2026
Pre-existing chromatin accessibility primes δ-cells for injury-induced endocrine plasticity.
Gräßlin, Jo 
ORCID: https://orcid.org/0000-0003-0641-9913, Chawla, Prateek, Subramanian, Padmapriya, Rajendran, Anuradha, Walda, Emilie Ida Christine, Froschauer, Alexander, Ninov, Nikolay and Junker, Jan Philipp ORCID: https://orcid.org/0000-0002-2826-8290
bioRxiv
: 2026.05.24.727280.
27 May 2026
In vivo single-cell RNA metabolic labeling resolves early transcriptional responders in the regenerating zebrafish heart.
Mintcheva, Janita ORCID: https://orcid.org/0000-0003-0793-6277, Tseng, Tzu-Lun ORCID: https://orcid.org/0000-0003-1319-0141, Goumenaki, Pinelopi, Neuschulz, Anika ORCID: https://orcid.org/0000-0001-6163-3344, Senoussi, Anis ORCID: https://orcid.org/0000-0002-7066-8917, Lelek, Sara, Lim, Khai Lone ORCID: https://orcid.org/0000-0003-0295-330X, Ming, Zhitao, Schäfer, Ronny, Hnatiuk, Alisa, Ninov, Nikolay ORCID: https://orcid.org/0000-0003-3286-6100, Beisaw, Arica ORCID: https://orcid.org/0000-0002-6658-6978, McGrail, Maura ORCID: https://orcid.org/0000-0001-9308-6189, Ben Lai, Shih-Lei ORCID: https://orcid.org/0000-0002-1409-4701, Panáková, Daniela ORCID: https://orcid.org/0000-0002-8739-6225, Stainier, Didier Y. R. ORCID: https://orcid.org/0000-0002-0382-0026 and Junker, Jan Philipp ORCID: https://orcid.org/0000-0002-2826-8290
Nature Communications 17
(1): 4073.
5 May 2026
Molecular evolution of animal aging.
Nussey, Daniel H., d'Adda di Fagagna, Fabrizio, Bardin, Allison J. ORCID: https://orcid.org/0000-0002-0200-4465, Blau, Helen, Brunet, Anne, Bulavin, Dmitry V., Guo, Longhua, Hara, Eiji ORCID: https://orcid.org/0000-0001-7821-3960, Junker, Jan Philipp ORCID: https://orcid.org/0000-0002-2826-8290, Gorbunova, Vera ORCID: https://orcid.org/0000-0001-8979-0333, Mittelbrunn, Maria ORCID: https://orcid.org/0000-0003-3487-8762, Rera, Michael ORCID: https://orcid.org/0000-0002-6574-6511, Reznick, Jane, Seluanov, Andrei ORCID: https://orcid.org/0000-0003-3400-538X, Schumacher, Björn ORCID: https://orcid.org/0000-0001-6097-5238, Teeling, Emma C., Valenzano, Dario Riccardo ORCID: https://orcid.org/0000-0002-8761-8289, Ye, Jing, Yun, Maximina H. ORCID: https://orcid.org/0000-0001-9019-2453, Garinis, George A. ORCID: https://orcid.org/0000-0002-3200-5004 and Gilson, Eric ORCID: https://orcid.org/0000-0001-5738-6723
EMBO Journal 45
(7): 2095-2111.
1 April 2026
In vivo RNA metabolic labeling identifies the sentinel cells of the regenerating zebrafish heart [bulk_slamseq].
Mintcheva, J. ORCID: https://orcid.org/0000-0003-0793-6277, Tseng, T., Goumenaki, P., Neuschulz, A. ORCID: https://orcid.org/0000-0001-6163-3344, Senoussi, A. ORCID: https://orcid.org/0000-0002-7066-8917, Schäfer, R., Lelek, S., Panakova, D. ORCID: https://orcid.org/0000-0002-8739-6225, Stainier, D. and Junker, J. ORCID: https://orcid.org/0000-0002-2826-8290
[Dataset]
30 March 2026
In vivo RNA metabolic labeling identifies the sentinel cells of the regenerating zebrafish heart [scrna-seq].
