Papers

Here's a list of papers that use Stellaris:

Here's some papers that use Stellaris RNA FISH. The list is definitely not complete–it's getting hard to keep up with all the different stuff people are doing with it! I put papers that I think made some sort of important technical contribution to the method in bold.

    • 1. Wang S, Sengel C, Emerson MM, Cepko CL. A Gene Regulatory Network Controls the Binary Fate Decision of Rod and Bipolar Cells in the Vertebrate Retina. Dev Cell. 2014 Aug 20.
    • 2. Yang B, Treweek JB, Kulkarni RP, Deverman BE, Chen C-K, Lubeck E, et al. Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing. Cell. 2014 Jul 31.
    • 3. Singer ZS, Yong J, Tischler J, Hackett JA, Altinok A, Surani MA, et al. Dynamic heterogeneity and DNA methylation in embryonic stem cells. Mol Cell. 2014 Jul 17;55(2):319–31.
    • 4. Ng A, Tan S, Singh G, Rizk P, Swathi Y, Tan TZ, et al. Lgr5 marks stem/progenitor cells in ovary and tubal epithelia. Nat Cell Biol. 2014 Jul 6.
    • 5. Abranches E, Guedes AMV, Moravec M, Maamar H, Svoboda P, Raj A, et al. Stochastic NANOG fluctuations allow mouse embryonic stem cells to explore pluripotency. Development. 2014 Jul;141(14):2770–9.
    • 6. Mohn F, Sienski G, Handler D, Brennecke J. The Rhino-Deadlock-Cutoff Complex Licenses Noncanonical Transcription of Dual-Strand piRNA Clusters in Drosophila. Cell. 2014 Jun 5;157(6):1364–79.
    • 7. Dimitrova N, Zamudio JR, Jong RM, Soukup D, Resnick R, Sarma K, et al. LincRNA-p21 Activates p21 In cis to Promote Polycomb Target Gene Expression and to Enforce the G1/S Checkpoint. Mol Cell. 2014 May 21.
    • 8. Lubeck E, Coskun AF, Zhiyentayev T, Ahmad M, Cai L. Single-cell in situ RNA profiling by sequential hybridization. Nature Methods. 2014 Mar 28;11(4):360–1.
    • 9. Paralkar VR, Mishra T, Luan J, Yao Y, Kossenkov AV, Anderson SM, et al. Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development. Blood. American Society of Hematology; 2014 Mar 20;123(12):1927–37.
    • 10. Facciponte JG, Ugel S, De Sanctis F, Li C, Wang L, Nair G, et al. Tumor endothelial marker 1-specific DNA vaccination targets tumor vasculature. J Clin Invest. American Society for Clinical Investigation; 2014 Mar 18;124(4):0–0.
    • 11. Lakdawala SS, Wu Y, Wawrzusin P, Kabat J, Broadbent AJ, Lamirande EW, et al. Influenza a virus assembly intermediates fuse in the cytoplasm. Heise MT, editor. PLoS Pathog. Public Library of Science; 2014 Mar;10(3):e1003971.
    • 12. Paralkar VR, Mishra T, Luan J, Yao Y, Kossenkov AV, Anderson SM, et al. Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development. Blood. American Society of Hematology; 2014 Feb 4;:blood–2013–12–544494.
    • 13. Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L, et al. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol. 2014 Feb;21(2):198–206.
    • 14. Jambo KC, Banda DH, Kankwatira AM, Sukumar N, Allain TJ, Heyderman RS, et al. Small alveolar macrophages are infected preferentially by HIV and exhibit impaired phagocytic function. Mucosal Immunol. 2014 Jan 29.
    • 15. Franz CJ, Renshaw H, Frezal L, Jiang Y, Félix M-A, Wang D. Orsay, Santeuil and Le Blanc viruses primarily infect intestinal cells in Caenorhabditis nematodes. Virology. 2014 Jan 5;448:255–64.
