Research

We study developmental rules and synthetically reconstruct tissue patterning

Many diseases arise from a breakdown in tissue structure, including cancers and congenital birth defects. We aim to reverse engineer the interactions between cells and their local environment that create and maintain the structure of tissues in the body.

We are particularly interested in learning to control patterning processes that occur in embryos, where the blueprint of adult tissues is established. We approach this by developing new cellular imaging, tissue construction, soft materials, and micro-scale engineering techniques.

We aim to reverse engineer the interactions between cells and their local environment that create and maintain the structure of tissues in the body.
cells_beacon3.png

SINGLE-CELL CONTRIBUTIONS TO TISSUE PATTERNING

The engineering rules that link single-cell phenotype to collective cell behavior are not well understood. Developmental processes such as cell intercalation, planar cell polarity, germ layer patterning, and body axis patterning are engineering black boxes because of this. We use cell sheet engineering, optogenetics, and single-cell analysis approaches to decode these engineering rules.   


Organ-scale hierarchical patterning of organoids

Organs such as the kidney have a repetitive spatial organization of functional units that is not currently engineerable. We aim to mimic aspects of branching and folding morphogenesis to give organoid models a repeatable mesoscale structure. These efforts will make organoid systems larger and more repeatable, improving their application in drug screens and regenerative medicine.

plotter_cells_crop.png

neuralcrest_crop.png

migratory and fate decisions in the neural crest

Neural crest cells constitute a traveling stem cell compartment that contribute to a staggering diversity of tissues in the body. Neural crest cells make highly coordinated, collective decisions to migrate and differentiate in embryos, in response to a complex set of cell-cell and cell-matrix cues. We aim to determine a minimal set of these cues to develop a code that prescribes neural crest decision-making in reconstituted tissues. These efforts will inform better models of human congenital disorders, a third of which result from neural crest dysfunction.


human-computer interfaces to tackle large image set analysis

High-throughput characterization of biological image data is a bottleneck in many scientific areas. We are crowd sourcing high-quality annotations from large groups of human workers with little formal scientific training. We have developed a publicly available website, quanti.us, in close collaboration with software engineering and computer science experts. Researchers can easily setup arbitrary image annotation jobs for problems where it is difficult or expensive to produce specific segmentation algorithms. These approaches enable training of tailored machine learning algorithms. Development of human-machine image analysis pipelines will make the scientific endeavor more nimble and quantitative for life scientists.

rawoverlays_clustered_indiv_stack_cleaned_bin2_8bitcolor.gif
 
BF_5x001_Composite_bged_smaller.png