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

GPSeq reveals the radial organization of chromatin in the cell nucleus.
Girelli, G. and Custodio, J. and Kallas, T. and Agostini, F. and Wernersson, E. and Spanjaard, B. and Mota, A. and Kolbeinsdottir, S. and Gelali, E. and Crosetto, N. and Bienko, M.
Nature Biotechnology 25 May 2020 (In Press)

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. and Vértesy, Á. and Betist, M.C. and Spanjaard, B. and Junker, J.P. and Berezikov, E. and 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. and Hu, B. and Mitic, N. and Olivares-Chauvet, P. and Janjuha, S. and 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. and Junker, J.P. and Gladka, M.M. and Molenaar, B. and Scholman, K.T. and Vigil-Garcia, M. and Versteeg, D. and de Ruiter, H. and Vermunt, M.W. and Creyghton, M.P. and Huibers, M.M.H. and de Jonge, N. and 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. and Junker, J.P. and Lyubimova, A. and 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. and Kruse, F. and Vasudevarao, M.D. and Junker, J.P. and Zebrowski, D.C. and Fischer, K. and Noel, E.S. and Gruen, D. and Berezikov, E. and Engel, F.B. and van Oudenaarden, A. and 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. and Junker, J.P. and Gill, M.E. and Mueller, J.L. and 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. and Chen, H.H. and Muñoz, J. and Musheev, M.U. and Kester, L. and Junker, J.P. and Mischerikow, N. and Arbab, M. and Kuijk, E. and Silberstein, L. and Kharchenko, P.V. and Geens, M. and Niehrs, C. and van de Velde, H. and van Oudenaarden, A. and 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. and Nicholls, P.K. and Soh, Y.Q.S. and Daniele, J.R. and Junker, J.P. and 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. and Junker, J.P. and Mokry, M. and Hatzis, P. and Koo, B.K. and Sasselli, V. and van der Flier, L.G. and Cuppen, E. and 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. and Peterson, K.A. and Nishi, Y. and Mao, J. and 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. and Noël, E.S. and Guryev, V. and Peterson, K.A. and Shah, G. and Huisken, J. and McMahon, A.P. and Berezikov, E. and 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. and Itzkovitz, S. and Junker, J.P. and Fan, Z.P. and 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. and Nishi, Y. and Ma, W. and Vedenko, A. and Shokri, L. and Zhang, X. and McFarlane, M. and Baizabal, J.M. and Junker, J.P. and van Oudenaarden, A. and Mikkelsen, T. and Bernstein, B.E. and Bailey, T.L. and Bulyk, M.L. and 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. and Valerius, M.T. and Duah, M. and Staser, K. and Hansard, J.K. and Guo, J.J. and McMahon, J. and Vaughan, J. and Faria, D. and Georgas, K. and Rumballe, B. and Ren, Q. and Krautzberger, A.M. and Junker, J.P. and Thiagarajan, R.D. and Machanick, P. and Gray, P.A. and van Oudenaarden, A. and Rowitch, D.H. and Stiles, C.D. and Ma, Q. and Grimmond, S.M. and Bailey, T.L. and 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. and Ziegler, F. and Rief, M.
Science 323 (5914): 633-637. 30 January 2009

Cysteine engineering of polyproteins for single-molecule force spectroscopy.
Dietz, H. and Bertz, M. and Schlierf, M. and Berkemeier, F. and Bornschloegl, T. and 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. and Hell, K. and Schlierf, M. and Neupert, W. and Rief, M.
Biophysical Journal 89 (5): L46-L48. November 2005


Applying synergy metrics to oncology combination screening data: agreements, disagreements and pitfalls.
Vlot, A.H.C. and Aniceto, N. and Menden, M.P. and 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. and Junker, J.P. and 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


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


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


Variability of an early developmental cell population underlies stochastic laterality defects.
Moreno-Ayala, R. and Olivares-Chauvet, P. and Schäfer, R. and Junker, J.P.
bioRxiv : 2020.07.20.212282. 20 July 2020

Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in wildtype and cloche/npas4l mutant zebrafish embryos.
McGarvey, A.C. and Kopp, W. and Vučićević, D. and Kempfer, R. and Mattonet, K. and Hirsekorn, A. and Bilić, I. and Trinks, A. and Merks, A.M. and Panáková, D. and Pombo, A. and Akalin, A. and Junker, J.P. and Stainier, D.Y.R. and Garfield, D. and Ohler, U. and Lacadie, S.A.
bioRxiv : 2020.06.26.173377. 26 June 2020

The transcriptome dynamics of single cells during the cell cycle.
Schwabe, D. and Formichetti, S. and Junker, J.P. and Falcke, M. and Rajewsky, N.
bioRxiv : 2019.12.23.887570. 26 December 2019

Spatial transcriptomics of C. elegans males and hermaphrodites identifies novel fertility genes.
Ebbing, A. and Vertesy, A. and Betist, M. and Spanjaard, B. and Junker, J.P. and van Oudenaarden, A. and Berezikov, E. and Korswagen, H.
bioRxiv : 348201. 15 June 2018

Massively parallel single cell lineage tracing using CRISPR/Cas9 induced genetic scars.
Spanjaard, B. and Hu, B. and Mitic, N. and Junker, J.P.
bioRxiv : 205971. 19 October 2017

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

This list was generated on Sat Sep 19 02:23:25 2020 CEST.
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