CURRICULUM VITAE – Samie R. Jaffrey, M.D., Ph.D.
`
`Department of Pharmacology
`Weill Medical College, Cornell University
`1300 York Avenue, Box 70
`
`New York, NY 10065
`
`
`Education
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`Office: (212) 746-6243
`Cell: (917) 589-7401
`Fax: (212) 746-6241
`email: srj2003@med.cornell.edu
`web: www.jaffreylab.org
`
`1999
`1999
`1992
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`M.D., Johns Hopkins University, School of Medicine
`Ph.D. in Neuroscience, Johns Hopkins University School of Medicine
`B.S. in Biology, Massachusetts Institute of Technology
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`2016 – present
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`2012 – present
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`2006 – 2012
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`2001 – 2006
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`1999 – 2001
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`1993 – 1997
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`1989 – 1992
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`Research and Professional Experience
`Greenberg-Starr Professor, Department of Pharmacology, Weill Medical
`College, Cornell University, New York, NY
`Professor of Pharmacology (with tenure), Weill Medical College, Cornell
`University, New York, NY
`Associate Professor of Pharmacology (with tenure), Weill Medical College,
`Cornell University, New York, NY
`Assistant Professor of Pharmacology, Weill Medical College, Cornell
`University, New York, NY
`Postdoctoral Fellow, Johns Hopkins University, School of Medicine,
`Department of Neuroscience
`1. “Chemical biology of protein modifications by nitric oxide”
`2. “Proteomic characterization of nitric oxide signaling”
`Dr. Solomon H. Snyder, postdoctoral advisor
`Graduate student, Johns Hopkins University, School of Medicine,
`Department of Neuroscience
`“Cloning and characterization of proteins that bind and regulate
`neuronal nitric oxide synthase”
`Dr. Solomon H. Snyder, graduate thesis advisor
`Undergraduate thesis research, Department of Biology, Massachusetts
`Institute of Technology
`“Metal binding properties of the HIV-1 RNA-binding protein Tat”
`Dr. Alan Frankel, undergraduate thesis advisor
`Selected Awards and Fellowships
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`2018
`2017
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`American Diabetes Association Visionary Award
`John J. Abel Award in Pharmacology, American Society of Pharmacology and
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`1
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`THORNE - EXHIBIT 1003
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`2017
`2017
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`2014
`2014
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`2013
`2013
`2011
`2009
`2006
`2006
`2006
`2006
`2005
`2003
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`2000
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`1999
`1993
`1989
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`Experimental Therapeutics
`Elected Member, American Society of Clinical Investigation
`Nature Methods “2016 Method of the Year – Epitranscriptome Analysis.” Highlighted the
`foundational role of the first epitranscriptome mapping technology Meyer, K.D., et al.,
`Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near
`stop codons. Cell, 149:1635-1646, 2012
`Siegel Family Award for Outstanding Medical Research
`American Society for Biochemistry and Molecular Biology 2014 Young Investigator
`Award
`NIH EUREKA Award
`Blavatnik Award for Young Scientists, 2013
`Faculty of 1000, All-time top-10 ranked publication (since 2001), for Paige et al., 2011
`NIH Director’s Transformative R01 award
`Postdoctoral Mentoring Award from the Weill Cornell Postdoctoral Association
`Irma T. Hirschl Scholar
`McKnight Foundation Technology Development Award
`Klingenstein Fellow in Neuroscience
`“New York 40 under 40” award, Crane’s New York Business Magazine
`Essel Investigator Award, National Alliance for Research on Schizophrenia and
`Depression
`National Alliance for Research on Schizophrenia and Depression Young
`Investigator Award
`Hans Prochaska Research Prize (Johns Hopkins University)
`Medical Scientist Training Program (Johns Hopkins)
`National Merit Scholar
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`Publications
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`Jaffrey, S.R., Haile, D.J., Klausner, R.D., Harford, J.B. The interaction between the iron-
`responsive element binding protein and its cognate RNA is highly dependent upon both
`RNA sequence and structure. Nucleic Acids Research, 21:4627-4631, 1993.
`Jaffrey, S.R., Cohen, N.A., Rouault, T.A., Klausner, R.D., Snyder, S.H. The iron-
`responsive element binding protein: A target for synaptic actions of nitric oxide. Proc. Natl.
`Acad. Sci. USA., 91:12994-8, 1994.
`Jaffrey, S.R., Snyder, S.H. Nitric oxide: A neural messenger. Annu. Rev. Cell and Dev.
`Biol., 11:471-40, 1995.
`Jaffrey, S.R., Snyder, S.H. PIN: An associated protein inhibitor of neuronal nitric oxide
`synthase. Science, 274:774-7, 1996.
`Zakhary, R., Poss, K.D., Jaffrey, S.R., Ferris, C.D., Tonegawa, S, Snyder, S.H. Targeted
`deletion of heme oxygenase-2 reveals neural role for carbon monoxide. Proc. Natl. Acad.
`Sci. U.S.A., 94:14848-53, 1997.
