Group Leader

Dr. Dominic Grün
Dr. Dominic Grün
Group Leader
Phone:+49 761 5108-490
Email:gruen@...

Lab Dominic Grün

Laboratory Dominic Grün

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Publications (2018-2005)

 *equal contributions, #co-corresponding authors

  • Tay TL, Sagar, Dautzenberg J, Grün D#, Prinz M# (2018): Unique microglia recovery population revealed by single-cell RNAseq following neurodegeneration. Acta Neuropathologica Communications 6(1): 87.
  • Costa F, Grün D#, Backofen R# (2018): GraphDDP: a graph-embedding approach to detect differentiation pathways in single-cell-data using prior class knowledge. Nature Communications 9(1): 3685.
  • Roovers EF, Kaaij LJT, Redl S, Bronkhorst AW, Wiebrands K, de Jesus Domingues AM, Huang HY, Han CT, Riemer S, Dosch R, Salvenmoser W, Grün D, Butter F, van Oudenaarden A, Ketting RF (2018): Tdrd6a Regulates the Aggregation of Buc into Functional Subcellular Compartments that Drive Germ Cell Specification. Developmental Cell 46(3): 285-301.
  • Grün D (2018): Revealing routes of cellular differentiation by single-cell RNA-seq. Current Opinion in Systems Biology 11: 9-17.
  • Boisset JC, Vivié J, Grün D, Muraro M, Lyubimova A, van Oudenaarden A (2018): Mapping the physical network of cellular interactions. Nature Methods 15(7): 547-553.
  • Lu TT, Heyne S, Dror E, Casas E, Leonhardt L, Boenke T, Yang CH, Sagar, Arrigoni L, Dalgaard K, Teperino R, Enders L, Selvaraj M, Ruf M, Raja SJ, Xie H, Boenisch U, Orkin SH, Lynn FC, Hoffman BG, Grün D, Vavouri T, Lempradl AM, Pospisilik JA (2018): The Polycomb-Dependent Epigenome Controls β Cell Dysfunction, Dedifferentiation, and Diabetes. Cell Metabolism 27(6): 1294-1308.
  • Herman JS, Sagar, Grün D (2018): FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data. Nature Methods 5(5): 379-386.
  • Sagar, Herman JS, Pospisilik JA, Grün D (2018): High-Throughput Single-Cell RNA Sequencing and Data Analysis. Methods Molecular Biology 2018 (1766), 257-283.
  • Felmlee DJ, Grün D, Baumert, TF (2017): Zooming in on liver zonation. Hepatology 67(2), 784-787.

  • Tay TL, Mai D, Dautzenberg J, Fernández-Klett F, Lin G, Sagar, Datta M, Drougard A, Stempfl T, Ardura-Fabregat A, Staszewski O, Margineanu A, Sporbert A, Steinmetz LM, Pospisilik JA, Jung S, Priller J, Grün D, Ronneberger O, Prinz M. (2017) A new fate mapping system reveals context-dependent random or clonal expansion of microglia. Nature Neuroscience 20(6): 793-803.

  • Herrtwich L, Nanda I, Evangelou K, Nikolova T, Horn V, Sagar, Erny D, Stefanowski J, Rogell R, Klein C, Gharun K, Follo M, Seidl M, Kremer B, Münke N, Senges J, Fliegauf M, Aschman T, Pfeifer D, Sarrazin S, Sieweke MH, Wagner D, Dierks C, Haaf T, Ness T, Zaiss MM, Voll RE, Deshmukh SD, Prinz M, Goldmann T, Hölscher C, Hauser AE, Lopez-Contreras AJ, Grün D, Gorgoulis V, Diefenbach A, Henneke P, Triantafyllopoulou, A (2016) DNA Damage Signaling Instructs Polyploid Macrophage Fate in Granulomas. Cell 167(5): 1264-1280.

  • Muraro MJ, Dharmadhikari G, Grün D, Groen N, Dielen T, Jansen E, van Gurp L, Engelse MA, Carlotti F, de Koning EJ, van Oudenaarden A (2016) A Single-Cell Transcriptome Atlas of the Human Pancreas. Cell Systems 3(4): 385-394.

