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Bayesian inference of transcriptional branching identifies regulators of early germ cell development in humans

https://doi.org/10.1101/167684
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Analysis of gene expression in PTHrP−/− mammary buds supports a role for BMP signaling and MMP2 in the initiation of ductal morphogenesis
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Expression of c‐KIT and Its Ligand, Stem Cell Factor, in Normal and Subfertile Human Testicular Tissue
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Tumor Necrosis Factor-α (TNF-α) Stimulates Proliferation of Mouse Primordial Germ Cells in Culture
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Origin, Migration, and Proliferation of Human Primordial Germ Cells
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Sur l'équilibre d'une masse fluide animée d'un mouvement de rotation
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Germ cell specification and pluripotency in mammals: a perspective from early embryogenesis
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Schwann cells produce tumor necrosis factor alpha: expression in injured and non-injured nerves
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Primordial Germ-Cell Development and Epigenetic Reprogramming in Mammals
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What Can Stem Cell Models Tell Us About Human Germ Cell Biology?
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Inhibition of the transcription factor Yin Yang 1 activity by S-nitrosation
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A Signaling Principle for the Specification of the Germ Cell Lineage in Mice
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.2014.12.013openalex-snapshot
SOX17 Is a Critical Specifier of Human Primordial Germ Cell Fate
inferredcites →https://doi.org/10.1016/j.cell.2015.04.053openalex-snapshot
A Unique Gene Regulatory Network Resets the Human Germline Epigenome for Development
inferredcites →https://doi.org/10.1016/j.cell.2015.05.012openalex-snapshot
DNA Demethylation Dynamics in the Human Prenatal Germline
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.cell.2016.03.023openalex-snapshot
Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos
inferredcites →https://doi.org/10.1016/j.devcel.2013.11.001openalex-snapshot
A Mesodermal Factor, T, Specifies Mouse Germ Cell Fate by Directly Activating Germline Determinants
inferredcites →https://doi.org/10.1016/j.mce.2004.09.012openalex-snapshot
Stem cell factor and c-Kit in human primordial germ cells and fetal ovaries
inferredcites →https://doi.org/10.1016/j.stem.2008.06.018openalex-snapshot
Establishment of Endoderm Progenitors by SOX Transcription Factor Expression in Human Embryonic Stem Cells
inferredcites →https://doi.org/10.1016/j.stem.2015.06.014openalex-snapshot
Robust In Vitro Induction of Human Germ Cell Fate from Pluripotent Stem Cells
inferredcites →https://doi.org/10.1016/j.stem.2017.03.007openalex-snapshot
Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal Niche Interactions
inferredcites →https://doi.org/10.1016/j.stemcr.2013.12.010openalex-snapshot
Nanog-Independent Reprogramming to iPSCs with Canonical Factors
inferredcites →https://doi.org/10.1016/j.stemcr.2015.04.014openalex-snapshot
Human Germline: A New Research Frontier
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Regulation and properties of extracellular signal-regulated protein kinases 1 and 2 in vitro.
