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List of works by Alexander van Oudenaarden

A Caenorhabditis elegans protein with a PRDM9-like SET domain localizes to chromatin-associated foci and promotes spermatocyte gene expression, sperm production and fertility.

scientific article published on 27 April 2018

A Gene Regulatory Program for Meiotic Prophase in the Fetal Ovary.

scientific article published on 17 September 2015

A Novel Sperm-Delivered Toxin Causes Late-Stage Embryo Lethality and Transmission Ratio Distortion in C. elegans ⬇️

scientific article published on July 26, 2011

A Single-Cell RNA Sequencing Study Reveals Cellular and Molecular Dynamics of the Hippocampal Neurogenic Niche

scientific article published in December 2017

A Single-Cell Transcriptome Atlas of the Human Pancreas

scientific article published on 28 September 2016

A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes

scientific article

A critical role for the Wnt effector Tcf4 in adult intestinal homeostatic self-renewal

scientific article

A general mechanism for network-dosage compensation in gene circuits

scientific article published on September 2010

A multistep epigenetic switch enables the stable inheritance of DNA methylation states

scientific article published on 14 January 2007

A physical sciences network characterization of non-tumorigenic and metastatic cells

scientific article published on January 2013

A predictive model of bifunctional transcription factor signaling during embryonic tissue patterning.

scientific article

A system of counteracting feedback loops regulates Cdc42p activity during spontaneous cell polarization

scientific article

A systems-level analysis of perfect adaptation in yeast osmoregulation

scientific article published on July 2009

A transcriptomic roadmap to α- and β-cell differentiation in the embryonic pancreas

scientific article published on 24 June 2019

A versatile genome-scale PCR-based pipeline for high-definition DNA FISH.

scientific article

Actin polymerization: forcing flat faces forward

scientific article published on June 2004

Allele-specific detection of single mRNA molecules in situ ⬇️

scientific article published on August 11, 2013

Amplitude control of cell-cycle waves by nuclear import

scientific article published on 25 April 2004

An in vitro model of early anteroposterior organization during human development

scientific article published on 11 June 2020

An organoid platform for ovarian cancer captures intra- and interpatient heterogeneity

scientific article published on 22 April 2019

Ascl2 acts as an R-spondin/Wnt-responsive switch to control stemness in intestinal crypts

scientific article

Attenuation of noise in ultrasensitive signaling cascades

scientific article

Biomimetic systems for studying actin-based motility

scientific article

Blastocyst-like structures generated solely from stem cells

scientific article published in Nature

Caenorhabditis elegans aristaless/Arx gene alr-1 restricts variable gene expression ⬇️

scientific article (publication date: 8 March 2011)

Cdx and T Brachyury Co-activate Growth Signaling in the Embryonic Axial Progenitor Niche

scientific article published on December 2016

Celebrating 100 years of Developmental Biology at the Hubrecht Institute

scientific article published on 5 June 2017

Cell Type Purification by Single-Cell Transcriptome-Trained Sorting

scientific article published on 01 October 2019

Cell intrinsic modulation of Wnt signaling controls neuroblast migration in C. elegans

scientific article published on 16 October 2014

Cells change their sensitivity to an EGF morphogen gradient to control EGF-induced gene expression

scientific article published on 11 May 2015

Cellular asymmetry and individuality in directional sensing

scholarly article

Cellular decision making and biological noise: from microbes to mammals

scientific article

Circadian gating of the cell cycle revealed in single cyanobacterial cells

scientific article published on March 2010

Circadian networks in human embryonic stem cell-derived cardiomyocytes

scientific article published on 23 May 2017

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

scientific article published in Scientific Reports

Constant growth rate can be supported by decreasing energy flux and increasing aerobic glycolysis

scientific article

Contributions of low molecule number and chromosomal positioning to stochastic gene expression

scientific article

Correction: Neuromesodermal progenitors are a conserved source of spinal cord with divergent growth dynamics

scientific article published on 08 September 2020

Correction: Neuromesodermal progenitors are a conserved source of spinal cord with divergent growth dynamics (doi: 10.1242/dev.166728)

