Geoffrey R. Schiebinger

Global StationaryOT: Trajectory inference for aging time courses of single-cell snapshots

This paper introduces a method to infer cell trajectories from aging time courses, improving accuracy in noisy data by leveraging temporal information.

DemuxHMM: Large-Scale Single-Cell Embryo Profiling via Recombination Barcoding

The paper introduces DemuxHMM, a recombination-aware demultiplexing method that improves scalability and performance for large-scale single-cell embryo profiling.

Single-cell transcriptomics reveals evolutionary reconfiguration of embryonic cell fate specification in the sea urchin Heliocidaris erythrogramma

The paper uses single-cell RNA sequencing to compare embryonic development in two sea urchin species, identifying evolutionary changes in cell fate specification and signaling.

Cellular proliferation biases clonal lineage tracing and trajectory inference

The paper identifies a statistical bias in lineage tracing and trajectory inference due to cell proliferation rates and shows how to improve trajectory inference methods to account for this bias.

Reconstruction of single cell lineage trajectories and identification of diversity in fates during the epithelial-to-mesenchymal transition

This study uses optimal transport analysis on scRNA-seq data to reconstruct EMT trajectories in MCF10A cells, identifying three distinct fates and novel genes associated with different EMT states.

The DNA-based global positioning system--a theoretical framework for large-scale spatial genomics

The paper introduces GPS-seq, a theoretical framework for spatial transcriptomics that uses DNA barcodes to enable large-scale, optics-free imaging of tissue sections at single-cell resolution.

Optimal transport analysis reveals trajectories in steady-state systems

This paper introduces StationaryOT, an optimal transport method to infer cell trajectories from single snapshots of equilibrium systems, validated on simulated and Arabidopsis root data.

Developmental Single-cell transcriptomics in the Lytechinus variegatus 1 Sea Urchin Embryo

The paper uses scRNA-seq and computational methods to study developmental trajectories and gene regulatory networks in sea urchin embryos, revealing lineage diversification and timing differences between species.

Hematopoiesis at single cell resolution spanning human development and maturation

The paper uses single cell RNA-seq to study human hematopoietic stem and progenitor cells (HSPCs) across development and aging, revealing age-related transcriptional changes and differentiation trajectories.

A Unified Framework for Lineage Tracing and Trajectory Inference

This paper introduces a unified framework that integrates lineage tracing with trajectory inference to improve accuracy in reconstructing developmental pathways.

Reconstruction of developmental landscapes by optimal-transport analysis of single-cell gene expression sheds light on cellular reprogramming.

Optimal transport converts a 65,781-cell reprogramming time course into probabilistic fates and trajectories, exposing alternative cell fates and a gene, Obox6, that improves reprogramming efficiency.