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Alexander van Oudenaarden, Ph.D. - Publications

Physics Massachusetts Institute of Technology, Cambridge, MA, United States 

133 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Baron CS, Kester L, Klaus A, Boisset JC, Thambyrajah R, Yvernogeau L, Kouskoff V, Lacaud G, van Oudenaarden A, Robin C. Single-cell transcriptomics reveal the dynamic of haematopoietic stem cell production in the aorta. Nature Communications. 9: 2517. PMID 29955049 DOI: 10.1038/s41467-018-04893-3  0.52
2018 Rivron NC, Frias-Aldeguer J, Vrij EJ, Boisset JC, Korving J, Vivié J, Truckenmüller RK, van Oudenaarden A, van Blitterswijk CA, Geijsen N. Blastocyst-like structures generated solely from stem cells. Nature. 557: 106-111. PMID 29720634 DOI: 10.1038/s41586-018-0051-0  0.52
2018 Loomans CJM, Williams Giuliani N, Balak J, Ringnalda F, van Gurp L, Huch M, Boj SF, Sato T, Kester L, de Sousa Lopes SMC, Roost MS, Bonner-Weir S, Engelse MA, Rabelink TJ, Heimberg H, ... ... van Oudenaarden A, et al. Expansion of Adult Human Pancreatic Tissue Yields Organoids Harboring Progenitor Cells with Endocrine Differentiation Potential. Stem Cell Reports. 10: 712-724. PMID 29539434 DOI: 10.1016/J.Stemcr.2018.02.005  0.36
2017 van den Brink SC, Sage F, Vértesy Á, Spanjaard B, Peterson-Maduro J, Baron CS, Robin C, van Oudenaarden A. Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations. Nature Methods. 14: 935-936. PMID 28960196 DOI: 10.1038/nmeth.4437  0.36
2016 Mooijman D, Dey SS, Boisset JC, Crosetto N, van Oudenaarden A. Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction. Nature Biotechnology. PMID 27347753 DOI: 10.1038/Nbt.3598  0.52
2016 Grün D, Muraro MJ, Boisset JC, Wiebrands K, Lyubimova A, Dharmadhikari G, van den Born M, van Es J, Jansen E, Clevers H, de Koning EJ, van Oudenaarden A. De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data. Cell Stem Cell. PMID 27345837 DOI: 10.1016/J.Stem.2016.05.010  0.52
2016 Beerling E, Seinstra D, de Wit E, Kester L, van der Velden D, Maynard C, Schäfer R, van Diest P, Voest E, van Oudenaarden A, Vrisekoop N, van Rheenen J. Plasticity between Epithelial and Mesenchymal States Unlinks EMT from Metastasis-Enhancing Stem Cell Capacity. Cell Reports. PMID 26947068 DOI: 10.1016/j.celrep.2016.02.034  0.36
2015 Grün D, van Oudenaarden A. Design and Analysis of Single-Cell Sequencing Experiments. Cell. 163: 799-810. PMID 26544934 DOI: 10.1016/j.cell.2015.10.039  1
2015 Kind J, Pagie L, de Vries SS, Nahidiazar L, Dey SS, Bienko M, Zhan Y, Lajoie B, de Graaf CA, Amendola M, Fudenberg G, Imakaev M, Mirny LA, Jalink K, Dekker J, ... van Oudenaarden A, et al. Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells. Cell. 163: 134-47. PMID 26365489 DOI: 10.1016/J.Cell.2015.08.040  0.52
2015 Grün D, Lyubimova A, Kester L, Wiebrands K, Basak O, Sasaki N, Clevers H, van Oudenaarden A. Single-cell messenger RNA sequencing reveals rare intestinal cell types. Nature. 525: 251-5. PMID 26287467 DOI: 10.1038/Nature14966  1
2015 Welling M, Chen HH, Muñoz J, Musheev MU, Kester L, Junker JP, Mischerikow N, Arbab M, Kuijk E, Silberstein L, Kharchenko PV, Geens M, Niehrs C, van de Velde H, van Oudenaarden A, et al. DAZL regulates Tet1 translation in murine embryonic stem cells. Embo Reports. PMID 26077710 DOI: 10.15252/Embr.201540538  0.36
2015 van de Wetering M, Francies HE, Francis JM, Bounova G, Iorio F, Pronk A, van Houdt W, van Gorp J, Taylor-Weiner A, Kester L, McLaren-Douglas A, Blokker J, Jaksani S, Bartfeld S, Volckman R, ... ... van Oudenaarden A, et al. Prospective derivation of a living organoid biobank of colorectal cancer patients. Cell. 161: 933-45. PMID 25957691 DOI: 10.1016/J.Cell.2015.03.053  1
2015 Schmiedel JM, Klemm SL, Zheng Y, Sahay A, Blüthgen N, Marks DS, van Oudenaarden A. Gene expression. MicroRNA control of protein expression noise. Science (New York, N.Y.). 348: 128-32. PMID 25838385 DOI: 10.1126/science.aaa1738  1