scientific article published on 22 January 2019

Correction: Spindle checkpoint silencing at kinetochores with submaximal microtubule occupancy (doi:10.1242/jcs.231589)

scientific article published on 12 September 2019

Coupling cellular oscillators—circadian and cell division cycles in cyanobacteria ⬇️

scientific article published on October 13, 2010

DAZL regulates Tet1 translation in murine embryonic stem cells

scientific article published on 15 June 2015

Dampening of expression oscillations by synchronous regulation of a microRNA and its target

scientific article

De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

scientific article

Deconvolving the roles of Wnt ligands and receptors in sensing and amplification ⬇️

scientific article published on January 1, 2013

Design and Analysis of Single-Cell Sequencing Experiments

scientific article

Differential Stoichiometry among Core Ribosomal Proteins ⬇️

scientific article

Differential stoichiometry among core ribosomal proteins

Direct cell reprogramming is a stochastic process amenable to acceleration

scientific article

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

scientific article published on December 2016

Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells

scientific article

Elastic instability in growing yeast colonies

scientific article

Elevated ATPase activity of KaiC applies a circadian checkpoint on cell division in Synechococcus elongatus

scientific article

Enhancement of cellular memory by reducing stochastic transitions

scientific article

Enteroendocrine and tuft cells support Lgr5 stem cells on Paneth cell depletion

scientific article published on 16 December 2019

Every cell is special: genome-wide studies add a new dimension to single-cell biology

scientific article

Exciting fluctuations: monitoring competence induction dynamics at the single-cell level

scientific article published on 16 May 2006

Expansion of Adult Human Pancreatic Tissue Yields Organoids Harboring Progenitor Cells with Endocrine Differentiation Potential.

scientific article published in March 2018

Feedback control of gene expression variability in the Caenorhabditis elegans Wnt pathway

scientific article

FuseFISH: robust detection of transcribed gene fusions in single cells

scientific article published on 27 December 2013

Gene expression. MicroRNA control of protein expression noise

scientific article

Genes methylated by DNA methyltransferase 3b are similar in mouse intestine and human colon cancer

scientific article

Genetic and phenotypic diversity in breast tumor metastases

scientific article published on 21 January 2014

Genome-wide RNA Tomography in the zebrafish embryo

scientific article published in October 2014

Genome-wide dissection of microRNA functions and cotargeting networks using gene set signatures

scientific article published on April 2010

Genome-wide maps of nuclear lamina interactions in single human cells

scientific article

Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation

scientific article

Growth landscape formed by perception and import of glucose in yeast

scientific article

H3K9me selectively blocks transcription factor activity and ensures differentiated tissue integrity

scientific article published on 04 November 2021

Heritable stochastic switching revealed by single-cell genealogy

scientific article

Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

scientific article published on 30 October 2013

How to regulate a gene: to repress or to activate?

scientific article published on 01 June 2012

Identification of molecular compartments and genetic circuitry in the developing mammalian kidney ⬇️

scientific article

Identifying the Stem Cell of the Intestinal Crypt: Strategies and Pitfalls ⬇️

scientific article published on October 5, 2012

Identity and dynamics of mammary stem cells during branching morphogenesis.

scientific article published on 30 January 2017

Imaging Single mRNA Molecules in Yeast

scientific article published on 01 March 2010

Imaging individual mRNA molecules using multiple singly labeled probes

scientific article

Induced Quiescence of Lgr5+ Stem Cells in Intestinal Organoids Enables Differentiation of Hormone-Producing Enteroendocrine Cells.

scientific article published on 17 November 2016

Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity

scientific article published on 23 January 2014

Integrated genome and transcriptome sequencing of the same cell

scientific article

Licensing of primordial germ cells for gametogenesis depends on genital ridge signaling

scientific article

LifeTime and improving European healthcare through cell-based interceptive medicine