`Jaffrey, S.R., Snowman, A.M., Eliasson, M.J.L., Cohen, N.A., Snyder, S.H. CAPON: A
`protein associated with neuronal nitric oxide synthase that regulates its interactions with
`PSD95. Neuron, 20:115-24, 1998.
`Snyder, S.H., Jaffrey, S.R., Zakhary, R. Nitric oxide and carbon monoxide: parallel roles
`as neural messengers. Brain Research Reviews, 26:167-175, 1998.
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`13.
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`14.
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`15.
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`Liang, J, Jaffrey, S.R., Guo, W., Snyder, S.H., Clardy, J. Structure of PIN/LC8 dimer with a
`bound peptide. Nature Structural Biology, 6:735-740, 1999.
`Ferris, C.D., Jaffrey, S.R., Sawa, A., Takahashi, M., Brady, S.D., Barrow, R.K., Tysoe,
`S.A., Wolosker, H, Baranano, D, Dore, S, Snyder, S.H. Heme oxygenase-1 prevents cell
`death by regulating cellular iron. Nature Cell Biology, 1:152-157, 1999.
`10. Snyder, S.H., Jaffrey, S.R. Vessels vivified by Akt acting on NO synthase. Nature Cell
`Biology, 1:E95-E96, 1999.
`11. Watkins, C.C., Sawa, A., Jaffrey, S.R., Blackshaw, S., Barrow, R.K., Snyder, S.H., Ferris,
`C.D. Insulin restores neuronal nitric oxide synthase expression and function that is lost in
`diabetic gastropathy. J. Clin. Invest, 106:373-384, 2000.
`12. Fang, M., Jaffrey, S.R.*, Sawa, A., Ye, K., Snyder, S.H. Dexras1: A G-protein coupled to
`neuronal nitric oxide synthase via CAPON. Neuron, 28:183-193, 2000. (*co-first author).
`Jaffrey, S.R., Erdjument-Bromage, H., Ferris, C.D., Tempst, P., Snyder, S.H. Protein S-
`nitrosylation: A physiologic signal for neuronal nitric oxide. Nature Cell Biology, 3:193-197,
`2001.
`Jaffrey, S.R., Snyder, S.H. The biotin switch method for the detection of S-nitrosylated
`proteins. Science STKE, www.stke.org/cgi/content/full/OC_sigtrans;2001/86, 2001.
`Jaffrey, S.R., Benfenati, F, Snowman, A.S., Snyder, S.H. Neuronal nitric oxide synthase
`localization mediated by a ternary complex with synapsin and CAPON. Proc. Natl. Acad.
`Sci. U.S.A., 99:3199-3204, 2002.
`Jaffrey, S.R., Fang, M., Snyder, S.H. Nitrosopeptide mapping: A novel methodology
`reveals S-nitrosylation of Dexras1 on a single cysteine residue. Chem. & Biol., 9:1329-
`1335, 2002.
`17. He, X., Gerona-Navarro, G., Jaffrey, S.R., Ligand discovery using small-molecule
`microarrays. J. Pharm. Exp. Therap., 313:1-7, 2005.
`Jaffrey, S.R. Detection and quantification of protein nitrosothiols. Methods in Enzymology,
`396:105-118, 2005.
`19. Wu, K.Y., Hengst, U, Macosko, E., Cox, L., Urquhart, E., Jeromin, A., Jaffrey, S.R. Local
`translation of RhoA regulates growth cone collapse. Nature, 436:1020-1024, 2005.
`20. Hengst, U., Cox, L.J., Macosko, E.Z., Jaffrey, S.R. Functional and selective RNA
`interference in developing axons and growth cones. Journal of Neuroscience, 26:5727-32,
`2006.
`21. Wu, K., Stessin, A., Kaminetsky, M., Hengst, U., Zippin, J., Buck, J., Levin, L.R., Jaffrey,
`S.R. Soluble adenylyl cyclase is required for netrin-1 signaling in nerve growth cones.
`Nature Neuroscience, 9:1257-1264, 2006.
`22. Paige, J.S., Jaffrey, S.R. Pharmacologic manipulation of nitric oxide signaling: Targeting
`NOS dimerization and protein-protein interactions. Curr. Topics Med. Chem. 7:97-114, 2007.
`23. Hengst, U.H., Jaffrey, S.R. Function and translational regulation of mRNA in developing
`axons. Semin. Cell & Dev. Biol. 18:209-15, 2007. PMCID: PMC3153311
`24. Cox, L.J., Hengst, U., Gurskaya, N.G., Lukyanov, K.A., Jaffrey, S.R. Intra-axonal translation
`and retrograde trafficking of CREB promotes neuronal survival. Nature Cell Biology, 10:149-
`159, 2008. PMCID: PMC3153364
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`25. Paige, J.S., Xu, G., Stancevic, B., Jaffrey, S.R. Nitrosothiol reactivity profiling identifies S-
`nitrosylated proteins with unexpected stability. Chemistry & Biology, 15:1307-1316, 2008.
