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Temporal mixture modelling of single-cell RNA-seq data resolves a CD4 + T cell fate bifurcation

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What this work says

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

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Kinetics and STAT4‐ or STAT6‐mediated regulation of genes involved in lymphocyte polarization to Th1 and Th2 cells

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Blood‐stage Plasmodium berghei infection leads to short‐lived parasite‐associated antigen presentation by dendritic cells

inferredcites →https://doi.org/10.1007/978-3-540-28650-9_4openalex-snapshot

Gaussian Processes in Machine Learning

inferredcites →https://doi.org/10.1016/j.cell.2013.04.007openalex-snapshot

Single Naive CD4+ T Cells from a Diverse Repertoire Produce Different Effector Cell Types during Infection

inferredcites →https://doi.org/10.1016/j.cell.2014.04.005openalex-snapshot

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

inferredcites →https://doi.org/10.1016/j.cell.2015.05.015openalex-snapshot

The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells

inferredcites →https://doi.org/10.1016/j.celrep.2014.04.011openalex-snapshot

Single-Cell RNA Sequencing Reveals T Helper Cells Synthesizing Steroids De Novo to Contribute to Immune Homeostasis

inferredcites →https://doi.org/10.1016/j.celrep.2015.05.042openalex-snapshot

CD8α− Dendritic Cells Induce Antigen-Specific T Follicular Helper Cells Generating Efficient Humoral Immune Responses

inferredcites →https://doi.org/10.1016/j.ejcb.2011.07.005openalex-snapshot

MAD1 and its life as a MYC antagonist: An update

inferredcites →https://doi.org/10.1016/j.immuni.2007.08.018openalex-snapshot

Real-Time Manipulation of T Cell-Dendritic Cell Interactions In Vivo Reveals the Importance of Prolonged Contacts for CD4+ T Cell Activation

inferredcites →https://doi.org/10.1016/j.immuni.2011.03.023openalex-snapshot

ICOS Receptor Instructs T Follicular Helper Cell versus Effector Cell Differentiation via Induction of the Transcriptional Repressor Bcl6

inferredcites →https://doi.org/10.1016/j.immuni.2011.03.024openalex-snapshot

Germinal Center B Cell and T Follicular Helper Cell Development Initiates in the Interfollicular Zone

inferredcites →https://doi.org/10.1016/j.immuni.2011.08.016openalex-snapshot

Differential Expression of Ly6C and T-bet Distinguish Effector and Memory Th1 CD4+ Cell Properties during Viral Infection

inferredcites →https://doi.org/10.1016/j.immuni.2011.09.009openalex-snapshot

Opposing Signals from the Bcl6 Transcription Factor and the Interleukin-2 Receptor Generate T Helper 1 Central and Effector Memory Cells

inferredcites →https://doi.org/10.1016/j.immuni.2011.11.012openalex-snapshot

Early Th1 Cell Differentiation Is Marked by a Tfh Cell-like Transition

inferredcites →https://doi.org/10.1016/j.immuni.2012.08.016openalex-snapshot

CXCR3 Chemokine Receptor-Ligand Interactions in the Lymph Node Optimize CD4+ T Helper 1 Cell Differentiation

inferredcites →https://doi.org/10.1016/j.immuni.2012.11.020openalex-snapshot

Persistent Antigen and Germinal Center B Cells Sustain T Follicular Helper Cell Responses and Phenotype

inferredcites →https://doi.org/10.1016/j.immuni.2013.02.020openalex-snapshot

Distinct Memory CD4+ T Cells with Commitment to T Follicular Helper- and T Helper 1-Cell Lineages Are Generated after Acute Viral Infection

inferredcites →https://doi.org/10.1016/j.immuni.2013.08.033openalex-snapshot

Sustained Interactions between T Cell Receptors and Antigens Promote the Differentiation of CD4+ Memory T Cells

