Publications
Be sure to check out our slidecasts, which are short recorded talks about the work in the papers. It's faster than reading!
If you are interested in getting started with single molecule RNA FISH yourself, check out this website. It has a lot of information and answers to many common questions.
If you want to count your spots, use this software. It is easy to use and gives good results.
Maamar, H., Cabili, N.M., Rinn, J.L., Raj, A. linc-HOXA1 is a non-coding RNA that represses Hoxa1 in cis. In press, Genes and Development.
Levesque, MJ, Raj, A Single chromosome transcriptional profiling reveals chromosome-level regulation of gene expression. Nature Methods, 2013, doi:10.1038/nmeth.2372. PDF, raw data+supplement+long version, slidecast
Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K, Lee CS, Flockhart RJ, Groff AF, Chow J, Johnston D, Kim GE, Spitale RC, Flynn RA, Zheng GX, Aiyer S, Raj A, Rinn JL, Chang HY, Khavari PA. Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature, 2013, doi:10.1038/nature11661. Link
Mirouze, N., Desai, Y., Raj, A., Dubnau, D. Spo0A-P imposes a temporal gate for the bimodal expression of competence in B. subtilis. PLoS Genetics, 2012, doi:10.1371/journal.pgen.1002586. PDF
Li, Fan; Zheng, Qi; Ryvkin, Paul; Dragomir, Isabelle; Desai, Yaanik; Aiyer, Subhadra; Valladares, Otto; Yang, Jamie; Bambina, Shelly; Sabin, Leah R.; Murray, John I.; Lamitina, Todd; Raj, Arjun; Cherry, Sara; Wang, Li-San; Gregory, Brian D. Global Analysis of RNA Secondary Structure in Two Metazoans. Cell Reports 2012; 1:69-82. PDF with Supplementary Information.
Nair G, Raj A. Time-lapse transcription. Science [perspective]. 2011 Apr 22; 332(6028):431-2. PDF.
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. J Clin Invest. 2011 May 2;121(5):1748-52. doi: 10.1172/JCI43169. PDF, Supplementary Information.
Batish M, Raj A, Tyagi S. Single molecule imaging of RNA in situ. Methods Mol Biol. 2011;714:3-13. PDF.
Raj A, Tyagi S. Detection of individual endogenous RNA transcripts in situ using multiple singly labeled probes. Method in Enzymology 2010; 472: 365-86. PDF.
Raj A*, Rifkin SA*, Andersen E, van Oudenaarden A. Variability in gene expression underlies incomplete penetrance. Nature, Feb 18 2010, doi:10.1038/nature08781 (* equal contributions). PDF, Supplementary Information, Data, Slidecast, News and Views, NPR, Cell Preview, NRC Handelsblad, Nat Rev Gen, Word cloud.
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. PNAS 2009; 106: 11667-72. PDF.
Raj A, van Oudenaarden A. Single-Molecule Approaches to Stochastic Gene Expression [Review article]. Ann. Rev. Biophysics 2009; 38: 255-70. PDF.
Raj A, van Oudenaarden A. Nature, Nurture or Chance: Stochastic Gene Expression and its Consequences [Review article]. Cell 2008; 135(2): 216-226. PDF.
Raj A, van den Boogard P, Rifkin SA, van Oudenaarden A, Tyagi S. Imaging individual mRNA molecules using multiple singly labeled probes. Nature Methods 2008; 5(10): 877-879. PDF, Supplementary material, Software.
To design your own probes, visit singlemoleculefish.com.
Maamar H*, Raj A*, Dubnau D. Noise in Gene Expression Determines Cell Fate in Bacillus Subtilis. Science, 2007 Jul 23; 317(5837): 526-9 (* equal contributions). PDF, Supplementary material, Movies
- Perspective by Mettetal and van Oudenaarden.
Raj A, Peskin CS, Tranchina D, Vargas DY, Tyagi S. Stochastic mRNA Synthesis in Mammalian Cells. PLoS Biol 2006; 4(10): e309. PDF, Supplementary material, Data
Raj A, Peskin CS. The influence of chromosome flexibility on chromosome transport during anaphase A. Proc Natl Acad Sci USA, 2006 Apr 4;103(14): 5349-54. PDF, Supplementary material
Vargas DY, Raj A, Marras SA, Kramer FR, Tyagi S. Mechanism of mRNA transport in the nucleus. Proc Natl Acad Sci USA, 2005 Nov 22;102(47): 17008-13. PDF, Supplementary material
Raj, A., T. Phan, R. P. Lin, and V. Angelopoulos, Wind survey of high-speed bulk flows and field-aligned beams in the near-Earth plasma sheet. J. Geophys. Res. 2002, 107(A12), 1419, PDF.
