Publications & References

Description of method

Other papers using single molecule FISH

  1. Itzkovitz S., Lyubimova A., Blat I. C., 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, in press.
  2.  Middelkoop T. C., Williams L., Yang P. T., Betist M. C., N. Ji, van Oudenaarden A., Kenyon C., Korswagen H. C. The thrombospondin repeat containing protein MIG-21 controls a left-right asymmetric Wnt signaling response in migrating C. elegans neuroblasts. Developmental Biology, in press.
  3. Seidel H. S., Ailion M., J. Li, van Oudenaarden A., Rockman M. V., Kruglyak L. A novel sperm-delivered toxin causes late-stage embryo lethality and transmission ratio distortion in C. elegans. PLoS Biology 9, e1001115 (2011).
  4. Harterink M., Kim D. H., Middelkoop T. C., Doan T. D., van Oudenaarden A., Korswagen H. C. Neuroblast migration along the anteroposterior axis of C. elegans is controlled by opposing gradients of Wnts and a secreted Frizzled-related protein. Development 138, 2915 (2011).
  5. Hebenstreit D., Fang M., Gu M., Charoensawan V., van Oudenaarden A., Teichmann S. A. RNA sequencing reveals two major classes of gene expression levels in metazoan cells. Molecular Systems Biology 7; doi: 10.1038/msb.2011.28 (2011).
  6.  Steine E. J., Ehrich M., Bell G. W., Raj A., Reddy S., van Oudenaarden A., Jaenisch R., Linhart H. G. Genes methylated by DNA methyltransferase 3b are similar in mouse intestine and human colon cancer. Journal of Clinical Investigation 121, 1748 (2011).
  7.  Itzkovitz S., van Oudenaarden A. Validating transcripts with probes and imaging technology. Nature Methods 8, S12 (2011).
  8. Topalidou I., van Oudenaarden A., Chalfie M. Caenorhabditis elegans aristaless/Arx gene alr-1 restricts variable gene expression. PNAS 108, 4063 (2011).
  9. Femino A., Fay F., Fogarty K., Singer R. Visualization of single RNA transcripts in situ. Science, 1998 280(5363) pp. 585-90.
  10. Vargas D., Raj A., Marras S., Kramer F., Tyagi S. Mechanism of mRNA transport in the nucleus. PNAS, 2005 102(47) pp. 17008-13.
  11. Raj A., Peskin C., Tranchina D., Vargas D., Tyagi S. Stochastic mRNA synthesis in mammalian cells. PLoS Biology, 2006 4(10) pp. e309.
  12. Maamar H., Raj A., Dubnau D. Noise in gene expression determines cell fate in B. subtilis. Science, 2007 317(5837) pp. 526-9.
  13. Raj A., Rifkin S.A., Andersen E., van Oudenaarden A. Variability in gene expression underlies incomplete penetrance. Nature, 2010 463(913) p. 913
  14. To T., Maheshri N., Noise can induce bimodality in positive transcriptional feedback loops without bistability. Science, 2010 327(5969), pp. 1142-5
  15. Little C., Tkačik G., Kneeland T., Wieschaus E., Gregor T., The Formation of the Bicoid Morphogen Gradient Requires Protein Movement from Anteriorly Localized mRNA. PLoS Biology, 2011 9(3): e1000596. doi:10.1371/journal.pbio.1000596
  16. Topalidou I., van Oudenaarden A., Chalfie M., Caenorhabditis elegans aristaless/Arx gene alr-1 restricts variable gene expression. PNAS, 2011 108(10): 4063-4068. doi: 10.1073/pnas.1101329108
  17. Nuclear import of APOBEC3F-labeled HIV-1 preintegration complexes. Burdicka, R.C.; Hub, W-S,; Pathaka, V.K. PNAS 2013, doi: 10.1073/pnas.1315996110.
  18. Axonal cap-dependent translation regulates presynaptic p35. Hsiao, K.; Bozdagi, O.; Benson, D.L. Dev Neurobiol. 2014 Mar;74(3):351-64. doi: 10.1002/dneu.22154.
  19. KIF14 Promotes AKT Phosphorylation and Contributes to Chemoresistance in Triple-Negative Breast Cancer. Singel, S.M.; Cornelius, C.; Zaganjor, E; Batten, K.; Sarode, V.R.; Buckley, D.L.; Peng, Y.; John, G.B.; Li, H.C.; Sadeghi, N.; Wright, W.E.; Lum, L,; Corson, T.W.; Shay, J.W. Neoplasia. 2014 Mar;16(3):247-256.e2. doi: 10.1016/j.neo.2014.03.008.
