I am a scientist with a broad, interdisciplinary background encompassing experimental biophysics, quantitative biochemistry, microscopy, and computation. I am currently developing software tools and a data science program for live cell, single molecule microscopy-based drug discovery at Eikon Therapeutics.

I received my Ph.D. from the California Institute of Technology in 2012 with Rob Phillips, where I used a brightfield microscopy assay, along with theoretical modeling, to make precise measurements of sequence-dependent DNA flexibility and its role in bacterial transcriptional regulation. I then completed postdoctoral research at the University of California, San Francisco, in Geeta Narlikar’s lab, where I used conventional biochemistry and a surface-attached fluorescence microscopy assay to study a class of essential enzymes called chromatin remodelers. My work led to several novel insights into these enzymes, including the first mechanistic dissection of a poorly characterized remodeler called INO80, with implications for INO80’s roles in transcriptional regulation and DNA damage repair.

I also develop software and tutorials for the community.

I am an avid runner and hiker; the image at the start of the CV section was taken on one of my favorite hikes in the Santa Cruz mountains.

Contact

johnson DOT stephanie076 AT gmail DOT com
Twitter: @StephL_Johnson
in/stephanie-johnson-phd

Johnson S.L., Narlikar G.J. (2020) ATP hydrolysis coordinates the activities of two motors in a dimeric chromatin remodeling enzyme. bioRxiv.

Armache J.P.*, Gamarra N.*, Johnson S.L., Leonard J.D., Wu S., Narlikar G.J., and Cheng Y. (2019) Electron cryo-microscopy structure of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome. eLIFE 8: e46057. (*equal contribution)

Gebala M., Johnson S.L., Narlikar G.J., and Herschlag D. (2019) Ion counting demonstrates a high electrostatic potential of the nucleosome. eLIFE 8: e44993.

Gamarra N., Johnson S.L., Trnka M., Burlingame A.L., and Narlikar G.J. (2018) The nucleosomal acidic patch relieves auto-inhibition by the ISWI remodeler SNF2h. eLIFE 7:e35322.

Zhou C.Y.*, Johnson S.L.*, Lee L.J., Longhurst A.D., Beckwith S.L., Johnson M.J., Morrison A.J., and Narlikar G.J. (2018) The yeast INO80 complex operates as a tunable DNA length-sensitive switch to regulate nucleosome sliding. Mol Cell 69: 677-688. (* equal contribution)

Zhou C.Y., Johnson S.L., Gamarra N.I., and Narlikar G.J. (2016) Mechanisms of ATP-dependent chromatin remodeling motors. Annu Rev Biophys 45: 153-81.

Chen Y.-J.*, Johnson S.*, Mulligan P.*, Spakowitz A., and Phillips R. (2014) Modulation of DNA loop lifetimes by the free energy of loop formation. Proc Natl Acad Sci 111(49):17402-17407. (* equal contribution)

Johnson S., van de Meent J.-W., Phillips R., Wiggins C., and Lindén M. (2014) Multiple Lac-mediated loops revealed by Bayesian statistics and tethered particle motion. Nucleic Acids Res 42(16): 10265-10277.

Johnson S.*, Chen Y.-J.*, and Phillips R. (2013) Poly(dA:dT)-rich DNAs are highly flexible in the context of DNA looping. PLOS ONE 8(10): e75799. (* equal contribution)

Boedicker J., Garcia H.G., Johnson S., and Phillips R. (2013) DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation. Physical Biology 10(6): 066005.

Johnson S., Lindén M., and Phillips R. (2012) Sequence dependence of transcription factor-mediated DNA looping. Nucleic Acids Res 40(16): 7728-7738.

Flemming E., Johnson S. (2007) Rosa’s roses: reduced vowels in American English. Journal of the International Phonetic Association 37: 83-86.

Long-form CV (pdf)

Professional Experience

2020 - present
Eikon Therapeutics
Software Engineer
Developing software tools and a data science program for live cell, single molecule microscopy-based drug discovery.

2019
Adecco for Google
Research Scientist Consultant
Worked with the Google Accelerated Science team to produce breakthroughs in the natural sciences by applying Google technologies.