`PMCID: PMC2628636
`26. Hengst, U., Deglincerti, A., Kim, H.J., Jeon, N.L., Jaffrey, S.R. Axonal elongation triggered
`by stimulus-induced local translation of a polarity complex protein. Nature Cell Biology,
`11:1024-30, 2009. PMCID: PMC2724225
`27. Rivieccio, M.A., Brochier, C., Willis, D.E., Walker, B.A., D’Annibale, M.A., McLaughlin, K.,
`Siddiq, A., Kozikowski, A.P., Jaffrey, S.R, Twiss, J.L., Ratan, R.R., Langley, B. HDAC6 is a
`target for protection and regeneration following injury in the nervous system. Proc. Natl.
`Acad. Sci. USA., 46:19599-19604, 2009. PMCID: PMC2780768
`28. Xu, G., Shin, S.Y., Jaffrey, S.R. Global profiling of protease cleavage sites by
`chemoselective labeling of protein N-termini. Proc. Natl. Acad. Sci. USA., 46:19310-19315,
`2009. PMCID: PMC2780798
`29. Xu, G., Paige, J.S., Jaffrey, S.R. Global analysis of lysine ubiquitination by ubiquitin
`remnant immunoaffinity profiling, Nature Biotechnology, 28:868-873, 2010. PMCID:
`PMC2946519
`30. Shin, S.Y., Almeida, R.D., Gerona-Navarro, G., Bracken, C., Jaffrey, S.R. Assembling
`ligands in situ using bioorthogonal boronate ester synthesis. Chemistry & Biology, 17: 1171-
`1176, 2010. PMCID: PMC3149976
`31. Xu, G., Jaffrey, S.R. N-CLAP: Global Profiling of N-Termini by Chemoselective Labeling of
`the α-Amine of Proteins. Cold Spring Harbor Protocols, doi:10.1101/pdb.prot5528, 2010.
`PMID: 21041401
`32. Cohen, M.S., Bas Orth, C., Kim, H.J. Jeon, N.L., Jaffrey, S.R. Neurotrophin-mediated
`dendrite-to-nucleus signaling revealed by microfluidic compartmentalization of dendrites.
`Proc. Natl. Acad. Sci. USA., 108:11246-11251, 2011. PMCID: PMC3131323
`33. Paige, J.S., Wu, K.Y., Jaffrey, S.R. RNA mimics of green fluorescent protein. Science,
`333:642-646, 2011.
`34. Xu, G., Shin, S.Y., Jaffrey, S.R. Chemoenzymatic labeling of protein C-termini for positive
`selection of C-terminal peptides. ACS Chem Biol, 6:1015-1020, 2011. PMCID: PMC3199308
`35. Xu, G., Jaffrey, S.R. The new landscape of protein ubiquitination. Nature Biotechnology,
`29:1098-1100, 2011. PMCID: PMC324807
`36. Baeza, J.L., de la Torre, B.G., Santiveri, C.M., Almeida, R.D., García-López, M.T., Gerona-
`Navarro, G., Jaffrey, S.R., Jiménez, M.A., Andreu, D., González-Muñiz, R., Martín-Martínez,
`M. Cyclic amino acid linkers stabilizing key loops of brain derived neurotrophic factor.
`Bioorg. Chem. Med. Lett., 22:444-448, 2012.
`37. Cohen, M.S., Ghosh, A.K., Kim, H.J., Jeon, N.L., Jaffrey, S.R. Chemical genetic-mediated
`spatial regulation of protein expression in neurons reveals an axonal function for WldS.
`Chemistry & Biology, 19:179-187, 2012. PMCID: PMC3292772
`38. Walker, B.A., Hengst, U., Kim, H.J., Jeon, N.L., Schmidt, E.F., Heintz, N., Milner, T.A.,
`Jaffrey, S.R., Reprogramming axonal behavior by axon-specific viral transduction. Gene
`Therapy, 19:947-55, 2012. PMCID: PMC3426632
`39. Paige, J.S., Ngyuen-Duc, T., Song, W., Jaffrey, S.R. Fluorescence imaging of cellular
`metabolites with RNA. Science, 335:1194, 2012. PMCID: PMC3303607
`40. Ji, S.-J., Jaffrey, S.R. Intra-axonal translation of SMAD1/5/8 mediates retrograde regulation
`of trigeminal ganglia subtype specification. Neuron, 74:95-107, 2012. PMCID: PMC3328135
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`41. Meyer, K.D., Saletore, Y., Zumbo, P., Elemento, O., Mason, C.E., Jaffrey, S.R.
`Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop
`codons. Cell, 149:1635-1646, 2012. PMCID: PMC3383396
`42. Deglincerti A., Jaffrey, S.R. Insights into the roles of local translation from the axonal
`transcriptome. Open Biology, 2:120079, 2012. PMCID: PMC3390793
`43. Walker, B.A., Ji., S.-J., Jaffrey, S.R. Intra-axonal translation of RhoA promotes axon growth
`inhibition by CSPG. Journal of Neuroscience, 32:14442-7, 2012. PMCID: PMC3509224
`44. Xu, G., Jaffrey, S.R. Comprehensive Profiling of Protein Ubiquitination for Drug Discovery.
