PIPages
Labs

Allon Klein

Harvard University, MA·Biomedical Engineering

Many of biology's key questions require measuring individual cells and their partners. For example: which genes a bacterium switches on, how immune cells respond to a pathogen, or how two cells signal to each other.

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Fields

Biomedical Engineering

Genetics

Biology

Topics

micro-capsules

droplet microfluidics

single-cell RNA-seq

Grants
4 known grants, through Jun 2029

What they work on

  1. Optimize single-lineage RNA-Seq in CAGE capsules and produce a benchmark bacterial Perturb-seq dataset that knocks down every E. coli transcription factor using CRISPR interference.
  2. Co-encapsulate human immune cells with microbes in CAGEs to read immune transcriptional responses together with pathogen identity, and test that capsules do not alter immune cell behavior.
  3. Build and benchmark a capsule prototype that screens millions of live cell–cell interactions for desirable ones, using receptor agonist and antagonist screens to measure false-positive and false-negative rates.
  4. Develop a capsule method that systematically maps how DNA sequence or signaling environment affects cell activity, and expand capsule chemistries and sizes from bacteria to organoids.
  5. Optimize Mosaic in Vivo Perturbation in zebrafish, using transposon-delivered CRISPR guide libraries and single-cell RNA-seq to measure the function of all transcription factors in eye development.
  6. Develop a capsule-based readout of cell type that scales to very large numbers of cells, and build validated whole-genome MVP CRISPR libraries.
  7. Benchmark CapFlow, capsule-amplified multiplexed mRNA flow cytometry, and CapCycle, cyclic imaging of 50 or more transcripts and surface proteins, for rapid profiling of the tumor microenvironment.

More about the research

Current methods examine only thousands of cells at a time, or struggle with bacteria at all. This lab builds micro-capsules, tiny shells with a hollow core and a semi-permeable wall that form around cells within droplets. Unlike oil-sealed droplets, capsules are sturdy, let small molecules pass through, and can be processed in ordinary water-based solutions. They also hold cells through many steps of growth, treatment, staining, imaging and sorting. Across four projects, the lab applies capsules and single-cell sequencing to bacteria, cell–cell interactions, tumors and zebrafish eye development.

Why it matters

These tools could let many labs study how genes control bacterial function and how the immune system responds to pathogens. They could also speed the discovery of therapeutic proteins and antibodies that change cell signaling. For cancer researchers, faster and cheaper profiling of tumor cells could help evaluate new drugs and identify cells that predict patient outcomes. The zebrafish screens could produce a catalog of gene function in the eye, relevant to eye diseases with large unmet medical needs.

Known grants

From NIH and NSF research grants. Labs often have other funding we can't see.

Mosaic in Vivo Perturbation (MVP) for systematic assessment of gene function in the eye

NIH · Sep 2024 – Jun 2029

Micro-capsule technology for high-throughput analyses of cell-cell interactions

NIH · Sep 2024 – Aug 2028

CAGE-Enabled Single-Lineage RNA-Seq for Bacterial PERTURB-Seq and Host-Pathogen Interaction Analysis

NIH · May 2026 – Apr 2028

Closest labs

Saeed Tavazoie

Columbia University, NY·Genetics

Identify the protein and DNA effectors of stochastic tuning, in which yeast cells use random gene-expression noise to adapt, using CRISPR interference, reporter assays and chemical, genetic and optogenetic perturbations of single cells in microfluidic devices.

Daniel Lim

University of California-San Francisco, CA·Neuroscience

Test whether the brain-specific lncRNA Pnky contains structural modules, such as a pseudoknot (a looped RNA fold), that are needed for its control of neuron production from neural stem cells.

Adam R. Abate

University of California-San Francisco, CA·Biomedical Engineering

Develop gigapixel PCR (gPCR), which pairs microfluidic-free self-assembled droplets with capillary electrophoresis readout, to quantify over 100 pathogen DNA targets in one reaction. Validate it against SeraCare reference standards.

The school

Harvard University: 42 labs on PI Pages, $1.5B a year on research, 712 research doctorates a year.

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