Alexander van Oudenaarden



  1. Junker J, van Oudenaarden A. Single-cell transcriptomics enters the age of mass production. Mol Cell. 2015;58:563-4 pubmed publisher
  2. Kester L, van Oudenaarden A. Single-Cell Transcriptomics Meets Lineage Tracing. Cell Stem Cell. 2018;23:166-179 pubmed publisher
    ..In this Review, we discuss transcriptome-based lineage trajectory prediction algorithms, single-cell genetic lineage tracing, and the promising combination of these techniques for stem cell and cancer research. ..
  3. Vértesy Á, Arindrarto W, Roost M, Reinius B, Torrens Juaneda V, Bialecka M, et al. Parental haplotype-specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells. Nat Commun. 2018;9:1873 pubmed publisher
    ..Altogether, we uncover the complexity and cell-to-cell heterogeneity of transcriptional and epigenetic remodeling in female human germ cells. ..
  4. Boisset J, Vivié J, Grün D, Muraro M, Lyubimova A, van Oudenaarden A. Mapping the physical network of cellular interactions. Nat Methods. 2018;15:547-553 pubmed publisher
    ..This strategy can be used to discover new niches or preferential interactions in a variety of organs. ..
  5. Junker J, Peterson K, Nishi Y, Mao J, McMahon A, van Oudenaarden A. A predictive model of bifunctional transcription factor signaling during embryonic tissue patterning. Dev Cell. 2014;31:448-60 pubmed publisher
    ..Our results provide a starting point for understanding gene regulation by bifunctional transcription factors during mammalian development. ..
  6. Grün D, Muraro M, Boisset J, Wiebrands K, Lyubimova A, Dharmadhikari G, et al. De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data. Cell Stem Cell. 2016;19:266-277 pubmed publisher
    ..We hope that StemID will accelerate the search for novel stem cells by providing concrete markers for biological follow-up and validation. ..
  7. Junker J, Noël E, Guryev V, Peterson K, Shah G, Huisken J, et al. Genome-wide RNA Tomography in the zebrafish embryo. Cell. 2014;159:662-75 pubmed publisher
    ..We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. ..
  8. Grün D, van Oudenaarden A. Design and Analysis of Single-Cell Sequencing Experiments. Cell. 2015;163:799-810 pubmed publisher
    ..We hope that these guidelines will enable a growing number of researchers to leverage the power of single-cell sequencing. ..
  9. Muraro M, Dharmadhikari G, Grün D, Groen N, Dielen T, Jansen E, et al. A Single-Cell Transcriptome Atlas of the Human Pancreas. Cell Syst. 2016;3:385-394.e3 pubmed publisher
    ..This resource will be useful for developing a deeper understanding of pancreatic biology and pathophysiology of diabetes mellitus. ..