We are a computational immunology lab at UNC-Chapel Hill, focused on extracting , organizing, and representing information from immune profiling technologies (CyTOF, Flow Cytometry, imaging CyTOF and single-cell RNA-seq). Our overall objective is to identify components of the immune system driving particular disease states that can be modulated for therapeutic effect.

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We are jointly located in Department of Computer Science and Computational Medicine Program at UNC. Our primary focus is in developing new computational methods for automated and efficient analysis of single-cell data profiling the immune system. We are specifically interested in designing new algorithms for extracting signals from high-throughput immune profiling modalities, such as flow and mass cytometry, single-cell RNA sequencing, and recently imaging mass cytometry. We are especially interested in studying how the brain and immune system influence each other, and implications in aging and neurodegeneration. scroll down to read about some of our recent projects!

Research

Featuizing and Creating Summaries of the Immune Sytem : We develop methods to encode the rich information about the immune system collected through modern high-throughput immune-profiling techniques, such as CyTOF and imaging CyTOF into a compact, mathematical abstraction. Such abstractions can be used in downstream clinical prediction tasks.

Metaclustering Approach for Automated Cell Population Discovery Across Multiple Samples. from Stanley et al. Nature Communications. 2020. [Paper]

Metaclustering Approach for Automated Cell Population Discovery Across Multiple Samples. from Stanley et al. Nature Communications. 2020. [Paper]

Set Modeling Meets Flow and Mass Cytometry. from Haidong Yi and Natalie Stanley. Proceedings of ACM-BCB 2021. [Paper on BioArXiv] [Published Paper]

Set Modeling Meets Flow and Mass Cytometry. from Haidong Yi and Natalie Stanley. Proceedings of ACM-BCB 2021. [Paper on BioArXiv] [Published Paper]

 

General. We are interested in developing methods to identify cellular correlates of particular disease states, as assayed with single-cell technologies (flow and mass cytometry and single-cell RNA sequencing). The algorithms we develop enable unsupervised automated cell-population discovery, extraction of biologically meaningful features, and comprehensive visualization. The ultimate goal of these algorithms is to uncover cell-types and signaling pathways that are implicated in some phenotype of interest. We develop our methods in a scalable way so that they can easily accommodate hundreds of samples with millions of cells.

 

Tracking Cell Populations Identified Automatically. Our recent work enables efficient automated cell-population discovery in hundreds of patient samples without throwing any information away. We can further study these identified cell-populations and identify differences in frequency or function of particular immune cell-types that differentiate particular patient phenotypes. These analyses can be used as a complement to or in place of manual gating.

 

Modeling Cytometry Data as Sets. Our recent work explores modeling flow and mass cytometry data as a collection of sets. A set representation is useful for samples profiled with flow and mass cytometry since 1) a variable number of cells are profiled per sample and 2) the order in which cells are profiled as no biological relevance. To predict patient phenotypes, our objective was therefore to predict a label for each set. This was achieved by applying a deep learning approaches for set classification.