Mintcheva, J. ORCID: https://orcid.org/0000-0003-0793-6277, Tseng, T., Goumenaki, P., Neuschulz, A. ORCID: https://orcid.org/0000-0001-6163-3344, Senoussi, A. ORCID: https://orcid.org/0000-0002-7066-8917, Schäfer, R., Lelek, S., Panakova, D. ORCID: https://orcid.org/0000-0002-8739-6225, Stainier, D. and Junker, J. ORCID: https://orcid.org/0000-0002-2826-8290
[Dataset]
30 March 2026
In vivo RNA metabolic labeling identifies the sentinel cells of the regenerating zebrafish heart [scslam-seq].
Mintcheva, J. ORCID: https://orcid.org/0000-0003-0793-6277, Tseng, T., Goumenaki, P., Neuschulz, A. ORCID: https://orcid.org/0000-0001-6163-3344, Senoussi, A. ORCID: https://orcid.org/0000-0002-7066-8917, Schäfer, R., Lelek, S., Panakova, D. ORCID: https://orcid.org/0000-0002-8739-6225, Stainier, D. and Junker, J. ORCID: https://orcid.org/0000-0002-2826-8290
[Dataset]
30 March 2026
Cell-autonomous control coupled with tissue context regulates the cessation of migration at the site of organ development.
Tarbashevich, Katsiaryna, Labbaf, Zahra, Ophaus, Moritz, Schick, Jan, Kühl, Lucas, Gross-Thebing, Sargon, Reichman-Fried, Michal, Hoffmann, Dennis, Stehling, Martin, Seggewiss, Jochen, Ruckert, Christian, Kroll, Johanna B. ORCID: https://orcid.org/0000-0003-4652-3598, Junker, Jan Philipp ORCID: https://orcid.org/0000-0002-2826-8290 and Raz, Erez ORCID: https://orcid.org/0000-0002-6347-3302
Development 153
(16): dev.205271.
20 February 2026
2025
Morphogenetic ovarian modules for oocyte production from germline stem cells.
Hart, Neta, Kroll, Johanna B. ORCID: https://orcid.org/0000-0003-4652-3598, Kumar, Vineet, Czukiewska, Sylwia M. ORCID: https://orcid.org/0000-0001-9151-9008, Bogoch, Yoel, Guler, Noga ORCID: https://orcid.org/0009-0004-8560-1995, Levy, Karine ORCID: https://orcid.org/0000-0003-0290-062X, Chuva de Sousa Lopes, Susana M., Junker, Jan Philipp ORCID: https://orcid.org/0000-0002-2826-8290 and Elkouby, Yaniv M. ORCID: https://orcid.org/0000-0002-9043-4106
Research Square
: rs-7325126/v1.
28 October 2025
Lineage origin and microenvironment shape neuroblastoma transcriptional state and plasticity.
Fresmann, Nora ORCID: https://orcid.org/0000-0002-9233-5101, Koeppke, Julia, Gauert, Anton ORCID: https://orcid.org/0000-0002-3013-5374, Senoussi, Anis ORCID: https://orcid.org/0000-0002-7066-8917, Olivares-Chauvet, Pedro ORCID: https://orcid.org/0009-0008-4684-255X, Schott, Marie ORCID: https://orcid.org/0009-0000-7393-2421, Hoefer, Lennart, Henssen, Anton G. ORCID: https://orcid.org/0000-0003-1534-778X, Rajewsky, Nikolaus ORCID: https://orcid.org/0000-0002-4785-4332, Spanjaard, Bastiaan ORCID: https://orcid.org/0000-0003-1309-8839, Hagemann, Anja I.H. ORCID: https://orcid.org/0000-0001-5491-4607 and Junker, Jan Philipp ORCID: https://orcid.org/0000-0002-2826-8290
bioRxiv
: 2025.10.13.682025.
