A. van Oudenaarden
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Population genomics of domestic and wild yeasts
Since the completion of the genome sequence of Saccharomyces cerevisiae in 1996 (refs 1, 2), there has been a large increase in complete genome sequences, accompanied by great advances in our… Expand
Imaging individual mRNA molecules using multiple singly labeled probes
- A. Raj, Patrick T C van den Bogaard, S. A. Rifkin, A. van Oudenaarden, Sanjay Tyagi
- Nature Methods
- 21 September 2008
We describe a method for imaging individual mRNA molecules in fixed cells by probing each mRNA species with 48 or more short, singly labeled oligonucleotide probes. This makes each mRNA molecule… Expand
Direct cell reprogramming is a stochastic process amenable to acceleration
Direct reprogramming of somatic cells into induced pluripotent stem (iPS) cells can be achieved by overexpression of Oct4, Sox2, Klf4 and c-Myc transcription factors, but only a minority of donor… Expand
Snowdrift game dynamics and facultative cheating in yeast
The origin of cooperation is a central challenge to our understanding of evolution. The fact that microbial interactions can be manipulated in ways that animal interactions cannot has led to a… Expand
MicroRNAs can generate thresholds in target gene expression
- Shankar Mukherji, M. Ebert, Grace X. Zheng, J. S. Tsang, P. Sharp, A. van Oudenaarden
- Medicine, Biology
- Nature Genetics
- 15 July 2011
MicroRNAs (miRNAs) are short, highly conserved noncoding RNA molecules that repress gene expression in a sequence-dependent manner. We performed single-cell measurements using quantitative… Expand
The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent ‘+4’ cell markers
Two types of stem cells are currently defined in small intestinal crypts: cycling crypt base columnar (CBC) cells and quiescent ‘+4’ cells. Here, we combine transcriptomics with proteomics to define… Expand
MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals.
MicroRNAs (miRNAs) are regulatory molecules that participate in diverse biological processes in animals and plants. While thousands of mammalian genes are potentially targeted by miRNAs, the… Expand
RNA sequencing reveals two major classes of gene expression levels in metazoan cells
- Daniel Hebenstreit, M. Fang, M. Gu, Varodom Charoensawan, A. van Oudenaarden, S. Teichmann
- Medicine, Biology
- Molecular systems biology
- 7 June 2011
The expression level of a gene is often used as a proxy for determining whether the protein or RNA product is functional in a cell or tissue. Therefore, it is of fundamental importance to understand… Expand
Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning.
In the vertebrate neural tube, regional Sonic hedgehog (Shh) signaling invokes a time- and concentration-dependent induction of six different cell populations mediated through Gli transcriptional… Expand
Replacement of Lost Lgr5-Positive Stem Cells through Plasticity of Their Enterocyte-Lineage Daughters.
Intestinal crypts display robust regeneration upon injury. The relatively rare secretory precursors can replace lost stem cells, but it is unknown if the abundant enterocyte progenitors that express… Expand