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.


Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting. Symmons O, Chang M, Mellis IA, Kalish JM, Park J, Suszták K, Bartolomei MS, Raj A. PLoS Genet. 2019 Jan 9;15(1):e1007874. doi: 10.1371/journal.pgen.1007874. pubmed.


Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation. Bartman CR, Hamagami N, Keller CA, Giardine B, Hardison RC, Blobel GA*, Raj A*. Mol Cell. 2019 Feb 7;73(3):519-532.e4. doi: 10.1016/j.molcel.2018.11.004. * Co-corresponding authors pubmed.

ClampFISH detects individual nucleic acid molecules using click chemistry-based amplification. Rouhanifard SH, Mellis IA, Dunagin M, Bayatpour S, Jiang CL, Dardani I, Symmons O, Emert B, Torre E, Cote A, Sullivan A, Stamatoyannopoulos JA, Raj A. Nat Biotechnol. 2018 Nov 12. doi: 10.1038/nbt.4286. pubmed.

Remodeling of the Collagen Matrix in Aging Skin Promotes Melanoma Metastasis and Affects Immune Cell Motility. Kaur A, Ecker BL, Douglass SM, Kugel CH 3rd, Webster MR, Almeida FV, Somasundaram R, Hayden J, Ban E, Ahmadzadeh H, Franco-Barraza J, Shah N, Mellis IA, Keeney F, Kossenkov A, Tang HY, Yin X, Liu Q, Xu X, Fane M, Brafford P, Herlyn M, Speicher DW, Wargo JA, Tetzlaff MT, Haydu LE, Raj A, Shenoy V, Cukierman E, Weeraratna AT. Cancer Discov. 2019 Jan;9(1):64-81. doi: 10.1158/2159-8290.CD-18-0193. pubmed. a tool for rapid, flexible, crowd-based annotation of images. Hughes AJ, Mornin JD, Biswas SK, Beck LE, Bauer DP, Raj A, Bianco S, Gartner ZJ. Nat Methods. 2018 Aug;15(8):587-590. doi: 10.1038/s41592-018-0069-0. pubmed.

IL-6 Mediates Cross-Talk between Tumor Cells and Activated Fibroblasts in the Tumor Microenvironment. Karakasheva TA, Lin EW, Tang Q, Qiao E, Waldron TJ, Soni M, Klein-Szanto AJ, Sahu V, Basu D, Ohashi S, Baba K, Giaccone ZT, Walker SR, Frank DA, Wileyto EP, Long Q, Dunagin MC, Raj A, Diehl JA, Wong KK, Bass AJ, Rustgi AK. Cancer Res. 2018 Sep 1;78(17):4957-4970. doi: 10.1158/0008-5472.CAN-17-2268. pubmed.

Gene expression distribution deconvolution in single-cell RNA sequencing. Wang J, Huang M, Torre E, Dueck H, Shaffer S, Murray J, Raj A, Li M, Zhang NR. Proc Natl Acad Sci U S A. 2018 Jul 10;115(28):E6437-E6446. doi: 10.1073/pnas.1721085115. pubmed.

SAVER: gene expression recovery for single-cell RNA sequencing. Huang M, Wang J, Torre E, Dueck H, Shaffer S, Bonasio R, Murray JI, Raj A, Li M, Zhang NR. Nat Methods. 2018 Jul;15(7):539-542. doi: 10.1038/s41592-018-0033-z. pubmed.

Torre E, Dueck H, Shaffer S, Gospocic J, Gupte R, Bonasio R, Kim J, Murray J, Raj A. Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH. Cell Syst. 2018 Feb 28;6(2):171-179.e5. doi: 10.1016/j.cels.2018.01.014 PDF, code and stuff, data on GEO.


Mellis IA, Gupte R, Raj A, Rouhanifard SH. Visualizing adenosine-to-inosine RNA editing in single mammalian cells. Nature Methods. 2017 Jun 12. doi: 10.1038/nmeth.4332 PDF, slideboard, code, data.

Shaffer SM, Dunagin MC, Torborg SR, Torre EA, Emert B, Krepler C, Beqiri M, Sproesser K, Brafford PA, Xiao M, Eggan E, Anastopoulos IN, Vargas-Garcia CA, Singh A, Nathanson KL, Herlyn M, Raj A. Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance. Nature. 2017 Jun 7. doi: 10.1038/nature22794 PDF, slidecast, data and code.