14 October 2025
Oxidative phosphorylation is required for cardiomyocyte re-differentiation and long-term fish heart regeneration.
Lekkos, Konstantinos, Hu, Zhilian, Nguyen, Phong D., Honkoop, Hessel, Sengul, Esra, Alonaizan, Rita, Koth, Jana, Ying, Jun, Lemieux, Madeleine E., Kenward, Alisha, Keeley, Sean, Spanjaard, Bastiaan ORCID: https://orcid.org/0000-0003-1309-8839, Kennedy, Brett W.C., Sun, Xin, Banecki, Katherine, Potts, Helen G., Ruggiero, Gennaro, Montgomery, James, Panáková, Daniela ORCID: https://orcid.org/0000-0002-8739-6225, Junker, Jan Philipp ORCID: https://orcid.org/0000-0002-2826-8290, Heather, Lisa C., Wang, Xiaonan, Gonzalez-Rosa, Juan Manuel, Bakkers, Jeroen and Mommersteeg, Mathilda T.M.
Nature Cardiovascular Research 4
(10): 1363-1380.
October 2025
LINNAEUS: simultaneous single-cell lineage tracing and cell type identification.
Spanjaard, B. ORCID: https://orcid.org/0000-0003-1309-8839 and Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290
Methods in Molecular Biology 2886
: 243-263.
3 January 2025
2024
Mapping lineage-traced cells across time points with moslin.
Lange, M., Piran, Z., Klein, M., Spanjaard, B. ORCID: https://orcid.org/0000-0003-1309-8839, Klein, D., Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290, Theis, F.J. and Nitzan, M. ORCID: https://orcid.org/0000-0003-0074-9196
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. ORCID: https://orcid.org/0000-0002-3486-9906, Conrad, T. ORCID: https://orcid.org/0000-0001-5618-6295, Mitic, N. ORCID: https://orcid.org/0000-0003-0141-1293, Vidal, R.O. ORCID: https://orcid.org/0000-0003-4217-2014, Obrusnik, T., Sai, S. ORCID: https://orcid.org/0000-0001-6865-341X, Nolte, C. ORCID: https://orcid.org/0000-0001-5398-3440, Semtner, M. ORCID: https://orcid.org/0000-0001-9379-9023 and Kettenmann, H. ORCID: https://orcid.org/0000-0001-8208-0291
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. ORCID: https://orcid.org/0000-0003-3722-8810, Wang, Q., Sagvekar, P. ORCID: https://orcid.org/0000-0003-4420-3806, Mintcheva, J. ORCID: https://orcid.org/0000-0003-0793-6277, Latting, S., Günther, S. ORCID: https://orcid.org/0000-0002-5594-4549, Ramadass, R., Yekelchyk, M., Preussner, J., Looso, M., Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290 and Stainier, D.Y.R.
Nature Communications 15
(1): 3637.
29 April 2024
Dissecting the spatiotemporal diversity of adult neural stem cells.
Mitic, N. ORCID: https://orcid.org/0000-0003-0141-1293, Neuschulz, A. ORCID: https://orcid.org/0000-0001-6163-3344, Spanjaard, B. ORCID: https://orcid.org/0000-0003-1309-8839, Schneider, J., Fresmann, N. ORCID: https://orcid.org/0000-0002-9233-5101, Novoselc, K.T., Strunk, T. ORCID: https://orcid.org/0009-0001-9420-7429, Münster, L., Olivares-Chauvet, P., Ninkovic, J. ORCID: https://orcid.org/0000-0002-4381-0041 and Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290
Molecular Systems Biology 20
(4): 321-337.
2 April 2024
Inference of differentiation trajectories by transfer learning across biological processes.
Jumde, G., Spanjaard, B. ORCID: https://orcid.org/0000-0003-1309-8839 and Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290
Cell Systems 15
(1): 75-82.e5.
17 January 2024
2023
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. ORCID: https://orcid.org/0000-0002-5159-9223, Feldman, H.A., Butcher, E.C., van Oudenaarden, A., Rafii, S., Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290 and Zon, L.I. ORCID: https://orcid.org/0000-0003-0860-926X
Developmental Cell 58
(12): 1037-1051.