scientific article published on 07 September 2020

Long-term expanding human airway organoids for disease modeling

scientific article published on 14 January 2019

Magneto-electric Aharonov–Bohm effect in metal rings

scientific article published in Nature

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

scientific article

Mapping the physical network of cellular interactions

scientific article published on 21 May 2018

MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals

scientific article

MicroRNAs can generate thresholds in target gene expression ⬇️

scientific article published on August 21, 2011

Microbiology. Necessary noise

scientific article published on 01 July 2007

Microbiology: Altruistic defence

scientific article published on September 2010

Nature, nurture, or chance: stochastic gene expression and its consequences

scientific article

Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning

scientific article

Neuroblast migration along the anteroposterior axis ofC. elegansis controlled by opposing gradients of Wnts and a secreted Frizzled-related protein ⬇️

scientific article published on June 8, 2011

Neuromesodermal progenitors are a conserved source of spinal cord with divergent growth dynamics

scientific article published on 09 November 2018

Noise propagation in gene networks

scientific article

Ongoing chromosomal instability and karyotype evolution in human colorectal cancer organoids

scientific article published on 29 April 2019

Optimality in the development of intestinal crypts

scientific article published on February 2012

Oral Mucosal Organoids as a Potential Platform for Personalized Cancer Therapy

scientific article published on 03 May 2019

Parental haplotype-specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells.

scientific article published on 14 May 2018

Patched Receptors Sense, Interpret, and Establish an Epidermal Hedgehog Signaling Gradient

scientific article published on 4 August 2016

Plasticity between Epithelial and Mesenchymal States Unlinks EMT from Metastasis-Enhancing Stem Cell Capacity

scientific article published on 2 March 2016

Polar-like trophoblast stem cells form an embryonic-abembryonic axis in blastoids.: Supplementary data

Population genomics of domestic and wild yeasts

scientific article

Predicting stochastic gene expression dynamics in single cells

scholarly article

Probing polymerization forces by using actin-propelled lipid vesicles

scientific article

Prospective derivation of a living organoid biobank of colorectal cancer patients.

scientific article published on May 2015

Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine

scientific article published on 17 March 2021

Publisher Correction: Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids

scientific article published on 01 March 2020

Quantitative time-lapse fluorescence microscopy in single cells

scientific article

RNA sequencing reveals two major classes of gene expression levels in metazoan cells

scientific article published on 07 June 2011

Reg4+ deep crypt secretory cells function as epithelial niche for Lgr5+ stem cells in colon

scientific article published on 29 August 2016

Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing

scientific article published on 13 January 2009

Replacement of Lost Lgr5-Positive Stem Cells through Plasticity of Their Enterocyte-Lineage Daughters

scientific article published on 27 January 2016

Robustness and epistasis in the C. elegans vulval signaling network revealed by pathway dosage modulation

scientific article published on 01 January 2013

Sequencing metabolically labeled transcripts in single cells reveals mRNA turnover strategies

scientific article

Single molecule fluorescent in situ hybridization (smFISH) of C. elegans worms and embryos ⬇️

scientific article published on December 13, 2012

Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration

scientific article published on 09 May 2019

Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase ⬇️

scientific article published on September 14, 2012

Single-Cell Sequencing of the Healthy and Diseased Heart Reveals Ckap4 as a New Modulator of Fibroblasts Activation

scientific article published on 31 January 2018

Single-Cell Transcriptomics Meets Lineage Tracing

scientific article published on 10 May 2018

Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction

scientific article published on 27 June 2016

Single-cell analysis reveals that noncoding RNAs contribute to clonal heterogeneity by modulating transcription factor recruitment

scientific article published on 19 January 2012

Single-cell analysis reveals that stochasticity and paracrine signaling control interferon-alpha production by plasmacytoid dendritic cells

scientific article published in Nature Communications

Single-cell analysis uncovers that metabolic reprogramming by ErbB2 signaling is essential for cardiomyocyte proliferation in the regenerating heart

scientific article published on 23 December 2019

Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids

scientific article published on 19 February 2020

Single-cell messenger RNA sequencing reveals rare intestinal cell types

scientific article

Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations.

scientific article published in September 2017

Single-cell transcriptomics enters the age of mass production.

scientific article published in May 2015

Single-cell transcriptomics reveal the dynamic of haematopoietic stem cell production in the aorta.

scientific article

Single-molecule approaches to stochastic gene expression

scientific article published on January 2009

Single-molecule mRNA detection and counting in mammalian tissue.