    • 16. Markey FB, Ruezinsky W, Tyagi S, Batish M. Fusion FISH Imaging: Single-Molecule Detection of Gene Fusion Transcripts In Situ. Pack S, editor. PLoS ONE. Public Library of Science; 2014;9(3):e93488.
    • 17. Spillane M, Ketschek A, Merianda TT, Twiss JL, Gallo G. Mitochondria Coordinate Sites of Axon Branching through Localized Intra-axonal Protein Synthesis. CellReports. 2013 Dec 26;5(6):1564–75.
    • 18. Semrau S, Crosetto N, Bienko M, Boni M, Bernasconi P, Chiarle R, et al. FuseFISH: Robust Detection of Transcribed Gene Fusions in Single Cells. CellReports. 2013 Dec 24.
    • 19. Conine CC, Moresco JJ, Gu W, Shirayama M, Conte D, Yates JR, et al. Argonautes Promote Male Fertility and Provide a Paternal Memory of Germline Gene Expression in C. elegans. Cell. 2013 Dec 19;155(7):1532–44.
    • 20. Lippmann ES, Estevez-Silva MC, Ashton RS. Defined human pluripotent stem cell culture enables highly efficient neuroepithelium derivation without small molecule inhibitors. Stem Cells. 2013 Dec 19;:n/a–n/a.
    • 21. Sinsimer KS, Lee JJ, Thiberge SY, Gavis ER. Germ Plasm Anchoring Is a Dynamic State that Requires Persistent Trafficking. CellReports. 2013 Dec 12;5(5):1169–77.
    • 22. Zheng C, Karimzadegan S, Chiang V, Chalfie M. Histone Methylation Restrains the Expression of Subtype-Specific Genes during Terminal Neuronal Differentiation inCaenorhabditis elegans. Ahringer J, editor. PLoS Genet. Public Library of Science; 2013 Dec;9(12):e1004017.
    • 23. O'Grady T, Cao S, Strong MJ, Concha M, Wang X, Bondurant SS, et al. Global Bidirectional Transcription of the Epstein-Barr Virus Genome During Reactivation. J Virol. American Society for Microbiology; 2013 Nov 20;:JVI.02989–13.
    • 24. Hsiao K, Bozdagi O, Benson DL. Axonal cap-dependent translation regulates presynaptic p35. Dev Neurobiol. 2013 Nov 19;:n/a–n/a.
    • 25. Burdick RC, Hu W-S, Pathak VK. Nuclear import of APOBEC3F-labeled HIV-1 preintegration complexes. Proc Natl Acad Sci USA. National Acad Sciences; 2013 Nov 18;:201315996.
    • 26. Jakobsen MR, Bak RO, Andersen A, Berg RK, Jensen SB, Jin T, et al. IFI16 senses DNA forms of the lentiviral replication cycle and controls HIV-1 replication. Proc Natl Acad Sci USA. National Acad Sciences; 2013 Nov 15;110(48):E4571–80.
    • 27. Alvarez-Dominguez JR, Hu W, Yuan B, Shi J, Park SS, Gromatzky AA, et al. Global discovery of erythroid long non-coding RNAs reveals novel regulators of red cell maturation. Blood. American Society of Hematology; 2013 Nov 7;:blood–2013–10–530683.
    • 28. Ji N, Middelkoop TC, Mentink RA, Betist MC, Tonegawa S, Mooijman D, et al. Feedback Control of Gene Expression Variability in the Caenorhabditis elegans Wnt Pathway. Cell. 2013 Nov 7;155(4):869–80.
    • 29. Zheng L, Sepúlveda LA, Lua RC, Lichtarge O, Golding I, Sokac AM. The maternal-to-zygotic transition targets actin to promote robustness during morphogenesis. Stern DL, editor. PLoS Genet. Public Library of Science; 2013 Nov;9(11):e1003901.
    • 30. Sahai-Hernandez P, Nystul TG. A dynamic population of stromal cells contributes to the follicle stem cell niche in the Drosophila ovary. Development. 2013 Oct 16.
