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van Oudenaarden group

For a full publication list search PubMed for articles by Alexander van Oudenaarden.
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D. Grün, A. Lyubimova, L. Kester, K. Wiebrands, O. Basak, N. Sasaki, H. Clevers, and A. van Oudenaarden,
Single-cell mRNA sequencing reveals rare intestinal cell types,
Nature doi:10.1038/nature14966 (2015)[pdf].

J. M. Schmiedel, S. L. Klemm, Y. Zheng, A. Sahay, N. Blüthgen, D. S. Marks and A. van Oudenaarden,
MicroRNA control of protein expression noise,
Science 348, 128 – 132 (2015)[pdf].

J. Schuijers, J. P. Junker, M. Mokry, P. Hatzis, B. K. Koo, V. Sasselli, L. G. van der Flier, E. Cuppen, A. van Oudenaarden, and H. Clevers,
Ascl2 acts as a R-spondin/Wnt-responsive switch to control stemness in intestinal crypts,
Cell Stem Cell 16, 158 – 170 (2015)[pdf].

S. S. Dey, L. Kester, B. Spanjaard, M. Bienko, and A. van Oudenaarden,
Integrated genome and transcriptome sequencing of the same cell,
Nature Biotechnology doi: 10.1038/nbt.3129 (2015)[pdf].

N. Crosetto, M. Bienko, and A. van Oudenaarden,
Spatially resolved transcriptomics and beyond,
Nature Reviews Genetics 16, 57 – 66 (2015) [pdf].

J. P. Junker, K. A. Peterson, Y. Nishi, J. Mao, A. P. McMahon, and A. van Oudenaarden,
A predictive model of bifunctional transcription factor signaling during embryonic tissue patterning,
Developmental Cell 31, 448 – 460 (2014)[pdf].

J. P. Junker, E. S. Noel, V. Guryev, K. A. Peterson, G. Shah, J. Huisken, A. P. McMahon, E. Berezikov, J. Bakkers, and A. van Oudenaarden,
Genome-wide RNA tomography in the zebrafish embryo,
Cell 159, 662 – 675 (2014)[pdf].

R. A. Mentink, T. C. Middelkoop L. Rella, N. Ji, C. Y. Tang, M. C. Betist, A. van Oudenaarden, and H. C. Korswagen,
Cell intrinsic modulation of Wnt signaling controls neuroblast migration in C. elegans,
Developmental Cell 31, 188 – 201 (2014)[pdf].

A. Barreca, C. Martinengo, L. Annaratone, L. Righi, A. Chiappella, M. Ladetto, A. Demurtas, L. Chiusa, A. Stacchini, N. Crosetto, A. van Oudenaarden, and R. Chiarle,
Inter- and intratumoral heterogeneity of BCL2 correlates with IgH expression and prognosis in follicular lymphoma,
Blood Cancer Journal Oct 10; 4:e249. doi: 10.1038/bcj.2014.67 (2014)[pdf].

N. Slavov, B. A. Budnik, D. Schwab, E. M. Airoldi, and A. van Oudenaarden,
Constant growth rate can be supported by decreasing energy flux and increasing aerobic glycolysis,
Cell Reports 7, 705 – 714 (2014)[pdf].

D. Grün, L. Kester, and A. van Oudenaarden,
Validation of noise models for single-cell transcriptomics,
Nature Methods 11, 637 – 640 (2014)[pdf].

S. Klemm, S. Semrau, K. Wiebrands, D. Mooijman, D. A. Faddah, R. Jaenisch, and A. van Oudenaarden,
Transcriptional profiling of cells sorted by RNA abundance,
Nature Methods 11, 549 – 551 (2014)[pdf].

J. P. Junker and A. van Oudenaarden,
Every cell is special: genome-wide studies add a new dimension to single-cell biology,
Cell 157, 8 – 11 (2014)[pdf].

V. Almendro, Y. K. Cheng, A. Randles, S. Itzkovitz, A. Marusyk, E. Ametller, X. Gonzalez-Farre, M. Muñoz, H. G. Russnes, A. Helland, I. H. Rye, A. L. Borresen-Dale, R. Maruyama, A. van Oudenaarden, M. Dowsett, R. L. Jones, J. Reis-Filho, P. Gascon, M. Gönen, F. Michor, and K. Polyak,
Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity,
Cell Reports 6, 514 – 527 (2014)[pdf].

V. Almendro, H. J. Kim, Y. K. Cheng, M. Gönen, S. Itzkovitz, P. Argani, A. van Oudenaarden, S. Sukumar, F. Michor, and K. Polyak,
Genetic and Phenotypic Diversity in Breast Tumor Metastases,
Cancer Research 74, 1 – 11 (2014)[pdf].

S. Semrau, N. Crosetto, M. Bienko, M. Boni, P. Bernasconi, R. Chiarle, and A. van Oudenaarden,
FuseFISH: Robust detection of transcribed gene fusions in single cells,
Cell Reports 6, 18 – 23 (2014)[pdf].

