The main focus of our group is single cell systems biology.  We use highly-multiplexed, super-resolution imaging to study gene regulatory networks in cells and organisms. 

We demonstrated a technique that can multiplex detection of 10,000 mRNAs or introns in single cells in culture or in mouse brain slices using sequential fluorescence in situ hybridization (seqFISH+) [link].  We also developed the transcriptome profiling method SPOTs [link] and, together with the Elowitz Lab at Caltech, the lineage tracing system MEMOIR [link].

The Cai Lab, 5-22-2019 at Ojai
Not pictured: Elsy, Mike, Nina, Noushin

News & Events

Congratulations to Elsy for being one of fifteen scientists awarded the 2019 HHMI Hanna H. Gray Fellowship! Click here to learn more!

Congratulations Dr. Yandong Zhang for a successful PhD defense!

Our new paper published in Nature!
"Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+"

Our new paper published in Cell!
"Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH"

Our new Nature Communications paper published!
"Identification of a neural crest stem cell niche by Spatial Genomic Analysis"

Our new Nature Methods paper published!
"Profiling the transcriptome with RNA SPOTs"

Our paper about MEMOIR is highligted on Caltech news!
"The Allen Discovery Center for Cell Lineage Tracing"

Our new paper published on Biophysical Journal!
"Multiplexed Dynamic Imaging of Genomic Loci by Combined CRISPR Imaging and DNA Sequential FISH"

Our recent paper about MEMOIR is highlighted by Nature News! "Systems biology: Molecular memoirs of a cellular family"

Our new Nature paper published!
"Synthetic recording and in situ readout of lineage information in single cells"

Demonstration of 200 mRNAs multiplexing in brain tissues!
"In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus"

Caltech    last update: 11/29/2017