Hsu SC, Gilgenast TG, Bartman CR, Edwards CR, Stonestrom AJ, Huang P, Emerson DJ, Evans P, Werner MT, Keller CA, Giardine B, Hardison RC, Raj A, Phillips-Cremins JE, Blobel GA. The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries. Mol Cell. 2017 Apr 6;66(1):102-116.e7. doi: 10.1016/j.molcel.2017.02.027. pubmed.

Casson CN, Doerner JL, Copenhaver AM, Ramirez J, Holmgren AM, Boyer MA, Siddarthan IJ, Rouhanifard SH, Raj A, Shin S. Neutrophils and Ly6Chi monocytes collaborate in generating an optimal cytokine response that protects against pulmonary Legionella pneumophila infection. PLoS Pathog. 2017 Apr 6;13(4):e1006309. doi: 10.1371/journal.ppat.1006309. pubmed.

Coté AJ, Raj A. FISHing Out the Details of CRISPR Genome Tracks. Biophys J. [Perspective] 2017 Mar 28;112(6):1045-1046. doi: 10.1016/j.bpj.2017.02.006. pubmed.

Beck LE, Raj A. Systems biology: Molecular memoirs of a cellular family. Nature. [Perspective] 2017 Jan 5;541(7635):38-39. doi: 10.1038/nature21101. pubmed.


Kotzin JJ, Spencer SP, McCright SJ, Kumar DB, Collet MA, Mowel WK, Elliott EN, Uyar A, Makiya MA, Dunagin MC, Harman CC, Virtue AT, Zhu S, Bailis W, Stein J, Hughes C, Raj A, Wherry EJ, Goff LA, Klion AD, Rinn JL, Williams A, Flavell RA, Henao-Mejia J. The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan. Nature (2016). doi:10.1038/nature19346 pubmed.

Dar RD, Shaffer SM, Singh A, Razooky BS, Simpson ML, Raj A, Weinberger LS. Transcriptional Bursting Explains the Noise-Versus-Mean Relationship in mRNA and Protein Levels. PLoS One 11, e0158298 (2016). pubmed.

Chen F, Wassie AT, Cote AJ, Sinha A, Alon S, Asano S, Daugharthy ER, Chang JB, Marblestone A, Church GM, Raj A, Boyden ES. Nanoscale imaging of RNA with expansion microscopy. Nat. Methods 13, 679–684 (2016). pubmed.

Hsiung CC, Bartman CR, Huang P, Ginart P, Stonestrom AJ, Keller CA, Face C, Jahn KS, Evans P, Sankaranarayanan L, Giardine B, Hardison RC, Raj A, Blobel GA. A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition. Genes Dev. 30, 1423–1439 (2016). pubmed.

Symmons O#, Raj A#. What’s Luck Got to Do with It: Single Cells, Multiple Fates, and Biological Nondeterminism. Molecular Cell 2016, doi:10.1016/j.molcel.2016.05.023. # corresponding authors. PDF.

Caroline R. Bartman, Sarah C. Hsu, Chris C-S. Hsiung, Arjun Raj#, and Gerd A. Blobel#. Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping. Molecular Cell 2016, doi:10.1016/j.molcel.2016.03.007. * equal contributions, # corresponding author. PDF, Slidecast.

Paul Ginart*, Jennifer M. Kalish*, Connie L. Jiang, Alice C. Yu, Marisa S. Bartolomei#, and Arjun Raj#. Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss-of-imprinting mutant. Genes and Development 2016, doi:10.1101/gad.275958.115T. * equal contributions, # corresponding author. PDF, supplement, Outlook from Park and Pfeifer, Data and code, Oligo list, Slidecast.

Cote AJ*, McLeod CM*, Farrell MJ, McClanahan PD, Dunagin MC, Raj A#, Mauck RL#. Single-cell differences in matrix gene expression do not predict matrix deposition. Nature Communications 2016, doi:10.1038/ncomms10865. * equal contributions, # corresponding author; orders randomly chosen. PDF, supplement, Data and code, Slidecast.