2015 Schuijers J, Junker JP, Mokry M, Hatzis P, Koo BK, Sasselli V, van der Flier LG, Cuppen E, van Oudenaarden A, Clevers H. Ascl2 acts as an R-spondin/Wnt-responsive switch to control stemness in intestinal crypts. Cell Stem Cell. 16: 158-70. PMID 25620640 DOI: 10.1016/J.Stem.2014.12.006  1
2015 Dey SS, Kester L, Spanjaard B, Bienko M, van Oudenaarden A. Integrated genome and transcriptome sequencing of the same cell. Nature Biotechnology. 33: 285-9. PMID 25599178 DOI: 10.1038/Nbt.3129  1
2015 Crosetto N, Bienko M, van Oudenaarden A. Spatially resolved transcriptomics and beyond. Nature Reviews. Genetics. 16: 57-66. PMID 25446315 DOI: 10.1038/nrg3832  0.52
2015 Kind J, Pagie L, deVries SS, Nahidiazar L, Dey SS, Bienko M, Zhan Y, Lajoie B, deGraaf CA, Amendola M, Fudenberg G, Imakaev M, Mirny LA, Jalink K, Dekker J, et al. Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells Cell. DOI: 10.1016/j.cell.2015.08.040  0.52
2014 Simmini S, Bialecka M, Huch M, Kester L, van de Wetering M, Sato T, Beck F, van Oudenaarden A, Clevers H, Deschamps J. Transformation of intestinal stem cells into gastric stem cells on loss of transcription factor Cdx2. Nature Communications. 5: 5728. PMID 25500896 DOI: 10.1038/Ncomms6728  1
2014 Junker JP, Peterson KA, Nishi Y, Mao J, McMahon AP, van Oudenaarden A. A predictive model of bifunctional transcription factor signaling during embryonic tissue patterning. Developmental Cell. 31: 448-60. PMID 25458012 DOI: 10.1016/J.Devcel.2014.10.017  1
2014 Junker JP, Noël ES, Guryev V, Peterson KA, Shah G, Huisken J, McMahon AP, Berezikov E, Bakkers J, van Oudenaarden A. Genome-wide RNA Tomography in the zebrafish embryo. Cell. 159: 662-75. PMID 25417113 DOI: 10.1016/J.Cell.2014.09.038  1
2014 Barreca A, Martinengo C, Annaratone L, Righi L, Chiappella A, Ladetto M, Demurtas A, Chiusa L, Stacchini A, Crosetto N, van Oudenaarden A, Chiarle R. Inter- and intratumoral heterogeneity of BCL2 correlates with IgH expression and prognosis in follicular lymphoma. Blood Cancer Journal. 4: e249. PMID 25303368 DOI: 10.1038/bcj.2014.67  0.52
2014 Slavov N, Budnik BA, Schwab D, Airoldi EM, van Oudenaarden A. Constant growth rate can be supported by decreasing energy flux and increasing aerobic glycolysis. Cell Reports. 7: 705-14. PMID 24767987 DOI: 10.1016/J.Celrep.2014.03.057  1
2014 Grün D, Kester L, van Oudenaarden A. Validation of noise models for single-cell transcriptomics. Nature Methods. 11: 637-40. PMID 24747814 DOI: 10.1038/nmeth.2930  1
2014 Klemm S, Semrau S, Wiebrands K, Mooijman D, Faddah DA, Jaenisch R, van Oudenaarden A. Transcriptional profiling of cells sorted by RNA abundance. Nature Methods. 11: 549-51. PMID 24681693 DOI: 10.1038/Nmeth.2910  1
2014 Junker JP, van Oudenaarden A. Every cell is special: genome-wide studies add a new dimension to single-cell biology. Cell. 157: 8-11. PMID 24679522 DOI: 10.1016/j.cell.2014.02.010  1
2014 Almendro V, Kim HJ, Cheng YK, Gönen M, Itzkovitz S, Argani P, van Oudenaarden A, Sukumar S, Michor F, Polyak K. Genetic and phenotypic diversity in breast tumor metastases. Cancer Research. 74: 1338-48. PMID 24448237 DOI: 10.1158/0008-5472.Can-13-2357-T  1
2014 Semrau S, Crosetto N, Bienko M, Boni M, Bernasconi P, Chiarle R, van Oudenaarden A. FuseFISH: robust detection of transcribed gene fusions in single cells. Cell Reports. 6: 18-23. PMID 24373969 DOI: 10.1016/j.celrep.2013.12.002  0.52
2014 Alvarez-Dominguez JR, Hu W, Yuan B, Shi J, Park SS, Gromatzky AA, van Oudenaarden A, Lodish HF. Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation. Blood. 123: 570-81. PMID 24200680 DOI: 10.1182/Blood-2013-10-530683  1
2013 Ji N, Middelkoop TC, Mentink RA, Betist MC, Tonegawa S, Mooijman D, Korswagen HC, van Oudenaarden A. Feedback control of gene expression variability in the Caenorhabditis elegans Wnt pathway. Cell. 155: 869-80. PMID 24209624 DOI: 10.1016/j.cell.2013.09.060  1