    • 31. Kim DH, Grün D, van Oudenaarden A. Dampening of expression oscillations by synchronous regulation of a microRNA and its target. Nat Genet. 2013 Sep 15.
    • 32. Kim DH, Grün D, van Oudenaarden A. Dampening of expression oscillations by synchronous regulation of a microRNA and its target. Nat Genet. Nature Publishing Group; 2013 Sep 15;:–.
    • 33. Shah K, Tyagi S. Barriers to transmission of transcriptional noise in a c-fos c-jun pathway. Molecular Systems Biology. 2013 Sep 10;9:687.
    • 34. Lorenowicz MJ, Macurkova M, Harterink M, Middelkoop TC, de Groot R, Betist MC, et al. Inhibition of late endosomal maturation restores Wnt secretion in C. elegans vps-29 retromer mutants. Cellular Signalling. 2013 Sep.
    • 35. Kennedy LM, Pham SCDL, Grishok A. Nonautonomous Regulation of Neuronal Migration by Insulin Signaling, DAF-16/FOXO, and PAK-1. CellReports. The Authors; 2013 Aug 28;:1–23.
    • 36. Menouni R, Champ S, Espinosa L, Boudvillain M, Ansaldi M. Transcription termination controls prophage maintenance in Escherichia coli genomes. Proc Natl Acad Sci USA. 2013 Aug 27;110(35):14414–9.
    • 37. Little SC, Tikhonov M, Gregor T. Precise developmental gene expression arises from globally stochastic transcriptional activity. Cell. 2013 Aug 15;154(4):789–800.
    • 38. Lyubimova A, Itzkovitz S, Junker JP, Fan ZP, Wu X, van Oudenaarden A. Single-molecule mRNA detection and counting in mammalian tissue. Nat Protoc. Nature Publishing Group; 2013 Aug 15;8(9):1743–58.
    • 39. Hansen CH, van Oudenaarden A. Allele-specific detection of single mRNA molecules in situ. Nature Methods. 2013 Aug;10(9):869–71.
    • 40. Levesque MJ, Ginart P, Wei Y, Raj A. Visualizing SNVs to quantify allele-specific expression in single cells. Nature Methods. 2013 Aug;10(9):865–7.
    • 41. Nair G, Walton T, Murray JI, Raj A. Gene transcription is coordinated with, but not dependent on, cell divisions during C. elegans embryonic fate specification. Development. 2013 Aug;140(16):3385–94.
    • 42. Faddah DA, Wang H, Cheng AW, Katz Y, Buganim Y, Jaenisch R. Single-Cell Analysis Reveals that Expression of Nanog Is Biallelic and Equally Variable as that of Other Pluripotency Factors in Mouse ESCs. Cell stem cell. 2013 Jul 3;13(1):23–9.
    • 43. Fang M, Xie H, Dougan SK, Ploegh H, van Oudenaarden A. Stochastic cytokine expression induces mixed T helper cell States. PLoS Biol. 2013 Jul;11(7):e1001618.
    • 44. Zopf CJ, Quinn K, Zeidman J, Maheshri N. Cell-cycle dependence of transcription dominates noise in gene expression. PLoS Comput Biol. 2013 Jul;9(7):e1003161.
    • 45. Castelnuovo M, Rahman S, Guffanti E, Infantino V, Stutz F, Zenklusen D. Bimodal expression of PHO84 is modulated by early termination of antisense transcription. Nat Struct Mol Biol. 2013 Jul;20(7):851–8.
    • 46. Doncic A, Skotheim JM. Feedforward regulation ensures stability and rapid reversibility of a cellular state. Mol Cell. 2013 Jun 27;50(6):856–68.
    • 47. Zhang X, Song Y, Shah AY, Lekova V, Raj A, Huang L, et al. Quantitative assessment of ratiometric bimolecular beacons as a tool for imaging single engineered RNA transcripts and measuring gene expression in living cells. Nucleic Acids Res. 2013 Jun 27.
