I am a data scientist at insitro, where I am part of the Computational Biology team. I focus on using classical and applied ML analysis techniques for imaging and sequencing-based high throughput screening efforts. My broad scientific 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 assays.
Previously, I was a computational biologist at Chan Zuckerberg Biohub SF. There I used single-cell and spatial transcriptomics technologies to study the fundamental cell biology of development and infectious disease. My focus was on developing downstream analysis methods for imaging-based spatial transcriptomics to study systems such as the developing zebrafish embryo.
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 resume here. Please feel free to reach out if you’d like to connect or chat.
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 and also heavily involved with the social dancing community as a teacher and DJ.
Contact
jhkliu42 at gmail dot com
Twitter: @jhliu42
LinkedIn: in/jonathan-liu-b004103b/
PhD in Physics, 2021
UC Berkeley
BS in Applied Physics, 2015
Caltech
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