2013 Teytelman L, Thurtle DM, Rine J, van Oudenaarden A. Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins. Proceedings of the National Academy of Sciences of the United States of America. 110: 18602-7. PMID 24173036 DOI: 10.1073/Pnas.1316064110  1
2013 Kim Dh, Grün D, van Oudenaarden A. Dampening of expression oscillations by synchronous regulation of a microRNA and its target. Nature Genetics. 45: 1337-44. PMID 24036951 DOI: 10.1038/ng.2763  1
2013 Lyubimova A, Itzkovitz S, Junker JP, Fan ZP, Wu X, van Oudenaarden A. Single-molecule mRNA detection and counting in mammalian tissue. Nature Protocols. 8: 1743-58. PMID 23949380 DOI: 10.1038/Nprot.2013.109  1
2013 Fang M, Xie H, Dougan SK, Ploegh H, van Oudenaarden A. Stochastic cytokine expression induces mixed T helper cell States. Plos Biology. 11: e1001618. PMID 23935453 DOI: 10.1371/Journal.Pbio.1001618  1
2013 Hansen CH, van Oudenaarden A. Allele-specific detection of single mRNA molecules in situ. Nature Methods. 10: 869-71. PMID 23934076 DOI: 10.1038/nmeth.2601  1
2013 Agus DB, Alexander JF, Arap W, Ashili S, Aslan JE, Austin RH, Backman V, Bethel KJ, Bonneau R, Chen WC, Chen-Tanyolac C, Choi NC, Curley SA, Dallas M, ... ... van Oudenaarden A, et al. A physical sciences network characterization of non-tumorigenic and metastatic cells. Scientific Reports. 3: 1449. PMID 23618955 DOI: 10.1038/Srep01449  1
2013 Neuert G, Munsky B, Tan RZ, Teytelman L, Khammash M, van Oudenaarden A. Systematic identification of signal-activated stochastic gene regulation. Science (New York, N.Y.). 339: 584-7. PMID 23372015 DOI: 10.1126/Science.1231456  1
2013 Barkoulas M, van Zon JS, Milloz J, van Oudenaarden A, Félix MA. Robustness and epistasis in the C. elegans vulval signaling network revealed by pathway dosage modulation. Developmental Cell. 24: 64-75. PMID 23328399 DOI: 10.1016/j.devcel.2012.12.001  1
2013 Tan RZ, Ji N, Mentink RA, Korswagen HC, van Oudenaarden A. Deconvolving the roles of Wnt ligands and receptors in sensing and amplification. Molecular Systems Biology. 9: 631. PMID 23295860 DOI: 10.1038/Msb.2012.64  1
2013 Bienko M, Crosetto N, Teytelman L, Klemm S, Itzkovitz S, van Oudenaarden A. A versatile genome-scale PCR-based pipeline for high-definition DNA FISH. Nature Methods. 10: 122-4. PMID 23263692 DOI: 10.1038/Nmeth.2306  1
2012 Peterson KA, Nishi Y, Ma W, Vedenko A, Shokri L, Zhang X, McFarlane M, Baizabal JM, Junker JP, van Oudenaarden A, Mikkelsen T, Bernstein BE, Bailey TL, Bulyk ML, Wong WH, et al. Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning. Genes & Development. 26: 2802-16. PMID 23249739 DOI: 10.1101/Gad.207142.112  1
2012 Ji N, van Oudenaarden A. Single molecule fluorescent in situ hybridization (smFISH) of C. elegans worms and embryos. Wormbook : the Online Review of C. Elegans Biology. 1-16. PMID 23242966 DOI: 10.1895/wormbook.1.153.1  1
2012 Barker N, van Oudenaarden A, Clevers H. Identifying the stem cell of the intestinal crypt: strategies and pitfalls. Cell Stem Cell. 11: 452-60. PMID 23040474 DOI: 10.1016/J.Stem.2012.09.009  1
2012 van Es JH, Sato T, van de Wetering M, Lyubimova A, Nee AN, Gregorieff A, Sasaki N, Zeinstra L, van den Born M, Korving J, Martens AC, Barker N, van Oudenaarden A, Clevers H. Dll1+ secretory progenitor cells revert to stem cells upon crypt damage. Nature Cell Biology. 14: 1099-104. PMID 23000963 DOI: 10.1038/Ncb2581  1
2012 Buganim Y, Faddah DA, Cheng AW, Itskovich E, Markoulaki S, Ganz K, Klemm SL, van Oudenaarden A, Jaenisch R. Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase. Cell. 150: 1209-22. PMID 22980981 DOI: 10.1016/j.cell.2012.08.023  1
2012 van Werven FJ, Neuert G, Hendrick N, Lardenois A, Buratowski S, van Oudenaarden A, Primig M, Amon A. Transcription of two long noncoding RNAs mediates mating-type control of gametogenesis in budding yeast. Cell. 150: 1170-81. PMID 22959267 DOI: 10.1016/J.Cell.2012.06.049  1