J. R. Alvarez-Dominguez, W. Hu, B. Yuan, J. Shi , S. S. Park, A. A. Gromatzk, A. van Oudenaarden, and H. F. Lodish,
Global discovery of erythroid long non-coding RNAs reveals novel regulators of red cell maturation,
Blood 123, 570 – 581 (2014)[pdf].

N. Ji, T. C. Middelkoop, R. A. Mentink, M. C. Betist, S. Tonegawa, D. Mooijman, H. C. Korswagen, and A. van Oudenaarden,
Feedback control of gene expression variability in the Caenorhabditis elegans Wnt pathway,
Cell 155, 869 – 880 (2013)[pdf].

L. Teytelman, D. M. Thurtle, J. Rine, and A. van Oudenaarden,
Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins,
Proceedings of the National Academy of Sciences USA 110, 18602 – 18607 (2013)[pdf].

D. H. Kim, D. Grün, and A. van Oudenaarden,
Dampening of expression oscillations by synchronous regulation of a microRNA and its target,
Nature Genetics 45, 1337 – 1344 (2013)[pdf].

A. Lyubimova, S. Itzkovitz, J. P. Junker, Z. P. Fan, X. Wu, and A. van Oudenaarden,
Single-molecule mRNA detection and counting in mammalian tissue,
Nature Protocols 8, 1743 – 1758 (2013)[pdf].

C. H. Hansen and A. van Oudenaarden,
Allele-specific detection of single mRNA molecules in situ,
Nature Methods 10, 869 – 871 (2013)[pdf].

M. Fang, H. Xie, S. K. Dougan, H. Ploegh, and A. van Oudenaarden,
Stochastic cytokine expression induces mixed T helper cell states,
PLoS Biology 11: e1001618. doi:10.1371/journal.pbio.1001618 (2013)[pdf].

G. Neuert, B. Munsky, R. Z. Tan, L. Teytelman, M. Khammash, and A. van Oudenaarden,
Systematic identification of signal-activated stochastic gene regulation,
Science 339, 584-587 (2013)[pdf].

M. Barkoulas, J. S. van Zon, J. Milloz, A. van Oudenaarden, and M. A. Félix,
Robustness and epistasis in the C. elegans vulval signaling network revealed by pathway dosage modulation,
Developmental Cell 24, 64-75 (2013)[pdf].

R. Z. Tan, N. Ji, R. A. Mentink, H. C. Korswagen, and A. van Oudenaarden,
Deconvolving the roles of Wnt ligands and receptors in sensing and amplification,
Molecular Systems Biology 9:631 doi:10.1038/msb.2012.64 (2013)[pdf].

M. Bienko, N. Crosetto, L. Teytelman, S. Klemm, S. Itzkovitz, and A. van Oudenaarden,
A versatile genome-scale PCR-based pipeline for high-definition DNA FISH,
Nature Methods 10, 122-124 (2013)[pdf].

N. Barker, A. van Oudenaarden, and H. Clevers,
Identifying the stem cell of the intestinal crypt: strategies and pitfalls,
Cell Stem Cell 11, 452-460 (2012)[pdf].

Y. Buganim, D. A. Faddah, A. W. Cheng, E. Itskovich, S. Markoulaki, K. Ganz, S. L. Klemm, A. van Oudenaarden, and R. Jaenisch,
Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase,
Cell 150, 1209-1212 (2012)[pdf].

B. Munsky, G. Neuert, and A. van Oudenaarden,
Using gene expression noise to understand gene regulation,
Science 336, 183-187 (2012)[pdf].

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,
Slug and sox9 cooperatively determine the mammary stem cell state,
Cell 148, 1015-1028 (2012)[pdf].

S. Bumgarner, G. Neuert, B. F. Voight, A. Symbor-Nagrabska, P. Grisafi, A. van Oudenaarden, and G. R. Fink,
Single-cell analysis reveals that noncoding RNAs contribute to clonal heterogeneity by modulating transcription factor recruitment,
Molecular Cell 45, 470-482 (2012)[pdf].

S. Itzkovitz, A. Lyubimova, I.C. Blat, M. Maynard, J. van Es, J. Lees, T. Jacks, H. Clevers, A. van Oudenaarden,
Single-molecule transcript counting of stem-cell markers in the mouse intestine,
Nature Cell Biology 14, 106-114 (2012)[pdf].

S. Itzkovitz, I. Blat, T. Jacks, H. Clevers, and A. van Oudenaarden,
Optimality in development of intestinal crypts,
Cell, 148, 608-619 (2012)[pdf].

S. Mukherji, M.S. Ebert, G. X. Y. Zheng, J.S. Tsang, P.A. Sharp, and A. van Oudenaarden,
MicroRNAs can generate thresholds in target gene expression,
Nature Genetics 43, 854-859 (2011)[pdf].

S. Itzkovitz and A. van Oudenaarden,
Validating transcripts with probes and imaging technology,
Nature Methods 8, S12-S19 (2011)[pdf].