19 June 2023
A single-cell RNA labeling strategy for measuring stress response upon tissue dissociation.
Neuschulz, A. ORCID: https://orcid.org/0000-0001-6163-3344, Bakina, O. ORCID: https://orcid.org/0000-0002-3486-9906, Badillo Lisakowski, V. ORCID: https://orcid.org/0000-0001-5906-2589, Olivares-Chauvet, P., Conrad, T. ORCID: https://orcid.org/0000-0001-5618-6295, Gotthardt, M. ORCID: https://orcid.org/0000-0003-1788-3172, Kettenmann, H. ORCID: https://orcid.org/0000-0001-8208-0291 and Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290
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. ORCID: https://orcid.org/0000-0002-7119-5381, Lacraz, G.P.A. ORCID: https://orcid.org/0000-0002-0373-3256, Vértesy, Á. ORCID: https://orcid.org/0000-0001-6075-5702, van Kampen, S.J. ORCID: https://orcid.org/0000-0002-4146-8481, Perini, I., de Ruiter, H., Versteeg, D., Brodehl, A. ORCID: https://orcid.org/0000-0001-9202-2343, van der Kraak, P., Giacca, M. ORCID: https://orcid.org/0000-0003-2927-7225, de Jonge, N., Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290, van Oudenaarden, A. ORCID: https://orcid.org/0000-0002-9442-3551, Vink, A. ORCID: https://orcid.org/0000-0002-9371-8788 and van Rooij, E. ORCID: https://orcid.org/0000-0002-2026-9408
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. ORCID: https://orcid.org/0000-0002-1205-604X, Maya-Mendoza, A., Galanos, P. and Bartek, J.
Cell Reports 42
(1): 111979.
31 January 2023
2022
Long-term imaging reveals behavioral plasticity during C. elegans dauer exit.
Preusser, F. ORCID: https://orcid.org/0000-0001-8231-2195, Neuschulz, A. ORCID: https://orcid.org/0000-0001-6163-3344, Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 and Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X
BMC Biology 20
(1): 277.
13 December 2022
Cluster-independent marker feature identification from single-cell omics data using SEMITONES.
Vlot, A.H.C. ORCID: https://orcid.org/0000-0001-9538-987X, Maghsudi, S. and Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116
Nucleic Acids Research 50
(18): e107.
14 October 2022
Cellular drivers of injury response and regeneration in the adult zebrafish heart.
Hu, B. ORCID: https://orcid.org/0000-0003-0751-885X, Lelek, S., Spanjaard, B. ORCID: https://orcid.org/0000-0003-1309-8839, Simões, M.G. ORCID: https://orcid.org/0000-0002-7340-9128, Aliee, H., Schäfer, R., Theis, F., Panáková, D. ORCID: https://orcid.org/0000-0002-8739-6225 and Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290
[Dataset]
16 August 2022
Morphine alleviates pain after heart cryonjury in zebrafish without impeding regeneration.
Lelek, S., Guedes Simões, M., Hu, B. ORCID: https://orcid.org/0000-0003-0751-885X, Alameldeen, A.M., Czajkowski, M.T. ORCID: https://orcid.org/0000-0002-0122-1943, Meyer, A.M. ORCID: https://orcid.org/0000-0002-4665-2077, Ferrara, F., Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290 and Pánákova, D. ORCID: https://orcid.org/0000-0002-8739-6225
[Dataset]
16 August 2022
Origin and function of activated fibroblast states during zebrafish heart regeneration.