2012 Muñoz J, Stange DE, Schepers AG, van de Wetering M, Koo BK, Itzkovitz S, Volckmann R, Kung KS, Koster J, Radulescu S, Myant K, Versteeg R, Sansom OJ, van Es JH, Barker N, ... van Oudenaarden A, et al. The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent '+4' cell markers. The Embo Journal. 31: 3079-91. PMID 22692129 DOI: 10.1038/Emboj.2012.166  1
2012 Slavov N, van Oudenaarden A. How to regulate a gene: to repress or to activate? Molecular Cell. 46: 551-2. PMID 22681881 DOI: 10.1016/J.Molcel.2012.05.035  1
2012 Schneider J, Skelton RL, Von Stetina SE, Middelkoop TC, van Oudenaarden A, Korswagen HC, Miller DM. UNC-4 antagonizes Wnt signaling to regulate synaptic choice in the C. elegans motor circuit. Development (Cambridge, England). 139: 2234-45. PMID 22619391 DOI: 10.1242/Dev.075184  1
2012 Yu J, Valerius MT, Duah M, Staser K, Hansard JK, Guo JJ, McMahon J, Vaughan J, Faria D, Georgas K, Rumballe B, Ren Q, Krautzberger AM, Junker JP, Thiagarajan RD, ... ... van Oudenaarden A, et al. Identification of molecular compartments and genetic circuitry in the developing mammalian kidney. Development (Cambridge, England). 139: 1863-73. PMID 22510988 DOI: 10.1242/Dev.074005  1
2012 Munsky B, Neuert G, van Oudenaarden A. Using gene expression noise to understand gene regulation. Science (New York, N.Y.). 336: 183-7. PMID 22499939 DOI: 10.1126/Science.1216379  1
2012 Slavov N, Airoldi EM, van Oudenaarden A, Botstein D. A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes. Molecular Biology of the Cell. 23: 1986-97. PMID 22456505 DOI: 10.1091/Mbc.E11-11-0961  1
2012 van Es JH, Haegebarth A, Kujala P, Itzkovitz S, Koo BK, Boj SF, Korving J, van den Born M, van Oudenaarden A, Robine S, Clevers H. A critical role for the Wnt effector Tcf4 in adult intestinal homeostatic self-renewal. Molecular and Cellular Biology. 32: 1918-27. PMID 22393260 DOI: 10.1128/MCB.06288-11  1
2012 Guo W, Keckesova Z, Donaher JL, Shibue T, Tischler V, Reinhardt F, Itzkovitz S, Noske A, Zürrer-Härdi U, Bell G, Tam WL, Mani SA, van Oudenaarden A, Weinberg RA. Slug and Sox9 cooperatively determine the mammary stem cell state. Cell. 148: 1015-28. PMID 22385965 DOI: 10.1016/J.Cell.2012.02.008  1
2012 Junker JP, van Oudenaarden A. When noisy neighbors are a blessing: analysis of gene expression noise identifies coregulated genes. Molecular Cell. 45: 437-8. PMID 22365826 DOI: 10.1016/j.molcel.2012.02.002  1
2012 Itzkovitz S, Blat IC, Jacks T, Clevers H, van Oudenaarden A. Optimality in the development of intestinal crypts. Cell. 148: 608-19. PMID 22304925 DOI: 10.1016/J.Cell.2011.12.025  1
2012 Bumgarner SL, Neuert G, Voight BF, Symbor-Nagrabska A, Grisafi P, van Oudenaarden A, Fink GR. Single-cell analysis reveals that noncoding RNAs contribute to clonal heterogeneity by modulating transcription factor recruitment. Molecular Cell. 45: 470-82. PMID 22264825 DOI: 10.1016/J.Molcel.2011.11.029  1
2012 Itzkovitz S, Lyubimova A, Blat IC, Maynard M, van Es J, Lees J, Jacks T, Clevers H, van Oudenaarden A. Single-molecule transcript counting of stem-cell markers in the mouse intestine. Nature Cell Biology. 14: 106-14. PMID 22119784 DOI: 10.1038/Ncb2384  1
2012 Middelkoop TC, Williams L, Yang PT, Luchtenberg J, Betist MC, Ji N, van Oudenaarden A, Kenyon C, Korswagen HC. The thrombospondin repeat containing protein MIG-21 controls a left-right asymmetric Wnt signaling response in migrating C. elegans neuroblasts. Developmental Biology. 361: 338-48. PMID 22074987 DOI: 10.1016/J.Ydbio.2011.10.029  1
2011 Mukherji S, Ebert MS, Zheng GX, Tsang JS, Sharp PA, van Oudenaarden A. MicroRNAs can generate thresholds in target gene expression. Nature Genetics. 43: 854-9. PMID 21857679 DOI: 10.1038/Ng.905  1
