Anders Sejr Hansen, PhD



Associate Professor of Biological Engineering


Single-molecule approaches in living cells
3D genome organization and gene regulation
Biophysics of nuclear organization


Computational & Systems Biology Initiative [CSBi]
Associate Member, Broad Institute of MIT and Harvard
Extramural member, Koch Institute for Integrative Cancer Research


Anders obtained his undergraduate and Master’s degree in Chemistry at Oxford University in 2010. He received his PhD in Chemistry and Chemical Biology from Harvard University in 2015, where he worked with Erin O’Shea and applied systems biology approaches to understand how cells can encode and transmit information in the dynamics of transcription factor activation. For his post-doc at UC Berkeley with Robert Tjian and Xavier Darzacq, Anders developed new imaging approaches for dissecting the dynamics of 3D genome organization with single-molecule resolution in living cells. Anders joined MIT as an Assistant Professor of Biological Engineering in early 2020.


Exquisite regulation of gene expression in time and space underlies essentially all biological processes. However, understanding gene regulation in mammals is challenging because mammalian genomes are enormous and largely non-coding. Specifically, mammalian genes are controlled by enhancers that can be hundreds of kilobases away from the genes they control. How the cell ensures that the right enhancer contacts and activates the right gene in 3D is not well understood. We are broadly interested in understanding the interplay between 3D genome organization and the regulation of gene expression, with a particular focus on development and disease.

We take a unique approach to these problems. Most biological processes are inherently dynamic, yet most current methods generate static snapshots and cannot report on dynamics. To overcome these limitations, we develop new experimental, optical and computational methods for following processes at the single-molecule level with millisecond and nanometer precision in time and space inside living cells. We integrate these approaches with traditional methods from genomics, biochemistry, genome-editing, stem cell differentiation and organoid modeling. Current areas of interest include:

  • The molecular mechanisms that regulate 3D genome organization
  • Regulation of 3D genome organization and transcription during development and their dysregulation in cancer
  • Developing new tools for following single-molecules inside of living cells
  • Developing predictive computational models of 3D genome organization
  • Applying and testing our understanding through synthetic biology approaches

Research Areas: 

Honors & Awards: 

K99/R00 Pathway to Independence, 2019-2023
NIH Director’s New Innovator Award, 2020-2025
Pew-Stewart Scholar in Cancer Research, 2021-2025