Burdick J, Walton T, Preston E, Zacharias A, Raj A, Murray JI. Overlapping cell population expression profiling and regulatory inference in C. elegans. BMC Genomics 2016, doi: 10.1186/s12864-016-2482-z. URL.


Kiwon Lee, Chris C.-S. Hsiung, Peng Huang, Arjun Raj, Gerd A. Blobel. Dynamic enhancer–gene body contacts during transcription elongation. Genes and Development 2015, doi:10.1101/gad.255265.114. URL.

Jie Xu, Xiomara Mercado-López, Jennifer T. Grier, Won-keun Kim, Lauren F. Chun, Edward B. Irvine, Yoandris Del Toro Duany, Alison Kell, Sun Hur, Michael Gale, Jr., Arjun Raj, Carolina B. López. Identification of a Natural Viral RNA Motif That Optimizes Sensing of Viral RNA by RIG-I. mBio 2015, doi:10.1128/mBio.01265-15. URL.

Mellis IA, Raj A. Half dozen of one, six billion of the other: What can small- and large-scale molecular systems biology learn from one another? Genome Research [Perspective piece for 20th anniversary edition] 2015, doi:10.1101/ gr.190579.115. PDF.

Nair G*, Abranches E*, Guedes A, Henrique D#, Raj A#. Heterogeneous lineage marker expression in naive embryonic stem cells is mostly due to spontaneous differentiation. Scientific Reports 2015, doi:10.1038/srep13339. * equal contributions, # corresponding author. PDF, Supplement, Supplementary Tables Repository.

Shaffer SM*, Joshi RP*, Chambers BS, Sterken D, Biaesch AG, Gabrieli DJ, Li Y, Feemster KA, Hensley SE#, Issadore D#, Raj A#. Multiplexed detection of viral infections using rapid in situ RNA analysis on a chip. Lab on a Chip 2015, doi:10.1039/c5lc00459d. * equal contributions, # corresponding author. PDF, Supplement, Sequences, Oligo list, Slidecast.

Shah NA, Levesque MJ, Raj A, Sarkar CA. Robust hematopoietic progenitor cell commitment in a noisy environment via suppression of a conflicting signal. J. Cell Sci 2015, doi:10.1242/jcs.158436. URL.

Padovan-Merhar O, Nair GP, Biaesch A, Mayer A, Scarfone S, Foley SW, Wu AR, Churchman LS, Singh A, Raj A. Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms. Molecular Cell 2015, doi:10.1016/j.molcel.2015.03.005. PDF, PDF+supplement, Data and code, Oligo list, Word cloud, Slidecast.

Cabili MN*#, Dunagin MC*, McClanahan PD, Biaesch A, Padovan-Merhar O, Regev A*, Rinn JL*#, Raj A*#. Localization and abundance analysis of human lncRNAs at single cell and single molecule resolution. Genome Biology 2015, doi:10.1186/s13059-015-0586-4. * equal contributions, # corresponding author. PDF, Supplement, Supplementary datasets Full dataset.

T Walton, E Preston, GP Nair, AL Zacharias, A Raj, JI Murray. The Bicoid Class Homeodomain Factors ceh-36/OTX and unc-30/PITX Cooperate in C. elegans Embryonic Progenitor Cells to Regulate Robust Development. PLOS Genetics 2015, doi:10.1371/journal.pgen.1005003.

Dunagin MC*, Cabili MN*, Rinn JL#, Raj A#. Visualization of lncRNA by Single-Molecule Fluorescence In Situ Hybridization. Meth in Mol Biology 2015, doi:10.1007/978-1-4939-2253-6_1. * equal contributions, # corresponding author. PDF.


Panda D, Pascual-Garcia P, Dunagin M, Tudorb M, Hopkins KC, Xua J, Golda B, Raj A, Capelson M, Cherry S. Nup98 promotes antiviral gene expression to restrict RNA viral infection in Drosophila. PNAS 2014, doi:10.1073/pnas.1410087111 pubmed.

