Academic Appointments

Honors & Awards

  • Career Award at the Scientific Interface, Burroughs-Wellcome Fund (2022-2027)
  • Science & SciLifeLab Prize for Young Scientists, Science & SciLifeLab (2020)
  • Nemko Prize in Cellular or Molecular Neuroscience, Society for Neuroscience (2019)
  • Harold M. Weintraub Graduate Student Award, Fred Hutchinson Cancer Research Center (2019)
  • Junior Fellowship, Harvard Society of Fellows (2019-2024)
  • Goldwater Scholarship, Goldwater Scholarship (2011-2012)
  • Churchill Scholarship, Winston Churchill Foundation of America (2012-2013)
  • Graduate Research Fellowship, National Science Foundation (2013-2016)
  • Hertz Fellowship, Fannie & John Hertz Foundation (2014-2018)

Professional Education

  • Junior Fellow, Harvard Society of Fellows (2024)
  • Ph.D., Stanford University, Neurosciences (2019)
  • M.Phil., University of Cambridge, Computational Biology (2013)
  • Sc.B., Brown University, Applied Mathematics-Biology (2012)

Contact

  • Academic
    wallen@stanford.edu
    University - Faculty Department: Department of Developmental Biology Position: Assistant Professor

Additional Info

  • Mail Code: 5329

2024-25 Courses

Stanford Advisees

All Publications

  • Alteration of genic 5-hydroxymethylcytosine patterning in olfactory neurons correlates with changes in gene expression and cell identity PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Colquitt, B. M., Allen, W. E., Barnea, G., Lomvardas, S. 2013; 110 (36): 14682-14687

    Abstract

    The modified DNA base 5-hydroxymethylcytosine (5hmC) is enriched in neurons where it may contribute to gene regulation and cellular identity. To determine how 5hmC influences gene expression in an in vivo neuronal population, we assessed the patterning and function of the base along the developmental lineage of the main olfactory epithelium-from multipotent stem cells through neuronal progenitors to mature olfactory sensory neurons (mOSNs). We find that 5hmC increases over gene bodies during mOSN development with substantial patterning occuring between the progenitor and mOSN stages. Although gene-body 5hmC levels correlate with gene expression in all three developmental cell types, this association is particularly pronounced within mOSNs. Overexpression of Tet3 in mOSNs markedly alters gene-body 5hmC levels and gene expression in a manner consistent with a positive role for 5hmC in transcription. Moreover, Tet3 overexpression disrupts olfactory receptor expression and the targeting of axons to the olfactory bulb, key molecular and anatomical features of the olfactory system. Our results suggest a physiologically significant role for gene-body 5hmC in transcriptional facilitation and the maintenance of cellular identity independent of its function as an intermediate to demethylation.

    View details for DOI 10.1073/pnas.1302759110

    View details for Web of Science ID 000323886200048

    View details for PubMedID 23969834

    View details for PubMedCentralID PMC3767503

  • An epigenetic trap stabilizes singular olfactory receptor expression. Cell Lyons, D. B., Allen, W. E., Goh, T., Tsai, L., Barnea, G., Lomvardas, S. 2013; 154 (2): 325-36

    Abstract

    The molecular mechanisms regulating olfactory receptor (OR) expression in the mammalian nose are not yet understood. Here, we identify the transient expression of histone demethylase LSD1 and the OR-dependent expression of adenylyl cyclase 3 (Adcy3) as requirements for initiation and stabilization of OR expression. As a transcriptional coactivator, LSD1 is necessary for desilencing and initiating OR transcription, but as a transcriptional corepressor, it is incompatible with maintenance of OR expression, and its downregulation is imperative for stable OR choice. Adcy3, a sensor of OR expression and a transmitter of an OR-elicited feedback, mediates the downregulation of LSD1 and promotes the differentiation of olfactory sensory neurons (OSNs). This novel, three-node signaling cascade locks the epigenetic state of the chosen OR, stabilizes its singular expression, and prevents the transcriptional activation of additional OR alleles for the life of the neuron.

    View details for DOI 10.1016/j.cell.2013.06.039

    View details for PubMedID 23870122

    View details for PubMedCentralID PMC3929589

  • An Epigenetic Signature for Monoallelic Olfactory Receptor Expression CELL Magklara, A., Yen, A., Colquitt, B. M., Clowney, E. J., Allen, W., Markenscoff-Papadimitriou, E., Evans, Z. A., Kheradpour, P., Mountoufaris, G., Carey, C., Barnea, G., Kellis, M., Lomvardas, S. 2011; 145 (4): 555-570

    Abstract

    Constitutive heterochromatin is traditionally viewed as the static form of heterochromatin that silences pericentromeric and telomeric repeats in a cell cycle- and differentiation-independent manner. Here, we show that, in the mouse olfactory epithelium, olfactory receptor (OR) genes are marked in a highly dynamic fashion with the molecular hallmarks of constitutive heterochromatin, H3K9me3 and H4K20me3. The cell type and developmentally dependent deposition of these marks along the OR clusters are, most likely, reversed during the process of OR choice to allow for monogenic and monoallelic OR expression. In contrast to the current view of OR choice, our data suggest that OR silencing takes place before OR expression, indicating that it is not the product of an OR-elicited feedback signal. Our findings suggest that chromatin-mediated silencing lays a molecular foundation upon which singular and stochastic selection for gene expression can be applied.

    View details for DOI 10.1016/j.cell.2011.03.040

    View details for Web of Science ID 000290560800009

    View details for PubMedID 21529909

    View details for PubMedCentralID PMC3094500