Overview
Our Interests
We are a group of scientists interested in understanding gene regulation, with an especial focus on the role of genome structure and development of advanced microscopy techniques. We value diversity, equity and inclusion as cornerstones of what makes science work. We aim to build an environment that embraces self-expression and acknowledges our diverse cultures, opportunities, and experiences rather than one that is color blind and culture blind. We enjoy building things, from molecules, to gene circuits, to microscopes, to software, and aspire to help build a welcoming community in the process.
We seek to understand the control of gene expression. Differences in gene expression underlie the tremendous variety of cell types in our bodies. 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. 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.
Research

Visualizing cis-regulation

Spatially resolved transcriptomics

Biophysical modelling

super-resolution microscopy of the 3D genome
People










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.
Lab News
Congratulations, Minhee!
Posted onMinhee Park was awarded a highly-competitive Damon Runyon postdoctoral fellowship. Congratulations, Minhee! You can read more about the fellowship and Minhee’s project here.
Congratulations, Dr. Leslie Mateo!
Posted onToday Leslie successfully defended her thesis, to cap off nearly four years in the lab. It was a beautiful presentation and the heartfelt remarks that followed led much of the audience to reach for tissues.
Congratulations, Dr. Aparna Rajpurkar!
Posted onThis morning Aparna successfully defended her thesis, the first grad student in the lab to reach this huge milestone. It was an excellent presentation, to top off years of hard work. Congratulations, Aparna!!! We celebrated via Zoom but are hopeful that a more traditional celebration will be possible soon.
Welcome, Kazuki and Geoff!
Posted onWe have recently added 2 new lab members. Kazuki Yoda is a 2nd year graduate student in biophysics and Geoffrey Lovely is a research scientist. Welcome to the lab!
Virtual pumpkin carving
Posted onThis year we kept the lab pumpkin carving tradition alive via Zoom. Nice work, everyone!
Congratulations, Sedona!
Posted onSedona has been awarded a 2020 Bio-X Graduate Fellowship! Congratulations! More information on the fellowship here.
VPUE summer research positions for Stanford undergrads
Posted onOur 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.
Check out Sedona and Alistair’s new review!
Posted onRead more about “Advances in chromatin imaging at kilobase-scale resolution” in Trends in Genetics here.
Welcome, Minhee!
Posted onWe are very excited to have Minhee Park join our lab as a postdoc. Welcome, Minhee!
Elephant seal walk at Ano Nuevo SP
Posted onMost 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!