`Current Pharmaceutical Design, 19:3315-28. 2013.
`45. Colak, D., Ji, S.-J., Porse, B.T., Jaffrey, S.R. Regulation of axon guidance by
`compartmentalized nonsense mediated mRNA decay. Cell, 6:1252-1265, 2013. PMCID:
`PMC3685487
`46. Strack, R.L., Jaffrey, S.R. New approaches for sensing metabolites and proteins in live cells
`using RNA. Current Opinion in Chemical Biology, 17:651-655, 2013. PMCID: PMC3742595
`47. Hess, M.E., Hess, S., Meyer, K.D., Verhagen, L.A.W., Koch, L., Brönneke, H.S., Dietrich,
`M.O., Jordan, S.D., Saletore, Y., Elemento, O., Belgardt, B.F., Franz, T., Horvath, T.L.,
`Rüther, U., Jaffrey, S.R., Kloppenburg, P., Brüning, J.C. The Fat Mass and Obesity
`Associated (Fto) Gene Regulates Activity of the Dopaminergic Midbrain Circuitry. Nature
`Neuroscience, 16:1042-1048, 2013.
`48. Song, W., Strack, R.L., Jaffrey, S.R. Imaging bacterial protein expression using genetically
`encoded RNA sensors. Nature Methods, 10:873-5, 2013. PMCID: PMC3758421
`49. Xu, G., Jaffrey, S.R. Proteomic Identification of Protein Ubiquitination Events. Biotechnology
`and Genetic Engineering Reviews, 29:73-109, 2013. PMCID: PMC3937853
`50. Curanovic, D., Cohen, M., Slagle, C.E., Singh, I., Leslie, C.S., Jaffrey, S.R. Transcriptome-
`wide profiling of stimulus-induced polyadenylation in living cells using a poly(A) trap. Nature
`Chemical Biology, 9:671-3, 2013. PMCID: PMC3805764
`51. Xu, G., Jiang, X. Jaffrey, S.R. A mental retardation-linked nonsense mutation in cereblon is
`rescued by proteasome inhibition. Journal of Biological Chemistry, 288:29573-29585, 2013.
`PMCID: PMC3795255
`52. Strack, R.L., Disney, M.D., Jaffrey, S.R. A superfolding Spinach2 reveals the dynamic
`nature of trinucleotide repeat-containing RNA. Nature Methods, 10:1219-1224, 2013.
`PMCID: PMC3852148
`53. Gerhardt, J., Tomishima, M.J., Zaninovic, N., Colak, D., Yan, Z., Zhan, Q., Rosenwaks, Z.,
`Jaffrey, S.R., and Schildkraut, C.L. The DNA replication program is altered at the FMR1
`locus in fragile X embryonic stem cells. Molecular Cell, 53:19-31, 2014. PMCID:
`PMC3920742
`54. Strack, R.L., Song, W., Jaffrey, S.R. Using Spinach-based sensors for fluorescence
`imaging of intracellular metabolites and proteins in living bacteria. Nature Protocols, 9:146-
`55, 2014.
`Lundquist, M.R., Storaska, A., Liu, T.-C., Larsen, S.D., Evans, T., Neubig, R.R., Jaffrey,
`S.R. Redox modification of nuclear actin by MICAL-2 regulates SRF signaling. Cell,
`156:563-576, 2014.
`56. Song, W., Strack, R.L., Svensen, N., Jaffrey, S.R. Plug-and-play fluorophores extend the
`spectral properties of Spinach. Journal of the American Chemical Society, 136:1198-201,
`2014. PMCID: PMC3929357
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`57.
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`Ji, S.-J., Jaffrey, S.R. Axonal transcription factors: Novel regulators of growth cone-to-
`nucleus signaling. Developmental Neurobiology, 74:245-258, 2014.
`58. Colak, D., Zaninovic, N., Cohen, M.S., Rosenwaks, Z., Yang, W.-Y., Gerhardt, J., Disney,
`M.D., Jaffrey, S.R. Promoter-bound trinucleotide repeat mRNA drives epigenetic silencing in
`Fragile X syndrome. Science, 343:1002-1005, 2014.
`59. Meyer, K.D., Jaffrey, S.R. The dynamic epitranscriptome: N6-methyladenosine and gene
`expression control. Nature Reviews Molecular Cell Biology, 15:313-26, 2014.
`60. Harkcom, W.T., Ghosh, A.K., Sung, M.S., Matov, A., Brown, K.D., Giannakakou, P., Jaffrey,
`S.R. NAD+ and SIRT3 control microtubule dynamics and reduce susceptibility to anti-
`microtubule agents. Proc. Natl. Acad. Sci. USA., 111:E2443-52, 2014.