inferredcites →https://doi.org/10.1016/j.immuni.2014.01.005openalex-snapshot

Molecular and Transcriptional Basis of CD4+ T Cell Dysfunction during Chronic Infection

inferredcites →https://doi.org/10.1016/j.immuni.2014.10.004openalex-snapshot

T Follicular Helper Cell Differentiation, Function, and Roles in Disease

inferredcites →https://doi.org/10.1016/j.patcog.2011.10.004openalex-snapshot

Overlapping Mixtures of Gaussian Processes for the data association problem

inferredcites →https://doi.org/10.1016/j.ymeth.2015.06.021openalex-snapshot

Computational assignment of cell-cycle stage from single-cell transcriptome data

inferredcites →https://doi.org/10.1016/s0092-8674(00)80702-3openalex-snapshot

A Novel Transcription Factor, T-bet, Directs Th1 Lineage Commitment

inferredcites →https://doi.org/10.1016/s0888-7543(03)00129-0openalex-snapshot

Identification of eight members of the Argonaute family in the human genome☆

inferredcites →https://doi.org/10.1038/nature13173openalex-snapshot

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

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/ni.2158openalex-snapshot

The transcriptional regulators Id2 and Id3 control the formation of distinct memory CD8+ T cell subsets

inferredcites →https://doi.org/10.1038/ni.3226openalex-snapshot

LEF-1 and TCF-1 orchestrate TFH differentiation by regulating differentiation circuits upstream of the transcriptional repressor Bcl6

inferredcites →https://doi.org/10.1038/ni.3229openalex-snapshot

The transcription factor TCF-1 initiates the differentiation of TFH cells during acute viral infection

inferredcites →https://doi.org/10.1038/ni.3461openalex-snapshot

Id2 reinforces TH1 differentiation and inhibits E2A to repress TFH differentiation

inferredcites →https://doi.org/10.1038/nmeth.3971openalex-snapshot

Diffusion pseudotime robustly reconstructs lineage branching

inferredcites →https://doi.org/10.1038/nprot.2014.006openalex-snapshot

Full-length RNA-seq from single cells using Smart-seq2

inferredcites →https://doi.org/10.1038/nrc1802openalex-snapshot

Common markers of proliferation

inferredcites →https://doi.org/10.1073/pnas.1408993111openalex-snapshot

Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape

inferredcites →https://doi.org/10.1073/pnas.1604178113openalex-snapshot

Transcriptional regulator Bhlhe40 works as a cofactor of T-bet in the regulation of IFN-γ production in i NKT cells

inferredcites →https://doi.org/10.1084/jem.192.11.1545openalex-snapshot

Follicular B Helper T Cells Express Cxc Chemokine Receptor 5, Localize to B Cell Follicles, and Support Immunoglobulin Production

inferredcites →https://doi.org/10.1084/jem.192.11.1553openalex-snapshot

Cxc Chemokine Receptor 5 Expression Defines Follicular Homing T Cells with B Cell Helper Function

inferredcites →https://doi.org/10.1084/jem.20042521openalex-snapshot

Antigen persistence is required throughout the expansion phase of a CD4+ T cell response

inferredcites →https://doi.org/10.1084/jem.20102144openalex-snapshot

The lineage-defining factors T-bet and Bcl-6 collaborate to regulate Th1 gene expression patterns

inferredcites →https://doi.org/10.1084/jem.20120219openalex-snapshot

Bcl6 expression specifies the T follicular helper cell program in vivo

inferredcites →https://doi.org/10.1084/jem.20141380openalex-snapshot

BCL6 orchestrates Tfh cell differentiation via multiple distinct mechanisms

inferredcites →https://doi.org/10.1089/cmb.2009.0175openalex-snapshot

A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series

inferredcites →https://doi.org/10.1093/bioinformatics/btv325openalex-snapshot

Diffusion maps for high-dimensional single-cell analysis of differentiation data

inferredcites →https://doi.org/10.1093/bioinformatics/btw372openalex-snapshot

Pseudotime estimation: deconfounding single cell time series

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/10.1109/tpami.2014.2318711openalex-snapshot

