Steven Blue

Senior Research Associate

 

 

Summary

As an undergraduate student at UC Irvine, Steven was a member of Dr. Marcelo Wood’s lab studying the inhibition of histone deacetylation on long-term memory formation and associated drug-seeking behavior in mouse models. In the summer of 2011, he interned at Allergan, Inc., assessing the efficacy of candidate compounds as therapies for macular degeneration. During his graduate studies, Steven conducted research in Dr. Craig Walsh’s lab studying the molecular, energetic, and metabolic triggers underlying programmed cell death signaling pathways.
In 2013, Steven joined Dr. Gene Yeo’s group to study RNA-protein interactions as a part of the ENCODE project. Specifically, he has primarily been characterizing antibodies targeting RNA-binding proteins (RBPs) and using them to reveal novel RBP binding targets via CLIP-seq methods. Additionally, Steven helps with managing the lab and overseeing day-to-day operational activities.Outside of lab, Steven enjoys outdoor activities including rock climbing, hiking, cycling.

 

Education

M.S., Biotechnology, University of California, Irvine, 2012

B.S., Biological Sciences, University of California, Irvine, 2010

 

Contact

sblue@health.ucsd.edu

Publications

  • Blue, S. M., Yee, B. A., Pratt, G. A., Mueller, J. R., Park, S. S., Shishkin, A. A., Starner, A. C., Van Nostrand, E. L., & Yeo, G. W. (2022). Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq. Nature Protocols. https://doi.org/10.1038/s41596-022-00680-z

  • Qin Y, Huttlin E, Winsnes C, Gosztyla ML, Wacheul L, Kelly MR, Blue SM, Zheng F, Chen M, Schaffer LV, Licon K, Bäckström A, Vaites LP, Lee JJ, Ouyang W, Liu SN, Zhang T, Silva E, Park J, Pitea A, Kreisberg JF, Gygi SP, Ma J, Harper JW, Yeo GW, Lafontaine DL, Lundberg E, Ideker T (2021). A multi-scale map of cell structure fusing protein images and interactions. Nature 600, 536–542. https://doi.org/10.1038/s41586-021-04115-9

  • Corley M, Flynn RA, Lee B, Blue SM, Chang HY, Yeo GW. Footprinting SHAPE-eCLIP Reveals Transcriptome-wide Hydrogen Bonds at RNA-protein Interfaces. Molecular Cell, 2020.

  • Batra R, Nelles DA, Roth DM, Krach F, Nutter CA, Tadokoro T, Thomas JD, Sznajder L, Blue SM, Gutierrez H, Liu P, Aigner S, Platoshyn O, Miyanohara A, Marsala M, Swanson MS, Yeo GW. The sustained expression of Cas9 targeting toxic RNAs reverses disease phenotypes in mouse models of myotonic dystrophy type 1. Nature Biomedical Engineering, 2020.

  • Bajaj J, Hamilton M, Shima Y, Chambers K, Spinler K, Van Nostrand E, Yee BA, Blue SM, Chen M, Rizzeri D, Chuah C, Oehler VG, Broome HE, Sasik R, Scott-Browne J, Rao A, Yeo GW, Reya T. An in vivo genome-wide CRISPR screen identifies the RNA-binding protein Staufen2 as a key regulator of myeloid leukemia. Nature Cancer, 2020.

  • Van Nostrand EL, Pratt GA, Yee BA, Wheeler E, Blue SM, Mueller J, Park SS, Garcia KE, Gelboin-Burkhart C, Nguyen TB, Rabano I, Stanton R, Sundararaman B, Wang R, Fu X-D, Graveley BR, Yeo GW. Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins. Genome Biology, 2020.

  • Batra R, Nelles DA, Pirie E, Blue SM, Marina RJ, Wang H, Chaim IA, Thomas JD, Zhang N, Nguyen V, Aigner S, Markmiller S, Xia G, Corbett KD, Swanson MS, Yeo GW. Elimination of Toxic Microsatellite Repeat Expansion RNA by RNA-Targeting Cas9. Cell. 2017 Aug 10.

  • Van Nostrand EL, Nguyen TB, Gelboin-Burkhart C, Wang R, Blue SM, Pratt GA, Louie AL, Yeo GW. Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP). Methods Mol Biol. 2017;1648:177-200. doi: 10.1007/978-1-4939-7204-3_14.

  • Van Nostrand EL, Gelboin-Burkhart C, Wang R, Pratt GA, Blue SM, Yeo GW. CRISPR/Cas9-mediated integration enables TAG-eCLIP of endogenously tagged RNA binding proteins. Methods. 2017 Apr 15;118-119:50-59. doi: 10.1016/j.ymeth.2016.12.007. Epub 2016 Dec 18.

  • Van Nostrand EL, Pratt GA, Shishkin AA, Gelboin-Burkhart C, Fang MY, Sundararaman B, Blue SM, Nguyen TB, Surka C, Elkins K, Stanton R, Rigo F, Guttman M, Yeo GW. Robust transcriptome-wide discovery of RNA-binding protein bindingsites with enhanced CLIP (eCLIP). Nat Methods. 2016 Jun;13(6):508-14. doi: 10.1038/nmeth.3810. Epub 2016 Mar 28.

  • Sundararaman B, Zhan L, Blue SM, Stanton R, Elkins K, Olson S, Wei X, Van, Nostrand EL, Pratt GA, Huelga SC, Smalec BM, Wang X, Hong EL, Davidson JM, Lécuyer E, Graveley BR, Yeo GW. Resources for the Comprehensive Discovery of Functional RNA Elements. Mol Cell. 2016 Mar 17;61(6):903-13. doi: 10.1016/j.molcel.2016.02.012.