Publications


Hu B*, Lelek S*, Spanjaard B*, Simoes M, Schäfer R, Aliee H, Theis F, Panáková D*, Junker JP*. “Cellular drivers of injury response and regeneration in the adult zebrafish heart” (*equal contribution). Submitted.

Holler K, Neuschulz A, Drewe-Boß P, Mintcheva J, Spanjaard B, Arsie R, Ohler U, Landthaler M, Junker JP. “Spatio-temporal mRNA dynamics in the early zebrafish embryo“. Submitted.

Lelek S, Simoes M, Hu B, Alameldeen A, Czajkowski M, Meyer AM, Ferrara F, Panáková D, Junker JP. “Morphine alleviates pain after heart cryoinjury in zebrafish without impeding regeneration”. Submitted.

Buchumenski I*, Holler K*, Appelbaum L, Eisenberg E, Junker JP*, Levanon EY*. “A-to-I RNA editing in zebrafish during development“ (*equal contribution). Under review.

McGarvey AC, Kopp W, Vučićević D, Kempfer R, Mattonet K, Hirsekorn A, Bilić I, Trinks A, Merks AM, Panáková D, Pombo A, Akalin A, Junker JP, Stainier DYR, Garfield D, Ohler U, Lacadie SA. “Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in wildtype and cloche/npas4l mutant zebrafish embryos”. Under review. Available as a preprint on bioRxiv, 2020, doi: 10.1101/2020.06.26.173377.

Moreno-Ayala R, Olivares-Chauvet P, Schäfer R, Junker JP. “Variability of an early developmental cell population underlies stochastic laterality defects”. In revision. Available as a preprint on bioRxiv, 2020, doi: 10.1101/2020.07.20.212282.

Hagedorn E, Perlin J, Mao C, Fernández-Maestre I, Freeman R, Daily M, D’Amato C, Wattrus S, Han T, Riquelme R, Li B, Redfield S, Collins S, Lichtig A, Yang S, Zhou Y, Kunar B, Gomez-Salinero J, Dinh TT, Pan J, Holler K, Butcher E, van Oudenaarden A, Rafii S, Junker JP, Zon L “Transcription factor induction of vascular blood stem cell niches in vivo”, In revision.

Schwabe D, Formichetti S, Junker JP, Falcke M, Rajewsky N. “The transcriptome dynamics of single cells during the cell cycle”. Molecular Systems Biology (in press). Available as a preprint on bioRxiv, doi: 10.1101/2019.12.23.887570.

Olivares-Chauvet P, Junker JP “Inclusion of temporal information in single cell transcriptomics”. International Journal of Biochemistry and Cell Biology, 2020, doi: 10.1016/j.biocel.2020.105745.

Yvernogeau L, Klaus A, Maas J, Morin-Poulard I, Weijts B, Schulte-Merker S, Berezikov E, Junker JP, Robin C “Multispecies RNA tomography reveals regulators of hematopoietic stem cell birth in the embryonic aorta”. Blood, 2020, doi: 10.1182/blood.2019004446.

Junker JP “Detouring the roadblocks in gene expression”. Nat Rev Mol Cell Biol, 2019, vol. 20 (4): p. 197

Ebbing A, Vértesy Á, Betist MC, Spanjaard B, Junker JP, Berezikov E, van Oudenaarden A & Korswagen HC “Spatial Transcriptomics of C. elegans Males and Hermaphrodites Identifies Sex-Specific Differences in Gene Expression Patterns”. Developmental Cell, 2018, vol. 47, p. 801–813.

Holler K, Junker JP “RNA tomography for spatially resolved transcriptomics (tomo-seq)”, Vertebrate Embryogenesis, Embryological, Cellular and Genetic Methods, 2nd Edition (Ed. F. Pelegri), 2018.

Spanjaard B*, Hu B*, Mitic N, Olivares Chauvet P, Janjuha S, Ninov N, Junker JP, “Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars” (*equal contribution), Nature Biotechnology, 2018, vol. 36, p. 469–473.

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

Lacraz G*, Junker JP*, Gladka M, Molenaar B, Scholman KT, 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” (*equal contribution), Circulation, 2017, vol. 136, p. 1396-1409.

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

Junker JP, 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 CC, Kruse F, Vasudevarao MD, Junker JP, Zebrowski DC, Fischer K, Noel ES, Grün D, Berezikov E, Engel FB, 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, vol. 36 (1), p. 36-49.