Fast Nonparametric Clustering of Structured Time-Series

inferredcites →https://doi.org/10.1126/science.1175870openalex-snapshot

Bcl6 and Blimp-1 Are Reciprocal and Antagonistic Regulators of T Follicular Helper Cell Differentiation

inferredcites →https://doi.org/10.1126/science.1247651openalex-snapshot

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

inferredcites →https://doi.org/10.1126/science.1260044openalex-snapshot

Antigen affinity, costimulation, and cytokine inputs sum linearly to amplify T cell expansion

inferredcites →https://doi.org/10.1145/1273496.1273557openalex-snapshot

Hierarchical Gaussian process latent variable models

inferredcites →https://doi.org/10.1146/annurev-immunol-030409-101212openalex-snapshot

Differentiation of Effector CD4 T Cell Populations

inferredcites →https://doi.org/10.1172/jci11902openalex-snapshot

Bonzo/CXCR6 expression defines type 1–polarized T-cell subsets with extralymphoid tissue homing potential

inferredcites →https://doi.org/10.1172/jci70698openalex-snapshot

Type I IFN signaling in CD8– DCs impairs Th1-dependent malaria immunity

inferredcites →https://doi.org/10.1182/blood-2004-11-4494openalex-snapshot

Balanced expression of CXCR5 and CCR7 on follicular T helper cells determines their transient positioning to lymph node follicles and is essential for efficient B-cell help

inferredcites →https://doi.org/10.1186/1471-2148-11-298openalex-snapshot

Rapid evolution and copy number variation of primate RHOXF2, an X-linked homeobox gene involved in male reproduction and possibly brain function

inferredcites →https://doi.org/10.1186/s13062-015-0045-xopenalex-snapshot

An atlas of mouse CD4+ T cell transcriptomes

inferredcites →https://doi.org/10.1214/08-aoas165openalex-snapshot

Horseshoes in multidimensional scaling and local kernel methods

inferredcites →https://doi.org/10.3389/fimmu.2014.00671openalex-snapshot

CD4 T-Cell Subsets in Malaria: TH1/TH2 Revisited

inferredcites →https://doi.org/10.4049/jimmunol.1202963openalex-snapshot

Bcl6 Expressing Follicular Helper CD4 T Cells Are Fate Committed Early and Have the Capacity To Form Memory

inferredcites →https://doi.org/10.4049/jimmunol.1300099openalex-snapshot

Id2-Mediated Inhibition of E2A Represses Memory CD8+ T Cell Differentiation

inferredcites →https://doi.org/10.4049/jimmunol.168.4.1723openalex-snapshot

Repeated Antigen Exposure Is Necessary for the Differentiation, But Not the Initial Proliferation, of Naive CD4+ T Cells

inferredcites →https://doi.org/10.4049/jimmunol.175.11.7109openalex-snapshot

CXCR5-Dependent Seeding of Follicular Niches by B and Th Cells Augments Antiviral B Cell Responses

inferredcites →https://doi.org/10.48550/arxiv.1206.5162openalex-snapshot

Fast Variational Inference in the Conjugate Exponential Family

What points at this work

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

inferred← citeshttps://doi.org/10.1073/pnas.1615590114openalex-snapshot

Diverse continuum of CD4 + T-cell states is determined by hierarchical additive integration of cytokine signals

inferred← citeshttps://doi.org/10.1093/nar/gkab004openalex-snapshot

Flexible comparison of batch correction methods for single-cell RNA-seq using BatchBench

inferred← citeshttps://doi.org/10.1101/132811openalex-snapshot

FORKS: Finding Orderings Robustly using k-means and Steiner trees

inferred← citeshttps://doi.org/10.1186/s13059-017-1192-4openalex-snapshot

Are cells from a snowman realistic? Cryopreserved tissues as a source for single-cell RNA-sequencing experiments

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