scientific article

Single-molecule transcript counting of stem-cell markers in the mouse intestine

scientific article published on 27 November 2011

Slug and Sox9 cooperatively determine the mammary stem cell state

scientific article

Snake Venom Gland Organoids

scientific article published on 01 January 2020

Snowdrift game dynamics and facultative cheating in yeast

scientific article published on 6 April 2009

Spatial Transcriptomics of C. elegans Males and Hermaphrodites Identifies Sex-Specific Differences in Gene Expression Patterns

scientific article published on 08 November 2018

Spatially Resolved Genome-wide Transcriptional Profiling Identifies BMP Signaling as Essential Regulator of Zebrafish Cardiomyocyte Regeneration

scientific article published on 31 December 2015

Spatially resolved transcriptomics and beyond.

scientific article

Spindle checkpoint silencing at kinetochores with submaximal microtubule occupancy

scientific article published on 17 June 2019

Stochastic Cytokine Expression Induces Mixed T Helper Cell States ⬇️

scientific article published on July 30, 2013

Stochastic gene expression in fluctuating environments

scientific article

Stochastic gene expression out-of-steady-state in the cyanobacterial circadian clock

scientific article

Stochastic gene expression: from single molecules to the proteome

scientific article published on 20 February 2007

Stochastic switching as a survival strategy in fluctuating environments

scientific article

Studying lineage decision-making in vitro: emerging concepts and novel tools

scientific article

Synthetic biology: The yin and yang of nature.

scientific article

Synthetic biology: understanding biological design from synthetic circuits

scientific article

Systematic identification of signal-activated stochastic gene regulation

scientific article

Tdrd6a Regulates the Aggregation of Buc into Functional Subcellular Compartments that Drive Germ Cell Specification

scientific article published on 01 August 2018

The Caenorhabditis elegans synthetic multivulva genes prevent ras pathway activation by tightly repressing global ectopic expression of lin-3 EGF

scientific article

The Human Cell Atlas

scientific article

The Human Cell Atlas

The Human Cell Atlas White Paper ⬇️

journal article from 'arXiv:1810.05192 [q-bio]' published in 2018

The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent '+4' cell markers

scientific article published on 12 June 2012

The Majority of CD45 Ter119 CD31 Bone Marrow Cell Fraction Is of Hematopoietic Origin and Contains Erythroid and Lymphoid Progenitors

scientific article published on 09 October 2018

The frequency dependence of osmo-adaptation in Saccharomyces cerevisiae

scientific article

The thrombospondin repeat containing protein MIG-21 controls a left-right asymmetric Wnt signaling response in migrating C. elegans neuroblasts

scientific article

Tomo-Seq Identifies SOX9 as a Key Regulator of Cardiac Fibrosis During Ischemic Injury.

scientific article published on 19 July 2017

Transcript counting in single cells reveals dynamics of rDNA transcription

scientific article

Transcription of two long noncoding RNAs mediates mating-type control of gametogenesis in budding yeast

scientific article

Transcriptional profiling of cells sorted by RNA abundance

scientific article

Transformation of intestinal stem cells into gastric stem cells on loss of transcription factor Cdx2.

scientific article

Troy+ brain stem cells cycle through quiescence and regulate their number by sensing niche occupancy

scientific article

UNC-4 antagonizes Wnt signaling to regulate synaptic choice in the C. elegans motor circuit ⬇️

scientific article published on June 1, 2012

Unravelling cellular relationships during development and regeneration using genetic lineage tracing

scientific article published on 05 November 2019

Using gene expression noise to understand gene regulation

scientific article

Validating transcripts with probes and imaging technology

scientific article published on 30 March 2011

Validation of noise models for single-cell transcriptomics

scientific article

Variability in gene expression underlies incomplete penetrance

scientific article

Viral genome imaging of hepatitis C virus to probe heterogeneous viral infection and responses to antiviral therapies

scientific article published on 26 April 2016

When it comes to decisions, myeloid progenitors crave positive feedback

scientific article published on 01 August 2006

When noisy neighbors are a blessing: analysis of gene expression noise identifies coregulated genes

scientific article published on 01 February 2012

Whole-organism clone tracing using single-cell sequencing.

scientific article published on 28 March 2018

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