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2013
Systematic identification of signal-activated stochastic gene regulation
G. Neuert, B. Munsky, R. Z. Tan, L. Teytelman, M. Khammash, and A. van Oudenaarden
Science 339, 584 (2013).
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Robustness and epistasis in the C. elegans vulval signaling network revealed by pathway dosage modulation
M. Barkoulas, J. S. van Zon, J. Milloz, A. van Oudenaarden, and M. A. Félix
Developmental Cell 24, 64 (2013).
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Deconvolving the roles of Wnt ligands and receptors in sensing and amplification
R. Z. Tan, N. Ji, R. A. Mentink, H. C. Korswagen, and A. van Oudenaarden
Molecular Systems Biology 9:631 doi:10.1038/msb.2012.64 (2013).
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A versatile genome-scale PCR-based pipeline for high-definition DNA FISH
M. Bienko, N. Crosetto, L. Teytelman, S. Klemm, S. Itzkovitz, and A. van Oudenaarden
Nature Methods 10, 122 (2013).
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2012
Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning
K. A. Peterson, Y. Nishi, W. Ma, A. Vedenko, L. Shokri, X. Zhang, M. McFarlane, J. M. Baizabal, J. P. Junker, A. van Oudenaarden, T. Mikkelsen, B. E. Bernstein, T. L. Bailey, M. L. Bulyk, W. H. Wong, and A. P. McMahon
Genes and Development 26, 2802 (2012).
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Single molecule fluorescent in situ hybridization (smFISH) of C. elegans worms and embryos
N. Ji, and A. van Oudenaarden
WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.153.1 (2012).
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Identifying the stem cell of the intestinal crypt: strategies and pitfalls
N. Barker, A. van Oudenaarden, and H. Clevers
Cell Stem Cell 11, 452 (2012).
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Dll1(+) secretory progenitor cells revert to stem cells upon crypt damage
J. H. van Es, T. Sato, M. van de Wetering, A. Lyubimova, A. N. Yee Nee, A. Gregorieff, N. Sasaki, L. Zeinstra, M. van den Born, J. Korving, A. C. Martens, N. Barker, A. van Oudenaarden, and H. Clevers
Nature Cell Biology 14, 1099 (2012).
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Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase
Y. Buganim, D. A. Faddah, A. W. Cheng, E. Itskovich, S. Markoulaki, K. Ganz, S. L. Klemm, A. van Oudenaarden, and R. Jaenisch
Cell 150, 1209 (2012).
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Transcription of two long noncoding RNAs mediates mating-type control of gametogenesis in budding yeast
F. J. van Werven, G. Neuert, N. Hendrick, A. Lardenois, S. Buratowski, A. van Oudenaarden, M. Primig, and A. Amon
Cell 150, 1170 (2012).
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The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent ‘+4’ cell markers
J. Munoz, D. E. Stange, A. G. Schepers, M. van de Wetering, B. Koo, S. Itzkovitz, R. Volckmann, K. S. Kung, J. Koster, S. Radulescu, K. Myant, R. Versteeg, O. J. Sansom, J. H. van Es, N. Barker, A. van Oudenaarden, S. Mohammed, A. Heck, and H. Clevers
EMBO Journal 31, 3079 (2012).
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How to regulate a gene: To repress or to activate?
N. Slavov and A. van Oudenaarden
Molecular Cell 45, 551 (2012).
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UNC-4 antagonizes Wnt signaling to regulate synaptic choice in the C. elegans motor circuit
J. Schneider, R. L. Skelton, S. E. Von Stetina, T. C. Middelkoop, A. van Oudenaarden, H. C. Korswagen, and D. M. Miller 3rd.
Development 139, 2234 (2012).
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Identification of molecular compartments and genetic circuitry in the developing mammalian kidney
J. Yu, M. T. Valerius, M. Duah, K. Staser, J. K. Hansard, J. J. Guo, J. McMahon, J. Vaughan, D. Faria, K. Georgas, B. Rumballe, Q. Ren, A. M. Krautzberger, J. P. Junker, R. D. Thiagarajan, P. Machanick, P. A. Gray, A. van Oudenaarden, D. H. Rowitch, C. D. Stiles, Q. Ma, S. M. Grimmond, T. L. Bailey, M. H. Little, and A. P. McMahon
Development 139, 1863 (2012).
