Modeling Gene Divergence Using Optimal Transport
We use optimal transport to look at gene expression as cells differentiate towards a final cell type in sea urchin.
Wasserstein Principal Curves
We demonstrate principal curves in Wasserstein (probability) space on a simulated dataset. We also show how to use the method for ordering data.
Celltype Timing Alignment Between Sea Urchin Species
Using optimal transport to compare developmental timing between sea urchin species.
DemuxHMM: Large-Scale Single-Cell Embryo Profiling via Recombination Barcoding
A new model for demultiplexing large scale scRNA-seq timecourses.
Principal Curves In Metric Spaces And The Space Of Probability Measures
We take a fresh look at the principal curves model in probability space and apply it to scRNA-seq time courses.
andrew-warren
Single-Cell Transcriptomics Reveals Evolutionary Reconfiguration of Embryonic Cell Fate Specification in the Sea Urchin Heliocidaris erythrogramma
We use optimal transport to analyze timing differences between He. urchin and Lv. urchin species.
abdull-j-massri
DNA-GPS: A theoretical framework for optics-free spatial genomics and synthesis of current methods
We develop a scalable framework to perform spatial transcriptomics on scRNA-seq data.
laura-greenstreet
Developmental single-cell transcriptomics in the Lytechinus variegatus sea urchin embryo
We use optimal transport to analyze a time series of sea urchin development and reconstruct published GRNs.
abdull-j-massri