2009

Synthetic biology: understanding biological design from synthetic circuits [review]
S. Mukherji and A. van Oudenaarden
Nature Reviews Genetics doi:10.1038/nrg2697 (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 doi:10.1038/nature08592 (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 [review]
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 [review]
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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Synthetic biology: The yin and yang of nature [review]
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 [review]
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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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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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 [review]
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 [review]
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 [review]
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 [review]
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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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 [review]
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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Biomimetic systems for studying actin-based motility [review]
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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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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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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Phase transition in a chain of quantum vortices
C. Bruder, L. I. Glazman, A. I. Larkin, J. E. Mooij, and A. van Oudenaarden
Physical Review B 59, 1383 (1999).
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1998

Manipulation of supported lipid bilayers
S. G. Boxer, J. T. Groves, N. Ulman, A. van Oudenaarden, J. Johnson, L. Kung, P. Cremer
Abstract of papers of the American chemical society 216, 254 (1998).

Scanning tunneling microscope tip as a positionable contact: probing a Josephson-junction array at subkelvin temperatures
J. W. G. Wildoer, A. van Oudenaarden, C. J. P. M. Harmans, and H. van Kempen
Journal of vacuum science and technology B 16, 2837 (1998).

One-dimensional Mott localization of quantum vortices in Josephson-junction arrays
A. van Oudenaarden, B. van Leeuwen, M. P. M. Robbens, and J. E. Mooij
Physical Review B 57, 11684 (1998).
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Giant higher harmonic generation in mesoscopic metal wires and rings interrupted by tunnel junctions
A. van Oudenaarden, Yu. V. Nazarov, and J. E. Mooij
Physical Review B 57, 8816 (1998).
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Magneto-electric Aharonov-Bohm effect in metal rings
Alexander van Oudenaarden, Michel H. Devoret, Yu.V. Nazarov, and J.E. Mooij
Nature 391, 768 (1998).
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1997

Conductance fluctuations in a metallic wire interrupted by a tunnel junction
A. van Oudenaarden, M. H. Devoret, E. H. Visscher, Yu. V. Nazarov, and J. E. Mooij
Physical Review Letters 78, 3539 (1997).
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1996

One-dimensional localization of quantum vortices in disordered Josephson junction arrays
A. van Oudenaarden, S.J.K. Vardy, and J.E. Mooij
Physical Review Letters 77, 4257 (1996).
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One-dimensional Mott insulator formed by quantum vortices in Josephson junction arrays
A. van Oudenaarden and J.E. Mooij
Physical Review Letters 76, 4947 (1996).
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Quantum vortices in periodic and disordered one-dimensional lattices
A. van Oudenaarden and J. E. Mooij
in 'Nanowires', NATO ASI Series,
edited by P. A. Serena and N. Garcia, 373 (1997).

Bloch vortices in one-dimensional Josephson junction arrays
A. van Oudenaarden, S. J. K. Vardy, and J. E. Mooij
in 'Proceedings of the 21^st international conference on low temperature physics, (Prague, 1996);
also published in Czechoslovak Journal of Physics 46 Suppl. S2, 707 (1996).

One-dimensional Mott insulator formed by quantum vortices in Josephson junction arrays
A. van Oudenaarden and J. E. Mooij
in 'Proceedings of 'Localization 96',
edited by T. Dietl (Jaszowiec, Poland, 1996), p. 79.

1995

Vortex dynamics in small arrays of underdamped Josephson junctions
A. van Oudenaarden, S. L. Yeung, and J. E. Mooij
in 'Macroscopic quantum phenomena and coherence in superconducting networks',
edited by C. Giovanella and M. Tinkham (World Scientific, Singapore, 1995).

1994

Internal stresses in amorphous FeNiB studied by neutron depolarization
M. de Jong, A. van Oudenaarden, J. Sietsma, M. Th. Rekveldt, and A. van den Beukel
Acta Physica Hungarica 75, 91 (1994).

Internal stress distribution in amorphous FeNiB studied by field dependent neutron depolarization
A. van Oudenaarden, M. de Jong, J. Sietsma, M. Th. Rekveldt, and A. van den Beukel
Journal of Magnetism and Magnetic Materials 133, 251 (1994).