On the public citation graph

A novel metric reveals previously unrecognized distortion in the analysis of scRNA-seq data

0 signed · 111 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.
Claim with ORCID
Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.
See reference health

What this work says

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

inferredcites →https://doi.org/10.1002/9780470747278openalex-snapshot
Nonnegative Matrix and Tensor Factorizations: Applications to Exploratory Multi-way Data Analysis and Blind Source Separation
inferredcites →https://doi.org/10.1007/978-3-540-45080-1_66openalex-snapshot
Nonlinear Dimension Reduction via Local Tangent Space Alignment
inferredcites →https://doi.org/10.1007/978-3-642-04277-5_18openalex-snapshot
On the Use of the Adjusted Rand Index as a Metric for Evaluating Supervised Classification
inferredcites →https://doi.org/10.1007/bf02289694openalex-snapshot
Nonmetric Multidimensional Scaling: A Numerical Method
inferredcites →https://doi.org/10.1007/s11741-004-0051-1openalex-snapshot
Principal manifolds and nonlinear dimensionality reduction via tangent space alignment
inferredcites →https://doi.org/10.1016/0893-6080(88)90023-8openalex-snapshot
Analysis of hidden units in a layered network trained to classify sonar targets
inferredcites →https://doi.org/10.1016/j.cageo.2018.12.005openalex-snapshot
Geochemical characterisation of rock hydration processes using t-SNE
inferredcites →https://doi.org/10.1016/j.ccell.2019.08.007openalex-snapshot
Tumor Cell Biodiversity Drives Microenvironmental Reprogramming in Liver Cancer
inferredcites →https://doi.org/10.1016/j.cell.2018.05.057openalex-snapshot
A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain
inferredcites →https://doi.org/10.1016/j.cell.2021.06.023openalex-snapshot
Molecular topography of an entire nervous system
inferredcites →https://doi.org/10.1016/j.coisb.2017.12.008openalex-snapshot
Manifold learning-based methods for analyzing single-cell RNA-sequencing data
inferredcites →https://doi.org/10.1016/j.cpc.2010.04.018openalex-snapshot
NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations
inferredcites →https://doi.org/10.1016/j.dss.2009.05.016openalex-snapshot
Modeling wine preferences by data mining from physicochemical properties
inferredcites →https://doi.org/10.1023/a:1009778005914openalex-snapshot
On Bias, Variance, 0/1—Loss, and the Curse-of-Dimensionality
inferredcites →https://doi.org/10.1037/h0071325openalex-snapshot
Analysis of a complex of statistical variables into principal components.
inferredcites →https://doi.org/10.1038/234034a0openalex-snapshot
Distance between Sets
inferredcites →https://doi.org/10.1038/nature25980openalex-snapshot
A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex
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.4038openalex-snapshot
Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain
inferredcites →https://doi.org/10.1038/nbt.4096openalex-snapshot
Integrating single-cell transcriptomic data across different conditions, technologies, and species
inferredcites →https://doi.org/10.1038/ncomms9687openalex-snapshot
Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression
inferredcites →https://doi.org/10.1038/nrg2934openalex-snapshot
RNA sequencing: advances, challenges and opportunities
inferredcites →https://doi.org/10.1038/nrg3833openalex-snapshot
Computational and analytical challenges in single-cell transcriptomics
inferredcites →https://doi.org/10.1038/s41467-017-02001-5openalex-snapshot
Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing
inferredcites →https://doi.org/10.1038/s41467-018-07931-2openalex-snapshot
Single-cell RNA-seq denoising using a deep count autoencoder
inferredcites →https://doi.org/10.1038/s41586-018-0414-6openalex-snapshot
RNA velocity of single cells
inferredcites →https://doi.org/10.1038/s41586-019-0969-xopenalex-snapshot
The single-cell transcriptional landscape of mammalian organogenesis
inferredcites →https://doi.org/10.1038/s41587-019-0071-9openalex-snapshot
A comparison of single-cell trajectory inference methods
inferredcites →https://doi.org/10.1038/s41596-020-00409-wopenalex-snapshot
Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data
inferredcites →https://doi.org/10.1080/14786440109462720openalex-snapshot
