Projects

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
A reservoir of stem-like CD8+ T cells in the tumor-draining lymph node preserves the ongoing antitumor immune response
Stem-like CD8+ T cells in dLN maintain stemness and protect antitumor T cells from terminal differentiation in the TME.

KA Connolly, M Kuchroo, A Venkat,…,NS Joshi. Science Immunology 2021.
Paper Manuscript Published
A reservoir of stem-like CD8+ T cells in the tumor-draining lymph node preserves the ongoing antitumor immune response
Beta cells are essential drivers of pancreatic ductal adenocarcinoma development
Disentangling the origin of β cells misexpressing pro-tumorigenic hormones in the context of obesity and other stressors.

C Garcia*, A Venkat*, DC McQuaid*,…,S Krishnaswamy, MD Muzumdar. In Revision.
Paper Yale Single Cell Symposium 2022 Manuscript in Revision
Beta cells are essential drivers of pancreatic ductal adenocarcinoma development
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
Inferring dynamic regulatory interaction graphs from time series data with perturbations
RiTINI infers time-varying interaction graphs to predict casual behavior of a system. D Bhaskar, S Magruder, E De Brouwer, A Venkat, F Wenkel, G Wolf, S Krishnaswamy. LoG Conference 2023.
Paper Code LoG 2023 Manuscript Published
Inferring dynamic regulatory interaction graphs from time series data with perturbations
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
Multiscale geometric and topological analyses for characterizing and predicting immune responses from single cell data
This review describes approaches to characterize immune heterogeneity at multiple resolutions.

A Venkat, D Bhaskar, S Krishnaswamy. Cell Trends in Immunology.
Paper Manuscript Published
Multiscale geometric and topological analyses for characterizing and predicting immune responses from single cell data
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
Revealing dynamic temporal regulatory networks driving cancer cell state plasticity with neural ODE-based optimal transport
TrajectoryNet learns continuous and cell-specific trajectories from longitudinal single-cell data.

A Tong*, M Kuchroo*, S Gupta, A Venkat,…,CL Chaffer, S Krishnaswamy. In Review.
Paper Code Manuscript in Review
Revealing dynamic temporal regulatory networks driving cancer cell state plasticity with neural ODE-based optimal transport