    • 48. Lee C, Zhang H, Baker AE, Occhipinti P, Borsuk ME, Gladfelter AS. Protein Aggregation Behavior Regulates Cyclin Transcript Localization and Cell-Cycle Control. Dev Cell. Elsevier; 2013 Jun 24;25(6):572–84.
    • 49. Graindorge A, Carre C, Gebauer F. Sex-lethal promotes nuclear retention of msl2 mRNA via interactions with the STAR protein HOW. Genes & development. 2013 Jun 20;27(12):1421–33.
    • 50. Guo Z, Driver I, Ohlstein B. Injury-induced BMP signaling negatively regulates Drosophila midgut homeostasis. J Cell Biol. 2013 Jun 10;201(6):945–61.
    • 51. Maamar H, Cabili MN, Rinn J, Raj A. linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis. Genes & development. 2013 Jun 1;27(11):1260–71.
    • 52. Messier V, Zenklusen D, Michnick SW. A nutrient-responsive pathway that determines M phase timing through control of B-cyclin mRNA stability. Cell. 2013 May 23;153(5):1080–93.
    • 53. Shepherd DP, Li N, Micheva-Viteva SN, Munsky B, Hong-Geller E, Werner JH. Counting small RNA in pathogenic bacteria. Anal Chem. 2013 May 21;85(10):4938–43.
    • 54. Skinner SO, Sepúlveda LA, Xu H, Golding I. Measuring mRNA copy number in individual Escherichia coli cells using single-molecule fluorescent in situ hybridization. Nat Protoc. 2013 May 16;8(6):1100–13.
    • 55. Cvetkovska V, Hibbert AD, Emran F, Chen BE. Overexpression of Down syndrome cell adhesion molecule impairs precise synaptic targeting. Nat Neurosci. Nature Publishing Group; 2013 May 12;16(6):677–82.
    • 56. Chou Y-Y, Heaton NS, Gao Q, Palese P, Singer R, Lionnet T. Colocalization of Different Influenza Viral RNA Segments in the Cytoplasm before Viral Budding as Shown by Single-molecule Sensitivity FISH Analysis. Whelan SPJ, editor. PLoS Pathog. 2013 May 9;9(5):e1003358.
    • 57. Tan DWM, Jensen KB, Trotter MWB, Connelly JT, Broad S, Watt FM. Single-cell gene expression profiling reveals functional heterogeneity of undifferentiated human epidermal cells. Development. 2013 Apr;140(7):1433–44.
    • 58. Minkovsky A, Barakat TS, Sellami N, Chin MH, Gunhanlar N, Gribnau J, et al. The pluripotency factor-bound intron 1 of Xist is dispensable for X chromosome inactivation and reactivation in vitro and in vivo. CellReports. 2013 Mar 28;3(3):905–18.
    • 59. Whitehead CL, Walker SP, Ye L, Mendis S, Kaitu'u-Lino TJ, Lappas M, et al. Placental Specific mRNA in the Maternal Circulation Are Globally Dysregulated in Pregnancies Complicated by Fetal Growth Restriction. Journal of Clinical Endocrinology & Metabolism. 2013 Mar 7;98(3):E429–36.
    • 60. Levesque MJ, Raj A. Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation. Nature Methods. 2013 Mar;10(3):246–8.
    • 61. Bolt MJ, Stossi F, Newberg JY, Orjalo A, Johansson HE, Mancini MA. Coactivators enable glucocorticoid receptor recruitment to fine-tune estrogen receptor transcriptional responses. Nucleic Acids Res. 2013 Feb 26.
    • 62. Neuert G, Munsky B, Tan RZ, Teytelman L, Khammash M, van Oudenaarden A. Systematic identification of signal-activated stochastic gene regulation. Science. 2013 Feb 1;339(6119):584–7.
