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Mapping Transcriptomic Vector Fields of Single Cells

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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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Regulation of Embryonic Stem Cell Pluripotency by Heat Shock Protein 90

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Relation of a New Interpretation of Stochastic Differential Equations to Ito Process

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The Potential Landscape of Genetic Circuits Imposes the Arrow of Time in Stem Cell Differentiation

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Silencing the Metallothionein-2A gene inhibits cell cycle progression from G1- to S-phase involving ATM and cdc25A signaling in breast cancer cells

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Real-Time Kinetics of Gene Activity in Individual Bacteria

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A Whole-Cell Computational Model Predicts Phenotype from Genotype

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CellNet: Network Biology Applied to Stem Cell Engineering

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Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

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Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

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Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

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A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

inferredcites →https://doi.org/10.1016/j.cell.2020.04.011openalex-snapshot

The Architecture of SARS-CoV-2 Transcriptome

inferredcites →https://doi.org/10.1016/j.cell.2020.09.056openalex-snapshot

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin

inferredcites →https://doi.org/10.1016/j.cell.2020.10.026openalex-snapshot

High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue

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Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe

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Gene Regulatory Networks Governing Pancreas Development

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Sequence homology between human PARP14 and the SARS-CoV-2 ADP ribose 1’-phosphatase

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SARS-CoV-2 Infection Boosts MX1 Antiviral Effector in COVID-19 Patients

inferredcites →https://doi.org/10.1016/j.isci.2021.102151openalex-snapshot

Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy

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Regularized vector field learning with sparse approximation for mismatch removal

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Bifurcation dynamics in lineage-commitment in bipotent progenitor cells

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Global view of bionetwork dynamics: adaptive landscape

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Exact stochastic simulation of coupled chemical reactions

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Expanding the Nucleoside Recoding Toolkit: Revealing RNA Population Dynamics with 6-Thioguanosine

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A synthetic oscillatory network of transcriptional regulators

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Taking a long, hard look

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Nascent transcript sequencing visualizes transcription at nucleotide resolution

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Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription

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Single-cell chromatin accessibility reveals principles of regulatory variation

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Synthetic recording and in situ readout of lineage information in single cells

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A single-cell survey of the small intestinal epithelium

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Whole-organism clone tracing using single-cell sequencing

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The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

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Multiplexed quantification of proteins and transcripts in single cells

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A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages

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Single-cell in situ RNA profiling by sequential hybridization

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Validation of noise models for single-cell transcriptomics

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Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput

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Simultaneous epitope and transcriptome measurement in single cells

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Reversed graph embedding resolves complex single-cell trajectories

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Thiol-linked alkylation of RNA to assess expression dynamics

inferredcites →https://doi.org/10.1038/s41467-019-11028-9openalex-snapshot

NASC-seq monitors RNA synthesis in single cells

inferredcites →https://doi.org/10.1038/s41576-018-0052-8openalex-snapshot

DNA-based memory devices for recording cellular events

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/s41586-019-1184-5openalex-snapshot

Molecular recording of mammalian embryogenesis

inferredcites →https://doi.org/10.1038/s41586-019-1369-yopenalex-snapshot

scSLAM-seq reveals core features of transcription dynamics in single cells

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A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

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A single-cell transcriptomic atlas characterizes ageing tissues in the mouse

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A comparison of single-cell trajectory inference methods

inferredcites →https://doi.org/10.1038/s41587-020-0480-9openalex-snapshot

Sci-fate characterizes the dynamics of gene expression in single cells

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Generalizing RNA velocity to transient cell states through dynamical modeling

inferredcites →https://doi.org/10.1038/s41587-020-0704-zopenalex-snapshot

RNA timestamps identify the age of single molecules in RNA sequencing

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Functional single-cell genomics of human cytomegalovirus infection

inferredcites →https://doi.org/10.1038/s41592-020-0880-2openalex-snapshot

ZipSeq: barcoding for real-time mapping of single cell transcriptomes

inferredcites →https://doi.org/10.1038/s41592-020-0935-4openalex-snapshot

Massively parallel and time-resolved RNA sequencing in single cells with scNT-seq

inferredcites →https://doi.org/10.1038/s41593-017-0056-2openalex-snapshot

Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing

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Potential landscape of high dimensional nonlinear stochastic dynamics with large noise

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A decomposition of irreversible diffusion processes without detailed balance

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Multiconfiguration molecular mechanics algorithm for potential energy surfaces of chemical reactions

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Quantifying the Waddington landscape and biological paths for development and differentiation

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Fundamental limits on dynamic inference from single-cell snapshots

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An Approach to Sensitivity Analysis of Computer Models: Part I—Introduction, Input Variable Selection and Preliminary Variable Assessment

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An Approach to Sensitivity Analysis of Computer Models: Part II—Ranking of Input Variables, Response Surface Validation, Distribution Effect and Technique Synopsis

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Potential in stochastic differential equations: novel construction

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Cancer as robust intrinsic state shaped by evolution: a key issues review

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Mapping between dissipative and Hamiltonian systems

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Dissecting newly transcribed and old RNA using GRAND-SLAM

inferredcites →https://doi.org/10.1093/nar/gkr1203openalex-snapshot

E2F7 represses a network of oscillating cell cycle genes to control S-phase progression

inferredcites →https://doi.org/10.1093/nar/gkx1190openalex-snapshot

JUNB governs a feed-forward network of TGFβ signaling that aggravates breast cancer invasion

inferredcites →https://doi.org/10.1096/fasebj.31.1_supplement.85.1openalex-snapshot