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Using gene expression noise to understand gene regulation
B. Munsky, G. Neuert, and A. van Oudenaarden
Science 336, 183 (2012).
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A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes
N. Slavov, E. Airoldi, A. van Oudenaarden, and D. Botstein
Molecular Biology of the Cell 23, 1986 (2012).
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A critical role for the Wnt effector Tcf4 in adult intestinal homeostatic self-renewal
J. H. van Es, A. Haegebarth, P. Kujala, S. Itzkovitz, B. K. Koo, S. F. Boj, J. Korving, M. van den Born, A. van Oudenaarden, S. Robine, H. Clevers
Molecular & Cellular Biology 32, 1918 (2012).
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Slug and sox9 cooperatively determine the mammary stem cell state
W. Guo, Z. Keckesova, J. L. Donaher, T. Shibue, V. Tischler, F. Reinhardt, S. Itzkovitz, A. Noske, U. Zürrer-Härdi, G. Bell, W. L. Tam, S. A. Mani, A. van Oudenaarden, and R. A. Weinberg
Cell 148, 1015 (2012).
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When noisy neighbors are a blessing: analysis of gene expression noise identifies coregulated genes
J. P. Junker and A. van Oudenaarden
Molecular Cell 45, 437 (2012).
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Optimality in the development of intestinal crypts
S. Itzkovitz, I. C. Blat, T. Jacks, H. Clevers, and A. van Oudenaarden
Cell 148, 608 (2012).
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Single-cell analysis reveals that noncoding RNAs contribute to clonal heterogeneity by modulating transcription factor recruitment
S. Bumgarner, G. Neuert, B. F. Voight, A. Symbor-Nagrabska, P. Grisafi, A. van Oudenaarden, and G. R. Fink
Molecular Cell 45, 470 (2012).
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Single-molecule transcript counting of stem-cell markers in the mouse intestine
S. Itzkovitz, A. Lyubimova, I. C. Blat, M. Maynard, J. van Es, J. Lees, T. Jacks, H. Clevers, and A. van Oudenaarden
Nature Cell Biology 14, 106 (2012).
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The thrombospondin repeat containing protein MIG-21 controls a left-right asymmetric Wnt signaling response in migrating C. elegans neuroblasts
T. C. Middelkoop, L. Williams, P. T. Yang, M. C. Betist, N. Ji, A. van Oudenaarden, C. Kenyon, and H. C. Korswagen
Developmental Biology 361, 338 (2012).
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2011
The Caenorhabditis elegans synthetic multivulva genes prevent Ras pathway activation by tightly repressing global ectopic expression of lin-3 EGF
A. M. Saffer, D. H. Kim, A. van Oudenaarden, and H. R. Horvitz
PLoS Genetics 7, e1002418 (2011).
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MicroRNAs can generate thresholds in target gene expression
S. Mukherji, M. S. Ebert, G. X. Y. Zheng, J. S. Tsang, P. A. Sharp, and A. van Oudenaarden
Nature Genetics 43, 854 (2011).
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A novel sperm-delivered toxin causes late-stage embryo lethality and transmission ratio distortion in C. elegans
H. S. Seidel, M. Ailion, J. Li, A. van Oudenaarden, M. V. Rockman, and L. Kruglyak
PLoS Biology 9, e1001115 (2011).
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Neuroblast migration along the anteroposterior axis of C. elegans is controlled by opposing gradients of Wnts and a secreted Frizzled-related protein
M. Harterink, D. H. Kim, T. C. Middelkoop, T. D. Doan, A. van Oudenaarden, and H. C. Korswagen
Development 138, 2915 (2011).
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RNA sequencing reveals two major classes of gene expression levels in metazoan cells
D. Hebenstreit, M. Fang, M. Gu, V. Charoensawan, A. van Oudenaarden, and S. A. Teichmann
Molecular Systems Biology
7; doi: 10.1038/msb.2011.28 (2011).