    • 63. Hartmann BM, Li W, Jia J, Patil S, Marjanovic N, Martínez-Romero C, et al. Mouse dendritic cell (DC) influenza virus infectivity is much lower than that for human DCs and is hemagglutinin subtype dependent. J Virol. American Society for Microbiology; 2013 Feb;87(3):1916–8.
    • 64. 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. 2013 Feb;10(2):122–4.
    • 65. Mazumder A, Tummler K, Bathe M, Samson LD. Single-cell analysis of ribonucleotide reductase transcriptional and translational response to DNA damage. Mol Cell Biol. 2013 Feb;33(3):635–42.
    • 66. Barkoulas M, van Zon JS, Milloz J, van Oudenaarden A, Félix M-A. Robustness and epistasis in the C. elegans vulval signaling network revealed by pathway dosage modulation. Dev Cell. 2013 Jan 14;24(1):64–75.
    • 67. Mazumder A, Tummler K, Bathe M, Samson LD. Single-Cell Analysis of Ribonucleotide Reductase Transcriptional and Translational Response to DNA Damage. Mol Cell Biol. 2013 Jan 10;33(3):635–42.
    • 68. Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K, et al. Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature. 2013 Jan 10;493(7431):231–5.
    • 69. 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 [Internet]. Nature Publishing Group; 2013 Jan 8;9(1):631. Available from: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=23295860&retmode=ref&cmd=prlinks
    • 70. Jakt LM, Moriwaki S, Nishikawa S. A continuum of transcriptional identities visualized by combinatorial fluorescent in situ hybridization. Development. 2013 Jan 1;140(1):216–25.
    • 71. Jasnos L, Aksoy FB, Hersi HM, Wantuch S, Sawado T. Identifying division symmetry of mouse embryonic stem cells: negative impact of DNA methyltransferases on symmetric self-renewal. Stem Cell Reports. Elsevier; 2013;1(4):360–9.
    • 72. Avendaño MS, Leidy C, Pedraza JM. Tuning the range and stability of multiple phenotypic states with coupled positive-negative feedback loops. Nat Commun. 2013;4:2605.
    • 73. Shaffer SM, Wu M-T, Levesque MJ, Raj A. Turbo FISH: A Method for Rapid Single Molecule RNA FISH. PLoS ONE. 2013;8(9):e75120.
    • 74. Denning DP, Hatch V, Horvitz HR. Both the caspase CSP-1 and a caspase-independent pathway promote programmed cell death in parallel to the canonical pathway for apoptosis in Caenorhabditis elegans. PLoS Genet. 2013;9(3):e1003341.
    • 75. Peterson KA, Nishi Y, Ma W, Vedenko A, Shokri L, Zhang X, et al. Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning. Genes & development. 2012 Dec 15;26(24):2802–16.
    • 76. Cochella L, Hobert O. Embryonic Priming of a miRNA Locus Predetermines Postmitotic NeuronalLeft/Right Asymmetry in C. elegans. Cell. Elsevier Inc; 2012 Dec 7;151(6):1229–42.
    • 77. Brewster RC, Jones DL, Phillips R. Tuning promoter strength through RNA polymerase binding site design in Escherichia coli. PLoS Comput Biol. 2012 Dec;8(12):e1002811.
    • 78. Patel T, Tursun B, Rahe DP, Hobert O. Removal of Polycomb repressive complex 2 makes C. elegans germ cells susceptible to direct conversion into specific somatic cell types. CellReports. 2012 Nov 29;2(5):1178–86.
    • 79. Xu S, Hafer N, Agunwamba B, Schedl P. The CPEB protein Orb2 has multiple functions during spermatogenesis in Drosophila melanogaster. PLoS Genet. 2012 Nov;8(11):e1003079.
    • 80. Kusek G, Campbell M, Doyle F, Tenenbaum SA, Kiebler M, Temple S. Asymmetric Segregation of the Double-Stranded RNA Binding Protein Staufen2 during Mammalian Neural Stem Cell Divisions Promotes Lineage Progression. Stem Cell. Elsevier Inc; 2012 Oct 5;11(4):505–16.
