Microscope building starts

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Nov 4th, 2016: Assembly of Microscope 1 finally begins, after waiting for renovations and supplies to arrive.   Here’s what the room looked like last month:     Now newly renovated, our optics table has been rigged and floated. Carly help move equipment into the new space. And Simon has assembled several beam expanders for each of the lasers.  They’re […]

Lab Overview

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Our Interest We are interested in studying 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. Differences in gene expression are encoded in the non-transcribed parts of our genome called cis regulatory elements. […]

Graduate Student Positions

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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

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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

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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.

Predictive modeling of genome structure

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Mathematical models allow us to develop rich predictions from quantitative measurement.  This approach to date has been vastly more successful in physics than molecular biology, where models have enable us to predict the existence of fundamental particles long before they are detected in nature, or determine the mass of celestial bodies that we could never put on a scale and […]


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Single molecule fluorescent in situ hybridization (FISH) is a powerful technique to label and count individual RNA molecules of a particular type inside a fixed cell or tissue.  It allows us to study the organization of RNAs within a cell and the organization of cell-types (classified by RNA expression) within a complex tissue or environment.  The ability to have precise […]

Visualizing cis-interactions in vivo

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In order to study the 3D DNA structures which regulate contacts between cis-regulatory elements (CREs) and their target transcribed elements (TEs), we are developing a super-resolution imaging approaches capable of resolving tens to hundreds of individual CREs, TEs, and intervening sequence in single cells of sectioned embryonic tissue and cultured cells at better than 20 nm resolution. We are applying this approach […]

3D Genome Structure

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Differences in gene expression arise due to differences in how accessible the sequence encoding a gene is to the transcription machinery of the cell. While we know much about the structure of DNA at small lengths scales (<1 kilobase) and at large length scales (whole chromosomes), we understand little about its organization at the intermediate scale of kilobases to megabases. […]