Professional Education

  • Bachelor of Science, Florida International University (1999)
  • Doctor of Philosophy, Florida State University (2013)
  • Master of Science, Florida International University (2003)

Stanford Advisors

Research & Scholarship

Current Research and Scholarly Interests

I aim to discern the molecular mechanisms driving lineage specification during embryonic development, neurogenesis, organogenesis and disease, with a long term goal of the development of tools for precision medicine at single cell, tissue, individual and population level.

My current research uses inner ear development as a model system. The inner ear is a complex structural and functional interconnected collection of sensory organs, responsible for our perception of sound, acceleration and balance. The inner ear semi-autonomously originates in early embryonic development from a patch of thickened ectoderm known as the otic placode. Advances in the understanding on otic development and lineage specification could lead to medical applications such as treating and identifying developmental disorders, as well as the development of in-vitro and in-vivo protocols for guided differentiation of sensory hair cells to cure deafness.

I am working to generate a cell atlas specific to the initiation of inner ear development, when the otic placode thickens and undergoes molecular and morphological changes to form an otocyst, which eventually develops into a fully functional inner ear. I aim to identify early otic-specific lineages, the molecular signatures specific to each, and describe the spatio-temporal dynamics of cells and genes during this developmental time frame.

I use computational tools to identify otic from non-otic cells in transgenic and wild type model organisms from multi-parallel qrtPCR from single cells, and concentrate on the otic populations for deep learning to accurately identify, characterize, and classify otic specific subpopulations. Computational approaches also allows us to determine the lineages composing the developing otic placode, to generate spatial and temporally accurate 3d models of organogenesis, and to design an otic cellular classifier using machine learning.

I use multidisciplinary approaches including: 1) microfluidic technology for the generation of single cell gene expression data, 2) computational and statistical multi-dimensional data analysis approaches in the form of supervised and unsupervised machine learning, 3) molecular biology tools such as transgenics, multi-parallel qRT-PCR, immuno-histochemistry, single molecule in-situ hybridization and 4) confocal microscopy.


All Publications

  • Single-cell analysis delineates a trajectory toward the human early otic lineage PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Ealy, M., Ellwanger, D. C., Kosaric, N., Stapper, A. P., Heller, S. 2016; 113 (30): 8508-8513


    Efficient pluripotent stem cell guidance protocols for the production of human posterior cranial placodes such as the otic placode that gives rise to the inner ear do not exist. Here we use a systematic approach including defined monolayer culture, signaling modulation, and single-cell gene expression analysis to delineate a developmental trajectory for human otic lineage specification in vitro. We found that modulation of bone morphogenetic protein (BMP) and WNT signaling combined with FGF and retinoic acid treatments over the course of 18 days generates cell populations that develop chronological expression of marker genes of non-neural ectoderm, preplacodal ectoderm, and early otic lineage. Gene expression along this differentiation path is distinct from other lineages such as endoderm, mesendoderm, and neural ectoderm. Single-cell analysis exposed the heterogeneity of differentiating cells and allowed discrimination of non-neural ectoderm and otic lineage cells from off-target populations. Pseudotemporal ordering of human embryonic stem cell and induced pluripotent stem cell-derived single-cell gene expression profiles revealed an initially synchronous guidance toward non-neural ectoderm, followed by comparatively asynchronous occurrences of preplacodal and otic marker genes. Positive correlation of marker gene expression between both cell lines and resemblance to mouse embryonic day 10.5 otocyst cells implied reasonable robustness of the guidance protocol. Single-cell trajectory analysis further revealed that otic progenitor cell types are induced in monolayer cultures, but further development appears impeded, likely because of lack of a lineage-stabilizing microenvironment. Our results provide a framework for future exploration of stabilizing microenvironments for efficient differentiation of stem cell-generated human otic cell types.

    View details for DOI 10.1073/pnas.1605537113

    View details for Web of Science ID 000380346200056

    View details for PubMedID 27402757

  • Assortative Mating Drives Linkage Disequilibrium between Sperm and Egg Recognition Protein Loci in the Sea Urchin Strongylocentrotus purpuratus MOLECULAR BIOLOGY AND EVOLUTION Stapper, A. P., Beerli, P., Levitan, D. R. 2015; 32 (4): 859-870


    Sperm and eggs have interacting proteins on their surfaces that influence their compatibility during fertilization. These proteins are often polymorphic within species, producing variation in gamete affinities. We first demonstrate the fitness consequences of various sperm bindin protein (Bindin) variants in the sea urchin Strongylocentrotus purpuratus, and assortative mating between males and females based on their sperm Bindin genotype. This empirical finding of assortative mating based on sperm Bindin genotype could arise by linkage disequilibrium (LD) between interacting sperm and egg recognition loci. We then examine sequence variation in eight exons of the sea urchin egg receptor for sperm Bindin (EBR1). We find little evidence of LD among the eight exons of EBR1, yet strong evidence for LD between sperm Bindin and EBR1 overall, and varying degrees of LD between sperm Bindin among the eight exons. We reject the alternate hypotheses of LD driven by shared evolutionary histories, population structure, or close physical linkage between these interacting loci on the genome. The most parsimonious explanation for this pattern of LD is that it represents selection driven by assortative mating based on interactions among these sperm and egg loci. These findings indicate the importance of ongoing sexual selection in the maintenance of protein polymorphisms and LD, and more generally highlight how LD can be used as an indication of current mate choice, as opposed to historic selection.

