Publications

2018

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


2017

Spanjaard B.; Junker J.P.
Methods for lineage tracing on the organism-wide level
Curr Opin Cell Biol, 2017, vol. 49, p. 16-21


Lacraz G., Junker J.P., Gladka M., Molenaar B., Scholman K. T. , Vigil-Garcia M., Versteeg D., de Ruiter H., Vermunt M., Creyghton M., Huibers M., de Jonge N., van Oudenaarden A., van Rooij E.
Tomo-seq identifies SOX9 as a key regulator of cardiac fibrosis during ischemic injury
Circulation, 2017, vol. 136, p. 1396-1409


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


2016

Junker J.P.; Spanjaard B.; Peterson-Maduro J.; Alemany A.; Hu B.; Florescu M.; van Oudenaarden A.
Massively parallel clonal analysis using CRISPR/Cas9 induced genetic scars
bioRxiv, 2016, doi: 10.1101/056499


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.
Spatially resolved genome-wide transcriptional profiling identifies BMP signaling as essential regulator of zebrafish cardiomyocyte regeneration
Developmental Cell, 2016,  36 (1), p. 36-49


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


2015

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


Welling M.; Chen H.H.; Munoz 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.
DAZL regulates Tet1 translation in murine embryonic stem cells
EMBO Reports, 2015, 16 (7), p. 791-802


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


Hu Y.C.; Nicholls P.K.; Soh Y.Q.S.; Daniele J.R.; Junker J.P.; van Oudenaarden A.; Page D.C.
Licensing of primordial germ cells for gametogenesis depends on genital ridge signaling
PLoS Genetics, 2015, 11 (3), 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.
Ascl2 acts as an R-spondin/Wnt-responsive switch to control stemness in intestinal crypts
Cell Stem Cell, 2015, 16 (2), p. 158-170


2014

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


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


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


2013

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


2012

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.
Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning
Genes & Development, 2012, 26 (24), p. 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.
Identification of molecular compartments and genetic circuitry in the developing mammalian kidney
Development, 2012, 139 (10), p. 1863-1873


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


2010

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


2009

Junker J.P.; Rief M.
Single-molecule force spectroscopy distinguishes target binding modes of calmodulin
PNAS, 2009, 106 (34), p. 14361-14366


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


2006

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


2005

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


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