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.
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.
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., 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.