LIII. On lines and planes of closest fit to systems of points in space
inferredcites →https://doi.org/10.1093/bib/bby076openalex-snapshot
Impact of similarity metrics on single-cell RNA-seq data clustering
inferredcites →https://doi.org/10.1093/bioinformatics/btz078openalex-snapshot
PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes
inferredcites →https://doi.org/10.1101/191056openalex-snapshot
Reconstruction of developmental landscapes by optimal-transport analysis of single-cell gene expression sheds light on cellular reprogramming
inferredcites →https://doi.org/10.1101/460154openalex-snapshot
Stem cell differentiation trajectories in Hydra resolved at single-cell resolution
inferredcites →https://doi.org/10.1101/655365openalex-snapshot
Accurate denoising of single-cell RNA-Seq data using unbiased principal component analysis
inferredcites →https://doi.org/10.1101/737577openalex-snapshot
Expression profiling of the mature C. elegans nervous system by single-cell RNA-Sequencing
inferredcites →https://doi.org/10.1105/tpc.18.00785openalex-snapshot
Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana
inferredcites →https://doi.org/10.1111/j.1469-1809.1936.tb02137.xopenalex-snapshot
THE USE OF MULTIPLE MEASUREMENTS IN TAXONOMIC PROBLEMS
inferredcites →https://doi.org/10.1126/science.290.5500.2319openalex-snapshot
A Global Geometric Framework for Nonlinear Dimensionality Reduction
inferredcites →https://doi.org/10.1126/science.290.5500.2323openalex-snapshot
Nonlinear Dimensionality Reduction by Locally Linear Embedding
inferredcites →https://doi.org/10.1126/science.aam8999openalex-snapshot
Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding
inferredcites →https://doi.org/10.1126/science.aao1082openalex-snapshot
The principles of cascading power limits in small, fast biological and engineered systems
inferredcites →https://doi.org/10.1126/science.aar3131openalex-snapshot
Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis
inferredcites →https://doi.org/10.1145/276698.276876openalex-snapshot
Approximate nearest neighbors
inferredcites →https://doi.org/10.1146/annurev-ecolsys-110512-135822openalex-snapshot
High-Throughput Genomic Data in Systematics and Phylogenetics
inferredcites →https://doi.org/10.1186/s13059-017-1305-0openalex-snapshot
Splatter: simulation of single-cell RNA sequencing data
inferredcites →https://doi.org/10.1186/s13059-017-1382-0openalex-snapshot
SCANPY: large-scale single-cell gene expression data analysis
inferredcites →https://doi.org/10.1186/s13059-019-1861-6openalex-snapshot
Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model
inferredcites →https://doi.org/10.1207/s15327906mbr0102_10openalex-snapshot
The Scree Test For The Number Of Factors
inferredcites →https://doi.org/10.12688/f1000research.9501.2openalex-snapshot
A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor
inferredcites →https://doi.org/10.1371/journal.pone.0191962openalex-snapshot
Semaphorin3A induces nerve regeneration in the adult cornea-a switch from its repulsive role in development
inferredcites →https://doi.org/10.1371/journal.pone.0205883openalex-snapshot
Single-cell RNA sequencing of the mammalian pineal gland identifies two pinealocyte subtypes and cell type-specific daily patterns of gene expression
inferredcites →https://doi.org/10.1524/auto.2011.0951openalex-snapshot
Simulation physiologischer Regelkreise mit der objektorientierten Modellbibliothek “HumanLib”
inferredcites →https://doi.org/10.15252/msb.20188746openalex-snapshot
Current best practices in single‐cell RNA‐seq analysis: a tutorial
inferredcites →https://doi.org/10.1587/transfun.e92.a.708openalex-snapshot
Fast Local Algorithms for Large Scale Nonnegative Matrix and Tensor Factorizations
inferredcites →https://doi.org/10.21105/joss.00861openalex-snapshot
UMAP: Uniform Manifold Approximation and Projection
inferredcites →https://doi.org/10.48550/arxiv.1201.0490openalex-snapshot
Scikit-learn: Machine Learning in Python
inferredcites →https://doi.org/10.48550/arxiv.1605.09370openalex-snapshot
Unsupervised Discovery of El Nino Using Causal Feature Learning on Microlevel Climate Data
inferredcites →https://doi.org/10.7554/elife.51254openalex-snapshot
Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments

