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Molecular Cross-Validation for Single-Cell RNA-seq

https://doi.org/10.1101/786269
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What this work says

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

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A New Look at the Statistical Model Identification
inferredcites →https://doi.org/10.1016/0377-0427(87)90125-7openalex-snapshot
Silhouettes: A graphical aid to the interpretation and validation of cluster analysis
inferredcites →https://doi.org/10.1016/j.cell.2015.05.002openalex-snapshot
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
inferredcites →https://doi.org/10.1016/j.cell.2015.11.013openalex-snapshot
Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors
inferredcites →https://doi.org/10.1016/j.cell.2016.07.054openalex-snapshot
Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics
inferredcites →https://doi.org/10.1016/j.cell.2018.05.061openalex-snapshot
Recovering Gene Interactions from Single-Cell Data Using Data Diffusion
inferredcites →https://doi.org/10.1038/nbt.3192openalex-snapshot
Spatial reconstruction of single-cell gene expression data
inferredcites →https://doi.org/10.1038/ncomms13942openalex-snapshot
Multiple Dirac cones at the surface of the topological metal LaBi
inferredcites →https://doi.org/10.1038/ncomms14049openalex-snapshot
Massively parallel digital transcriptional profiling of single cells
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/s41586-018-0590-4openalex-snapshot
Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris
inferredcites →https://doi.org/10.1038/s41587-019-0379-5openalex-snapshot
Droplet scRNA-seq is not zero-inflated
inferredcites →https://doi.org/10.1038/s41592-018-0229-2openalex-snapshot
Deep generative modeling for single-cell transcriptomics
inferredcites →https://doi.org/10.1038/s41592-019-0686-2openalex-snapshot
SciPy 1.0: fundamental algorithms for scientific computing in Python
inferredcites →https://doi.org/10.1038/s41593-017-0029-5openalex-snapshot
Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex
inferredcites →https://doi.org/10.1093/nar/gkp889openalex-snapshot
BioNumbers—the database of key numbers in molecular and cell biology
inferredcites →https://doi.org/10.1101/426239openalex-snapshot
Quasi-universality in single-cell sequencing data
inferredcites →https://doi.org/10.1101/632216openalex-snapshot
Systematic comparative analysis of single cell RNA-sequencing methods
inferredcites →https://doi.org/10.1109/cvpr.2019.00223openalex-snapshot
Noise2Void - Learning Denoising From Single Noisy Images
inferredcites →https://doi.org/10.1109/tac.1974.1100705openalex-snapshot
A new look at the statistical model identification
inferredcites →https://doi.org/10.1126/science.aaf7907openalex-snapshot
Whole-organism lineage tracing by combinatorial and cumulative genome editing
inferredcites →https://doi.org/10.1126/science.aaq1723openalex-snapshot
Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics
inferredcites →https://doi.org/10.1126/science.aar4362openalex-snapshot
Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo
inferredcites →https://doi.org/10.1126/science.aaw3381openalex-snapshot
Lineage tracing on transcriptional landscapes links state to fate during differentiation
inferredcites →https://doi.org/10.1137/1.9781611972740.22openalex-snapshot
Clustering with Bregman Divergences
inferredcites →https://doi.org/10.1142/9789813279827_0033openalex-snapshot
Parameter tuning is a key part of dimensionality reduction via deep variational autoencoders for single cell RNA transcriptomics
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/10.1214/08-aoas227openalex-snapshot
Bi-cross-validation of the SVD and the nonnegative matrix factorization
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/10.13140/rg.2.2.29485.95202openalex-snapshot
Learning Image Restoration without Clean Data
inferredcites →https://doi.org/10.17863/cam.64134openalex-snapshot
SciPy 1.0: fundamental algorithms for scientific computing in Python
inferredcites →https://doi.org/10.48550/arxiv.1803.04189openalex-snapshot
Noise2Noise: Learning Image Restoration without Clean Data