2011 Seidel HS, Ailion M, Li J, van Oudenaarden A, Rockman MV, Kruglyak L. A novel sperm-delivered toxin causes late-stage embryo lethality and transmission ratio distortion in C. elegans. Plos Biology. 9: e1001115. PMID 21814493 DOI: 10.1371/Journal.Pbio.1001115  1
2011 Hebenstreit D, Fang M, Gu M, Charoensawan V, van Oudenaarden A, Teichmann SA. RNA sequencing reveals two major classes of gene expression levels in metazoan cells. Molecular Systems Biology. 7: 497. PMID 21654674 DOI: 10.1038/Msb.2011.28  1
2011 Harterink M, Kim DH, Middelkoop TC, Doan TD, van Oudenaarden A, Korswagen HC. Neuroblast migration along the anteroposterior axis of C. elegans is controlled by opposing gradients of Wnts and a secreted Frizzled-related protein. Development (Cambridge, England). 138: 2915-24. PMID 21653614 DOI: 10.1242/dev.064733  1
2011 Steine EJ, Ehrich M, Bell GW, Raj A, Reddy S, van Oudenaarden A, Jaenisch R, Linhart HG. Genes methylated by DNA methyltransferase 3b are similar in mouse intestine and human colon cancer. The Journal of Clinical Investigation. 121: 1748-52. PMID 21490393 DOI: 10.1172/Jci43169  1
2011 Itzkovitz S, van Oudenaarden A. Validating transcripts with probes and imaging technology. Nature Methods. 8: S12-9. PMID 21451512 DOI: 10.1038/nmeth.1573  1
2011 Balázsi G, van Oudenaarden A, Collins JJ. Cellular decision making and biological noise: from microbes to mammals. Cell. 144: 910-25. PMID 21414483 DOI: 10.1016/J.Cell.2011.01.030  1
2011 Topalidou I, van Oudenaarden A, Chalfie M. Caenorhabditis elegans aristaless/Arx gene alr-1 restricts variable gene expression. Proceedings of the National Academy of Sciences of the United States of America. 108: 4063-8. PMID 21368126 DOI: 10.1073/pnas.1101329108  1
2010 Pando BF, van Oudenaarden A. Coupling cellular oscillators--circadian and cell division cycles in cyanobacteria. Current Opinion in Genetics & Development. 20: 613-8. PMID 20947336 DOI: 10.1016/j.gde.2010.09.001  1
2010 Youk H, Raj A, van Oudenaarden A. Imaging single mRNA molecules in yeast. Methods in Enzymology. 470: 429-46. PMID 20946820 DOI: 10.1016/S0076-6879(10)70017-3  1
2010 Acar M, Pando BF, Arnold FH, Elowitz MB, van Oudenaarden A. A general mechanism for network-dosage compensation in gene circuits. Science (New York, N.Y.). 329: 1656-60. PMID 20929850 DOI: 10.1126/Science.1190544  1
2010 Youk H, van Oudenaarden A. Microbiology: Altruistic defence. Nature. 467: 34-5. PMID 20811443 DOI: 10.1038/467034A  1
2010 Tan RZ, van Oudenaarden A. Transcript counting in single cells reveals dynamics of rDNA transcription. Molecular Systems Biology. 6: 358. PMID 20393578 DOI: 10.1038/Msb.2010.14  1
2010 Tsang JS, Ebert MS, van Oudenaarden A. Genome-wide dissection of microRNA functions and cotargeting networks using gene set signatures. Molecular Cell. 38: 140-53. PMID 20385095 DOI: 10.1016/J.Molcel.2010.03.007  1
2010 Yang Q, Pando BF, Dong G, Golden SS, van Oudenaarden A. Circadian gating of the cell cycle revealed in single cyanobacterial cells. Science (New York, N.Y.). 327: 1522-6. PMID 20299597 DOI: 10.1126/Science.1181759  1
2010 Dong G, Yang Q, Wang Q, Kim YI, Wood TL, Osteryoung KW, van Oudenaarden A, Golden SS. Elevated ATPase activity of KaiC applies a circadian checkpoint on cell division in Synechococcus elongatus. Cell. 140: 529-39. PMID 20178745 DOI: 10.1016/J.Cell.2009.12.042  1
2010 Raj A, Rifkin SA, Andersen E, van Oudenaarden A. Variability in gene expression underlies incomplete penetrance. Nature. 463: 913-8. PMID 20164922 DOI: 10.1038/Nature08781  0.96
2009 Youk H, van Oudenaarden A. Growth landscape formed by perception and import of glucose in yeast. Nature. 462: 875-9. PMID 20016593 DOI: 10.1038/Nature08653  1
2009 Mukherji S, van Oudenaarden A. Synthetic biology: understanding biological design from synthetic circuits. Nature Reviews. Genetics. 10: 859-71. PMID 19898500 DOI: 10.1038/nrg2697  1