    • 81. Voronina E, Paix A, Seydoux G. The P granule component PGL-1 promotes the localization and silencing activity of the PUF protein FBF-2 in germline stem cells. Development. 2012 Oct;139(20):3732–40.
    • 82. van Werven FJ, Neuert G, Hendrick N, Lardenois A, Buratowski S, van Oudenaarden A, et al. Transcription of two long noncoding RNAs mediates mating-type control of gametogenesis in budding yeast. Cell. 2012 Sep 14;150(6):1170–81.
    • 83. Buganim Y, Faddah DA, Cheng AW, Itskovich E, Markoulaki S, Ganz K, et al. Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase. Cell. 2012 Sep 14;150(6):1209–22.
    • 84. Zhong FL, Batista LFZ, Freund A, Pech MF, Venteicher AS, Artandi SE. TPP1 OB-fold domain controls telomere maintenance by recruiting telomerase to chromosome ends. Cell. 2012 Aug 3;150(3):481–94.
    • 85. Muñoz J, Stange DE, Schepers AG, van de Wetering M, Koo B-K, Itzkovitz S, et al. The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent “+4” cell markers. EMBO J. 2012 Jul 18;31(14):3079–91.
    • 86. Gao Q, Chou Y-Y, Doğanay S, Vafabakhsh R, Ha T, Palese P. The influenza A virus PB2, PA, NP, and M segments play a pivotal role during genome packaging. J Virol. 2012 Jul;86(13):7043–51.
    • 87. Purvis JE, Karhohs KW, Mock C, Batchelor E, Loewer A, Lahav G. p53 dynamics control cell fate. Science. 2012 Jun 15;336(6087):1440–4.
    • 88. Chou Y-Y, Vafabakhsh R, Doğanay S, Gao Q, Ha T, Palese P. One influenza virus particle packages eight unique viral RNAs as shown by FISH analysis. Proc Natl Acad Sci USA. 2012 Jun 5;109(23):9101–6.
    • 89. Lubeck E, Cai L. Single-cell systems biology by super-resolution imaging and combinatorial labeling. Nature Methods. Nature Publishing Group; 2012 Jun 3;9(7):743–8.
    • 90. Schneider J, Skelton RL, Stetina von SE, Middelkoop TC, van Oudenaarden A, Korswagen HC, et al. UNC-4 antagonizes Wnt signaling to regulate synaptic choice in the C. elegans motor circuit. Development. 2012 Jun;139(12):2234–45.
    • 91. van Es JH, Haegebarth A, Kujala P, Itzkovitz S, Koo B-K, Boj SF, et al. A critical role for the Wnt effector Tcf4 in adult intestinal homeostatic self-renewal. Mol Cell Biol. 2012 May;32(10):1918–27.
    • 92. Yu J, Valerius MT, Duah M, Staser K, Hansard JK, Guo J-J, et al. Identification of molecular compartments and genetic circuitry in the developing mammalian kidney. Development. 2012 May;139(10):1863–73.
    • 93. Batish M, van den Bogaard P, Kramer FR, Tyagi S. Neuronal mRNAs travel singly into dendrites. Proc Natl Acad Sci USA. 2012 Mar 20;109(12):4645–50.
    • 94. Guo W, Keckesova Z, Donaher JL, Shibue T, Tischler V, Reinhardt F, et al. Slug and Sox9 cooperatively determine the mammary stem cell state. Cell. 2012 Mar 2;148(5):1015–28.
    • 95. Bumgarner SL, Neuert G, Voight BF, Symbor-Nagrabska A, Grisafi P, van Oudenaarden A, et al. Single-cell analysis reveals that noncoding RNAs contribute to clonal heterogeneity by modulating transcription factor recruitment. Mol Cell. 2012 Feb 24;45(4):470–82.