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Reviews of Chromosome Studies in Urological Tumors. III. Cytogenetics and Genes in Testicular Tumors
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DNA methylation and chromatin accessibility profiling of mouse and human fetal germ cells
inferredcites →https://doi.org/10.1038/nature06403openalex-snapshot
Nanog safeguards pluripotency and mediates germline development
inferredcites →https://doi.org/10.1038/nature06968openalex-snapshot
The ground state of embryonic stem cell self-renewal
inferredcites →https://doi.org/10.1038/nature09303openalex-snapshot
Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification
inferredcites →https://doi.org/10.1038/nature11918openalex-snapshot
PRC1 coordinates timing of sexual differentiation of female primordial germ cells
inferredcites →https://doi.org/10.1038/nature12417openalex-snapshot
Induction of mouse germ-cell fate by transcription factors in vitro
inferredcites →https://doi.org/10.1038/nature12745openalex-snapshot
Derivation of novel human ground state naive pluripotent stem cells
inferredcites →https://doi.org/10.1038/nature16480openalex-snapshot
NANOG alone induces germ cells in primed epiblast in vitro by activation of enhancers
inferredcites →https://doi.org/10.1038/nature22812openalex-snapshot
Principles of early human development and germ cell program from conserved model systems
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.3569openalex-snapshot
Wishbone identifies bifurcating developmental trajectories from single-cell data
inferredcites →https://doi.org/10.1038/ncb2798openalex-snapshot
A tripartite transcription factor network regulates primordial germ cell specification in mice
inferredcites →https://doi.org/10.1038/nchembio.137openalex-snapshot
Small molecule–mediated disruption of Wnt-dependent signaling in tissue regeneration and cancer
inferredcites →https://doi.org/10.1038/ncomms11056openalex-snapshot
Loss of MAX results in meiotic entry in mouse embryonic and germline stem cells
inferredcites →https://doi.org/10.1038/nmeth.4402openalex-snapshot
Reversed graph embedding resolves complex single-cell trajectories
inferredcites →https://doi.org/10.1038/nprot.2016.131openalex-snapshot
Self-organization of human embryonic stem cells on micropatterns
inferredcites →https://doi.org/10.1038/nrc1568openalex-snapshot
Testicular germ-cell tumours in a broader perspective
inferredcites →https://doi.org/10.1038/nrg.2016.88openalex-snapshot
Specification and epigenetic programming of the human germ line
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/10.1038/nsmb.3365openalex-snapshot
Xist-dependent imprinted X inactivation and the early developmental consequences of its failure
inferredcites →https://doi.org/10.1038/protex.2018.094openalex-snapshot
Generating Gastruloids from Mouse Embryonic Stem Cells
inferredcites →https://doi.org/10.1038/s41556-017-0013-zopenalex-snapshot
Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation
inferredcites →https://doi.org/10.1038/s41556-018-0147-7openalex-snapshot
Self-assembly of embryonic and two extra-embryonic stem cell types into gastrulating embryo-like structures
inferredcites →https://doi.org/10.1038/s41586-018-0150-yopenalex-snapshot
Self-organization of a human organizer by combined Wnt and Nodal signalling
inferredcites →https://doi.org/10.1038/s41586-018-0414-6openalex-snapshot
RNA velocity of single cells
inferredcites →https://doi.org/10.1038/sj.onc.1201787openalex-snapshot
Identification of the critical region of 12p over-representation in testicular germ cell tumors of adolescents and adults
inferredcites →https://doi.org/10.1042/bsr20160441openalex-snapshot
Proliferation in culture of primordial germ cells derived from embryonic stem cell: induction by retinoic acid
inferredcites →https://doi.org/10.1042/bst20160173openalex-snapshot
Molecular architecture of polycomb repressive complexes
inferredcites →https://doi.org/10.1073/pnas.1408993111openalex-snapshot
Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape
inferredcites →https://doi.org/10.1093/bioinformatics/btr261openalex-snapshot
DREME: motif discovery in transcription factor ChIP-seq data
inferredcites →https://doi.org/10.1093/bioinformatics/btw329openalex-snapshot
Inferring the perturbation time from biological time course data
inferredcites →https://doi.org/10.1093/bioinformatics/btw372openalex-snapshot
Pseudotime estimation: deconfounding single cell time series
inferredcites →https://doi.org/10.1093/bioinformatics/bty498openalex-snapshot
A descriptive marker gene approach to single-cell pseudotime inference
inferredcites →https://doi.org/10.1093/bioinformatics/bty533openalex-snapshot