Hu, B. ORCID: https://orcid.org/0000-0003-0751-885X, Lelek, S., Spanjaard, B. ORCID: https://orcid.org/0000-0003-1309-8839, El-Sammak, H. ORCID: https://orcid.org/0000-0002-0178-1457, Simões, M.G. ORCID: https://orcid.org/0000-0002-7340-9128, Mintcheva, J. ORCID: https://orcid.org/0000-0003-0793-6277, Aliee, H., Schäfer, R., Meyer, A.M. ORCID: https://orcid.org/0000-0002-4665-2077, Theis, F. ORCID: https://orcid.org/0000-0002-2419-1943, Stainier, D.Y.R. ORCID: https://orcid.org/0000-0002-0382-0026, Panáková, D. ORCID: https://orcid.org/0000-0002-8739-6225 and Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290
Nature Genetics 54
(8): 1227-1237.
August 2022
Transient activated fibroblasts contribute to zebrafish heart regeneration.
Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290 and Panáková, D. ORCID: https://orcid.org/0000-0002-8739-6225
Nature Genetics 54
(8): 1076-1077.
August 2022
Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos.
McGarvey, A.C. ORCID: https://orcid.org/0000-0003-3838-1139, Kopp, W. ORCID: https://orcid.org/0000-0003-0376-0032, Vučićević, D. ORCID: https://orcid.org/0000-0002-1162-6709, Mattonet, K. ORCID: https://orcid.org/0000-0002-9705-8086, Kempfer, R. ORCID: https://orcid.org/0000-0002-8588-8576, Hirsekorn, A., Bilić, I. ORCID: https://orcid.org/0000-0002-2730-1634, Gil, M. ORCID: https://orcid.org/0000-0002-3885-7806, Trinks, A. ORCID: https://orcid.org/0000-0001-9983-1506, Merks, A.M. ORCID: https://orcid.org/0000-0001-5677-7204, Panáková, D. ORCID: https://orcid.org/0000-0002-8739-6225, Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290, Stainier, D.Y.R. ORCID: https://orcid.org/0000-0002-0382-0026, Garfield, D. ORCID: https://orcid.org/0000-0002-8790-797X, Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116 and Lacadie, S.A. ORCID: https://orcid.org/0000-0002-0893-5340
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. ORCID: https://orcid.org/0000-0002-5154-3318, Chawla, P., Hnatiuk, A., Kamel, M., Silva, L.D., Spanjaard, B. ORCID: https://orcid.org/0000-0003-1309-8839, 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. ORCID: https://orcid.org/0000-0002-2826-8290 and Ninov, N. ORCID: https://orcid.org/0000-0003-3286-6100
Development 149
(2): dev199853.
January 2022
2021
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. ORCID: https://orcid.org/0000-0002-2826-8290, 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
Single-cell genomics to study developmental cell fate decisions in zebrafish.
Moreno-Ayala, R. ORCID: https://orcid.org/0000-0002-8614-1239 and Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290
Briefings in Functional Genomics 20
(6): 420–426.
November 2021
Spatio-temporal mRNA tracking in the early zebrafish embryo.
Holler, K. ORCID: https://orcid.org/0000-0002-5159-9223, Neuschulz, A. ORCID: https://orcid.org/0000-0001-6163-3344, Drewe-Boß, P. ORCID: https://orcid.org/0000-0002-5459-9771, Mintcheva, J. ORCID: https://orcid.org/0000-0003-0793-6277, Spanjaard, B. ORCID: https://orcid.org/0000-0003-1309-8839, Arsiè, R. ORCID: https://orcid.org/0000-0002-7869-7624, Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116, Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734 and Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290
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. ORCID: https://orcid.org/0000-0002-5159-9223, Appelbaum, L. ORCID: https://orcid.org/0000-0002-9248-5919, Eisenberg, E. ORCID: https://orcid.org/0000-0001-8681-3202, Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290 and Levanon, E.Y. ORCID: https://orcid.org/0000-0002-3641-4198
Nucleic Acids Research 49
(8): 4325-4337.
7 May 2021
Mit Einzelzell-Genomik die Entscheidungen von Zellen verfolgen [Deciphering cell fate decisions using single cell genomics].
Hu, B. ORCID: https://orcid.org/0000-0003-0751-885X and Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290
BIOspektrum 27
(1): 25-27.
February 2021
Variability of an early developmental cell population underlies stochastic laterality defects.
