developmental cell population underlies stochastic laterality defects.
Moreno-Ayala, R., Olivares-Chauvet, P., Schäfer, R. and Junker, J.P.
Cell Reports 34 (2): 108606. 12 January 2021

The transcriptome dynamics of single cells during the cell cycle.
Schwabe, D., Formichetti, S., Junker, J.P., Falcke, M. and Rajewsky, N.
Molecular Systems Biology 16 (11): e9946. 1 November 2020

GPSeq reveals the radial organization of chromatin in the cell nucleus.
Girelli, G., Custodio, J., Kallas, T., Agostini, F., Wernersson, E., Spanjaard, B., Mota, A., Kolbeinsdottir, S., Gelali, E., Crosetto, N. and Bienko, M.
Nature Biotechnology 38 (10): 1184-1193. October 2020

Multispecies RNA tomography reveals regulators of hematopoietic stem cell birth in the embryonic aorta.
Yvernogeau, L., Klaus, A., Maas, J., Morin-Poulard, I., Weijts, B., Schulte-Merker, S., Berezikov, E., Junker, J.P. and Robin, C.
Blood 136 (7): 831-844. 13 August 2020

Inclusion of temporal information in single cell transcriptomics.
Olivares-Chauvet, P. and Junker, J.P.
International Journal of Biochemistry and Cell Biology 122 : 105745. May 2020

RNA tomography for spatially resolved transcriptomics (Tomo-seq).
Holler, K. and Junker, J.P.
Methods in Molecular Biology 1920 : 129-141. 2019

Spatial transcriptomics of C. elegans males and hermaphrodites identifies sex-specific differences in gene expression patterns.
Ebbing, A., Vértesy, Á., Betist, M.C., Spanjaard, B., Junker, J.P., Berezikov, E., van Oudenaarden, A. and Korswagen, H.C.
Developmental Cell 47 (6): 801-813. 17 December 2018

Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars.
Spanjaard, B., Hu, B., Mitic, N., Olivares-Chauvet, P., Janjuha, S., Ninov, N. and Junker, J.P.
Nature Biotechnology 36 (5): 469-473. May 2018

Tomo-seq identifies SOX9 as a key regulator of cardiac fibrosis during ischemic injury.
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. and van Rooij, E.
Circulation 136 (15): 1396-1409. 10 October 2017

Patched receptors sense, interpret and establish an epidermal Hedgehog signalling gradient.
Adolphe, C., Junker, J.P., Lyubimova, A., van Oudenaarden, A. and Wainwright, B.
Journal of Investigative Dermatology 137 (1): 179-186. January 2017

Spatially resolved genome-wide transcriptional profiling identifies BMP signaling as essential regulator of zebrafish cardiomyocyte regeneration.
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. and Bakkers, J.
Developmental Cell 36 (1): 36-49. 11 January 2016

A gene regulatory program for meiotic prophase in the fetal ovary.
Soh, Y.Q.S., Junker, J.P., Gill, M.E., Mueller, J.L., van Oudenaarden, A. and Page, D.C.
PLoS Genetics 11 (9): e1005531. 17 September 2015

DAZL regulates Tet1 translation in murine embryonic stem cells.
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. and Geijsen, N.
EMBO Reports 16 (7): 791-802. July 2015

Licensing of primordial germ cells for gametogenesis depends on genital ridge signaling.
Hu, Y.C., Nicholls, P.K., Soh, Y.Q.S., Daniele, J.R., Junker, J.P., van Oudenaarden, A. and Page, D.C.
PLoS Genetics 11 (3): e1005019. 4 March 2015

Ascl2 acts as an R-spondin/Wnt-responsive switch to control stemness in intestinal crypts.
Schuijers, J., Junker, J.P., Mokry, M., Hatzis, P., Koo, B.K., Sasselli, V., van der Flier, L.G., Cuppen, E., van Oudenaarden, A. and Clevers, H.
Cell Stem Cell 16 (2): 158-170. 5 February 2015

A predictive model of bifunctional transcription factor signaling during embryonic tissue patterning.
Junker, J.P., Peterson, K.A., Nishi, Y., Mao, J., McMahon, A.P. and van Oudenaarden, A.
Developmental Cell 31 (4): 448-460. 24 November 2014

Genome-wide RNA tomography in the zebrafish embryo.
Junker, J.P., Noël, E.S., Guryev, V., Peterson, K.A., Shah, G., Huisken, J., McMahon, A.P., Berezikov, E., Bakkers, J. and van Oudenaarden, A.
Cell 159 (3): 662-675. 23 October 2014