What points at this work

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

inferred← citeshttps://doi.org/10.1016/j.cels.2023.08.004openalex-snapshot
Studying stochastic systems biology of the cell with single-cell genomics data
inferred← citeshttps://doi.org/10.1016/j.cmet.2022.11.009openalex-snapshot
Single-cell transcriptomic and spatial landscapes of the developing human pancreas
inferred← citeshttps://doi.org/10.1016/j.cmpb.2024.108337openalex-snapshot
A self-supervised embedding of cell migration features for behavior discovery over cell populations
inferred← citeshttps://doi.org/10.1016/j.csbj.2025.08.020openalex-snapshot
Smmit: A pipeline for integrating multiple single-cell multi-omics samples
inferred← citeshttps://doi.org/10.1016/j.gastha.2022.07.015openalex-snapshot
Cellular and Transcriptional Heterogeneity in the Intrahepatic Biliary Epithelium
inferred← citeshttps://doi.org/10.1016/j.stem.2021.03.020openalex-snapshot
Cascade diversification directs generation of neuronal diversity in the hypothalamus
inferred← citeshttps://doi.org/10.1038/s41467-020-18695-zopenalex-snapshot
Mapping the bacterial metabolic niche space
inferred← citeshttps://doi.org/10.1038/s41467-021-22851-4openalex-snapshot
Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces
inferred← citeshttps://doi.org/10.1038/s41467-024-45891-yopenalex-snapshot
Statistical method scDEED for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters
inferred← citeshttps://doi.org/10.1038/s41467-025-60434-9openalex-snapshot
Assessing and improving reliability of neighbor embedding methods: a map-continuity perspective
inferred← citeshttps://doi.org/10.1038/s41586-024-08453-2openalex-snapshot
Mapping cells through time and space with moscot
inferred← citeshttps://doi.org/10.1038/s41587-026-03220-2openalex-snapshot
Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data
inferred← citeshttps://doi.org/10.1038/s41592-021-01346-6openalex-snapshot
CellRank for directed single-cell fate mapping
inferred← citeshttps://doi.org/10.1038/s41592-025-02832-xopenalex-snapshot
Monod: model-based discovery and integration through fitting stochastic transcriptional dynamics to single-cell sequencing data
inferred← citeshttps://doi.org/10.1038/s41598-020-70353-yopenalex-snapshot
Single-cell RNA sequencing uncovers heterogenous transcriptional signatures in macrophages during efferocytosis
inferred← citeshttps://doi.org/10.1038/s43588-022-00380-4openalex-snapshot
Dynamic visualization of high-dimensional data
inferred← citeshttps://doi.org/10.1073/pnas.2313719121openalex-snapshot
Principled and interpretable alignability testing and integration of single-cell data
inferred← citeshttps://doi.org/10.1088/2632-2153/ad9079openalex-snapshot
Characterizing out-of-distribution generalization of neural networks: application to the disordered Su–Schrieffer–Heeger model
inferred← citeshttps://doi.org/10.1093/bib/bbac387openalex-snapshot
How does the structure of data impact cell–cell similarity? Evaluating how structural properties influence the performance of proximity metrics in single cell RNA-seq data
inferred← citeshttps://doi.org/10.1093/bib/bbaf287openalex-snapshot
Evaluating discrepancies in dimensionality reduction for time-series single-cell RNA-sequencing data
inferred← citeshttps://doi.org/10.1093/bioadv/vbab026openalex-snapshot
Dimensional reduction of phenotypes from 53 000 mouse models reveals a diverse landscape of gene function
inferred← citeshttps://doi.org/10.1093/cvr/cvac040openalex-snapshot
Single-cell transcriptomes in the heart: when every epigenome counts
inferred← citeshttps://doi.org/10.1093/gigascience/giae056openalex-snapshot
TooManyCellsInteractive: A visualization tool for dynamic exploration of single-cell data
inferred← citeshttps://doi.org/10.1093/nargab/lqaa053openalex-snapshot
Untangling biological factors influencing trajectory inference from single cell data
inferred← citeshttps://doi.org/10.1093/nargab/lqaa102openalex-snapshot
Erratum: Untangling biological factors influencing trajectory inference from single cell data.
inferred← citeshttps://doi.org/10.1101/2020.04.02.022632openalex-snapshot
Transcriptomic entropy benchmarks stem cell-derived cardiomyocyte maturation against endogenous tissue at single cell level