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Genes methylated by DNA methyltransferase 3b are similar in mouse intestine and human colon cancer
E. J. Steine, M. Ehrich, G. W. Bell, A. Raj, S. Reddy, A. van Oudenaarden, R. Jaenisch, and H. G. Linhart
Journal of Clinical Investigation 121, 1748 (2011).
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Validating transcripts with probes and imaging technology
S. Itzkovitz and A. van Oudenaarden
Nature Methods 8, S12 (2011).
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Cellular decision making and biological noise: from microbes to mammals
G. Balázsi, A. van Oudenaarden, and J. J. Collins
Cell 144, 910 (2011).
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Caenorhabditis elegans aristaless/Arx gene alr-1 restricts variable gene expression
I. Topalidou, A. van Oudenaarden, and M. Chalfie
PNAS 108, 4063 (2011).
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2010
Coupling cellular oscillators - Circadian and cell division cycles in cyanobacteria
B. Pando and A. van Oudenaarden
Current Opinion in Genetics & Development 20, 613 (2010).
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Imaging single mRNA molecules in yeast
H. Youk, A. Raj, and A. van Oudenaarden
Methods in Enzymology 470, 429 (2010).
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A general mechanism for network-dosage compensation in gene circuits
M. Acar, B. F. Pando, F. H. Arnold, M. B. Elowitz, and A. van Oudenaarden
Science 329, 1656 (2010).
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Altruistic defence
H. Youk and A. van Oudenaarden
Nature 467, 34 (2010).
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Transcript counting in single cells reveals dynamics of rDNA transcription
R. Z. Tan and A. van Oudenaarden
Molecular Systems Biology 6; doi:10.1038/msb.2010.14 (2010).
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Genome-wide dissection of microRNA functions and cotargeting networks using gene set signatures
J. S. Tsang, M. S. Ebert, and A. van Oudenaarden
Molecular Cell 38, 140 (2010).
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Circadian gating of the cell cycle
revealed in single cyanobacterial cells
Q. Yang, B. F. Pando, G. Dong, S. S. Golden, and A. van Oudenaarden
Science 327, 1522 (2010).
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Elevated ATPase activity of KaiC applies a circadian checkpoint on cell division in Synechococcus elongatus
G. Dong, Q. Yang, Q. Wang, Y. Kim, T. L. Wood, K. W. Osteryoung, A. van Oudenaarden, and S. S. Golden
Cell 140, 529 (2010).
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Variability in gene expression underlies incomplete penetrance
A. Raj, S. A. Rifkin, E. Andersen, and A. van Oudenaarden
Nature 463, 913 (2010).
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2009
Growth landscape formed by perception and import of glucose in yeast
H. Youk and A. van Oudenaarden
Nature 462, 875 (2009).
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Synthetic biology: understanding biological design from synthetic circuits
S. Mukherji and A. van Oudenaarden
Nature Reviews Genetics 10, 859 (2009).
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Direct cell reprogramming is a stochastic process amenable to acceleration
J. Hanna, K. Saha, B. Pando, J. van Zon, C. J. Lengner, M. P. Creyghton, A. van Oudenaarden, and R. Jaenisch
Nature 462, 595 (2009).
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A systems-level analysis of perfect
adaptation in yeast osmoregulation
D. Muzzey, C. A. Gómez-Uribe, J. T. Mettetal,
and A. van Oudenaarden
Cell 138, 160 (2009).
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Quantitative time-lapse fluorescence microscopy in single cells
D. Muzzey and
A. van Oudenaarden
Annual Review of Cell and Developmental Biology 25, 301 (2009).
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Many human large
intergenic noncoding RNAs associate with chromatin-modifying complexes
and affect gene expression
A. M. Khalil, M. Guttman, M. Huarte, M. Garber, A. Raj, D. Rivea Morales,
K. Thomas, A. Presser, B. E. Bernstein, A. van Oudenaarden, A. Regev,
E. S. Lander, and J. L. Rinn
PNAS 106, 11667 (2009).
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Single-molecule approaches to stochastic
gene expression
A. Raj and A. van Oudenaarden
Annual Review of Biophysics 38,
255 (2009).