2009 Hanna J, Saha K, Pando B, van Zon J, Lengner CJ, Creyghton MP, van Oudenaarden A, Jaenisch R. Direct cell reprogramming is a stochastic process amenable to acceleration. Nature. 462: 595-601. PMID 19898493 DOI: 10.1038/Nature08592  1
2009 Muzzey D, Gómez-Uribe CA, Mettetal JT, van Oudenaarden A. A systems-level analysis of perfect adaptation in yeast osmoregulation. Cell. 138: 160-71. PMID 19596242 DOI: 10.1016/J.Cell.2009.04.047  1
2009 Muzzey D, van Oudenaarden A. Quantitative time-lapse fluorescence microscopy in single cells. Annual Review of Cell and Developmental Biology. 25: 301-27. PMID 19575655 DOI: 10.1146/annurev.cellbio.042308.113408  1
2009 Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, Regev A, Lander ES, Rinn JL. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proceedings of the National Academy of Sciences of the United States of America. 106: 11667-72. PMID 19571010 DOI: 10.1073/Pnas.0904715106  1
2009 Raj A, van Oudenaarden A. Single-molecule approaches to stochastic gene expression. Annual Review of Biophysics. 38: 255-70. PMID 19416069 DOI: 10.1146/Annurev.Biophys.37.032807.125928  1
2009 Gore J, Youk H, van Oudenaarden A. Snowdrift game dynamics and facultative cheating in yeast. Nature. 459: 253-6. PMID 19349960 DOI: 10.1038/Nature07921  1
2009 Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V, Tsai IJ, Bergman CM, Bensasson D, O'Kelly MJ, van Oudenaarden A, et al. Population genomics of domestic and wild yeasts. Nature. 458: 337-41. PMID 19212322 DOI: 10.1038/Nature07743  1
2009 Gore J, van Oudenaarden A. Synthetic biology: The yin and yang of nature. Nature. 457: 271-2. PMID 19148089 DOI: 10.1038/457271A  1
2009 James SA, O'Kelly MJ, Carter DM, Davey RP, van Oudenaarden A, Roberts IN. Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing. Genome Research. 19: 626-35. PMID 19141593 DOI: 10.1101/gr.084517.108  1
2008 Raj A, van Oudenaarden A. Nature, nurture, or chance: stochastic gene expression and its consequences. Cell. 135: 216-26. PMID 18957198 DOI: 10.1016/J.Cell.2008.09.050  1
2008 Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A, Tyagi S. Imaging individual mRNA molecules using multiple singly labeled probes. Nature Methods. 5: 877-9. PMID 18806792 DOI: 10.1038/nmeth.1253  0.96
2008 Acar M, Mettetal JT, van Oudenaarden A. Stochastic switching as a survival strategy in fluctuating environments. Nature Genetics. 40: 471-5. PMID 18362885 DOI: 10.1038/Ng.110  1
2008 Mettetal JT, Muzzey D, Gómez-Uribe C, van Oudenaarden A. The frequency dependence of osmo-adaptation in Saccharomyces cerevisiae. Science (New York, N.Y.). 319: 482-4. PMID 18218902 DOI: 10.1126/Science.1151582  1
2008 Upadhyaya A, Baraban M, Wong J, Matsudaira P, van Oudenaarden A, Mahadevan L. Power-limited contraction dynamics of Vorticella convallaria: an ultrafast biological spring. Biophysical Journal. 94: 265-72. PMID 17933875 DOI: 10.1529/Biophysj.107.108852  1
2007 Chabot JR, Pedraza JM, Luitel P, van Oudenaarden A. Stochastic gene expression out-of-steady-state in the cyanobacterial circadian clock. Nature. 450: 1249-52. PMID 18097413 DOI: 10.1038/nature06395  1
2007 Kaufmann BB, Yang Q, Mettetal JT, van Oudenaarden A. Heritable stochastic switching revealed by single-cell genealogy. Plos Biology. 5: e239. PMID 17803359 DOI: 10.1371/Journal.Pbio.0050239  1
2007 Mettetal JT, van Oudenaarden A. Microbiology. Necessary noise. Science (New York, N.Y.). 317: 463-4. PMID 17656711 DOI: 10.1126/science.1146747  1
2007 Tsang J, Zhu J, van Oudenaarden A. MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. Molecular Cell. 26: 753-67. PMID 17560377 DOI: 10.1016/J.Molcel.2007.05.018  1
2007 Kaufmann BB, van Oudenaarden A. Stochastic gene expression: from single molecules to the proteome. Current Opinion in Genetics & Development. 17: 107-12. PMID 17317149 DOI: 10.1016/J.Gde.2007.02.007  1