inferred← citeshttps://doi.org/10.1101/2021.11.04.467087openalex-snapshot
Absence of enterotypes in the human gut microbiomes reanalyzed with non-linear dimensionality reduction methods
inferred← citeshttps://doi.org/10.1101/2022.06.03.494765openalex-snapshot
A lack of distinct cell identities in single-cell measurements: revisiting Waddington’s landscape
inferred← citeshttps://doi.org/10.1101/2022.06.11.495771openalex-snapshot
Monod : model-based discovery and integration through fitting stochastic transcriptional dynamics to single-cell sequencing data
inferred← citeshttps://doi.org/10.1101/2023.04.21.537839openalex-snapshot
scDEED: a statistical method for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters
inferred← citeshttps://doi.org/10.1101/2023.05.11.540374openalex-snapshot
Mapping cells through time and space with moscot
inferred← citeshttps://doi.org/10.1101/2023.08.03.551836openalex-snapshot
Is your data alignable? Principled and interpretable alignability testing and integration of single-cell data
inferred← citeshttps://doi.org/10.1101/2023.11.13.566337openalex-snapshot
cellstruct: Metrics scores to quantify the biological preservation between two embeddings
inferred← citeshttps://doi.org/10.1101/2025.04.28.651069openalex-snapshot
From Pairwise Distances to Neighborhood Preservation: Benchmarking Dimensionality Reduction Algorithms for CyTOF, scRNA-seq, and CITE-seq
inferred← citeshttps://doi.org/10.1101/2025.06.05.658097openalex-snapshot
Robust self-supervised machine learning for single cell embeddings and annotations
inferred← citeshttps://doi.org/10.1101/2025.08.26.672474openalex-snapshot
DeepAtlas: a tool for effective manifold learning
inferred← citeshttps://doi.org/10.1109/sampta59647.2023.10301403openalex-snapshot
On Manifold Learning in Plato’s Cave: Remarks on Manifold Learning and Physical Phenomena
inferred← citeshttps://doi.org/10.1146/annurev-biodatasci-101424-121439openalex-snapshot
Mapping, Modeling, and Reprogramming Cell-Fate Decision-Making Systems
inferred← citeshttps://doi.org/10.1177/14738716261434908openalex-snapshot
Demystifying UMAP artifacts: An interactive study on diagnosis and steering using 3D probes
inferred← citeshttps://doi.org/10.1186/s13059-019-1898-6openalex-snapshot
Accuracy, robustness and scalability of dimensionality reduction methods for single-cell RNA-seq analysis
inferred← citeshttps://doi.org/10.1186/s13059-023-03067-9openalex-snapshot
GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership
inferred← citeshttps://doi.org/10.12688/f1000research.184395.1openalex-snapshot
Finding stable clusterings of single-cell RNA-seq data
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1008569openalex-snapshot
Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1009305openalex-snapshot
Transcriptomic entropy benchmarks stem cell-derived cardiomyocyte maturation against endogenous tissue at single cell level
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1010492openalex-snapshot
RNA velocity unraveled
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1011288openalex-snapshot
The specious art of single-cell genomics
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1012014openalex-snapshot
Clustering and visualization of single-cell RNA-seq data using path metrics
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1012386openalex-snapshot
Binomial models uncover biological variation during feature selection of droplet-based single-cell RNA sequencing
inferred← citeshttps://doi.org/10.21873/cgp.20284openalex-snapshot
Machine Learning Approaches on High Throughput NGS Data to Unveil Mechanisms of Function in Biology and Disease
inferred← citeshttps://doi.org/10.4018/979-8-3693-1886-7.ch002openalex-snapshot
Data Visualization in Large Scale Based on Trained Data
inferred← citeshttps://doi.org/10.70675/bd56dad7z8c68z4b89z8585zeee85b54c61dopenalex-snapshot
Mécanismes développementaux orchestrant la différenciation des cellules souches pluripotentes induites en cellules souches hématopoïétiques
inferred← citeshttps://doi.org/10.7717/peerj.15838openalex-snapshot
Absence of enterotypes in the human gut microbiomes reanalyzed with non-linear dimensionality reduction methods
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.