Cellular Signaling

AAnet resolves a continuum of spatially-localized cell states to unveil tumor complexity
AAnet is a neural network for nonlinear archetypal analysis of single-cell data.

A Venkat*, S Youlten*,…,S Krishnaswamy, CL Chaffer. Cancer Discovery In Revision.
Paper Code CSHL Systems Immunology 2021 Manuscript in Revision
AAnet resolves a continuum of spatially-localized cell states to unveil tumor complexity
Directed Scattering for Knowledge Graph-based Cellular Signaling Analysis
DSAE employs a directed version of a geometric scattering transform for embedding nodes of directed graphs.

A Venkat*, J Chew*, F Cardoso Rodriguez, CJ Tape, M Perlmutter, S Krishnaswamy. ICASSP 2024.
Paper Code GSP 2023 Manuscript Published
Directed Scattering for Knowledge Graph-based Cellular Signaling Analysis
Graph Fourier MMD for Signals on Graphs
GFMMD embeds signals defined on graphs via an optimal witness function.

S Leone, A Tong, G Huguet, A Venkat, G Wolf, S Krishnaswamy. SampTA 2023.
Paper Code SAMPTA 2023 Manuscript Published
Graph Fourier MMD for Signals on Graphs
Mapping the gene space at single-cell resolution with gene signal pattern analysis
GSPA learns gene-gene relationships from single-cell data by embedding the gene space.

A Venkat, S Leone, S Youlten, E Fagerberg, J Attanasio, NS Joshi, S Krishnaswamy. Nature Computational Science 2024.
Paper Blog Post Code ISMB 2021 Immunology 2023 Manuscript Published
Mapping the gene space at single-cell resolution with gene signal pattern analysis
PD-1 maintains CD8 T cell tolerance towards cutaneous neoantigens
PD-1 avoids immunopathology by preventing CD8 T cells to attain fully functional state.

M Damo, N Hornick, A Venkat,…,S Krishnaswamy, N Joshi. Nature 2023.
Paper Manuscript Published
PD-1 maintains CD8 T cell tolerance towards cutaneous neoantigens
Single-cell analysis reveals transcriptional dynamics in primary parathyroid tissue
The first parathyroid single-cell atlas of primary parathyroid tissue.

A Venkat*, M Carlino*, B Lawton*,…,S Krishnaswamy, D Krause. Genome Research 2024.
Paper HypoPara Think Tank 2022 Code Manuscript Published
Single-cell analysis reveals transcriptional dynamics in primary parathyroid tissue