Alexander van Oudenaarden

Alexander van Oudenaarden performed his PhD research in the field of experimental solid state physics at Delft University of Technology. He obtained his PhD degree in 1998 and received the ‘Andries Miedema’ Award for best PhD-research in the field of condensed matter physics in the Netherlands. From 1998 to 1999, he was a postdoctoral fellow at Stanford University collaborating with Steven Boxer and Julie Theriot. He joined the MIT faculty in 2000. In 2001, he was named an Alfred Sloan Research Fellow, a Keck Career Development Professor in Biomedical Engineering, and received the NSF CAREER award. He was promoted to Associate Professor with tenure in 2004. In 2008 he was promoted to full Professor of Physics at MIT and received a John Simon Guggenheim Fellowship and the NIH Director’s Pioneer Award. From 2009 to 2012 he was the director of the NIH/NCI-funded Physical Sciences-Oncology center at MIT. In 2012 he started as director of the Hubrecht Institute and was awarded an ERC Advanced Investigator award and NWO VICI award. In 2014 he became a member of the Royal Netherlands Academy of Arts and Sciences.

Other activities:

  • Professor at Utrecht University
  • Member of the Royal Netherlands Academy of Arts and Sciences
  • Member at the National Scientific Advisory Board (NKI)
  • Member of the advisory editorial board of Molecular Systems Biology
  • Member of the scientific advisory board at European Molecular Biology Laboratory (EMBL)
  • Member of the scientific advisory board at Max Planck institutes
  • Member of the scientific advisory board at Whitehead Institute for Biomedical research