Moreno-Ayala, R. ORCID: https://orcid.org/0000-0002-8614-1239, Olivares-Chauvet, P., Schäfer, R. and Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290
Cell Reports 34
(2): 108606.
12 January 2021
2020
The transcriptome dynamics of single cells during the cell cycle.
Schwabe, D. ORCID: https://orcid.org/0000-0003-2825-3352, Formichetti, S. ORCID: https://orcid.org/0000-0002-7907-2239, Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290, Falcke, M. ORCID: https://orcid.org/0000-0001-7137-1114 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Molecular Systems Biology 16
(11): e9946.
1 November 2020
Cellular drivers of injury response and regeneration in the adult zebrafish heart (zebrafish).
[Dataset]
5 October 2020
Morphine alleviates pain after heart cryoinjury in zebrafish without impeding regeneration.
Lelek, S., Simões, M. ORCID: https://orcid.org/0000-0002-7340-9128, Hu, B. ORCID: https://orcid.org/0000-0003-0751-885X, Alameldeen, A.M.A., Czajkowski, M.T. ORCID: https://orcid.org/0000-0002-0122-1943, Meyer, A.M. ORCID: https://orcid.org/0000-0002-4665-2077, Ferrara, F., Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290 and Panáková, D. ORCID: https://orcid.org/0000-0002-8739-6225
bioRxiv
: 2020.10.01.322560.
2 October 2020
GPSeq reveals the radial organization of chromatin in the cell nucleus.
Girelli, G. ORCID: https://orcid.org/0000-0003-4264-6494, Custodio, J., Kallas, T., Agostini, F. ORCID: https://orcid.org/0000-0002-5453-2737, Wernersson, E. ORCID: https://orcid.org/0000-0003-4778-1660, Spanjaard, B. ORCID: https://orcid.org/0000-0003-1309-8839, Mota, A., Kolbeinsdottir, S., Gelali, E. ORCID: https://orcid.org/0000-0003-0067-5473, Crosetto, N. ORCID: https://orcid.org/0000-0002-3019-6978 and Bienko, M. ORCID: https://orcid.org/0000-0002-6499-9082
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. ORCID: https://orcid.org/0000-0002-2826-8290 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. ORCID: https://orcid.org/0000-0002-2826-8290
International Journal of Biochemistry and Cell Biology 122
: 105745.
May 2020
2019
Applying synergy metrics to oncology combination screening data: agreements, disagreements and pitfalls.
Vlot, A.H.C. ORCID: https://orcid.org/0000-0001-9538-987X, Aniceto, N., Menden, M.P., Ulrich-Merzenich, G. and Bender, A.
Drug Discovery Today 24
(12): 2286-2298.
December 2019
Detouring the roadblocks in gene expression.
Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290
Nature Reviews Molecular Cell Biology 20
(4): 197.
April 2019
RNA tomography for spatially resolved transcriptomics (Tomo-seq).
Holler, K. ORCID: https://orcid.org/0000-0002-5159-9223 and Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290
Methods in Molecular Biology 1920
: 129-141.
2019
2018
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. ORCID: https://orcid.org/0000-0003-1309-8839, Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290, 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. ORCID: https://orcid.org/0000-0003-1309-8839, Hu, B. ORCID: https://orcid.org/0000-0003-0751-885X, Mitic, N. ORCID: https://orcid.org/0000-0003-0141-1293, Olivares-Chauvet, P., Janjuha, S., Ninov, N. and Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290
Nature Biotechnology 36
(5): 469-473.
May 2018
2017
Methods for lineage tracing on the organism-wide level.
Spanjaard, B. ORCID: https://orcid.org/0000-0003-1309-8839 and Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290
Current Opinion in Cell Biology 49
: 16-21.
December 2017
Tomo-seq identifies SOX9 as a key regulator of cardiac fibrosis during ischemic injury.
