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 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. Undergraduates interested in working on a summer research project in 2018 are encouraged […]

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 […]

MERFISH

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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 […]

3-D 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. […]