Dimitrova N, Zamudio JR, Jong RM, Soukup D, Resnick R, Sarma K, Ward AJ, Raj A, Lee JT, Sharp PA, Jacks T. LincRNA-p21 Activates p21 In cis to Promote Polycomb Target Gene Expression and to Enforce the G1/S Checkpoint. Molecular Cell 2014, doi:10.1016/j.molcel.2014.04.025 pubmed.

Abranches E, Guedes AM, Moravec M, Maamar H, Svoboda P, Raj A, Henrique D. Stochastic NANOG fluctuations allow mouse embryonic stem cells to explore pluripotency. Development 2014, doi:10.1242/dev.108910 pubmed.

Weis B, Schmidt J, Maamar H, Raj A, Lin H, Tóth C, Riedmann K, Raddatz G, Seitz HK, Ho AD, Lyko F, Linhart HG. Inhibition of intestinal tumor formation by deletion of the DNA methyltransferase 3a. Oncogene 2014, doi:10.1038/onc.2014.114 pubmed.

Ginart P., Raj A. RNA sequencing in situ. Nature Biotechnology 2014 [News and Views], doi:10.1038/nbt.2921 PDF.

Nair, G. An intuitive derivation of the expectation-maximization algorithm. Rajlab, brief communication. PDF.

Facciponte JG, Ugel S, De Sanctis F, Li C, Wang L, Nair G, Sehgal S, Raj A, Matthaiou E, Coukos G, Facciabene A. Tumor endothelial marker 1-specific DNA vaccination targets tumor vasculature. Journal of Clinical Investigation 2014, doi:10.1172/JCI67382. pubmed.

Paralkar VR, Mishra T, Luan J, Yao Y, Kossenkov AV, Anderson SM, Dunagin M, Pimkin M, Gore M, Sun D, Konuthula N, Raj A, An X, Mohandas N, Bodine DM, Hardison RC, Weiss MJ. Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development. Blood 2014, doi:10.1182/blood-2013-12-544494. pubmed.

Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L, McClanahan P, Hendrickson DG, Sauvageau M, Kelley DR, Morse M, Engreitz J, Lander ES, Guttman M, Lodish HF, Flavell R, Raj A, Rinn JL. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nature SMB 2014, doi:10.1038/nsmb.2764. pubmed.


Shaffer, S.M., Wu, M., Levesque, M.J., Raj, A. Turbo FISH: A method for rapid single molecule RNA FISH. PLoS ONE 8(9): e75120, 2013, doi:10.1371/journal.pone.0075120. PDF, protocol, live demo.

Padovan-Merhar, O., Raj, A. Using variability in gene expression as a tool for studying gene regulation. WIREs Syst Biol Med [review article], 2013, doi: 10.1002/wsbm.1243. PDF.

Levesque, M.J., Ginart, P., Wei, Y., Raj, A. Visualizing SNVs to quantify allele-specific expression in single cells. Nature Methods, 2013, doi:10.1038/nmeth.2589. PDF, supplement, slidecast

Nair, G., Walton, T., Murray, J.I.*, Raj, A.* Gene transcription is coordinated with but not dependent on cell divisions during C. elegans embryonic fate specification. Development, 2013, doi:10.1242/dev.098012. (* co-corresponding authors) PDF, supplement, slidecast

Zhang, X., Song, Y., Shah, A.Y., Lekova, V., Raj, A., Huang, L., Behlke, M.A., Tsourkas, A. Quantitative assessment of ratiometric bimolecular beacons as a tool for imaging single engineered RNA transcripts and measuring gene expression in living cells. Nucleic Acids Research, 2013, doi:10.1093/nar/gkt561. link.

Maamar, H., Cabili, N.M., Rinn, J.L., Raj, A. linc-HOXA1 is a non-coding RNA that represses Hoxa1 in cis. Genes and Development, 2013, doi:10.1101/gad.217018.113. PDF, supplement, slidecast

Levesque, MJ, Raj, A Single chromosome transcriptional profiling reveals chromosome-level regulation of gene expression. Nature Methods, 2013, doi:10.1038/nmeth.2372. PDF, PDF + supplement, 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


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

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

Man, I'm getting old...

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.

Gibbons, M. Raj, A. Strichartz, R. S. The Finite Element Method on the Sierpinski Gasket. Constructive Approximation, 2001, 17(4): 561-588, PDF, website.