Single-molecule mRNA detection and counting in mammalian tissue.
Lyubimova, A., Itzkovitz, S., Junker, J.P., Fan, Z.P., Wu, X. and van Oudenaarden, A.
Nature Protocols 8 (9): 1743-1758. September 2013

Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning.
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. and McMahon, A.P.
Genes & Development 26 (24): 2802-2816. 15 December 2012

Identification of molecular compartments and genetic circuitry in the developing mammalian kidney.
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. and McMahon, A.P.
Development 139 (10): 1863-1873. May 2012

Evidence for a broad transition-state ensemble in calmodulin folding from single-molecule force spectroscopy.
Junker, J.P. and Rief, M.
Angewandte Chemie International Edition 49 (19): 3306-3309. 26 April 2010

Single-molecule force spectroscopy distinguishes target binding modes of calmodulin.
Junker, J.P. and Rief, M.
Proceedings of the National Academy of Sciences of the United States of America 106 (34): 14361-14366. 25 August 2009

Ligand-dependent equilibrium fluctuations of single calmodulin molecules.
Junker, J.P., Ziegler, F. and Rief, M.
Science 323 (5914): 633-637. 30 January 2009

Cysteine engineering of polyproteins for single-molecule force spectroscopy.
Dietz, H., Bertz, M., Schlierf, M., Berkemeier, F., Bornschloegl, T., Junker, J.P. and Rief, M.
Nature Protocols 1 (1): 80-84. 2006

Influence of substrate binding on the mechanical stability of mouse dihydrofolate reductase.
Junker, J.P., Hell, K., Schlierf, M., Neupert, W. and Rief, M.
Biophysical Journal 89 (5): L46-L48. November 2005

Review

Single-cell genomics to study developmental cell fate decisions in zebrafish.
Moreno-Ayala, R. and Junker, J.P.
Briefings in Functional Genomics 20 (6): 420–426. November 2021

Mit Einzelzell-Genomik die Entscheidungen von Zellen verfolgen [Deciphering cell fate decisions using single cell genomics].
Hu, B. and Junker, J.P.
BIOspektrum 27 (1): 25-27. February 2021

Applying synergy metrics to oncology combination screening data: agreements, disagreements and pitfalls.
Vlot, A.H.C., Aniceto, N., Menden, M.P., Ulrich-Merzenich, G. and Bender, A.
Drug Discovery Today 24 (12): 2286-2298. December 2019

Methods for lineage tracing on the organism-wide level.
Spanjaard, B. and Junker, J.P.
Current Opinion in Cell Biology 49 : 16-21. December 2017

Tomo-seq: A method to obtain genome-wide expression data with spatial resolution.
Kruse, F., Junker, J.P., van Oudenaarden, A. and Bakkers, J.
Methods in Cell Biology 135 : 299-307. 2016

Every cell is special: genome-wide studies add a new dimension to single-cell biology.
Junker, J.P. and van Oudenaarden, A.
Cell 157 (1): 8-11. 27 March 2014

Letter

Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations.
van den Brink, S.C., Sage, F., Vertesy, A., Spanjaard, B., Peterson-Maduro, J., Baron, C.S., Robin, C. and van Oudenaarden, A.
Nature Methods 14 (10): 935-936. 29 September 2017

Editorial

Transient activated fibroblasts contribute to zebrafish heart regeneration.
Junker, J.P. and Panáková, D.
Nature Genetics 54 (8): 1076-1077. August 2022

Detouring the roadblocks in gene expression.
Junker, J.P.
Nature Reviews Molecular Cell Biology 20 (4): 197. April 2019

Single-cell transcriptomics enters the age of mass production.
Junker, J.P. and van Oudenaarden, A.
Molecular Cell 58 (4): 563-564. 21 May 2015

When noisy neighbors are a blessing: analysis of gene expression noise identifies coregulated genes.
Junker, J.P. and van Oudenaarden, A.
Molecular Cell 45 (4): 437-438. 24 February 2012

Preprint

Morphine alleviates pain after heart cryoinjury in zebrafish without impeding regeneration.
Lelek, S., Simões, M., Hu, B., Alameldeen, A.M.A., Czajkowski, M.T., Meyer, A.M., Ferrara, F., Junker, J.P. and Panáková, D.
bioRxiv : 2020.10.01.322560. 2 October 2020

Massively parallel clonal analysis using CRISPR/Cas9 induced genetic scars.
Junker, J.P., Spanjaard, B., Peterson-Maduro, J., Alemany, A., Hu, B., Florescu, M. and van Oudenaarden, A.
bioRxiv : 056499. 4 January 2017