2007 Lim HN, van Oudenaarden A. A multistep epigenetic switch enables the stable inheritance of DNA methylation states. Nature Genetics. 39: 269-75. PMID 17220888 DOI: 10.1038/Ng1956  1
2006 Muzzey D, van Oudenaarden A. When it comes to decisions, myeloid progenitors crave positive feedback. Cell. 126: 650-2. PMID 16923384 DOI: 10.1016/J.Cell.2006.08.007  1
2006 Samadani A, Mettetal J, van Oudenaarden A. Cellular asymmetry and individuality in directional sensing. Proceedings of the National Academy of Sciences of the United States of America. 103: 11549-54. PMID 16864788 DOI: 10.1073/Pnas.0601909103  1
2006 Tsang J, van Oudenaarden A. Exciting fluctuations: monitoring competence induction dynamics at the single-cell level. Molecular Systems Biology. 2: 2006.0025. PMID 16738573 DOI: 10.1038/Msb4100064  1
2006 Mettetal JT, Muzzey D, Pedraza JM, Ozbudak EM, van Oudenaarden A. Predicting stochastic gene expression dynamics in single cells. Proceedings of the National Academy of Sciences of the United States of America. 103: 7304-9. PMID 16648266 DOI: 10.1073/Pnas.0509874103  1
2006 Tharp WG, Yadav R, Irimia D, Upadhyaya A, Samadani A, Hurtado O, Liu SY, Munisamy S, Brainard DM, Mahon MJ, Nourshargh S, van Oudenaarden A, Toner MG, Poznansky MC. Neutrophil chemorepulsion in defined interleukin-8 gradients in vitro and in vivo. Journal of Leukocyte Biology. 79: 539-54. PMID 16365152 DOI: 10.1189/Jlb.0905516  1
2005 Ozbudak EM, Becskei A, van Oudenaarden A. A system of counteracting feedback loops regulates Cdc42p activity during spontaneous cell polarization. Developmental Cell. 9: 565-71. PMID 16198298 DOI: 10.1016/j.devcel.2005.08.014  1
2005 Becskei A, Kaufmann BB, van Oudenaarden A. Contributions of low molecule number and chromosomal positioning to stochastic gene expression. Nature Genetics. 37: 937-44. PMID 16086016 DOI: 10.1038/Ng1616  1
2005 Acar M, Becskei A, van Oudenaarden A. Enhancement of cellular memory by reducing stochastic transitions. Nature. 435: 228-32. PMID 15889097 DOI: 10.1038/Nature03524  1
2005 Pedraza JM, van Oudenaarden A. Noise propagation in gene networks. Science (New York, N.Y.). 307: 1965-9. PMID 15790857 DOI: 10.1126/science.1109090  1
2004 Upadhyaya A, van Oudenaarden A. Actin polymerization: forcing flat faces forward. Current Biology : Cb. 14: R467-9. PMID 15203017 DOI: 10.1016/J.Cub.2004.06.010  1
2004 Thattai M, Van Oudenaarden A. Stochastic gene expression in fluctuating environments Genetics. 167: 523-530. PMID 15166174 DOI: 10.1534/genetics.167.1.523  1
2004 Nguyen B, Upadhyaya A, Van Oudenaarden A, Brenner MP. Elastic Instability in Growing Yeast Colonies Biophysical Journal. 86: 2740-2747. PMID 15111392 DOI: 10.1016/S0006-3495(04)74327-1  1
2004 Becskei A, Boselli MG, van Oudenaarden A. Amplitude control of cell-cycle waves by nuclear import Nature Cell Biology. 6: 451-457. PMID 15107861 DOI: 10.1038/ncb1124  1
2004 Ozbudak EM, Thattai M, Lim HN, Shraiman BI, Van Oudenaarden A. Multistability in the lactose utilization network of Escherichia coli. Nature. 427: 737-40. PMID 14973486 DOI: 10.1038/Nature02298  1
2003 Mittal N, Budrene EO, Brenner MP, Van Oudenaarden A. Motility of Escherichia coli cells in clusters formed by chemotactic aggregation Proceedings of the National Academy of Sciences of the United States of America. 100: 13259-13263. PMID 14597724 DOI: 10.1073/Pnas.2233626100  1
2003 Upadhyaya A, van Oudenaarden A. Biomimetic systems for studying actin-based motility. Current Biology : Cb. 13: R734-44. PMID 13678615 DOI: 10.1016/J.Cub.2003.08.051  1
2003 Upadhyaya A, Chabot JR, Andreeva A, Samadani A, van Oudenaarden A. Probing polymerization forces by using actin-propelled lipid vesicles. Proceedings of the National Academy of Sciences of the United States of America. 100: 4521-6. PMID 12657740 DOI: 10.1073/Pnas.0837027100  1
2002 Thattai M, Van Oudenaarden A. Attenuation of noise in ultrasensitive signaling cascades Biophysical Journal. 82: 2943-2950. PMID 12023217  1