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

Soh YQS*, Junker JP*, Gill M, Mueller J, Page DC, van Oudenaarden A: “A Gene Regulatory Program for Meiotic Prophase in the Fetal Ovary” (*equal contribution), PLoS Genetics, 2015, 11(9): e1005531

Junker JP, van Oudenaarden A: “Single Cell Transcriptomics Enters the Age of Mass Production”, Molecular Cell, 2015, vol. 58 (4), p. 563–564.

Welling M, Chen HH, Munoz J, Musheev MU, Kester L, Junker JP, Mischerikov N, Arbab M, Kuijk E, Silberstein L, Kharchenko PV, Geens M, Niehrs C, van de Velde H, van Oudenaarden A, Heck AJR, Geijsen N: “DAZL regulates Tet1 translation in murine embryonic stem cells”, EMBO Reports, 2015, vol. 16 (7), p. 791-802.

Hu YC, Nicholls PK, Soh YQS, Danielle JR, Junker JP, van Oudenaarden A, Page DC: “Licensing of Primordial Germ Cells for Gametogenesis Depends on Genital Ridge Signaling”, PLoS Genetics, 2015, vol. 11 (3), p. e1005019.

Schuijers J, Junker JP, Mokry M, Hatzis P, Koo BK, Sasselli V, van der Flier L, 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, vol. 16 (2), p.158–170. 

Junker JP, Peterson KA, Nishi Y, Mao J, McMahon AP, van Oudenaarden A: “A Predictive Model of Bifunctional Transcription Factor Signaling”, Developmental Cell, 2014, vol. 31 (4), p. 448–460.

Junker JP, Noël ES, Guryev V, Peterson KA, Shah G, Huisken J, McMahon AP, Berezikov E, Bakkers J, van Oudenaarden A: “Genome-wide RNA Tomography in the Zebrafish Embryo”, Cell, 2014, vol. 159 (3), p. 662–675.

Junker JP, van Oudenaarden A: “Every Cell Is Special: Genome-wide Studies Add a New Dimension to Single-Cell Biology”, Cell, 2014, vol. 157 (1), p. 8–11

Lyubimova A, Itzkovitz S, Junker JP, Wu X , Fan ZP, van Oudenaarden A: “Single-molecule mRNA Detection and Counting in Mammalian Tissue”, Nature Protocols, 2013, vol. 8 (9), p. 1743–1758.

Peterson KA, Nishi Y, Ma W, Vedenko A, Shokri L, Zhang X, McFarlane M, Baizabal JM, Junker JP, van Oudenaarden A, Mikkelsen T, Bernstein BE, Bailey TL, Bulyk ML, Wong WH, McMahon AP: “Neural-specific Sox2 Input and Differential Gli-binding Affinity Provide Context and Positional Information in Shh-directed Neural Patterning”, Genes & Development, 2012, vol. 26 (24), p. 2802–2816.

Yu J, Valerius TM, Duah M, Staser K, Hansard JK, Guo JJ, McMahon J, Vaughan J, Faria D, Georgas K, Rumballe B, Ren Q, Krautzberger AM, Junker JP, Thiagarajan RD, Machanick P, Gray PA, van Oudenaarden A, Rowitch DH, Stiles CD, Ma Q, Grimmond SM, Bailey TK, Little MH, McMahon AP: “Identification of Molecular Compartments and Genetic Circuitry in the Developing Mammalian Kidney”, Development, 2012, vol. 139 (10), p. 1863–1873.

Junker JP, van Oudenaarden A: “When Noisy Neighbors are a Blessing: Analysis of Gene Expression Noise Identifies Coregulated Genes”, Molecular Cell, 2012, vol. 45 (4), p. 437–438.

Junker JP, Rief M: “Evidence for a Broad Transition-State Ensemble in Calmodulin Folding from Single-Molecule Force Spectroscopy”, Angewandte Chemie, 2010, vol. 49 (19), p. 3306–3309.

Junker JP, Rief M: “Single-Molecule Force Spectroscopy Distinguishes Target Binding Modes of Calmodulin”, PNAS, 2009, vol. 106 (34), p. 14361–14366.

Junker JP, Ziegler F, Rief M: “Ligand-Dependent Equilibrium Fluctuations of Single Calmodulin Molecules”, Science, 2009, vol. 323 (5914), p. 633–637.

Dietz H, Bertz M, Schlierf M, Berkemeier F, Bornschlögl T, Junker JP, Rief M: “Cysteine Engineering of Polyproteins for Single Molecule Force Spectroscopy”, Nature Protocols, 2006, vol. 1 (1), p. 80–84.

Junker JP, Hell K, Schlierf M, Neupert W, Rief M: “Influence of Substrate Binding on the Mechanical Stability of Mouse Dihydrofolate Reductase”, Biophysical Journal, 2005, vol. 89 (5), p. L46–48.


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