click here for an extended CV

Team members van Oudenaarden

Nigel Pearson

MS student
n.pearson@hubrecht.eu

Nigel Pearson

Susanne van den Brink

PhD Student
susanne.brink@hubrecht.eu

Susanne van den Brink

Siddharth Dey

Postdoc
http://siddharthdey.com

Siddharth Dey

Lennart Kester

PhD Student
l.kester@hubrecht.eu

Lennart Kester

Judith Vivié

Single-cell sequencing facility
j.vivie@hubrecht.eu

Judith Vivié

Maya Sen

Postdoc
m.sen@hubrecht.eu

Maya Sen

Josi Peterson

Technician
j.peterson@hubrecht.eu

Josi Peterson

Kay Wiebrands

PhD Student
k.wiebrands@hubrecht.eu

Kay Wiebrands

Jean-Charles Boisset

Postdoc
j.boisset@hubrecht.eu

Jean-Charles Boisset

Reinier van der Linden

Technician
r.linden@hubrecht.eu

Reinier van der Linden

Dylan Mooijman

PhD Student
d.mooijman@hubrecht.eu

Dylan Mooijman

Valerie van der Schier

M.S. student
v.schier@hubrecht.eu

Valerie van der Schier

Aditya Barve

Postdoc
a.barve@hubrecht.eu

Aditya Barve

Alexander van Oudenaarden


a.vanoudenaarden@hubrecht.eu

oudenaarden

Anna van Oudenaarden

Senior Researcher
anna.oudenaarden@hubrecht.eu

Anna van Oudenaarden

Mauro Muraro

PhD Student
m.muraro@hubrecht.eu

Maura Muraro

Maria Florescu

PhD Student
m.florescu@hubrecht.eu

Maria Florescu.jpg

Buys de Barbanson

PhD student
b.barbanson@hubrecht.eu

Buys de Barbanson

Christoph Geisenberger

Postdoc
c.geisenberger@hubrecht.eu

Christoph Geisenberger

Abel Vertesy

PhD Student
a.vertesy@hubrecht.eu

Abel Vertesyweb

Nico Battich

Postdoc
n.battich@hubrecht.eu

Nico Battich

Anna Alemany Arias

Postdoc
a.alemany@hubrecht.eu

Anna Alemany Arias

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More information

Post-doc Period Current Position
Attila Becskei 2003-2005 Professor
Biozentrum, Universitat Basel, The Center for Molecular Life Sciences, Switzerland
Magda Bienko 2011-2014 Assistant Professor
Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
Nicola Crosetto 2011-2014 Assistant Professor
Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
Jeff Gore 2006-2009 Associate Professor
Department of Physics, MIT, Cambridge, MA, USA
Dominic Grün 2012-2015 Assistant Professor
Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
Shalev Itzkovitz 2010-2012 Assistant Professor
Weizmann Instiute, Israel
Jan-Philipp Junker 2010-2015 Assistant Professor
Max Delbrück center for Molecular Medicine, Germany
Han Lim 2002-2005 Associate Professor
Department of Integrative Biology, University of California, Berkeley, CA, USA
Gregor Neuert 2006-2012 Assistant Professor
Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
Arjun Raj 2006-2009 Assistant Professor
Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
Scott Rifkin 2006-2009 Assistant Professor
Section of Ecology, Behavior and Evolution, UCSD, San Diego, CA, USA
Azadeh Samadani 2003-2006 Assistant Professor
Department of Physics, Brandeis University, MA, USA
Stefan Semrau 2010-2015 Assistant Professor
Leiden Institute of Physics, Leiden, The Netherlands
Nikolai Slavov 2010-2015 Assistant Professor
Department of Bioengineering, Northeastern University, Boston, MA, USA
Leonid Teytelman 2009-2013 Co-founder and CEO
Protocols.io, CA, USA
Arpita Upadhyaya 2002-2005 Assistant Professor
Department of Physics, University of Maryland, College Park, MD, USA
Jeroen van Zon 2008-2012 Assistant Professor
AMOLF, Amsterdam, The Netherlands
PhD student Period Current Position
Murat Acar 2003-2007 Assistant Professor
Department of Molecular, Cellular, and Developmental Biology, Yale University, CT, USA
Jeff Chabot 2000-2005 Senior Scientist
Department of Systems Biology, Pfizer, Cambridge, MA, USA
Miaoqing Fang 2007-2012 Software Engineer
Facebook, CA, USA
Clinton Hansen 2009-2014 Postdoc
Harvard Medical School, Boston, MA, USA
Ni Ji 2009-2013 Postdoc
Harvard University. Cambridge, MA, USA
Ben Kaufmann 2003-2007 Senior Scientist
Amyris Inc, CA, USA
Dong hyun Kim 2007-2012 Medical School
South Korea
Sandy Klemm 2009-2014 Postdoc
Stanford University, CA, USA
Jialing Li 2007-2012  Yahoo, Sunnyvale, CA, USA
Ya Lin 2010-2014 Microsoft
Cambridge, MA, USA
Jay Mettetal 2004-2007 Associate Director
AstraZeneca, London
Shankar Mukherji 2005-2010 Postdoc
Harvard University, Cambridge, MA, USA
Dale Muzzey 2005-2009 Scientist
Counsyl Biotech, CA, USA
Mei Lyn Ong 2007-2011 Agency for Science, Technology and Research
Singapore
Michael O’Kelly 2003-2007 Bugcrowd Inc., CA, USA
Ertugrul Ozbudak 2000-2004 Associate Professor
Albert Einstein College of Medicine, New York, USA
Bernardo Pando 2005-2010 Morgan Stanley, New York, USA
Annalisa Pawlosky 2007-2013 Postdoc
Stanford University, CA, USA
Juan Pedraza 2001-2005 Professor
Department of Physics, Universidad de los Andes, Bogota, Colombia
Apratim Sahay 2009-2015 Charles River Watershed Association, Cambridge, MA, USA
Rui Zhen Tan 2007-2011 Agency for Science, Technology and Research
Singapore
Mukund Thattai 2000-2004 Professor
NCBS, Bangalore, India
John Tsang 2005-2008 Investigator
National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
Qiong Yang 2004-2009 Assistant Professor
Department of Physics, University of Michigan, Ann Arbor, MI, USA
Hyun Youk 2007-2011 Assistant Professor
Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
Yannan Zheng 2009-2015 Data Scientist
AvantCredit, Chicago, IL, USA

Research

single_cell

Van Oudenaarden: Quantitative biology of development & stem cells

The van Oudenaarden lab is using a combination of experimental, computational, and theoretical approaches to quantitatively understand decision‐making in single cells with a focus on questions in developmental and stem cell biology. We are particularly interested in how cells use gene networks to make robust decisions even in the presence of significant fluctuations in gene expression. We use and develop a wide range of single-cell methods including single-cell sequencing and quantitative imaging tools.

Read research

Key publications

M. J. Muraro, G. Dharmadhikari, D. Grün, N. Groen, T. Dielen, E. Jansen, L. van Gurp, M. A. Engelse, F. Carlotti, E.J.P. de Koning, and A. van Oudenaarden
A single-cell transcriptome atlas of the human pancreas
Cell Systems http://dx.doi.org/10.1016/j.cels.2016.09.002 (2016) [pdf]

D. Mooijman, S. S. Dey, J. C. Boisset, N. Crosetto, and A. van Oudenaarden
Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction
Nature Biotechnology 34, 852 – 856 (2016) [pdf]

D. Grün, M. J. Muraro, J. C. Boisset, K. Wiebrands, A. Lyubimova, G. Dharmadhikari, M. van den Born, J. van Es, E. Jansen, H. Clevers, E.J.P. de Koning, and A. van Oudenaarden
De novo prediction of stem cell identity using single-cell transcriptome data
Cell Stem Cell 19, 266 – 277 (2016) [pdf]

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 525, 251 – 255 (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]

S. S. Dey, L. Kester, B. Spanjaard, M. Bienko, and A. van Oudenaarden
Integrated genome and transcriptome sequencing of the same cell
Nature Biotechnology 33, 285 – 289 (2015) [pdf]

Selected publications

For a full publication list click here. PDFs are for personal use only.

