Lacra Bintu is an Assistant Professor in the Bioengineering Department at Stanford. Her lab performs single-cell measurements of chromatin and gene regulation dynamics, and uses these data to develop predictive models of basic biological processes and improve mammalian cell engineering.

Lacra started working on the theory of gene regulation as an undergraduate with Jané Kondev from Brandeis University and Rob Phillips from Caltech. As a Physics PhD student in the lab of Carlos Bustamante at U.C. Berkeley, she used single-molecule methods to tease apart the molecular mechanisms of transcription through nucleosomes. She transitioned to studying the dynamics of epigenetic regulation in live cells during her postdoctoral fellowship with Michael Elowitz at Caltech. She started her own interdisciplinary lab at Stanford in January 2017.

Academic Appointments

Honors & Awards

  • Career Award at the Scientific Interface, Burroughs Wellcome Fund (2015-2020)
  • Postdoctoral Fellowship, Jane Coffin Childs Memorial Fund for Medical Research (2011-2014)
  • Beckman Fellowship, California Institute of Technology (2011-2014)
  • Harold M. Weintraub Graduate Student Award, Fred Hutchinson Center (2011)
  • Outstanding Graduate Student Instructor Award, University of California, Berkeley (2006)
  • Doris Brewer Cohen Endowment Award for best senior thesis, Brandeis University (2005)
  • Wien International Scholarship, Brandeis University (2001-2005)

Professional Education

  • Postdoctoral Fellow, California Institute of Technology, Biology and Biological Engineering (2016)
  • Ph.D., University of California, Berkeley, Physics (2010)
  • B.S., Brandeis University, Physics, Mathematics, Neuroscience (2005)

2020-21 Courses

Stanford Advisees

Graduate and Fellowship Programs

All Publications

  • Mapping chromatin modifications at the single cell level. Development (Cambridge, England) Ludwig, C. H., Bintu, L. 2019; 146 (12)


    Understanding chromatin regulation holds enormous promise for controlling gene regulation, predicting cellular identity, and developing diagnostics and cellular therapies. However, the dynamic nature of chromatin, together with cell-to-cell heterogeneity in its structure, limits our ability to extract its governing principles. Single cell mapping of chromatin modifications, in conjunction with expression measurements, could help overcome these limitations. Here, we review recent advances in single cell-based measurements of chromatin modifications, including optimization to reduce DNA loss, improved DNA sequencing, barcoding, and antibody engineering. We also highlight several applications of these techniques that have provided insights into cell-type classification, mapping modification co-occurrence and heterogeneity, and monitoring chromatin dynamics.

    View details for DOI 10.1242/dev.170217

    View details for PubMedID 31249006

  • Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements. Nature communications Tycko, J., Wainberg, M., Marinov, G. K., Ursu, O., Hess, G. T., Ego, B. K., Li, A., Truong, A., Trevino, A. E., Spees, K., Yao, D., Kaplow, I. M., Greenside, P. G., Morgens, D. W., Phanstiel, D. H., Snyder, M. P., Bintu, L., Greenleaf, W. J., Kundaje, A., Bassik, M. C. 2019; 10 (1): 4063


    Pooled CRISPR-Cas9 screens are a powerful method for functionally characterizing regulatory elements in the non-coding genome, but off-target effects in these experiments have not been systematically evaluated. Here, we investigate Cas9, dCas9, and CRISPRi/a off-target activity in screens for essential regulatory elements. The sgRNAs with the largest effects in genome-scale screens for essential CTCF loop anchors in K562 cells were not single guide RNAs (sgRNAs) that disrupted gene expression near the on-target CTCF anchor. Rather, these sgRNAs had high off-target activity that, while only weakly correlated with absolute off-target site number, could be predicted by the recently developed GuideScan specificity score. Screens conducted in parallel with CRISPRi/a, which do not induce double-stranded DNA breaks, revealed that a distinct set of off-targets also cause strong confounding fitness effects with these epigenome-editing tools. Promisingly, filtering of CRISPRi libraries using GuideScan specificity scores removed these confounded sgRNAs and enabled identification of essential regulatory elements.

    View details for DOI 10.1038/s41467-019-11955-7

    View details for PubMedID 31492858