Lacraz, G.P.A., Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290, 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
Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations.
van den Brink, S.C. ORCID: https://orcid.org/0000-0003-3683-7737, Sage, F., Vertesy, A. ORCID: https://orcid.org/0000-0001-6075-5702, Spanjaard, B. ORCID: https://orcid.org/0000-0003-1309-8839, Peterson-Maduro, J., Baron, C.S., Robin, C. and van Oudenaarden, A.
Nature Methods 14
(10): 935-936.
29 September 2017
Massively parallel clonal analysis using CRISPR/Cas9 induced genetic scars.
Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290, Spanjaard, B. ORCID: https://orcid.org/0000-0003-1309-8839, Peterson-Maduro, J., Alemany, A., Hu, B. ORCID: https://orcid.org/0000-0003-0751-885X, Florescu, M. and van Oudenaarden, A.
bioRxiv
: 056499v2.
4 January 2017
Patched receptors sense, interpret and establish an epidermal Hedgehog signalling gradient.
Adolphe, C., Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290, Lyubimova, A., van Oudenaarden, A. and Wainwright, B.
Journal of Investigative Dermatology 137
(1): 179-186.
January 2017
2016
Spatially resolved genome-wide transcriptional profiling identifies BMP signaling as essential regulator of zebrafish cardiomyocyte regeneration.
Wu, C.C. ORCID: https://orcid.org/0000-0003-3903-2512, Kruse, F., Vasudevarao, M.D., Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290, 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
Tomo-seq: A method to obtain genome-wide expression data with spatial resolution.
Kruse, F., Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290, van Oudenaarden, A. and Bakkers, J.
Methods in Cell Biology 135
: 299-307.
2016
2015
A gene regulatory program for meiotic prophase in the fetal ovary.
Soh, Y.Q.S., Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290, 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. ORCID: https://orcid.org/0000-0002-2826-8290, 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
Single-cell transcriptomics enters the age of mass production.
Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290 and van Oudenaarden, A.
Molecular Cell 58
(4): 563-564.
21 May 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. ORCID: https://orcid.org/0000-0002-2826-8290, 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. ORCID: https://orcid.org/0000-0002-2826-8290, 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
2014
A predictive model of bifunctional transcription factor signaling during embryonic tissue patterning.
Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290, 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. ORCID: https://orcid.org/0000-0002-2826-8290, 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
Every cell is special: genome-wide studies add a new dimension to single-cell biology.
Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290 and van Oudenaarden, A.
Cell 157
(1): 8-11.
27 March 2014
2013
Single-molecule mRNA detection and counting in mammalian tissue.
Lyubimova, A., Itzkovitz, S., Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290, Fan, Z.P., Wu, X. and van Oudenaarden, A.
Nature Protocols 8
(9): 1743-1758.
September 2013
2012
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. ORCID: https://orcid.org/0000-0002-2826-8290, 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. ORCID: https://orcid.org/0000-0002-2826-8290, 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
When noisy neighbors are a blessing: analysis of gene expression noise identifies coregulated genes.
Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290 and van Oudenaarden, A.
Molecular Cell 45
(4): 437-438.
24 February 2012
2010
Evidence for a broad transition-state ensemble in calmodulin folding from single-molecule force spectroscopy.
Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290 and Rief, M.
Angewandte Chemie International Edition 49
(19): 3306-3309.
26 April 2010
2009
Single-molecule force spectroscopy distinguishes target binding modes of calmodulin.
Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290 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. ORCID: https://orcid.org/0000-0002-2826-8290, Ziegler, F. and Rief, M.
Science 323
(5914): 633-637.
30 January 2009
2006
Cysteine engineering of polyproteins for single-molecule force spectroscopy.
Dietz, H., Bertz, M., Schlierf, M., Berkemeier, F., Bornschloegl, T., Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290 and Rief, M.
Nature Protocols 1
(1): 80-84.
2006
2005
Influence of substrate binding on the mechanical stability of mouse dihydrofolate reductase.
Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290, Hell, K., Schlierf, M., Neupert, W. and Rief, M.
Biophysical Journal 89
(5): L46-L48.
November 2005
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