2002 Ozbudak EM, Thattai M, Kurtser I, Grossman AD, van Oudenaarden A. Regulation of noise in the expression of a single gene. Nature Genetics. 31: 69-73. PMID 11967532 DOI: 10.1038/Ng869  1
2001 Thattai M, Van Oudenaarden A. Intrinsic noise in gene regulatory networks Proceedings of the National Academy of Sciences of the United States of America. 98: 8614-8619. PMID 11438714 DOI: 10.1073/pnas.151588598  1
1999 van Oudenaarden A, Theriot JA. Cooperative symmetry-breaking by actin polymerization in a model for cell motility. Nature Cell Biology. 1: 493-9. PMID 10587645 DOI: 10.1038/70281  1
1999 van Oudenaarden A, Boxer SG. Brownian ratchets: molecular separations in lipid bilayers supported on patterned arrays. Science (New York, N.Y.). 285: 1046-8. PMID 10446046 DOI: 10.1126/Science.285.5430.1046  1
1999 Cameron LA, Footer MJ, van Oudenaarden A, Theriot JA. Motility of ActA protein-coated microspheres driven by actin polymerization. Proceedings of the National Academy of Sciences of the United States of America. 96: 4908-13. PMID 10220392 DOI: 10.1073/Pnas.96.9.4908  1
1999 Bruder C, Glazman LI, Larkin AI, Mooij JE, Van Oudenaarden A. Phase transition in a chain of quantum vortices Physical Review B - Condensed Matter and Materials Physics. 59: 1383-1395.  1
1998 Van Oudenaarden A, Devoret MH, Nazarov YV, Mooij JE. Magneto-electric Aharonov-Bohm effect in metal rings Nature. 391: 768-770. DOI: 10.1038/35808  1
1998 Wildöer JWG, Van Oudenaarden A, Harmans CJPM, Van Kempen H. Scanning tunneling microscope tip as a positionable contact: Probing a Josephson-junction array at subkelvin temperatures Journal of Vacuum Science and Technology B: Microelectronics and Nanometer Structures. 16: 2837-2840.  1
1998 Van Oudenaarden A, Van Leeuwen B, Robbens MPM, Mooij JE. One-dimensional Mott localization of quantum vortices in Josephson-junction arrays Physical Review B - Condensed Matter and Materials Physics. 57: 11684-11690.  1
1998 Van Oudenaarden A, Nazarov YV, Mooij JE. Giant higher harmonic generation in mesoscopic metal wires and rings interrupted by tunnel junctions Physical Review B - Condensed Matter and Materials Physics. 57: 8816-8818.  1
1997 Van Oudenaarden A, Devoret MH, Visscher EH, Nazarov YV, Mooij JE. Conductance fluctuations in a metallic wire interrupted by a tunnel junction Physical Review Letters. 78: 3539-3542. DOI: 10.1103/Physrevlett.78.3539  1
1996 van Oudenaarden A, Várdy SJ, Mooij JE. One-Dimensional Localization of Quantum Vortices in Disordered Josephson Junction Arrays. Physical Review Letters. 77: 4257-4260. PMID 10062488  1
1996 van Oudenaarden A, Mooij JE. One-Dimensional Mott Insulator Formed by Quantum Vortices in Josephson Junction Arrays. Physical Review Letters. 76: 4947-4950. PMID 10061420  1
1996 van Oudenaarden A, Vády SJK, Mooij JE. Bloch vortices in One-dimensional josephson junction arrays Czechoslovak Journal of Physics. 46: 707-708. DOI: 10.1007/BF02583661  1
1996 Van Oudenaarden A, Várdy SJK, Mooij JE. One-dimensional localization of quantum vortices in disordered josephson junction arrays Physical Review Letters. 77: 4257-4260.  1
1996 Van Oudenaarden A, Mooij JE. One-dimensional Mott insulator formed by quantum vortices in Josephson junction arrays Physical Review Letters. 76: 4947-4950.  1
1994 van Oudenaarden A, de Jong M, Sietsma J, Rekveldt MT, van den Beukel A. Internal stress distribution in amorphous Fe40Ni40B20 studied by field dependent neutron depolarization Journal of Magnetism and Magnetic Materials. 133: 251-254. DOI: 10.1016/0304-8853(94)90538-X  1
1994 de Jong M, van Oudenaarden A, Sietsma J, Th. Rekveldt M, van den Beukel A. Internal stresses in amorphous Fe40Ni40B20 studied with neutron depolarization Acta Physica Hungarica. 75: 91-100. DOI: 10.1007/Bf03156562  1
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