Publications



2017

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



van den Brink S.C.; Sage F.; Vertesy A.; Spanjaard B.; Peterson-Maduro J.; Baron C.S.; Robin C.; van Oudenaarden A.
Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations
Nature Methods 14 (10): 935-936 (2017-09-29)



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 137 (1): 179-186 (2017-01)



2016

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 36 (1): 36-49 (2016-01-11)



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 135: 299-307 (2016)



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 11 (9): e1005531 (2015-09-17)



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 16 (7): 791-802 (2015-07)



Junker J.P.; van Oudenaarden A.
Single-cell transcriptomics enters the age of mass production
Molecular Cell 58 (4): 563-564 (2015-05-21)



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 11 (3): e1005019 (2015-03-04)



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 16 (2): 158-170 (2015-02-05)



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 31 (4): 448-460 (2014-11-24)



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 159 (3): 662-675 (2014-10-23)



Junker J.P.; van Oudenaarden A.
Every cell is special: genome-wide studies add a new dimension to single-cell biology
Cell 157 (1): 8-11 (2014-03-27)



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 8 (9): 1743-1758 (2013-09)



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 26 (24): 2802-2816 (2012-12-15)



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 139 (10): 1863-1873 (2012-05)



Junker J.P.; van Oudenaarden A.
When noisy neighbors are a blessing: analysis of gene expression noise identifies coregulated genes
Molecular Cell 45 (4): 437-438 (2012-02-24)



2010

Junker J.P.; Rief M.
Evidence for a broad transition-state ensemble in calmodulin folding from single-molecule force spectroscopy
Angewandte Chemie International Edition in English 49 (19): 3306-3309 (2010-04-26)



2009

Junker J.P.; Rief M.
Single-molecule force spectroscopy distinguishes target binding modes of calmodulin
Proceedings of the National Academy of Sciences of the United States of America 106 (34): 14361-14366 (2009-08-25)



Junker J.P.; Ziegler F.; Rief M.
Ligand-dependent equilibrium fluctuations of single calmodulin molecules
Science 323 (5914): 633-637 (2009-01-30)



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 1 (1): 80-84 (2006)



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 89 (5): L46-L48 (2005-11)