    • 96. Itzkovitz S, Blat IC, Jacks T, Clevers H, van Oudenaarden A. Optimality in the development of intestinal crypts. Cell. 2012 Feb 3;148(3):608–19.
    • 97. Trcek T, Chao JA, Larson DR, Park HY, Zenklusen D, Shenoy SM, et al. Single-mRNA counting using fluorescent in situ hybridization in budding yeast. Nat Protoc. 2012 Feb;7(2):408–19.
    • 98. Li F, Zheng Q, Ryvkin P, Dragomir I, Desai Y, Aiyer S, et al. Global analysis of RNA secondary structure in two metazoans. CellReports. 2012 Jan 26;1(1):69–82.
    • 99. Nédelec S, Peljto M, Shi P, Amoroso MW, Kam LC, Wichterle H. Concentration-dependent requirement for local protein synthesis in motor neuron subtype-specific response to axon guidance cues. J Neurosci. 2012 Jan 25;32(4):1496–506.
    • 100. Middelkoop TC, Williams L, Yang P-T, Luchtenberg J, Betist MC, Ji N, et al. The thrombospondin repeat containing protein MIG-21 controls a left-right asymmetric Wnt signaling response in migrating C. elegans neuroblasts. Dev Biol. 2012 Jan 15;361(2):338–48.
    • 101. Singh A, Razooky BS, Dar RD, Weinberger LS. Dynamics of protein noise can distinguish between alternate sources of gene-expression variability. Molecular Systems Biology. 2012;8:607.
    • 102. Kuhlman TE, Cox EC. Gene location and DNA density determine transcription factor distributions in Escherichia coli. Molecular Systems Biology. 2012;8:610.
    • 103. Trcek T, Larson DR, Moldón A, Query CC, Singer RH. Single-molecule mRNA decay measurements reveal promoter- regulated mRNA stability in yeast. Cell. 2011 Dec 23;147(7):1484–97.
    • 104. Burga A, Casanueva MO, Lehner B. Predicting mutation outcome from early stochastic variation in genetic interaction partners. Nature. 2011 Dec 8;480(7376):250–3.
    • 105. Saffer AM, Kim DH, van Oudenaarden A, Horvitz HR. The Caenorhabditis elegans synthetic multivulva genes prevent ras pathway activation by tightly repressing global ectopic expression of lin-3 EGF. PLoS Genet. 2011 Dec;7(12):e1002418.
    • 106. Topalidou I, Chalfie M. Shared gene expression in distinct neurons expressing common selector genes. Proc Natl Acad Sci USA. 2011 Nov 29;108(48):19258–63.
    • 107. Itzkovitz S, Lyubimova A, Blat IC, Maynard M, van Es J, Lees J, et al. Single-molecule transcript counting of stem-cell markers in the mouse intestine. Nat Cell Biol. Nature Publishing Group; 2011 Nov 27;14(1):106–14.
    • 108. Vargas DY, Shah K, Batish M, Levandoski M, Sinha S, Marras SAE, et al. Single-molecule imaging of transcriptionally coupled and uncoupled splicing. Cell. 2011 Nov 23;147(5):1054–65.
    • 109. Korzelius J, The I, Ruijtenberg S, Prinsen MBW, Portegijs V, Middelkoop TC, et al. Caenorhabditis elegans Cyclin D/CDK4 and Cyclin E/CDK2 Induce Distinct Cell Cycle Re-Entry Programs in Differentiated Muscle Cells. PLoS Genet. Public Library of Science; 2011 Nov 10;7(11):e1002362.
    • 110. Korzelius J, The I, Ruijtenberg S, Prinsen MBW, Portegijs V, Middelkoop TC, et al. Caenorhabditis elegans cyclin D/CDK4 and cyclin E/CDK2 induce distinct cell cycle re-entry programs in differentiated muscle cells. PLoS Genet. 2011 Nov;7(11):e1002362.
    • 111. 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. 2011 Jul;138(14):2915–24.