Education/training

2013 - 2019
University of California, San Francisco
Postdoctoral fellow in Biochemistry and Biophysics
Mechanistic dissection of ATP-dependent chromatin remodeling motors using a combined ensemble biochemistry and single-molecule biophysics approach.
Advisor: Geeta Narlikar

2012
California Institute of Technology
Postdoctoral scholar in Applied Physics
Role of DNA sequence and bacterial architectural proteins in transcriptional regulation.
Advisor: Rob Phillips

2006 - 2012
California Institute of Technology
Ph.D. in Biochemistry and Molecular Biophysics
Thesis: DNA mechanics and transcriptional regulation in the E. coli lac operon.
Advisor: Rob Phillips

2002 - 2006
Stanford University
B.S. with honors in Biological Sciences
Minor in Symbolic Systems (individually designed, combining computer science and linguistics)
Honors thesis: A molecular helping hand: Towards an understanding of the force dependence of transcription through roadblocks.
Advisor: Steven Block

Awards/fellowships

Best Poster Prize at the 2016 American Society for Biochemistry and Molecular Biology special symposium on Transcriptional Regulation: Chromatin and RNA Polymerase II (October 10, 2016).

Leukemia and Lymphoma Society Career Development Program Fellow (2014-2017).

National Science Foundation Graduate Research Fellowship (2008-2011).

Virginia Gilloon Fellowship for Women in Science and Engineering (California Institute of Technology internal fellowship) (2006).

Graduated from Stanford University with Distinction and Honors (2006).

Phi Beta Kappa (2006).

Talks

“Regulation of rapid nucleosome sliding by the INO80 chromatin remodeling complex”, talk given at the 2018 Biophysics of Nuclear Organization and Function QB3 Symposium, Berkeley, CA, July 24, 2018.

“Mechanism of nucleosome sliding in yeast INO80 as revealed by single-molecule FRET”, talk given at the 2017 EMBO conference The Nucleosome: from Atoms to Genomes, Heidelberg, Germany, August 31, 2017.

“Protomer coordination in a dimeric chromatin remodeling motor”, Best Poster Prize talk at the 2016 American Society for Biochemistry and Molecular Biology special symposium on Transcriptional Regulation: Chromatin and RNA Polymerase II, Snowbird, UT, October 10, 2016.

“Transcription factor mediated looping and the role of DNA flexibility”, talk given at the Coarse-Grain Mechanics of DNA: Part II from Electrons to Oligomers CECAM conference at the Swiss Federal Institute of Technology Lausanne (EPFL), Switzerland, September 1, 2011.

Teaching/mentoring

2014 - 2016: Direct supervisor for two San Francisco State masters students as part of a joint UCSF-SF State program aimed at recruiting under-represented minorities into post-graduate STEM programs.

2007 - 2010: Mentored two Caltech undergraduates on their senior thesis projects (in physics and applied physics), and a summer undergraduate research assistant.

2009, 2010, 2012: Teaching assistant for BE/APh 161: Physical Biology of the Cell at the California Institute for Technology (graduate course in the application of statistical mechanics to problems in biology). Head TA 2009 and 2010.

2007, 2008, 2009, 2011: Teaching assistant for BE/APh 262: Physical Biology Bootcamp at the California Institute for Technology (week-long intensive introductory biophysics lab course).

2008: Teaching assistant for Bi 1: Biology and Biophysics of Viruses at the California Institute for Technology (introductory biology for non-majors).

2006: Teaching assistant for Bi/Ch 110: Introduction to Biochemistry at the California Institute for Technology.

Traces, single-molecule FRET analysis code

Slopey, for the quantification of single-molecule FRET trajectories containing fast, non-instantaneous transitions (see these slides for an introduction to Slopey and its application to the analysis of a chromatin remodeler’s reaction mechanism)

Histograms vs CDFs, on the uses of histograms, KDEs, and CDFs for cluster analysis

Are my data exponentially distributed?, on how to determine underlying distributions that your data could be drawn from

Bootstrapped error calculations, on estimating errors based on a bootstrapping method