`61. Warner, K.D., Chen, M.C., Song, W., Strack, R.L., Thorn, A., Jaffrey, S.R., Ferré-D’Amaré,
`A.R. Structural basis for activity of highly efficient RNA mimics of green fluorescent protein.
`Nature Struct. Mol. Biol., 21:658-663, 2014.
`62. Filonov, G.S., Moon, J.D., Svensen, N, Jaffrey, S.R. Broccoli: Rapid selection of an RNA
`mimic of green fluorescent protein by fluorescence-based selection and directed evolution.
`Journal of the American Chemical Society, 136:16299-16308, 2014.
`63. Jaffrey, S.R. An expanding universe of mRNA modifications. Nature Struct. Mol. Biol.,
`21:945-946, 2014.
`64. Brown, K.D., Maqsood, S., Huang, J.-Y., Pan, Y., Harkcom, W., Li, W., Sauve, A., Verdin,
`E., Jaffrey, S.R. Activation of SIRT3 by the NAD+ precursor nicotinamide riboside protects
`from noise-induced hearing loss, Cell Metabolism, 20:1059-1068, 2014.
`65. Witkin K.L., Hanlon S.E., Strasburger J.A., Coffin J.M., Jaffrey S.R., Howcroft T.K., Dedon
`P.C., Steitz J.A., Daschner P.J., Read-Connole E. RNA editing, epitranscriptomics, and
`processing in cancer progression. Cancer Biol Ther. 16:21-7, 2015.
`66. Strack, R.L., Jaffrey, S.R. Live-cell imaging of mammalian RNAs with Spinach2. Methods in
`Enzymology, 550:129-46, 2015.
`67. You, M., Jaffrey, S.R. Designing optogenetically controlled RNA for regulating biological
`systems. Ann. N.Y. Acad. Sci., 1352:13-9, 2015.
`68. Deglincerti, A., Liu, Y., Colak, D., Hengst, U., Xu, G., Jaffrey, S.R. Coupled local translation
`and degradation regulate growth cone collapse. Nature Communications, 6:6888, doi:
`10.1038/ncomms7888, 2015.
`69. Filonov, G.S. Kam, C.W., Song, W., Jaffrey, S.R. In-gel imaging of RNA processing using
`Broccoli reveals optimal aptamer expression strategies. Chemistry & Biology, 22:649-60,
`2015.
`70. You, M., Litke, J.L., Jaffrey, S.R. Imaging metabolite dynamics in living cells using a
`Spinach-based riboswitch. Proc. Natl. Acad. Sci. USA., 112:E2756-65, 2015.
`Linder, B., Grozhik, A.V., Olarerin-George, A.O., Meydan, C., Mason, C.E., Jaffrey, SR.
`Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome.
`Nature Methods, 12:767-772, 2015.
`Lu, Z., Filonov, G.S., Noto, J.J., Schmidt, C.A., Hatkevich-O’Donnell, T., Wen, Y., Jaffrey,
`S.R., Matera, A.G. Metazoan tRNA introns generate stable circular RNAs. RNA, 21:1554-
`65, 2015.
`73. You, M., Jaffrey, S.R. Structure and Mechanism of RNA Mimics of Green Fluorescent
`Protein. Annual Review of Biophysics, 44:187-206, 2015.
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`74. Liu, Y., Huang, X., He, X., Zhou, Y., Jiang X., Chen-Kiang, S., Jaffrey, S.R., Xu, G. A novel
`effect of thalidomide and its analogs: suppression of cereblon ubiquitination enhances
`ubiquitin ligase function. FASEB J., 29:4829-39, 2015.
`75. Miyawaki, A., Jaffrey, S.R. Editorial overview: Molecular imaging: Cellular imaging
`approaches. Current Opinion in Chemical Biology, 27:v-vi, 2015.
`76. Zhou, J., Wan, J., Gao, X., Zhang, X., Jaffrey, S.R., Qian, S.-B. Dynamic m6A mRNA
`methylation directs translational control of heat shock response. Nature, 526:591-4, 2015.
`77. Meyer, K.D., Patil, D.P., Zhou, J., Zinoviev, A., Skabkin, M.A., Elemento, O., Pestova, T.V.,
`Qian, S.-B., Jaffrey, S.R. 5'UTR m6A promotes cap-independent translation. Cell,
`163:999-1010, 2015.
`78. Svensen, N., Jaffrey, S.R. Fluorescent RNA aptamers as a tool to study RNA-modifying
`enzymes. Cell Chemical Biology, 23:415-25, 2016. Selected for the “Cell Chemical Biology
`Best of 2016” issue.
`79. Frye, M., Jaffrey, S.R., Pan T., Rechavi G., Suzuki T. RNA modifications: what have we
`learned and where are we headed? Nat. Rev. Genetics, 17:365-72, 2016.
`80. Kim, J.Y., Jaffrey, S.R. Separating neuronal compartments gives clues as to local effect of
`ubiquitin conjugates in synaptogenesis. J. Cell Biol., 212:851-3, 2016.