  • Grün D#, Muraro MJ, Boisset JC, Wiebrands K, Lyubimova A, Dharmadhikari G, van den Born M, van Es J, Jansen E, Clevers H, de Koning EJP, van Oudenaarden A# (2016) De Novo Prediction of Stem Cell Identity Using Single-Cell Transcriptome Data. Cell Stem Cell 19(2): 266-77.

  • Wu CC, Kruse F, Vasudevarao MD, Junker JP, Zebrowski DC, Fischer K, Noël ES, Grün D, Berezikov E, Engel FB, van Oudenaarden A, Weidinger G, Bakkers J (2016) Spatially Resolved Genome-wide Transcriptional Profiling Identifies BMP Signaling as Essential Regulator of Zebrafish Cardiomyocyte Regeneration. Developmental Cell 36(1): 36-49.

  • Grün D and van Oudenaarden A. (2015) Design and analysis of single cell sequencing experiments. Cell 163(4): 799-810.

  • Grün D*, Lyubimova A, Kester L, Wiebrands K, Basak O, Sasaki N, Clevers H, van Oudenaarden A. (2015) Single-cell mRNA sequencing reveals rare intestinal cell types. Nature 525: 251-255.

  • Grün D*, Kester L*, van Oudenaarden A. (2014) Validation of noise models for single-cell transcriptomics enables genome-wide quantification of stochastic gene expression. Nature Methods 11(6): 637-40.

  • Stoeckius M*, Grün D*, Kirchner M, Ayoub S, Torti F, Piano F, Herzog M, Selbach M, Rajewsky N. (2014) Identification of a novel mRNA turnover mechanism in the oocyte-to-embryo transition of C. elegans. EMBO Journal 33(16): 1751-66.

  • Stoeckius M*, Grün D*, Rajewsky N. (2014) Paternal RNA contributions in the C. elegans zygote. EMBO Journal 33(16): 1740-50.

  • Grün D*, Kirchner M*, Thierfelder N*, Stoeckius M, Selbach M, Rajewsky N. (2014) Conservation of mRNA and protein expression during development of C. elegans. Cell Reports 6(3): 565-77.

  • Kim DH, Grün D, van Oudenaarden A. (2013) Dampening of expression oscillations by synchronous regulation of a microRNA and its target. Nature Genetics 45(11): 1337-44.

  • Onal P*, Grün D*, Adamidi C*, Rybak A, Solana J, Wang Y, Rahn HP, Chen W, Ziebold U, Rajewsky N (2012) Molecular determinants of pluripotency are deeply conserved between mammalian and planarian stem cells. EMBO Journal 31(12): 2755-69.

  • Jungkamp AC, Stoeckius M, Mecenas D, Grün D, Mastrobuoni G, Kempa S, Rajewsky N (2011) In vivo and transcriptome-wide identification of RNA-binding protein target sites. Molecular Cell 44(5): 828-40.
  • Adamidi C*, Wang Y*, Grün D*, Mastrobuoni G*, You X*, Tolle D, Dodt M, Mackowiak SD, Gogol-Doering A, Oenal P, Rybak A, Ross E, Alvarado AS, Kempa S, Dieterich C, Rajewsky N, Chen W (2011) De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics. Genome Research 21(7): 1193-1200.
  • Grün D, Rajewsky N (2008) Computational prediction of microRNA targets in vertebrates, fruitflies and nematodes. MicroRNAs: From Basic Science to Disease Biology: 172-186.

  • Lall S*, Grün D*, Krek A, Chen K, Wang YL, Dewey CN, Sood P, Colombo T, Bray N, Macmenamin P, Kao HL, Gunsalus KC, Pachter L, Piano F, Rajewsky N (2006) A genome-wide map of conserved microRNA targets in C. elegans. Current Biology 16(5): 460-471.

  • Grün D, Wang YL, Langenberger D, Gunsalus KC, Rajewsky N (2005) microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Computational Biology 1(1): e13.

  • Krek A*, Grün D*, Poy MN*, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, Rajewsky N (2005) Combinatorial microRNA target predictions. Nature Genetics 37(5): 495-500.
 
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