At the Raychaudhuri Lab, we study the basis of immune mediated disease using techniques in human genetics, bioinformatics, and systems biology.
Below, please click each figure to visit the associated publication.
- Distinct HLA Associations with Rheumatoid Arthritis Subsets Defined by Serological Subphenotype
- Fast, sensitive and accurate integration of single-cell data with Harmony
- Early progression to active tuberculosis is a highly heritable trait driven by 3q23 in Peruvians
- Defining Inflammatory Cell States in Rheumatoid Arthritis Joint Synovial Tissues by Integrating Single-cell Transcriptomics and Mass Cytometry
- IMPACT: Genomic annotation of cell-state-specific regulatory elements inferred from the epigenome of bound transcription factors
- Lymphocyte innateness is defined by underlying transcriptional states reflecting a balance between proliferation and effector functions
Soumya Raychaudhuri's Twitter
Autoimmune variants were enriched in cell-state-dependent eQTLs, such as an RA variant near ORMDL3 strongest in cytotoxic CD8+ T cells. This suggests that cell state context is important for disease-associated eQTLs. t.co/OZwL7aulEn
In some instances, multiple independent SNP effects acting on the same gene might respond differently to cell-state differences. t.co/nU48rMsl0S
Over one-third of the 6,511 cis-eQTLs had state-dependent effects, which we could calculate at single-cell resolution. t.co/Db88w79feh
We modeled eQTLs with a Poisson mixed effects model robust to single-cell sparsity and differential expression that can occur with cell-state changes. t.co/dBL1Z1F2oE
Here, we modeled continuous T cell states at single-cell resolution by integrating RNA and 31 T cell surface proteins. t.co/C2CUjk7pmr