  20. Defining Estrogenic Mechanisms of Bisphenol A Analogs through High Throughput Microscopy-Based Contextual Assays. Stossi, F.; Bolt, M.J.; Ashcroft, F.J.; Lamerdin, J.E.; Melnick, J.S.; Powell, R.T.; Dandekar, R.D.; Mancini, M.G.; Walker, C.L.; Westwick, J.K.; Mancini, M.A. Chemistry & Biology 2014, doi: 10.1016/j.chembiol.2014.03.013.
  21. Identification of a novel multiple kinase inhibitor with potent antiviral activity against influenza virus by reducing viral polymerase activity. Sasaki, Y.; Kakisaka, M.; Chutiwitoonchai, N.; Tajima, S.; Hikono, H.; Saito, T.; Aida, Y. Biochem Biophys Res Commun. 2014 Jul 18;450(1):49-54., doi: 10.1016/j.bbrc.2014.05.058.
  22. LincRNA-p21 Activates p21 In cis to Promote Polycomb Target Gene Expression and to Enforce the G1/S Checkpoint. Dimitrova, N.; Zamudio, JR.; Jong, RM.; Soukup, D.; Resnick, R.; Sarma, K.; Ward, AJ.; Raj, A.; Lee, JT.;  Sharp, PA.; Jacks, T.  Mol Cell. 2014 Jun 5;54(5):777-90, doi: 10.1016/j.molcel.2014.04.025.
  23. The Rhino-Deadlock-Cutoff Complex Licenses Noncanonical Transcription of Dual-Strand piRNA Clusters in Drosophila. Mohn, F.;  Sienski, G.; Handler,  D.; Brennecke, J. Cell. 2014 Jun 5;157(6):1364-1379, doi: 10.1016/j.cell.2014.04.031.
  24. Most Human Proteins Made in Both Nucleus and Cytoplasm Turn Over within Minutes. Baboo, S.; Bhushan, B.; Jiang, H.; Grovenor, CR.; Pierre, P.; Davis, BG.; Cook, PR. PLoS One. 2014 Jun 9;9(6):e99346. doi: 10.1371/journal.pone.0099346.
  25. MicroRNA binding to the HIV-1 Gag protein inhibits Gag assembly and virus production. Chen, AK.; Sengupta, P.; Waki, K.; Van Engelenburg, SB.; Ochiya, T.; Ablan, SD.; Freed, EO.; Lippincott-Schwartz, J. Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):E2676-83, doi: 10.1073/pnas.1408037111.
  26. Lgr5 marks stem/progenitor cells in ovary and tubal epithelia. Ng, A.; Tan, S.; Singh, G.; Rizk, P.; Swathi, Y.; Tan, TZ.; Huang, RY.; Leushacke, M.; Barker, N. Nat Cell Biol. 2014 Aug;16(8):745-57, doi: 10.1038/ncb3000.
  27. Genetic Basis for Saccharomyces cerevisiae Biofilm in Liquid Medium.
    Andersen, KS.; Bojsen, RK.; Sørensen, LG.; Nielsen, MW.; Lisby, M.; Folkesson, A.; Regenberg, B. G3 (Bethesda). 2014 Jul 9, doi: 10.1534/g3.114.010892.
  28. Identification of genes in toxicity pathways of trinucleotide-repeat RNA in C. elegans. Garcia, SM.; Tabach, Y.; Lourenço, GF.; Armakola, M.; Ruvkun, G.Nat Struct Mol Biol. 2014 Aug;21(8):712-20, doi: 10.1038/nsmb.2858.
  29. Hira-Mediated H3.3 Incorporation Is Required for DNA Replication and Ribosomal RNA Transcritpion in the Mouse Zygote. Lin, CJ.; Koh, FM.; Wong, P.; Conti, M.; Ramalho-Santos, M. Dev Cell. 2014, Jul 30, doi: 10.1016/j.devcel.2014.06.022.
  30. The Translational Regulators GCN-1 and ABCF-3 Act Together to Promote Apoptosis in C. elegans. Hirose, T.; Horvitz, HR PLoS Genet  2014, doi: 10.1371/journal.pgen.1004512.
  31. A Gene Regulatory Network Controls the Binary Fate Decision of Rod and Bipolar Cells in the Vertebrate Retina. Wang, S.; Sengel, C.; Emerson, MM.; Cepko, CL. Dev Cell  2014, doi: 10.1016/j.devcel.2014.07.018.
  32. Single yeast cells vary in transcription activity not in delay time after a metabolic shift. Schwabe, A.; Bruggeman, FJ. Nat Commun  2014, doi: 10.1038/ncomms5798.
  33. Nup98 promotes antiviral gene expression to restrict RNA viral infection in Drosophila. Panda, D.; Pascual-Garcia, P.; Dunagin, M.; Tudor, M.; Hopkins, KC.; Xu, J.; Gold, B.; Raj, A.; Capelson, M.; Cherry, S. Proc Natl Acad Sci U S A  2014, doi: 10.1073/pnas.141008711.
