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Topslam: Waddington Landscape Recovery for Single Cell Experiments

https://doi.org/10.1101/057778
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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The molecular and mathematical basis of Waddington's epigenetic landscape: A framework for post‐Darwinian biology?
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Simultaneous Localization and Mapping
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Simultaneous Localization and Mapping
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Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development
inferredcites →https://doi.org/10.1016/j.cell.2015.10.039openalex-snapshot
Design and Analysis of Single-Cell Sequencing Experiments
inferredcites →https://doi.org/10.1016/j.copbio.2016.04.015openalex-snapshot
Single-cell gene expression profiling and cell state dynamics: collecting data, correlating data points and connecting the dots
inferredcites →https://doi.org/10.1016/j.devcel.2010.02.012openalex-snapshot
Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst
inferredcites →https://doi.org/10.1038/nature02168openalex-snapshot
The International HapMap Project
inferredcites →https://doi.org/10.1038/nbt.2038openalex-snapshot
Single-cell dissection of transcriptional heterogeneity in human colon tumors
inferredcites →https://doi.org/10.1038/nbt.2859openalex-snapshot
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
inferredcites →https://doi.org/10.1038/nbt.3102openalex-snapshot
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
inferredcites →https://doi.org/10.1038/nbt.3569openalex-snapshot
Wishbone identifies bifurcating developmental trajectories from single-cell data
inferredcites →https://doi.org/10.1038/ncb2709openalex-snapshot
Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis
inferredcites →https://doi.org/10.1038/nmeth0411-311openalex-snapshot
Single-cell genomics
inferredcites →https://doi.org/10.1038/nsmb.2660openalex-snapshot
Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells
inferredcites →https://doi.org/10.1063/1.4816376openalex-snapshot
Potential and flux field landscape theory. I. Global stability and dynamics of spatially dependent non-equilibrium systems
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Effects of environmental enrichment on gene expression in the brain
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A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series
inferredcites →https://doi.org/10.1093/bib/bbp046openalex-snapshot
Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing
inferredcites →https://doi.org/10.1093/bioinformatics/bts385openalex-snapshot
A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst
inferredcites →https://doi.org/10.1093/bioinformatics/bts714openalex-snapshot
Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments
inferredcites →https://doi.org/10.1093/bioinformatics/btu134openalex-snapshot
Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data
inferredcites →https://doi.org/10.1093/bioinformatics/btw201openalex-snapshot
SCell: integrated analysis of single-cell RNA-seq data
inferredcites →https://doi.org/10.1098/rsif.2012.0434openalex-snapshot
Quasi-potential landscape in complex multi-stable systems
inferredcites →https://doi.org/10.1101/026872openalex-snapshot
Bayesian Gaussian Process Latent Variable Models for pseudotime inference in single-cell RNA-seq data
inferredcites →https://doi.org/10.1101/gr.110882.110openalex-snapshot
Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq
inferredcites →https://doi.org/10.1109/tpami.2014.2318711openalex-snapshot
Fast Nonparametric Clustering of Structured Time-Series
inferredcites →https://doi.org/10.1126/science.1245316openalex-snapshot
Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells
inferredcites →https://doi.org/10.1162/089976699300016728openalex-snapshot
Mixtures of Probabilistic Principal Component Analyzers
inferredcites →https://doi.org/10.1186/1752-0509-5-85openalex-snapshot
A deterministic map of Waddington's epigenetic landscape for cell fate specification
inferredcites →https://doi.org/10.1261/rna.1947110openalex-snapshot
Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression
inferredcites →https://doi.org/10.1371/journal.pgen.0030160openalex-snapshot
PCA-Correlated SNPs for Structure Identification in Worldwide Human Populations
inferredcites →https://doi.org/10.2307/1293653openalex-snapshot
Principles of Development and Differentiation C. H. Waddington
inferredcites →https://doi.org/10.4324/9781315765471openalex-snapshot
The Strategy of the Genes
inferredcites →https://doi.org/10.48550/arxiv.1411.7432openalex-snapshot
Metrics for Probabilistic Geometries

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/9781119487845.ch31openalex-snapshot
Modelling Gene Expression Dynamics with Gaussian Process Inference
inferred← citeshttps://doi.org/10.1002/9781394372683.ch1openalex-snapshot
A Brief Conceptual History of Epigenetics, and More Besides
inferred← citeshttps://doi.org/10.1002/cyto.a.23976openalex-snapshot
Learning Pathway Dynamics from Single‐Cell Proteomic Data: A Comparative Study
inferred← citeshttps://doi.org/10.1007/978-1-4939-9224-9_7openalex-snapshot
Quantitative Modelling of the Waddington Epigenetic Landscape
inferred← citeshttps://doi.org/10.1038/s41587-019-0071-9openalex-snapshot
A comparison of single-cell trajectory inference methods
inferred← citeshttps://doi.org/10.1093/bfgp/elx029openalex-snapshot
The Human Cell Atlas: Technical approaches and challenges
inferred← citeshttps://doi.org/10.1093/bioinformatics/btx022openalex-snapshot
NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty1009openalex-snapshot
DensityPath: an algorithm to visualize and reconstruct cell state-transition path on density landscape for single-cell RNA sequencing data
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty533openalex-snapshot
GrandPrix: scaling up the Bayesian GPLVM for single-cell data
inferred← citeshttps://doi.org/10.1101/191056openalex-snapshot
Reconstruction of developmental landscapes by optimal-transport analysis of single-cell gene expression sheds light on cellular reprogramming
inferred← citeshttps://doi.org/10.1101/710640openalex-snapshot
Mathematical modeling with single-cell sequencing data
inferred← citeshttps://doi.org/10.1109/tcbb.2018.2847690openalex-snapshot
A Branch Point on Differentiation Trajectory is the Bifurcating Event Revealed by Dynamical Network Biomarker Analysis of Single-Cell Data
inferred← citeshttps://doi.org/10.1186/s12859-021-04330-1openalex-snapshot
Velo-Predictor: an ensemble learning pipeline for RNA velocity prediction
inferred← citeshttps://doi.org/10.12688/f1000research.131861.1openalex-snapshot
Single-cell transcriptional uncertainty landscape of cell differentiation
inferred← citeshttps://doi.org/10.14418/wes01.2.354openalex-snapshot
A Synthetic Portal into the Genome for Controlled Transgenesis in Human Pluripotent Stem Cells
inferred← citeshttps://doi.org/10.25088/complexsystems.29.4.779openalex-snapshot
A Review of Complex Systems Approaches to Cancer Networks
inferred← citeshttps://doi.org/10.32657/10220/45611openalex-snapshot
Mathematical modeling and simulation of stem cell differentiation and reprogramming by Waddington's epigenetic landscape
inferred← citeshttps://doi.org/10.3934/mbe.2022395openalex-snapshot
Comparison of cell state models derived from single-cell RNA sequencing data: graph versus multi-dimensional space
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