Here we list some papers that can provide context for addressing the proposed challenges

Single-cell Sequencing Method

SPLiT-seq publication https://www.science.org/doi/10.1126/science.aam8999

• Scale Biosciences workflow is based on the concept of combinatorial indexing introduced in the SPLiT-seq paper

Pseudotime Trajectory Analysis

Benchmark of Pseudotime Trajectory Analyses https://www.nature.com/articles/s41587-019-0071-9

• Benchmarked 45 methods with many datasets

Review of Pseudotime Trajectory Analyses https://www.sciencedirect.com/science/article/pii/S2452310021000299

• Review of trajectory analyses

11 Grand Challenges in single-cell science https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1926-6

• Slightly an old paper but the concepts hold true.
• Generalizing trajectory inference is the fourth challenge

CellRank https://www.nature.com/articles/s41592-021-01346-6

• One pseudotime estimation approach

Lamian https://www.nature.com/articles/s41467-023-42841-y

• Pseudotime estimation approach for multi-sample data

Differential Expression Across Pseudotime Trajectory

PseudotimeDE https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02341-y

• Method for detecting genes differentially expressed across a pseudotime

Trajectory-based differential expression analysis for single-cell sequencing data https://www.nature.com/articles/s41467-020-14766-3

• A method for differential expression analysis across pseudotimes

Cardiomyocyte Differentiations

Review of iPSC-derived cardiomyocytes https://www.sciencedirect.com/science/article/pii/S2666166722004403?via%3Dihub

• Provides a review of the field of iPSC-derived cardiomyocytes to provide biological theory, context and