Jonathan Liu

Jonathan Liu

Data Scientist II, Computational Biology

Chan-Zuckerberg Biohub

About Me

I am a computational biologist in the Quantitative Cell Sciences team of the data science platform at the Chan Zuckerberg Biohub in San Francisco. There I use single-cell and spatial transcriptomics technologies to study the fundamental cell biology of development and infectious disease. My current focus is on developing downstream analysis methods for imaging-based spatial transcriptomics to study systems such as the developing zebrafish embryo. I also have an interest in developing statistical analyses for single-cell atlas datasets. My broad research interests lie at the intersection of emerging technologies and the immediate data analysis, and I particularly enjoy working closely with experimentalists to maximize the investigatory power of cutting-edge scientific instrumentation.

Before coming to the Biohub, I did my undergraduate studies in Applied Physics at Caltech and got a PhD in Physics at UC Berkeley, where I studied the biophysics of gene regulatory networks with Hernan Garcia. There, I focused on developing statistical techniques and models to quantify biophysical parameters from eukaryotic transcriptional data acquired through live cell imaging. I also spent a year working in origins-of-life research with Dieter Braun at the Ludwig Maximilian University in Munich, Germany, under the sponsorship of the U.S. Fulbright Student Fellowship. Although my background is in traditional physics, I have picked up a lot of familiarity with biology along the way and often inhabit the border between physics and biology, as well as between theory and experiment.

Check out my CV here as well as my resume here. Please feel free to reach out if you’d like to connect or chat. I am also available for technical consultation for matters regarding single-cell and/or spatial biology.

Outside of research, I am deeply committed to science communication and community building. I have given numerous talks to wide range of audiences, both expert and nonexpert, and regularly write scientific articles for the Berkeley Science Review. For the past few years, I have also been involved with industry-academia connections, serving on the team of Beyond Academia, a student-run organization at UC Berkeley that brings together hundreds of PhDs in industry every year.

Beyond my scientific life, I am an active collaborative pianist in the Bay Area. In my free time I enjoy reading speculative fiction, running, cooking, and social dancing.


jonathan dot liu at czbiohub dot org

Twitter: @jhliu42

LinkedIn: in/jonathan-liu-b004103b/


  • Spatial and single-cell biology
  • Statistical inference
  • Modeling
  • Computational image analysis


  • PhD in Physics, 2021

    UC Berkeley

  • BS in Applied Physics, 2015




Data Scientist II, Computational Biology

Chan-Zuckerberg Biohub

Jan 2023 – Present San Francisco, California

Data Scientist, Computational Biology

Chan-Zuckerberg Biohub

Aug 2021 – Dec 2022 San Francisco, California

Graduate Student Researcher

Garcia Lab, UC Berkeley

Aug 2016 – Jul 2021 Berkeley, California
Funded by Department of Defense NDSEG fellowship.

Visiting Researcher

Braun Lab, LMU Munich

Sep 2015 – Jul 2016 Munich, Germany
Funded by U.S. Fulbright Scholar program.

Selected Publications

Jonathan Liu*, Vanessa Tran*, Venkata Naga Pranathi Vemuri, Ashley Byrne, Michael Borja, Yang Joon Kim, Snigdha Agarwal, Ruofan Wang, Kyle Awayan, Abhishek Murti, Aris Taychameekiatchai, Bruce Wang, George Emanuel, Jiang He, John Haliburton, Angela Oliveira Pisco, Norma Neff. (2022) Concordance of MERFISH spatial transcriptomics with bulk and single-cell RNA sequencing. *Life Science Alliance*. (*equal contribution)

The COVID Tissue Atlas Consortium. (2022) Comprehensive characterization of the transcriptional response to COVID-19 in multiple organs reveals shared signatures across tissues. bioRxiv.

Yang Joon Kim, Kaitlin Rhee, Jonathan Liu, Selene Jeammet, Meghan A Turner, Stephen J Small, Hernan G Garcia. (2022) Predictive modeling reveals that higher-order cooperativity drives transcriptional repression in a synthetic developmental enhancer. eLife.

Jonathan Liu, Donald Hansen, Elizabeth Eck, Yang Joon Kim, Meghan A Turner, Simon Alamos, Hernan G Garcia. (2021) Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage. PLoS Computational Biology.

Elizabeth Eck*, Jonathan Liu*, Maryam Kazemzadeh-Atoufi, Sydney Ghoreishi, Shelby Blythe, Hernan G Garcia. (2020) Quantitative dissection of transcription in development yields evidence for transcription factor-driven chromatin accessibility eLife 2020;9:e56429. (*equal contribution)

Matthias Morasch, Jonathan Liu, Christina F Dirscherl, Alan Ianeselli, Alexandra Kühnlein, Kristian Le Vay, Philipp Schwintek, Saidul Islam, Mérina K Corpinot, Bettina Scheu, Donald B Dingwell, Petra Schwille, Hannes Mutschler, Matthew W Powner, Christof B Mast, Dieter Braun. (2019) Heated gas bubbles enrich, crystallize, dry, phosphorylate and encapsulate prebiotic molecules Nature Chemistry 11:779–788