Lgr5 Stem Cell‐based organoids in human disease

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Epigenetic state network approach for describing cell phenotypic transitions

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Quasi-potential landscape in complex multi-stable systems

inferredcites →https://doi.org/10.1101/2019.12.31.892190openalex-snapshot

Correlated Gene Modules Uncovered by Single-Cell Transcriptomics with High Detectability and Accuracy

inferredcites →https://doi.org/10.1101/592089openalex-snapshot

Modeling latent flows on single-cell data using the Hodge decomposition

inferredcites →https://doi.org/10.1101/710640openalex-snapshot

Mathematical modeling with single-cell sequencing data

inferredcites →https://doi.org/10.1103/physreve.96.040402openalex-snapshot

Emergent Lévy behavior in single-cell stochastic gene expression

inferredcites →https://doi.org/10.1103/physrevlett.94.128701openalex-snapshot

Cell Fates as High-Dimensional Attractor States of a Complex Gene Regulatory Network

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Robust Point Matching via Vector Field Consensus

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Principal Graph and Structure Learning Based on Reversed Graph Embedding

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Requirement for ErbB2/ErbB signaling in developing cartilage and bone

inferredcites →https://doi.org/10.1126/sciadv.aba9319openalex-snapshot

Live-cell imaging and analysis reveal cell phenotypic transition dynamics inherently missing in snapshot data

inferredcites →https://doi.org/10.1126/science.aaa6090openalex-snapshot

Spatially resolved, highly multiplexed RNA profiling in single cells

inferredcites →https://doi.org/10.1126/science.aab1601openalex-snapshot

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

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.aal3753openalex-snapshot

Multipotent peripheral glial cells generate neuroendocrine cells of the adrenal medulla

inferredcites →https://doi.org/10.1126/science.aau5324openalex-snapshot

Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region

inferredcites →https://doi.org/10.1126/science.aav3751openalex-snapshot

Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation

inferredcites →https://doi.org/10.1126/science.aaw1219openalex-snapshot

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

inferredcites →https://doi.org/10.1126/science.aaw3381openalex-snapshot

Lineage tracing on transcriptional landscapes links state to fate during differentiation

inferredcites →https://doi.org/10.1126/science.aax3072openalex-snapshot

Sequencing metabolically labeled transcripts in single cells reveals mRNA turnover strategies

inferredcites →https://doi.org/10.1126/science.aba7667openalex-snapshot

Species-specific pace of development is associated with differences in protein stability

inferredcites →https://doi.org/10.1126/science.aba7668openalex-snapshot

Species-specific segmentation clock periods are due to differential biochemical reaction speeds

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A human cell atlas of fetal gene expression

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Tracking development at the cellular level

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Imaging vector fields using line integral convolution

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Dimensionality Reduction Via Graph Structure Learning

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The Glial Nature of Embryonic and Adult Neural Stem Cells

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Developmental trajectory of prehematopoietic stem cell formation from endothelium

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4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells

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dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments

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Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics

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Protein velocity and acceleration from single-cell multiomics experiments

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An Introduction to Systems Biology

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An Introduction to Systems Biology

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Dynamical Systems for Biological Modeling

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A Correspondence Between Bayesian Estimation on Stochastic Processes and Smoothing by Splines

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Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis

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Cell Fate Decision as High-Dimensional Critical State Transition

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From Understanding the Development Landscape of the Canonical Fate-Switch Pair to Constructing a Dynamic Landscape for Two-Step Neural Differentiation

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The MITF paralog tfec is required in neural crest development for fate specification of the iridophore lineage from a multipotent pigment cell progenitor

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UMAP: Uniform Manifold Approximation and Projection

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On the Mathematics of RNA Velocity I: Theoretical Analysis

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The Strategy of the Genes

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Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention

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The Strategy of the Genes: A Discussion of Some Aspects of Theoretical Biology

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Thyroid hormone regulates distinct paths to maturation in pigment cell lineages

What points at this work

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

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Single-Cell Analysis of the Transcriptome and Epigenome

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Single‐Cell RNA Sequencing for Precision Oncology: Current State-of-Art

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Differentiation reveals latent features of aging and an energy barrier in murine myogenesis

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Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe

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Current progress and potential opportunities to infer single-cell developmental trajectory and cell fate

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The emergence and promise of single-cell temporal-omics approaches

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Spatio-temporal mRNA tracking in the early zebrafish embryo

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Dissecting transition cells from single-cell transcriptome data through multiscale stochastic dynamics

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Lineage tracing meets single-cell omics: opportunities and challenges

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Generalizing RNA velocity to transient cell states through dynamical modeling

inferred← citeshttps://doi.org/10.1038/s41587-022-01209-1openalex-snapshot

CoSpar identifies early cell fate biases from single-cell transcriptomic and lineage information

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Massively parallel and time-resolved RNA sequencing in single cells with scNT-seq

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CellRank for directed single-cell fate mapping

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Computing the Riemannian curvature of image patch and single-cell RNA sequencing data manifolds using extrinsic differential geometry

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Dynamics of transcriptional and post-transcriptional regulation

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Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball patterned arrays

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Genomic sequences and RNA binding proteins predict RNA splicing kinetics in various single-cell contexts

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Transiently increased intercommunity regulation characterizes concerted cell phenotypic transition

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RNA velocity unraveled

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