    • 112. So L-H, Ghosh A, Zong C, Sepúlveda LA, Segev R, Golding I. General properties of transcriptional time series in Escherichia coli. Nat Genet. 2011 Jun;43(6):554–60.
    • 113. Steine EJ, Ehrich M, Bell GW, Raj A, Reddy S, van Oudenaarden A, et al. Genes methylated by DNA methyltransferase 3b are similar in mouse intestine and human colon cancer. J Clin Invest. 2011 May;121(5):1748–52.
    • 114. Larson DR, Zenklusen D, Wu B, Chao JA, Singer RH. Real-time observation of transcription initiation and elongation on an endogenous yeast gene. Science. 2011 Apr 22;332(6028):475–8.
    • 115. Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature. 2011 Apr 7;472(7341):120–4.
    • 116. Little SC, Tkacik G, Kneeland TB, Wieschaus EF, Gregor T. The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized mRNA. PLoS Biol. 2011 Mar;9(3):e1000596.
    • 117. Waks Z, Klein AM, Silver PA. Cell-to-cell variability of alternative RNA splicing. Molecular Systems Biology. 2011;7:506.
    • 118. 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. 2011;7:497.
    • 119. Batish M, Raj A, Tyagi S. Single molecule imaging of RNA in situ. Methods Mol Biol. 2011;714:3–13.
    • 120. Zong C, So L-H, Sepúlveda LA, Skinner SO, Golding I. Lysogen stability is determined by the frequency of activity bursts from the fate-determining gene. Molecular Systems Biology. 2010 Nov 30;6:440.
    • 121. Tan RZ, van Oudenaarden A. Transcript counting in single cells reveals dynamics of rDNA transcription. Molecular Systems Biology. 2010 Apr 13;6:358.
    • 122. To T-L, Maheshri N. Noise can induce bimodality in positive transcriptional feedback loops without bistability. Science. 2010 Feb 26;327(5969):1142–5.
    • 123. Raj A, Rifkin SA, Andersen E, van Oudenaarden A. Variability in gene expression underlies incomplete penetrance. Nature. 2010 Feb 18;463(7283):913–8.
    • 124. Raj A, Tyagi S. Detection of individual endogenous RNA transcripts in situ using multiple singly labeled probes. Meth Enzymol. 2010;472:365–86.
    • 125. Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA. 2009 Jul 14;106(28):11667–72.
    • 126. Lu J, Tsourkas A. Imaging individual microRNAs in single mammalian cells in situ. Nucleic Acids Res. 2009 Jun 10.
    • 127. Raj A, van Oudenaarden A. Single-molecule approaches to stochastic gene expression. Annual review of biophysics. 2009;38:255–70.
    • 128. Zenklusen D, Larson DR, Singer RH. Single-RNA counting reveals alternative modes of gene expression in yeast. Nat Struct Mol Biol. 2008 Dec;15(12):1263–71.
    • 129. Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A, Tyagi S. Imaging individual mRNA molecules using multiple singly labeled probes. Nature Methods. 2008 Oct;5(10):877–9.
    • 130. Maamar H, Raj A, Dubnau D. Noise in gene expression determines cell fate in Bacillus subtilis. Science. 2007 Jul 27;317(5837):526–9.
    • 131. Raj A, Peskin CS, Tranchina D, Vargas DY, Tyagi S. Stochastic mRNA synthesis in mammalian cells. PLoS Biol. 2006 Oct;4(10):e309.
    • 132. Vargas DY, Raj A, Marras SAE, Kramer FR, Tyagi S. Mechanism of mRNA transport in the nucleus. Proc Natl Acad Sci USA. 2005 Nov 22;102(47):17008–13.
    • 133. Levsky JM, Shenoy SM, Pezo RC, Singer RH. Single-cell gene expression profiling. Science. 2002 Aug 2;297(5582):836–40.
    • 134. Femino AM, Fay FS, Fogarty K, Singer RH. Visualization of single RNA transcripts in situ. Science. 1998 Apr 24;280(5363):585–90.