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.tibtech.2024.07.006openalex-snapshot
Concepts and new developments in droplet-based single cell multi-omics
inferred← citeshttps://doi.org/10.1038/s41467-020-20092-5openalex-snapshot
Single-cell atlas of the first intra-mammalian developmental stage of the human parasite Schistosoma mansoni
inferred← citeshttps://doi.org/10.1038/s41467-021-23949-5openalex-snapshot
Single cell derived mRNA signals across human kidney tumors
inferred← citeshttps://doi.org/10.1038/s41467-024-46045-wopenalex-snapshot
scCASE: accurate and interpretable enhancement for single-cell chromatin accessibility sequencing data
inferred← citeshttps://doi.org/10.1038/s41467-024-54187-0openalex-snapshot
HOX gene expression in the developing human spine
inferred← citeshttps://doi.org/10.1038/s41467-025-59880-2openalex-snapshot
A CRISPR/Cas9-based enhancement of high-throughput single-cell transcriptomics
inferred← citeshttps://doi.org/10.1038/s41586-024-07869-0openalex-snapshot
A γδ T cell–IL-3 axis controls allergic responses through sensory neurons
inferred← citeshttps://doi.org/10.1038/s41586-024-08105-5openalex-snapshot
Immune responses in checkpoint myocarditis across heart, blood and tumour
inferred← citeshttps://doi.org/10.1038/s41587-025-02694-wopenalex-snapshot
Defining and benchmarking open problems in single-cell analysis
inferred← citeshttps://doi.org/10.1038/s41591-024-02895-xopenalex-snapshot
Single-cell transcriptomic analyses reveal distinct immune cell contributions to epithelial barrier dysfunction in checkpoint inhibitor colitis
inferred← citeshttps://doi.org/10.1073/pnas.2209124120openalex-snapshot
An empirical Bayes method for differential expression analysis of single cells with deep generative models
inferred← citeshttps://doi.org/10.1093/biostatistics/kxac047openalex-snapshot
Inference after latent variable estimation for single-cell RNA sequencing data
inferred← citeshttps://doi.org/10.1093/jimmun/vkag141.533openalex-snapshot
A multimodal atlas of COVID-19 severity identifies hallmarks of dysregulated immunity 2258066
inferred← citeshttps://doi.org/10.1093/nargab/lqag095openalex-snapshot
A systematic assessment of single-cell language model configurations
inferred← citeshttps://doi.org/10.1101/2020.06.08.140673openalex-snapshot
Monet: An open-source Python package for analyzing and integrating scRNA-Seq data using PCA-based latent spaces
inferred← citeshttps://doi.org/10.1101/2021.11.15.468733openalex-snapshot
Erasure of Biologically Meaningful Signal by Unsupervised scRNAseq Batch-correction Methods
inferred← citeshttps://doi.org/10.1101/2023.09.15.557794openalex-snapshot
Immune Responses in Checkpoint Myocarditis Across Heart, Blood, and Tumor
inferred← citeshttps://doi.org/10.1101/2023.09.21.558277openalex-snapshot
Simultaneous estimation of gene regulatory network structure and RNA kinetics from single cell gene expression
inferred← citeshttps://doi.org/10.1101/2023.10.13.562243openalex-snapshot
A General Single-Cell Analysis Framework via Conditional Diffusion Generative Models
inferred← citeshttps://doi.org/10.1101/2025.11.19.689204openalex-snapshot
Lymphotoxin-driven cancer cell eradication by tumoricidal CD8 + TIL
inferred← citeshttps://doi.org/10.1126/sciadv.abd3311openalex-snapshot
Tumor to normal single-cell mRNA comparisons reveal a pan-neuroblastoma cancer cell
inferred← citeshttps://doi.org/10.1126/sciimmunol.aeb9068openalex-snapshot
Multiomic analysis of malignant ascites defines RORC -expressing dendritic cells at sites of metastasis
inferred← citeshttps://doi.org/10.1186/s13059-020-02132-xopenalex-snapshot
A systematic evaluation of single-cell RNA-sequencing imputation methods
inferred← citeshttps://doi.org/10.1186/s13059-020-02136-7openalex-snapshot
pipeComp, a general framework for the evaluation of computational pipelines, reveals performant single cell RNA-seq preprocessing tools
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/10.3389/fonc.2021.716042openalex-snapshot
Deciphering the Immune–Tumor Interplay During Early-Stage Lung Cancer Development via Single-Cell Technology
inferred← citeshttps://doi.org/10.64898/2026.06.02.729664openalex-snapshot
Auditable recovery of single-cell RNA-seq zeros with SPARE
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