References¶
- Bergen20
Bergen, V. et al. (2020), Generalizing RNA velocity to transient cell states through dynamical modeling, Nature Biotechnology.
- Coifman05
Coifman et al. (2005), Geometric diffusions as a tool for harmonic analysis and structure definition of data: Diffusion maps, PNAS.
- GPCCA18
Reuter, B. et al. (2018), Generalized Markov State Modeling Method for Nonequilibrium Biomolecular Dynamics: Exemplified on Amyloid β Conformational Dynamics Driven by an Oscillating Electric Field., Journal of Chemical Theory and Computation.
- Haghverdi16
Haghverdi et al. (2016), Diffusion pseudotime robustly reconstructs branching cellular lineages, Nature Methods.
- Li2020
Li, T. et al. (2020), On the Mathematics of RNA Velocity I: Theoretical Analysis, bioRxiv.
- Lung20
Strunz, M. et al. (2020), Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis, Nature Communications.
- Macosko15
Macosko, E. Z. et al., (2015), Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets, Cell.
- MAGIC18
Van Dijk, D. et al. (2018), Recovering Gene Interactions from Single-Cell Data Using Data Diffusion, Cell.
- Manno18
La Manno et al. (2018), RNA velocity of single cells, Nature.
- Morris18
Biddy, B.A., Kong, W., Kamimoto, K. et al. (2018), Single-cell mapping of lineage and identity in direct reprogramming., Nature 564, 219–224.
- Panc19
Bastidas-Ponce et al. (2019), Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis, Development.
- Reuter19
Reuter, B. et al. (2019), Generalized Markov modeling of nonreversible molecular kinetics, The Journal of Chemical Physics.
- Robinson10
Robinson, M. D. et al. (2010), A scaling normalization method for differential expression analysis of RNA-seq data, Genome Biology.
- Setty19
Setty et al. (2019), Characterization of cell fate probabilities in single-cell data with Palantir, Nature Biotechnology.
- Tolver16
Tolver (2016), An introduction to Markov chains, Recuperado el 15.
- Weinreb18
Weinreb et al. (2018), Fundamental limits on dynamic inference from single-cell snapshots, PNAS.
- Wolf18
Wolf et al. (2018), Scanpy: large-scale single-cell gene expression data analysis, Genome Biology.
- Wolf19
Wolf et al. (2019), PAGA: Graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells, Genome Biology.