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 3-D organization of the genome. While interactions between regulatory elements and genes are long-range, they still occur only on the same chromosome (in cis) and are not known beyond the scale of a couple of megabases, suggesting physical proximity of the elements is necessary for regulation. Moreover, if a regulatory element is artificially placed directly adjacent to a new promoter that it does not normally regulate, it will typically activate transcription from that promoter, indicating that physical proximity is generally sufficient for regulation.  The genome must therefore be folded in such a way to allow communication between all the sequences that need to interact and to segregate those that should not interact.  What this 3-D organization looks like, how it is established, how it changes over development, and what the consequences are for the control of gene expression are all poorly understood questions, which our lab is working to answer.

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

Interested in learning about single-molecule imaging and programming instrument control software?  Join the lab as an undergraduate researcher and assist with programming our two super-resolution Stochastic Optical Reconstruction Microscopy setups!  Previous experience with Matlab or Python is advantageous.  Commitment 4-10 hrs/wk.

See all positions

Lab News


VPUE summer research positions for Stanford undergrads

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Our lab (and others in Developmental Biology) have positions available for current Stanford undergrads to participate in 10-week summer research projects sponsored by the VPUE.  Contact Alistair if you’re interested: boettiger *at* stanford *dot* edu More information on the program is available here.  Applications are due April 1.


Elephant seal walk at Ano Nuevo SP

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Most of the lab braved wet and windy weather to visit Ano Nuevo State Park during the elephant seal pupping and mating season.  Fortunately for us, seals are more active on cold, rainy days and we came came very close to one seal, witnessed a couple of fights, and heard lots of noisy pups. It’s definitely worth a visit!


DevBio retreat in Monterey

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We had another great departmental retreat in Monterey, CA!  Aparna and Leslie both gave excellent talks on their latest findings and we had a chance to hear about the cool work going on in other developmental biology labs. We also spotted some playful dolphins and whales from the hotel — maybe next year we’ll remember to bring binoculars!


Leslie awarded an HHMI Gilliam Fellowship!

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Leslie Mateo was awarded a 2019 Gilliam Fellowship from the Howard Hughes Medical Institute. This award recognizes Leslie’s amazing work, her passion for supporting underrepresented minorities in science, and her leadership potential as a future PI. Congratulations, Leslie! The grant will also provide training to both Leslie and Alistair on creating inclusive environments and promoting diversity in academic science.  You can […]


Poster presentations today at Keystone

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The lab has two poster presentations this evening as part of the Keystone 3D Genome Conference (X6) Leslie Mateo will present “Applying ORCA to visualize chromatin organization and transcription in Drosophila embryos at single-cell resolution” Sedona Murphy & Aparna Rajpurkar will present “Exploring the role of phase transition and polycomb compaction during Drosophila embryogenesis.”


New paper out today!

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  The lab has a new paper online today in Nature. The paper uses a novel imaging approach to visualize chromatin and gene expression in single cells in Drosophila embryos. You can hear more about the research at the Keystone Symposium on the 3D Genome.  Alistair is presenting a talk this evening and Leslie is presenting a poster on Tuesday evening.