`81. Filonov, G.S., Jaffrey, S.R. RNA Imaging with Dimeric Broccoli in Live Bacterial and
`Mammalian Cells. Curr. Protoc. Chem. Biol., 8:1-28, 2016.
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`82. Meyer, K.D., Jaffrey, S.R. Expanding the diversity of DNA base modifications with N⁶-
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`84.
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`methyldeoxyadenosine. Genome Biol., 17:5, 2016.
`83. Svensen, N., Jaffrey, S.R. Peptide synthesis on a next-generation DNA sequencing
`platform. ChemBioChem, 17:1628-35, 2016.
`Laptenok, S.P., Conyard J., Bulman Page, P.C., Chan Y., You, M., Jaffrey, S.R., Meech,
`S.R. Photoacid Behaviour in a Fluorinated Green Fluorescent Protein Chromophore:
`Ultrafast Formation of Anion and Zwitterion States, Chemical Science, 7:5747-5752, 2016
`85. Yang, W.-Y., He, F., Strack, R., Oh, S. Y., Frazer, M., Jaffrey, S., Todd, P.K., Disney,
`Matthew. Small Molecule Recognition and Tools to Study Modulation of r(CGG)exp in
`Fragile X-Associated Tremor Ataxia Syndrome. ACS Chem Bio., 11:2456-65, 2016.
`86. Wu, J., Jaffrey, S.R. Tracking translation one mRNA at a time. Nature Biotechnology,
`34:723-4, 2016.
`87. Chakraborty, K., Veetil, A.T., Jaffrey, S.R., Krishnan, Y. Nucleic Acid-Based Nanodevices in
`Biological Imaging. Annu. Rev. Biochem., 85:349-73, 2016.
`88. Filonov G.S., Jaffrey S.R. Preface, Methods in Enzymology, 572:xv-xvi, 2016
`89.
`Litke J.L., You M., Jaffrey S.R., Developing Fluorogenic Riboswitches for Imaging
`Metabolite Concentration Dynamics in Bacterial Cells. Methods in Enzymology, 572:315-33,
`2016
`90. Patil, D.P., Chen, C.-K., Pickering, B.F., Chow A., Jackson C., Guttman, M., Jaffrey, S.R.
`m6A RNA methylation promotes XIST-mediated transcriptional repression. Nature, 537:369-
`73, 2016.
`91. Mauer, J., Luo, X., Blanjoie, A., Jiao, X., Grozhik, A.V., Patil, D.P., Vasseur, J.-J., Chen, Q.,
`Gross, S.S., Elemento, O., Debart, F., Kiledjian, M., Jaffrey, S.R. Reversible methylation of
`m6Am in the 5’ cap controls mRNA stability. Nature, 541:371-375, 2017.
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`92. Jaffrey, S.R.*, and Kharas, M.G.* Emerging links between m6A and misregulated mRNA
`methylation in cancer. Genome Medicine, 9:2, 2017.
`93. Olarerin-George A.O., Jaffrey S.R. MetaPlotR: a Perl/R pipeline for plotting metagenes of
`nucleotide modifications and other transcriptomic sites. Bioinformatics, 33:1563-1564, 2017.
`94. Grozhik A.V., Linder B., Olarerin-George A.O., Jaffrey S.R. Mapping m6A at Individual-
`Nucleotide Resolution Using Crosslinking and Immunoprecipitation (miCLIP). Methods
`Molecular Biology, 1562:55-78, 2017.
`95. Kan, L., Grozhik, A.V., Vedanayagam, J., Patil, D.P., Pang, N., Lim, K.-S., Huang, Y.-C.,
`Joseph, B., Lin, C.-J., Despic, V., Guo, J., Yan, D., Kondo, S., Deng, W.-M., Dedon, P.C.,
`Jaffrey, S.R., Lai, E.C. The m6A pathway facilitates sex determination in Drosophila. Nature
`Communications, 8:15737, 2017.
`96. Warner, K.D., Sjekloća, L., Song, W., Filonov, G.S., Jaffrey, S.R., Ferré-D’Amaré, A.R. A
`homodimer interface without base pairs in an RNA mimic of red fluorescent protein. Nature
`Chemical Biology, 13:1195-1201, 2017.
`97. Song, W., Filonov, G.S., Kim, H., Hirsch, M., Li, X., Moon, J. D., Jaffrey, S. R. Imaging RNA
`polymerase III transcription using a photostable RNA-fluorophore complex. Nature Chemical
`Biology, 13:1187-1194, 2017.
`98. Vu, L.P., Pickering, B.F., Cheng, Y., Zaccara, S., Nguyen, D., Minuesa, G., Chou, T., Chow,
`A., Saletore, Y., MacKay, M., Schulman, J., Famulare, C., Patel, M., Klimek, V. M., Garrett-
`Bakelman, F.E., Melnick, A., Carroll, M., Mason, C. E., Jaffrey, S.R.*, and Kharas, M.G.*
`The N6-methyladenosine (m6A)-forming enzyme METTL3 controls myeloid differentiation of
`normal hematopoietic and leukemia cells. Nature Medicine, 23:1369-1376, 2017.