  34. Multifunctional roles for the protein translocation machinery in RNA anchoring to the endoplasmic reticulum. Jagannathan, S.; Hsu, JC.; Reid, DW.; Chen, Q.; Thompson, WJ.; Moseley, AM.; Nicchitta, CV. J Biol Chem.  2014, doi: 10.1074/jbc.M114.580688.
  35. Rejuvenation of Meiotic Cohesion in Oocytes during Prophase I Is Required for Chiasma Maintenance and Accurate Chromosome Segregation. Weng, KA.; Jeffreys, CA.; Bickel, SE. PLoS Genet. 2014, doi: 10.1371/journal.pgen.1004607.
  36. The translation elongation factor eEF1A1 couples transcription to translation during heat shock response. Vera, M.; Pani, B.; Griffiths, LA.; Muchardt, C.; Abbott, CM.; Singer, RH.; Nudler, E. Elife. 2014, doi: 10.7554/eLife.03164.
  37. Translational Control of the Oogenic Program by Components of OMA Ribonucleoprotein Particles in Caenorhabditis elegans. Spike, CA.; Coetzee, D.; Nishi, Y.; Guven-Ozkan, T.; Oldenbroek, M.; Yamamoto, I.; Lin, R.; Greenstein, D. Genetics 2014, doi: 10.1534/genetics.114.168823.
  38. Inter- and intratumoral heterogeneity of BCL2 correlates with IgH expression and prognosis in follicular lymphoma. Barreca, A.; Matinengo, C.; Annaratone, L.; Righi, L.; Chiappella, A.; Ladetto, M.; Demurtas, A.; Chiusa, L.; Stacchini, A.; Crosetto, N.; van Oudenaarden, A.; Chiarle, R. Blood Cancer J.  2014, doi: 10.1038/bcj.2014.67.
  39. Luminal signalling links cell communication to tissue architecture during organogenesis. Durdu, S.; Iskar, M.; Revenu, C.; Schieber, N.; Kunze, A.; Bork, P.; Schwab, Y.; Gilmour, D. Nature 2014, doi: 10.1038/nature13852.
  40. Mechanisms of translational repression of the Smcp mRNA in round spermatids. Cullinane, DL.; Chowdhury, TA.; Kleene, KC. Reproduction 2014, doi: 10.1530/REP-14-0394.
  41. Activation of the chicken type I IFN response by infectious bronchitis coronavirus. Kint, J.; Fernandez-Gutierrez, M.; Maier, HJ.; Britton, P.; Langereis, MA.; Koumans, J.; Wiegertjes, GF.; Forlenza, M. Virol. 2014, Nov 5. pii: JVI.02671-14.
  42. Autophagy supports genomic stability by degrading retrotransposon RNA. Guo, H.; Chitiprolu, M.; Gagnon, D.; Meng, L.; Perez-Iratxeta, C.; Lagace, D.; Gibbings, D. Nat. Commun. 2014, doi: 10.1038/ncomms6276.
  43. Kinetic competition during the transcription cycle results in stochastic RNA processing. Coulon, A.; Ferguson, ML.; de Turris, V.; Palangat, M.; Chow, CC.; Larson, DR. Elife. 2014, doi: 10.7554/eLife.03939.
  44. Self-Digitization Microfluidic Chip for Absolute Quantification of mRNA in Single Cells. Thompson, AM.; Gansen, A.; Paguirigan, AL.; Kreutz, JE.; Radich, JP.; Chiu, DT. Anal Chem. 2014, doi: 10.1021/ac5035924.
  45. Proteostatic Control of Telomerase Function through TriC-Mediated Folding of TCAB1. Freund, A.; Zhong, FL.; Venteicher, AS.; Meng. Z.; Veenstra, TD.; Frydman, J.; Artandi, SE. Cell. 2014, doi: 10.1016/j.cell.2014.10.059.
  46. Inside single cells: quantitative analysis with advanced optics and nanomaterials. Cui, Y.; Irudayaraj, J. Wiley Interdiscip Rev Nanomed Nanobiotechnol. 2014, doi: 10.1002/wnan.1321.
  47. Novel Small Leucine-Rich Protein Chondroadherin-like (CHADL) is Expressed in Cartilage and Modulates Chondrocyte Differentiation. Tillgren, V.; Ho, JC.; Onnerfjord, P.; Kalamajski, S. J Biol Chem. 2014, Dec 1. pii: jbc.M114.593541.
  48. Profiling T Cell Activation Using Single-Molecule Fluorescence In Situ Hybridization and Flow Cytometry. Bushkin, Y.; Radford, F.; Pine, R.; Lardizabat, A.; Mangura, BT.; Gennaro, ML.; Tyagi, S. The Journal of Immunology 2014.

Other mentions & references