    View details for DOI 10.1093/molbev/msv010

    View details for Web of Science ID 000353560900003

    View details for PubMedID 25618458

  • Alteration of forest structure modifies the distribution of scale insect, Stigmacoccus garmilleri, in Mexican tropical montane cloud forests JOURNAL OF INSECT SCIENCE Gamper, H. A., Koptur, S., Garcia-Franco, J., Stapper, A. P. 2011; 11


    Stigmacoccus garmilleri Foldi (Hemiptera: Margarodidae) is an ecologically important honeydew-producing scale insect associated with oak trees (Quercus spp.) in highland forests of Veracruz, Mexico. The honeydew exudates of S. garmilleri serve as a significant nutrient source to many species of birds, insects, and sooty molds. Oak trees found in the forest interior, forest edge, and those scattered in pasture areas support scale insect colonies, though the pattern of insect infestations on trees within these varying landscape types has not been elucidated. This study aims to describe the distribution of scale insect infestation and any distinctions in honeydew production based on tree location. Scale insect density, honeydew volume, and sugar concentration were surveyed throughout a continuous landscape that included both patches of forest and scattered pasture trees. In addition, the anal filament through which the honeydew drop is secreted was also measured and was experimentally removed to test and measure regrowth. Scale insect densities on tree trunks were greatest on pasture trees, while intermediate densities were found on trees at the forest edge, and low densities on interior forest trees, suggesting that trees in disturbed areas are more susceptible to scale insect infestation. Trees with small diameters at breast height had significantly higher insect densities than trees with medium to large diameters. Trunk aspect (North, South, East, and West) was not a significant determinant of scale insect density. In forested areas higher densities of scale insects were found at three meters height in comparison to lower heights. Sugar concentrations and drop volumes of honeydew in forest and pasture areas were not significantly different. However, scale-insect anal tubes/filaments were significantly longer in pasture than they were in forests. Sugar concentrations of honeydew appeared to be positively correlated with temperature and negatively correlated with relative humidity. Experiments indicated that anal filaments could grow approximately 4 mm every 24 hours, and average tube growth was significantly faster in pasture than in forest, suggesting that there may be a physiological effect on the insect due to landscape disturbance. The results obtained in this study describe the increases in scale insect infestation of trees with forest disturbance. The effect of these increased scale insect densities on the host tree physiology is still to be resolved.

    View details for Web of Science ID 000294996000003

    View details for PubMedID 22239677



    Gamete-recognition proteins often, but not always, evolve rapidly. We explored how variation in sperm bindin influences reproductive success of the sea urchin Strongylocentrotus purpuratus during group spawning in the sea. Despite large variation in male and female abundance and neighbor distances, males with common genotypes had higher reproductive success than males with rare genotypes. However, males with a relatively uncommon proline-for-serine substitution were the most successful. Females also showed a fitness consequence of sperm-bindin genotype, suggesting linkage disequilibrium between the sperm-bindin locus and the egg receptor locus. Females with common genotypes had higher reproductive success than rare genotypes, but females with relatively uncommon insertions were most successful. Overall, these results suggest that rare male proteins are selected against, as supported by molecular evidence of purifying selection and probably caused by poor matches to the female receptor protein. Within the pool of moderately common to common alleles, however, individuals with less-common functional variants were favored and probably maintained by negative frequency-dependent selection. These results support the hypothesis that sperm availability and sexual conflict influence the evolution of gamete recognition systems in broadcast spawners and highlight the benefits of combining fitness measures with molecular signatures for estimation of patterns of selection.

    View details for DOI 10.1111/j.1558-5646.2009.00850.x

    View details for Web of Science ID 000274713800013

    View details for PubMedID 19796148

  • Alginate production affects Pseudomonas aeruginosa biofilm development and architecture, but is not essential for biofilm formation JOURNAL OF MEDICAL MICROBIOLOGY Stapper, A. P., Narasimhan, G., Ohman, D. E., Barakat, J., Hentzer, M., Molin, S., Kharazmi, A., Hoiby, N., Mathee, K. 2004; 53 (7): 679-690


    Extracellular polymers can facilitate the non-specific attachment of bacteria to surfaces and hold together developing biofilms. This study was undertaken to qualitatively and quantitatively compare the architecture of biofilms produced by Pseudomonas aeruginosa strain PAO1 and its alginate-overproducing (mucA22) and alginate-defective (algD) variants in order to discern the role of alginate in biofilm formation. These strains, PAO1, Alg+ PAOmucA22 and Alg- PAOalgD, tagged with green fluorescent protein, were grown in a continuous flow cell system to characterize the developmental cycles of their biofilm formation using confocal laser scanning microscopy. Biofilm Image Processing (BIP) and Community Statistics (COMSTAT) software programs were used to provide quantitative measurements of the two-dimensional biofilm images. All three strains formed distinguishable biofilm architectures, indicating that the production of alginate is not critical for biofilm formation. Observation over a period of 5 days indicated a three-stage development pattern consisting of initiation, establishment and maturation. Furthermore, this study showed that phenotypically distinguishable biofilms can be quantitatively differentiated.

    View details for DOI 10.1099/jmm.0.45539-0

    View details for Web of Science ID 000222535400015

    View details for PubMedID 15184541