GrandPrix: scaling up the Bayesian GPLVM for single-cell data
inferredcites →https://doi.org/10.1093/bioinformatics/bty603openalex-snapshot
Branch-recombinant Gaussian processes for analysis of perturbations in biological time series
inferredcites →https://doi.org/10.1093/bioinformatics/bty664openalex-snapshot
GPseudoRank: a permutation sampler for single cell orderings
inferredcites →https://doi.org/10.1093/molehr/gaq052openalex-snapshot
Human primordial germ cells migrate along nerve fibers and Schwann cells from the dorsal hind gut mesentery to the gonadal ridge
inferredcites →https://doi.org/10.1093/nar/gkw377openalex-snapshot
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
inferredcites →https://doi.org/10.1093/nar/gkw430openalex-snapshot
TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis
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/10.1101/170118openalex-snapshot
Fundamental limits on dynamic inference from single cell snapshots
inferredcites →https://doi.org/10.1101/gad.13.4.424openalex-snapshot
Bmp4 is required for the generation of primordial germ cells in the mouse embryo
inferredcites →https://doi.org/10.1105/tpc.112.102046openalex-snapshot
Arabidopsis Defense against Botrytis cinerea : Chronology and Regulation Deciphered by High-Resolution Temporal Transcriptomic Analysis
inferredcites →https://doi.org/10.1111/j.1365-2605.2006.00742.xopenalex-snapshot
The equilibrium of XIAP and Smac/DIABLO expression is gradually deranged during the development and progression of testicular germ cell tumours
inferredcites →https://doi.org/10.1126/science.1105396openalex-snapshot
Common and Distinct Elements in Cellular Signaling via EGF and FGF Receptors
inferredcites →https://doi.org/10.1126/science.aal1810openalex-snapshot
Assembly of embryonic and extraembryonic stem cells to mimic embryogenesis in vitro
inferredcites →https://doi.org/10.1126/science.aar5780openalex-snapshot
The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution
inferredcites →https://doi.org/10.1146/annurev.cellbio.20.010403.095114openalex-snapshot
FUNDAMENTALS OF PLANARIAN REGENERATION
inferredcites →https://doi.org/10.1186/1471-2105-14-128openalex-snapshot
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
inferredcites →https://doi.org/10.1186/gb-2007-8-2-r24openalex-snapshot
Quantifying similarity between motifs
inferredcites →https://doi.org/10.1186/s13059-016-0975-3openalex-snapshot
SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data
inferredcites →https://doi.org/10.1186/s13059-018-1440-2openalex-snapshot
BGP: identifying gene-specific branching dynamics from single-cell data with a branching Gaussian process
inferredcites →https://doi.org/10.1242/dev.041160openalex-snapshot
Conditional knockdown of Nanog induces apoptotic cell death in mouse migrating primordial germ cells
inferredcites →https://doi.org/10.1242/dev.050146openalex-snapshot
The role of FGF/Erk signaling in pluripotent cells
inferredcites →https://doi.org/10.1242/dev.117598openalex-snapshot
LIF signaling in stem cells and development
inferredcites →https://doi.org/10.1242/dev.129.10.2367openalex-snapshot
Depletion of definitive gut endoderm in Sox17 -null mutant mice
inferredcites →https://doi.org/10.15252/embj.201695862openalex-snapshot
In vitro expansion of mouse primordial germ cell‐like cells recapitulates an epigenetic blank slate
inferredcites →https://doi.org/10.1609/aaai.v28i1.8904openalex-snapshot
Automatic Construction and Natural-Language Description of Nonparametric Regression Models
inferredcites →https://doi.org/10.48550/arxiv.1610.08733openalex-snapshot
GPflow: A Gaussian process library using TensorFlow
inferredcites →https://doi.org/10.7554/elife.21064openalex-snapshot
PCGF6-PRC1 suppresses premature differentiation of mouse embryonic stem cells by regulating germ cell-related genes
inferredcites →https://doi.org/10.7554/elife.22345openalex-snapshot
Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition

What points at this work

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

inferred← citeshttps://doi.org/10.1093/bioinformatics/bty603openalex-snapshot
Branch-recombinant Gaussian processes for analysis of perturbations in biological time series
inferred← citeshttps://doi.org/10.1146/annurev-biodatasci-080917-013452openalex-snapshot
From Tissues to Cell Types and Back: Single-Cell Gene Expression Analysis of Tissue Architecture
inferred← citeshttps://doi.org/10.1186/s13059-018-1440-2openalex-snapshot
BGP: identifying gene-specific branching dynamics from single-cell data with a branching Gaussian process
inferred← citeshttps://doi.org/10.26508/lsa.202201706openalex-snapshot
Origin and segregation of the human germline
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