01
Genetic Perturbations
We use state-of-the-art genetic perturbation assays to map how biological systems change in response to perturbations of genes and regulatory elements—millions of cells at a time.
Functional Perturbation Lab
Based at the New York Genome Center, we study how biological systems respond to precise perturbations. Our research involves highly scalable multimodal experimental approaches to investigate causal mechanisms in biology.
Our work
Research areas
02
Technology Development
Develop new single-cell tools that capture more cells and modalities, improve data quality, and reduce costs.
03
Neurological Disease Biology
Use genetic perturbations in human models of neurological disease to uncover disease mechanisms and advance therapeutic development.
Publications
Relevant publications
Genome-wide single-cell perturbation screens with VIPerturb-seq
Bradu A, Blair JD, Grabski IN, Mascio I, Lee J, McCormick C, Satija R · bioRxiv · February 13, 2026 · PMCID: PMC12919025
Iterative, multimodal, and scalable single-cell profiling for discovery and characterization of signaling regulators
Blair JD, Bradu A, Dalgarno C, Grabski IN, Satija R · bioRxiv · August 30, 2025 · PMCID: PMC12407899
Phospho-seq: integrated, multi-modal profiling of intracellular protein dynamics in single cells
Blair JD, Hartman A, Zenk F, Wahle P, Brancati G, Dalgarno C, Treutlein B, Satija R · Nature Communications · 16(1):1346 · PMCID: PMC11794950
mTORC1 activation drives astrocyte reactivity in cortical tubers and brain organoid models of TSC
Li TL, Blair JD, Yoo T, Grant GA, Hockemeyer D, Porter BE, Bateup HS · bioRxiv · March 18, 2025 · PMCID: PMC11908165
Genetically engineered human cortical spheroid models of tuberous sclerosis
Blair JD, Hockemeyer D, Bateup HS · Nature Medicine · 24(10):1568–1578 · PMCID: PMC6261470
Resources
Tools & resources
ProtocolsExperimental protocols and supporting materialsProbeMakerDesign custom DNA probes for use in 10x FLEX experimentsCRISPR Seed FinderScan TSS windows for PAM-proximal seed matchesCRISPR Seed Hit BrowserBrowse guide- and gene-level seed hits for the Dolcetto library only, with differential-expression overlaysFlex v2 Cost CalculatorEstimate hybridization, GEM lane, and sequencing costs
Source and documentation on GitHub The lab
People
Platform Lead
John Blair, PhD
John Blair received his PhD from the University of California, Berkeley, where he worked in Dr. Helen Bateup's lab and established human neuronal models of Tuberous Sclerosis. This work combined 3D human stem cell differentiation, CRISPR-mediated stem cell engineering, and single-cell sequencing. He completed his postdoctoral training in Dr. Rahul Satija's lab at the New York Genome Center, where he developed multimodal technologies for single-cell sequencing with intracellular protein quantification and perturbations—including Phospho-seq and FlexPlex—as well as VIPerturb-seq for large-scale Perturb-seq in fixed samples.
Full bibliographyCollaborations
Collaborations
We welcome sponsored research projects, subcontracts, and collaborative grant applications. Please fill out the form below to reach out and someone will be in contact with you shortly.
Contact the labContact
Contact
Emailjblair@nygenome.org
LocationNew York Genome Center
101 Avenue of the Americas
New York, NY 10013
101 Avenue of the Americas
New York, NY 10013