Scott Alan Holley, PhD

Associate Professor of Molecular, Cellular, and Developmental Biology

Departments & Organizations

Animal Organogenesis

Yale Combined Program in the Biological and Biomedical Sciences (BBS): Biochemistry, Biophysics and Structural Biology: Cell Cycle and Signal Transduction | Molecular Cell Biology, Genetics and Development: Development; Imaging (super-resolution); Quantitative/Systems Biology

Office of Cooperative Research

Faculty Research


My doctoral research at the University of Chicago with Chip Ferguson demonstrated the conservation of dorsal-ventral patterning mechanisms between insects and vertebrates, identified noggin as a BMP inhibitor and originated concept of facilitated morphogen diffusion. I was a Damon Runyon Cancer Research Foundation Postdoctoral Fellow with Nobel Laureate Christiane Nüsslein-Volhard at the Max Planck Institute for Developmental Biology in Tübingen, Germany. As a postdoc, I discovered the zebrafish segmentation clock, a genetic mechanism that leads to vertebral defects such as scoliosis when perturbed in humans. My lab at Yale studies systems developmental biology, biophysics and biomechanics of vertebral column development in zebrafish. We combine in vivo biophysics, embryology, genetics, live imaging and systems level data analysis and computer modeling to study pattern formation and morphogenesis. Our experimental approach is driven by the idea that quantitative in vivo analysis will lead to fundamental insights into the emergence of biological organization from the collective interaction of its constituent parts. My lab’s research has been supported by grants from the NIH, NSF, the American Cancer Society and the March of Dimes.

Education & Training

PhD University of Chicago,
Postdoctoral Fellow Max Planck Institut für Entwicklungsbiologie, Tübingen, Germany

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Contact Info

Scott Alan Holley, PhD
Lab Location
Kline Biology Tower
219 Prospect Street, Ste 1038

New Haven, CT 06511
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Office Location
Kline Biology Tower
219 Prospect Street, Ste 1034

New Haven, CT 06511
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Mailing Address
Dept. of MCDB
P.O. Box 208103

New Haven, CT 06520-8103

Holley Lab

Research Image 1

Figure 1. To the left is a photograph of a live zebrafish embryo during the first day of development. Somites are the repeated structures that give rise to the vertebral column and skeletal muscle. New somites are created in the tailbud, which is also the leading edge of the extending trunk and tail. The schematic to the right summarizes differences in the flow of migrating cells in the blue, green and cyan regions of the tailbud.

Research Image 2

Figure 2. Cell movement within the tailbud was imaged, cells were tracked and average cell velocities over a 10 micron radius were calculated in 3D and projected onto a 2-D surface. The warmer colors indicate regions of higher cell velocities. The arrows indicate 2-D projection of the averaged 3-D velocity vectors.

Research Image 3

Figure 3. High-resolution fluorescent in situ hybridization of the oscillating expression of two segmentation clock genes her1 (green) and deltaC (red). Nuclei are blue. These stripes of gene expression sweep though the tissue in a reiterated, wave-like fashion from posterior (right) to anterior (left). This striped pattern created by the “segmentation clock” presages the segmental pattern of morphological somites and, ultimately, the vertebral column.