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Snowdrift game dynamics and facultative
cheating in yeast
J. Gore, H Youk, and A. van Oudenaarden
Nature 459, 253 (2009).
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Population genomics of domestic and
wild yeasts
G. Liti, D. M. Carter, A. M. Moses, J. Warringer,
L. Parts, S. A. James, R. P. Davey, I. N. Roberts, A. Burt, V. Koufopanou,
I. J. Tsai, C. M. Bergman, D. Bensasson, M. J. O'Kelly, A. van Oudenaarden,
D. B. Barton, E. Bailes, A. N. Nguyen, M. Jones, M. A. Quail, I. Goodhead,
S. Sims, F. Smith, A. Blomberg, R. Durbin, and E. J. Louis
Nature 458, 337 (2009).
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The yin and yang
of nature
J. Gore and A. van Oudenaarden
Nature 457, 271 (2009).
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Repetitive
sequence variation and dynamics in the ribosomal DNA array of Saccharomyces
cerevisiae as revealed by whole-genome resequencing
S.
A. James, M. J. O'Kelly, D. M. Carter, R. P. Davey, A. van Oudenaarden,
and I. N. Roberts
Genome Research 19, 626 (2009).
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2008
Nature, nurture, or chance: Stochastic
gene expression and its consequences
A. Raj and A. van Oudenaarden
Cell 135, 216 (2008).
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Imaging individual mRNA molecules
using multiple singly labeled probes
A. Raj, P. van den Bogaard, S. A. Rifkin,
A. van Oudenaarden, and S. Tyagi
Nature Methods 5, 877 (2008).
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Design Website | Spot Detection
Software
Stochastic switching as a survival
strategy in fluctuating environments
M. Acar, J. T. Mettetal, and A. van Oudenaarden
Nature Genetics 40, 471 (2008).
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The frequency dependence of osmo-adaptation
in Saccharomyces cerevisiae
J. T. Mettetal, D. Muzzey, C. Gomez-Uribe,
and A. van Oudenaarden
Science 319, 482 (2008).
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Power-limited
contraction dynamics of Vorticella convallaria: an ultrafast biological
spring
A. Upadhyaya, M. Baraban, J. Wong, A. van
Oudenaarden, and L. Mahadevan
Biophysical Journal 94, 265 (2008).
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| New & Notable
2007
Stochastic gene
expression out-of-steady-state in the cyanobacterial circadian clock
J. R. Chabot, J. M. Pedraza, P. Luitel,
and A. van Oudenaarden
Nature
450, 1249 (2007).
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Heritable stochastic
switching revealed by single-cell genealogy
B. B. Kaufmann, Q. Yang, J. T. Mettetal,
and A. van Oudenaarden
PLoS Biology
5, e239 (2007).
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Necessary noise
J. T. Mettetal and A. van Oudenaarden
Science 317, 463 (2007).
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MicroRNA-mediated feedback and feedforward
loops are recurrent network motifs in mammals
J. Tsang, J. Zhu, and A. van Oudenaarden
Molecular Cell 26, 753 (2007).
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Stochastic gene
expression: from single molecules to the proteome
B. B. Kaufmann and A. van Oudenaarden
Current Opinion in Genetics and Development
17, 107 (2007).
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A multistep
epigenetic switch enables the stable inheritance of DNA methylation
states
H. N. Lim and A. van Oudenaarden
Nature Genetics
39, 269 (2007).
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2006
When it comes to decisions, myeloid
progenitors crave positive feedback
D. Muzzey and A. van Oudenaarden
Cell 126, 650 (2006).
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Cellular asymmetry and individuality
in directional sensing
A. Samadani, J. T. Mettetal, and A. van Oudenaarden
PNAS 103, 11549 (2006).
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Exciting fluctuations: monitoring
competence induction dynamics at the single-cell level
J. Tsang and A. van Oudenaarden
Molecular Systems Biology 2, doi:10.1038/msb4100064 (2006).
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Predicting stochastic gene expression
dynamics in single cells
J. T. Mettetal, D. Muzzey, J. M. Pedraza, E. M.
Ozbudak, and A. van Oudenaarden
PNAS 103, 7304 (2006).