`99. Meyer K.D., Jaffrey S.R. Rethinking m6A Readers, Writers, and Erasers. Annual Review
`of Cell and Developmental Biology, 33:319-342, 2017.
`100. Dumelie, J., Jaffrey S.R. Defining the location of promoter-associated R-loops at near-
`nucleotide resolution using bisDRIP-seq. eLIFE, 6:e28306, 2017
`101. Grozhik, A.V., Jaffrey S.R. Shrinking maps of RNA modifications. Nature, 551:174-176,
`2017.
`102. Kim, J.Y., Deglincerti, A. Jaffrey S.R. Staufen1-mediated decay pathway influences the
`local transcriptome in axons. Translation, 5:e1414016, 2017
`103. Patil, D.P., Pickering, B.F., Jaffrey S.R. Reading m6A in the transcriptome: m6A-binding
`proteins. Trends in Cell Biology, 28:113-127, 2018.
`104. Wu, B., Su, S., Patil, D.P., Liu, H., Gan, J., Jaffrey S.R., Ma, J. Molecular basis for the
`specific and multivariant recognitions of RNA substrates by human hnRNP A2/B1. Nature
`Communications, 9:420, 2018.
`105. Jaffrey S.R. RNA-Based Fluorescent Biosensors for Detecting Metabolites in vitro and in
`Living Cells. Adv. Pharmacology, 82:187-203, 2018
`106. Grozhik, A.V., Jaffrey S.R. Distinguishing RNA modifications from noise in epitranscriptome
`maps. Nature Chemical Biology, 14:215-225, 2018
`107. Mauer J., Jaffrey S.R. FTO, m6Am, and the hypothesis of reversible epitranscriptomic
`mRNA modifications. FEBS Letters, 592:2012-2022, 2018
`108. Jaffrey S.R., Wilkinson M.F. Nonsense-mediated RNA decay in the brain: emerging
`modulator of neural development and disease. Nature Reviews Neuroscience, 19:715-728,
`2018
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`8
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`109. Mauer, J., Sindelar, M., Despic, V., Guez, T., Hawley, B.R., Vasseur, J.-J., Rentmeister, A.,
`Gross, S.S., Pellizzoni, L., Debart, F., Goodarzi, H., Jaffrey, S.R. FTO controls reversible
`m6Am RNA methylation during snRNA biogenesis. Nature Chemical Biology, 15:340-347,
`2019
`110. You, M., Litke, J.L., Wu, R., and Jaffrey, S.R. Detection of Low-Abundance Metabolites in
`Live Cells Using an RNA Integrator. Cell Chemical Biology, 26:471-481, 2019
`111. Litke, J., Jaffrey, S.R. Highly efficient cellular expression of circular RNA aptamers and
`devices using autocatalytic transcripts. Nature Biotechnology, 37:667-675, 2019.
`112. Muthmann, N., Guez, T., Vasseur, J.-J., Jaffrey, S.R., Debart, F., Rentmeister A.
`Combining chemical synthesis and enzymatic methylation to access short RNAs with
`various 5′ caps. ChemBioChem, 20:1693-1700, 2019
`113. Hawley, B.R., Jaffrey, S.R. Simultaneous mapping of m6A and m6Am at single-nucleotide
`resolution using miCLIP. Current Protocols in Molecular Biology, in press, 2019
`114. Filonov, G.S., Song, W., Jaffrey, S.R. Spectral tuning by a single nucleotide controls the
`fluorescence properties of a fluorogenic aptamer. Biochemistry, 58:1560-1564, 2019
`115. Boulias, K., Diana Toczydłowska-Socha, D., Hawley, B.R., Liberman- Isakov, N.,
`Takashima, K., Zaccara, S., Guez, T., Vasseur, J.-J., Debart, F., Aravind, K., Jaffrey, S.R.*,
`Greer, E.L.* Identification of the m6Am methyltransferase PCIF1 reveals the location and
`functions of m6Am in the transcriptome, Molecular Cell, 75:631-643e8, 2019
`116. Ries, R.J., Zaccara, S., Klein, P., Olarerin-George, A., Namkoong, S., Pickering, B.F., Patil,
`D.P., Kwak, H., Lee, J.H., Jaffrey, S.R. m6A enhances the phase separation potential of
`mRNA, Nature, 571:424-428, 2019
`117. Costa, R.O., Martins, H., Martins, L.F., Cwetsch, A.W., Mele, M., Pedro, J.R., Tomé, D.,
`Jeon, N.L., Cancedda, L., Jaffrey, S.R., Almeida, R.D. Synaptogenesis stimulates a
`proteasome-mediated ribosome reduction in axons, Cell Reports, 28:p864-876.e6, 2019
`118. Wu, J., Zaccara, S., Khuperkar, D., Kim, H., Tanenbaum, M.E., Jaffrey, S.R. Live imaging of
`mRNA using RNA-stabilized fluorogenic proteins, Nature Methods, 16:862-865, 2019
`119. Cheng, Y., Luo, H., Izzo, F., Pickering,B.F., Nguyen, D., Myers, R., Schurer, A., Gourkanti,
`S., Brüning, J.C., Vu, L.P., Jaffrey, S.R., Landau, D., Kharas, M.G. RNA methylation
`maintains hematopoietic stem cell identity and symmetric commitment, Cell Reports,
`28:p1703-1716.e6, 2019
`120. van Tran, N., Ernst, F.G.M., Hawley, B.Rr, Zorbas, C., Ulryck, N., Hackert, P., Bohnsack,
`K.E., Bohnsack, M.T., Jaffrey, S.R., Graille, M., Lafontaine, D.L.J. The human 18S rRNA
`m6A methyltransferase METTL5 is stabilized by TRMT112. Nucleic Acids Res, 47:719-7733.
