Our Interests

We seek to understand the control of gene expression. Differences in gene expression underlie the tremendous variety of cell types in our bodies and account for most of the innate differences between you and me or between me and chimpanzee. These differences are encoded in the non-transcribed parts of our genome called cis regulatory elements, regions that bind proteins (in a sequence dependent manner), which regulate transcription of surrounding genes. Surprisingly, these regulatory elements can be very far away (in linear-sequence) from the transcribed elements they control, frequently tens to hundreds of thousands of basepairs apart.  A major direction in the lab is to understand how such long-range interactions occur, how they achieve target specificity, and how they may be reprogrammed by alterations to the genome sequence.


We believe the answers to these questions require understanding the 3D organization of the genome. While interactions between regulatory elements and transcribed elements are long-range, they still occur only on the same chromosome (in cis) and are not known beyond the scale of a couple megabases. This is one line of evidence suggesting physical proximity of the elements is necessary for regulatory interaction. Moreover, if one regulatory element is artificially inserted immediately next to a transcribed element that it does not normally regulate, it will generally start to modify transcription, indicating that physical proximity is generally sufficient for regulatory interaction.  Nonetheless, it is not well understood how the genome is organized in the 3D environment of the nucleus to promote the correct interactions and avoid potentially deleterious ones or what mechanisms regulate this organization.

Our tools

To answer these questions we need new tools.  Our lab is engaged in using developing and combining new technologies to enable this research, including:

  • super-resolution imaging
  • single molecule microscopy
  • genetic engineering
  • next generation sequencing approaches
  • mathematical and biophysical modeling

See our research projects below for some examples of this approach in action.


Visualizing cis-regulation

Visualizing cis-interactions in vivo

Spatially resolved transcriptomics


super-resolution microscopy of the 3D genome

3D Genome Structure


Positions Available

Graduate Student Positions

Ask me about rotation projects!  Graduate students from any program interested in gene regulation, genome structure, advanced microscopy, and/or quantitative biology are encouraged to visit. Please contact Alistair by email: boettiger at stanford dot edu to set up a time.   Potential Rotation Projects: Imaging insulator activity in action. Structural relationships of enhancers and promoters in development. Advanced error-correction codes […]

Postdoctoral Positions

Postdoctoral positions available.  Please send a C.V. and contact information for three references to boettiger at stanford dot edu. Additional information on working and living in the Stanford area and the resources available to postdocs: Stanford Office of Postdoctoral Affairs. http://postdocs.stanford.edu/

Undergraduate Research Positions

Available immediately: advanced optics research assistant. Interested in learning about single molecule imaging? Design and assembly of optics? Programming instrument control software?  Join the lab as an undergraduate researcher and assist in the building and/or programming of our first super-resolution Stochastic Optical Reconstruction Microscopy setup!  Previous course experience in optics, electromagnetism, or python advantageous but not required.  Commitment 4-10 hrs/wk.

See all positions