G. Balázsi, A. van Oudenaarden, and J.J. Collins,
Cellular decision-making and biological noise: from microbes to mammals,
Cell 144, 910-925 (2011)[pdf].

M. Acar, B.F. Pando, F.H. Arnold, M.B. Elowitz, and A. van Oudenaarden,
A general mechanism for network-dosage compensation in gene networks,
Science 329, 1656-1660 (2010)[pdf].

J.S. Tsang, M.S. Ebert, and A. van Oudenaarden,
Genome-wide dissection of microRNA functions and cotargeting networks using gene set signatures,
Molecular Cell 38, 140-153 (2010)[pdf].

Q. Yang, B. F. Pando, G. Dong, S. S. Golden, and A. van Oudenaarden,
Circadian gating of the cell cycle revealed in single cyanobacterial cells,
Science 327, 1522-1526 (2010)[pdf].

A. Raj, S.A. Rifkin, E. Andersen, and A. van Oudenaarden,
Variability in gene expression underlies incomplete penetrance,
Nature 463, 913918 (2010)[pdf].

H. Youk and A. van Oudenaarden,
Growth landscape formed by perception and import of glucose in yeast,
Nature 462, 875-880 (2009)[pdf].

S. Mukherji and A. van Oudenaarden,
Synthetic biology: Understanding biological design from synthetic circuits,
Nature Review Genetics 10, 859-871 (2009)[pdf].

J. Hanna, K. Saha, B. Pando, J. van Zon, C.J. Lengner, M.P. Creyghton, A. van Oudenaarden, and R. Jaenisch,
Direct cell reprogramming is a stochastic process amenable to acceleration,
Nature 462, 595-603 (2009)[pdf].

D. Muzzey, C. Gomez-Uribe, J.T. Mettetal, and A. van Oudenaarden,
A systems-level analysis of perfect adaptation in yeast osmoregulation,
Cell 138, 160-171 (2009)[pdf].

J. Gore, H. Youk, and A. van Oudenaarden,
Snowdrift game dynamics and facultative cheating in yeast,
Nature 459, 253-256 (2009)[pdf].

A. Raj and A. van Oudenaarden,
Nature, nurture, or chance: Stochastic gene expression and its consequences,
Cell 135, 216-226 (2008)[pdf].

A. Raj, P. van den Bogaard, S.A. Rifkin, A. van Oudenaarden, and S. Tyagi,
Imaging individual mRNA molecules using multiple singly labeled probes,
Nature Methods 5, 877-879 (2008)[pdf].

M. Acar, J.T. Mettetal, and A. van Oudenaarden,
Stochastic switching as a survival strategy in fluctuating environments,
Nature Genetics 40, 471-475 (2008)[pdf].

J.T. Mettetal, D. Muzzey, C. Gomez-Uribe, and A. van Oudenaarden,
The frequency dependence of osmo-adaptation in Saccharomyces cerevisiae,
Science 319, 482-484 (2008)[pdf].

J.R. Chabot, J.M. Pedraza, P. Luitel, and A. van Oudenaarden,
Stochastic gene expression out-of-steady-state in the cyanobacterial circadian clock,
Nature 450, 1249-1252 (2007)[pdf].

J. Tsang, J. Zhu, and A. van Oudenaarden,
MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals,
Molecular Cell 26, 753-767 (2007)[pdf].

H.N. Lim and A. van Oudenaarden,
A multistep epigenetic switch enables the stable inheritance of DNA methylation states,
Nature Genetics 39, 269-275 (2007)[pdf].

A. Becskei, B.B. Kaufmann, and A. van Oudenaarden,
Contributions of low molecule number and chromosomal positioning to stochastic gene expression,
Nature Genetics 37, 937-944 (2005)[pdf].

M. Acar, A. Becskei, and A. van Oudenaarden,
Enhancement of cellular memory by reducing stochastic transitions,
Nature 435, 228 (2005)[pdf].

J.M. Pedraza and A. van Oudenaarden,
Noise propagation in gene networks,
Science 307, 1965-1969 (2005)[pdf].

A. Becskei, M.G. Boselli, and A. van Oudenaarden,
Amplitude control of cell-cycle waves by nuclear import,
Nature Cell Biology 6, 451 (2004)[pdf].

E.M. Ozbudak, M. Thattai, H.N. Lim, B.I. Shraiman, and A. van Oudenaarden,
Multistability in the lactose utilization network of Escherichia coli,
Nature 427, 737 (2004)[pdf].

E. Ozbudak, M. Thattai, I. Kurtser, A.D. Grossman and A. van Oudenaarden,
Regulation of noise in the expression of a single gene,
Nature Genetics 31, 69 (2002)[pdf].

M. Thattai and A. van Oudenaarden,
Intrinsic noise in gene regulatory networks,
Proceedings of the National Academy of Sciences USA 98, 8614 (2001)[pdf].

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