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Neutrophil chemorepulsion
in defined interleukin-8 gradients in vitro and in vivo.
W. G. Tharp, R. Yadav, D. Irimia, A. Upadhyaya,
A. Samadani, O. Hurtado, S. Y. Liu, S. Munisamy, D. M. Brainard, M.
J. Mahon, S. Nourshargh, A. van Oudenaarden, M. G. Toner, M. C. Poznansky
Journal of Leukocyte Biology 79, 539 (2006).
PubMed
Noise in gene regulatory
networks [book chapter]
J. M. Pedraza and
A. van Oudenaarden
in 'Complex Systems Science in BioMedicine' (Kluwer Academic, New York,
2006).
2005
A system of
counteracting feedback loops regulates Cdc42p actvity during spontaneous
cell polarization
E. M. Ozbudak, A. Becskei, and A. van
Oudenaarden
Developmental Cell 9, 565 (2005).
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| Current Biology Dispatch |
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Contributions
of low molecule number and chromosomal positioning to stochastic gene
expression
A. Becskei, B. B. Kaufmann, and A. van
Oudenaarden
Nature Genetics
37, 937 (2005).
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Enhancement
of cellular memory by reducing stochastic transitions
M. Acar, A. Becskei, and A. van Oudenaarden
Nature
435, 228 (2005).
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Noise propagation
in gene networks
J. M. Pedraza and A. van Oudenaarden
Science 307, 1965 (2005).
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2004
Actin polymerization:
forcing flat faces forward
A. Upadhyaya and A. van Oudenaarden
Current Biology 14, R467 (2004).
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Stochastic gene
expression in fluctuating environments
M. Thattai and A. van Oudenaarden
Genetics 167, 523 (2004).
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Amplitude control
of cell-cycle waves by nuclear import
A. Becskei, M. G. Boselli, and A. van Oudenaarden
Nature Cell Biology 6, 451 (2004).
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Elastic instability
in growing yeast colonies
B. Nguyen, A. Upadhyaya, A. van Oudenaarden,
and M. P. Brenner
Biophysical Journal 86, 2740 (2004).
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Multistability
in the lactose utilization network of Escherichia coli
E. M. Ozbudak, M. Thattai, H. N. Lim, B.
I. Shraiman, and A. van Oudenaarden
Nature 427, 737 (2004).
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2003
Motility of
Escherichia coli cells in clusters formed by chemotactic aggregation
N. Mittal, E. O. Budrene, M. P. Brenner,
and A. van Oudenaarden
PNAS 100, 13259 (2003).
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| Movies
Biomimetic systems
for studying actin-based motility
A. Upadhyaya and A. van Oudenaarden
Current Biology 13, R734 (2003).
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Probing polymerization
forces by using actin-propelled lipid vesicles
A. Upadhyaya, J. R. Chabot, A. Andreeva,
A. Samadani, and A. van Oudenaarden
PNAS 100, 4521 (2003).
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| Movies
2002
Attenuation
of noise in ultrasensitive signaling cascades
M. Thattai and A. van Oudenaarden
Biophysical Journal 82, 2943 (2002).
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Regulation of
noise in the expression of a single gene
E. M. Ozbudak, M. Thattai, I. Kurtser,
A. D. Grossman, and A. van Oudenaarden
Nature Genetics 31, 69 (2002).
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| News & Views
2001
Intrinsic noise
in gene regulatory networks
M. Thattai and A. van Oudenaarden
PNAS 98, 8614 (2001).
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1999
Cooperative
symmetry breaking by actin filament polymerization in a model for cell
motility
A. van Oudenaarden and J. A. Theriot
Nature Cell Biology 1, 493 (1999).
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Brownian ratchets:
a lipid bilayer supported by a patterned array
A. van Oudenaarden and S. G. Boxer
Science 285, 1046 (1999).
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Motility of
ActA protein-coated microspheres driven by actin polymerization
L. A. Cameron, M. J. Footer, A. van Oudenaarden,
and J. A. Theriot
PNAS 96, 4908 (1999).
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