2016

M. J. Muraro, G. Dharmadhikari, D. Grün, N. Groen, T. Dielen, E. Jansen, L. van Gurp, M. A. Engelse, F. Carlotti, E.J.P. de Koning, and A. van Oudenaarden
A single-cell transcriptome atlas of the human pancreas
Cell Systems http://dx.doi.org/10.1016/j.cels.2016.09.002 (2016) [pdf]

D. Mooijman, S. S. Dey, J. C. Boisset, N. Crosetto, and A. van Oudenaarden
Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction
Nature Biotechnology 34, 852 – 856 (2016) [pdf]

D. Grün, M. J. Muraro, J. C. Boisset, K. Wiebrands, A. Lyubimova, G. Dharmadhikari, M. van den Born, J. van Es, E. Jansen, H. Clevers, E.J.P. de Koning, and A. van Oudenaarden
De novo prediction of stem cell identity using single-cell transcriptome data
Cell Stem Cell 19, 266 – 277 (2016) [pdf]

E. Beerling, D. Seinstra, E. de Wit, L. Kester, D. van der Velden, C. Maynard, R. Schäfer, P. van Diest, E. Voest, A. van Oudenaarden, N. Vrisekoop, and J. van Rheenen
Plasticity between epithelial and mesenchymal states unlinks EMT from metastasis-enhancing stem cell capacity
Cell Reports 14, 2281 – 2288 (2016) [pdf]

P. W. Tetteh, O. Basak, H. F. Farin, K. Wiebrands, K. Kretzschmar, H. Begthel, M. van den Born, J. Korving, F. de Sauvage, J. H. van Es, A. van Oudenaarden, and H. Clevers
Replacement of lost Lgr5-positive stem cells through plasticity of their enterocyte-lineage daughters
Cell Stem Cell 18, 203 – 213 (2016) [pdf]

C. C. Wu, F. Kruse, M. D. Vasudevarao, J. P. Junker, D. C. Zebrowski, K. Fischer, E. S. Noël, D. Grün, E. Berezikov, F. B. Engel, A. van Oudenaarden, G. Weidinger, and J. Bakkers
Spatially resolved genome-wide transcriptional profiling identifies BMP signaling as essential regulator of zebrafish cardiomyocyte regeneration
Developmental Cell 36, 36 – 49 (2016) [pdf]

2015

S. Semrau and A. van Oudenaarden
Studying lineage decision-making in vitro: emerging concepts and novel tools
Annual Review of Cell and Developmental Biology 31, 317 – 345 (2015) [pdf]

D. Grün and A. van Oudenaarden
Design and analysis of single-cell sequencing experiments
Cell 163, 799 – 810 (2015) [pdf]

N. Slavov, S. Semrau, E. Airoldi, B. Budnik, and A. van Oudenaarden
Differential stoichiometry among core ribosomal proteins
Cell Reports 13, 865 – 873 (2015) [pdf]

J. Kind, L. Pagie, S. S. de Vries, L. Nahidiazar, S. S. Dey, M. Bienko, Y. Zhan, B. Lajoie, C. A. de Graaf, M. Amendola, G. Fudenberg, M. Imakaev, L. A. Mirny, K. Jalink, J. Dekker, A. van Oudenaarden, and B. van Steensel
Genome-wide maps of nuclear lamina interactions in single human cells
Cell 63, 134 – 147 (2015) [pdf]

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 525, 251 – 255 (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]

J. S. van Zon, S. Kienle, G. Huelsz-Prince, M. Barkoulas, and A. van Oudenaarden
Cells change their sensitivity to an EGF morphogen gradient to control EGF-induced gene expression
Nature Communications 6: 7053 doi:10.1038/ncomms8053 (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 33, 285 – 289 (2015) [pdf]

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

2014

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]

2013

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]

2012

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]

2011

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]

2010

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]

2009

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]

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

2008

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]

2007

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]

2005

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]

2004

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]

2002

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]

2001

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