Alexander van Oudenaarden

NOTCH-driven oscillations control cell fate decisions during intestinal homeostasis

The paper shows that NOTCH-driven Hes1 oscillations with different periods control cell fate decisions in intestinal stem cells, influencing secretory and absorptive lineage commitment.

Random mtDNA mutagenesis maps genotype-phenotype associations across metabolic contexts and lineages

The paper introduces mtDIVE, a random mtDNA mutagenesis platform, to study genotype-phenotype associations in metabolic contexts and lineages, revealing lineage-specific effects and mutation-specific impacts.

Oncogenic fusions induce an extensive cancer-restricted cryptic proteome in Ewing sarcoma

The paper shows EWSR1::FLI1 fusion drives the production of cancer-specific neoproteins in Ewing sarcoma, revealing a reversible dark proteome with therapeutic potential.

Single-Cell Inference of Structural States Of Ribosomes

SCISSOR infers global translation activity in single cells using ribosomal RNA protection signatures, revealing cell cycle and differentiation-related translation variations in human and murine cells.

Mechanical strain of the intestinal epithelium directs absorptive lineage maturation

This study shows that mechanical strain on intestinal organoids reduces the maturity of absorptive lineage cells by expanding early-stage enterocytes and downregulating maturation programs.

Single-cell co-mapping reveals relationship between chromatin state and gene expression in early zebrafish development

The paper uses single-cell multimodal data to show how chromatin states and gene expression interact during early zebrafish development, revealing lineage-specific transcription factor regulation.

Unified function of FACT in mammalian chromatin replication and transcription, dissolving and restoring nucleosomes to counteract genome aggregation

This study shows that FACT is essential for chromatin replication and transcription by disrupting and reassembling nucleosomes, preventing genome aggregation.

WEE1 inhibitors trigger GCN2-mediated activation of the integrated stress response

This study shows WEE1 inhibitors trigger the integrated stress response via GCN2 activation, leading to translational shutdown, which can be mitigated by low-dose or combination treatments.

Dynamic Ribosomal RNA Methylation Regulates Translation in the Hematopoietic System and is Essential for Stem Cell Fitness

The paper identifies rRNA methylation dynamics as a mechanism regulating translation efficiency and HSC fitness during hematopoietic differentiation.

Latent plasticity of the human pancreas across development, health, and disease.

The paper constructs a single-cell multiomics atlas of the human pancreas across development, health, and T2D, identifying plastic cell states and lineage trajectories.

THE NSL COMPLEX PROMOTES NEURAL DEVELOPMENT BY PREVENTING R-LOOP INDUCED REPLICATION STRESS

This study shows the NSL complex prevents R-loop induced replication stress during neural development, leading to developmental abnormalities when disrupted.

Time-resolved and multifactorial profiling in single cells resolves the order of heterochromatin formation events during X-chromosome inactivation

The paper introduces Dam&ChIC, a method for time-resolved chromatin profiling in single cells, revealing that genome-lamina detachment precedes H3K27me3 accumulation during X-chromosome inactivation.

Acute multi-level response to defective de novo chromatin assembly in S-phase

This study investigates the acute effects of CAF-1 loss on chromatin assembly during S-phase, revealing multi-level responses including replication slowdown and histone modification changes.

Detection of histone modifications and full-length transcriptome in single cells identifies sequential epigenetic perceptiveness to lineage commitment

The paper develops T-ChIC to detect histone modifications and full-length transcripts in single cells, revealing sequential epigenetic changes during lineage commitment in gastruloids.

COORDINATION BETWEEN EMBRYO GROWTH AND TROPHOBLAST MIGRATION UPON IMPLANTATION DELINEATES MOUSE EMBRYOGENESIS

This study develops an engineered uterus-like microenvironment to study mouse embryo implantation, revealing coordination between trophoblast migration and embryo growth.

Transcription factor induction of vascular blood stem cell niches in vivo

This study identifies transcription factors that induce vascular blood stem cell niches in vivo, enabling synthetic niche generation and potential therapeutic applications.

Deconvolving multiplexed histone modifications in single cells

The paper introduces scChIX, a method to map multiple histone modifications in single cells by combining experimental and computational approaches, revealing chromatin state transitions in immune cells.

Hierarchical chromatin regulation during blood formation uncovered by single cell sortChIC

The paper develops sortChIC to map histone modifications in mouse hematopoietic cells, revealing hierarchical chromatin regulation during blood formation.

Acceleration of genome replication uncovered by single-cell nascent DNA sequencing

This study measures DNA replication speeds in human cells using single-cell sequencing and finds replication accelerates during S-phase, limited by transcriptional activity early in the phase.

Droplet-based Single-cell Total RNA-seq Reveals Differential Non-Coding Expression and Splicing Patterns during Mouse Development

The paper introduces VASA-seq, a method for total single-cell RNA-seq in mice, revealing non-coding RNA expression and alternative splicing during development.

Strand-specific single-cell methylomics reveals distinct modes of DNA demethylation dynamics during early mammalian development

The paper introduces a single-cell methylomics method to study DNA demethylation dynamics in early mammalian development and finds distinct active and passive demethylation modes in mouse and human embryos.

Functional modules from variable genes: Leveraging percolation to analyze noisy, high-dimensional data

The paper introduces a density-based clustering method using percolation theory to identify functionally related gene modules from noisy, high-dimensional RNA sequencing data across different organisms.

Embryonic signals perpetuate polar-like trophoblast stem cells and pattern the blastocyst axis.

The paper shows that embryonic signals convert trophoblast stem cells into polar-like cells that pattern the blastocyst axis in vitro.

Cell type purification by single-cell transcriptome-trained sorting

GateID combines single-cell transcriptomics with FACS to purify cell types without specific antibodies or transgenes.

Dynamics of Meiotic Sex Chromosome Inactivation and Pachytene Activation in Mice Spermatogenesis

The paper maps gene expression changes during meiotic prophase-I in mice spermatogenesis, identifying key transitions and gene regulation patterns.

Combined quantification of intracellular (phospho-)proteins and transcriptomics from fixed single cells.

The paper introduces RAID, a method to analyze both transcriptomes and intracellular phosphoproteins from fixed single cells, showing its ability to detect heterogeneity in cellular responses.

Tdrd6a regulates the aggregation of Buc into functional subcellular compartments that drive germ cell specification

This study identifies Tdrd6a as a regulator of Buc protein aggregation, which is essential for forming subcellular compartments that drive germ cell specification in zebrafish.

Spatial transcriptomics of C. elegans males and hermaphrodites identifies novel fertility genes

The paper uses spatial transcriptomics to identify novel fertility genes in C. elegans by analyzing gene expression patterns in males and hermaphrodites.

Sharq, a versatile preprocessing and QC pipeline for Single Cell RNA-seq

Sharq preprocesses single cell RNA-seq data from fastq files to gene expression tables, addressing amplification biases and providing quality control diagnostics.

Neuromesodermal Progenitors are a Conserved Source of Spinal Cord with Divergent Growth Dynamics

The paper traces neuromesodermal progenitors in zebrafish embryos to show they contribute to spinal cord and mesoderm with distinct growth dynamics across species.