`2019.
`121. Linder, B., Jaffrey, S.R. Discovering and Mapping the Modified Nucleotides That Comprise
`the Epitranscriptome of mRNA. Cold Spring Harb Perspect Biol., 11:pii a032201, 2019.
`122. Dey, S.K., Jaffrey, S.R. RIBOTACs: Small molecules target RNA for degradation. Cell
`Chemical Biology, 26:1047-1049, 2019.
`123. Wang, J., Chew, B.L.A., Lai, Y., Dong, H., Xu, L., Balamkundu, S., Cai, W.M., Cui, L., Liu,
`C.F., Fu, X.-Y., Lin, Z., Shi, P.-Y., Lu, T.K., Luo, D., Jaffrey, S.R., Dedon, P.C. Quantifying
`the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA. Nucleic Acids
`Res, 47:e130. 2019
`124. Kim, H., Jaffrey, S.R. A Fluorogenic RNA-Based Sensor Activated by Metabolite-Induced
`RNA Dimerization. Cell Chem Biol. 26:P1725-1731.E6, 2019.
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`125. Grozhik, A.V., Olarerin-George, A.O., Sindelar, M., Li, X., Gross, S.S., Jaffrey, S.R.
`Antibody cross-reactivity accounts for widespread appearance of m1A in 5'UTRs. Nat
`Commun. 10:5126, 2019
`126. Li, X., Kim, H., Litke, J.L., Wu, J., Jaffrey, S.R. Fluorophore-promoted RNA folding and
`photostability enable imaging of single Broccoli-tagged mRNAs in live mammalian cells.
`Angewandte Chemie Intl. Ed., 59:4511-4518, 2020
`127. McIntyre, A.B.R., Gokhale, N.S., Cerchietti, L., Jaffrey, S.R., Horner, S.M., Mason, C.E.
`Limits in the detection of m6A changes using MeRIP/m6A-seq. Scientific Reports, 10:6590,
`2020.
`128. Zaccara, S., Jaffrey, S.R. A unified model for the function of YTHDF proteins in regulating
`m6A-modified mRNA. Cell, 181:1582-1595, 2020
`129. Wu, J., Jaffrey, S.R. Imaging mRNA trafficking in living cells using fluorogenic proteins.
`Curr. Opinion Cell Biol., 57:177-183, 2020
`130. Li, X., Mo, L., Litke, J.L., Dey, S.K., Suter, S.R., Jaffrey SR. Imaging Intracellular S-
`Adenosyl Methionine Dynamics in Live Mammalian Cells with a Genetically Encoded Red
`Fluorescent RNA-Based Sensor. J. Am. Chem Soc. 142:14117-14124, 2020.
`131. Xi, L., Carroll, T., Matos, I., Luo, J.-D., Polak, L., Pasolli, H.A., Brüning, J.C., Jaffrey, S.R.,
`Fuchs, E. m6A RNA Methylation Impacts Fate Choices during Skin Morphogenesis. eLIFE,
`in press, 2020.
`
`
`
`Book Chapters
`
`
`1. Jaffrey, S.R. “Nitric Oxide, Donors, & Inhibitors,” Basic and Clinical Pharmacology, 10th ed.
`Ed. Bertram G. Katzung. McGraw-Hill (New York, NY), 2006.
`2. Jaffrey, S.R. “Nitric Oxide, Donors, & Inhibitors,” Basic and Clinical Pharmacology, 11th ed.
`Ed. Bertram G. Katzung. McGraw-Hill (New York, NY), 2009.
`3. Jaffrey, S.R. “Nitric Oxide, Donors, & Inhibitors,” Basic and Clinical Pharmacology, 12th ed.
`Ed. Bertram G. Katzung. McGraw-Hill (New York, NY), 2012.
`4. Jaffrey, S.R. “RNA mimics of green fluorescent protein,” McGraw-Hill Yearbook of Science &
`Technology. McGraw-Hill (New York, NY), 2012.
`5. Jaffrey, S.R. “RNA,” in Optical Probes in Biology. Taylor & Francis Group LLC (New York,
`NY), 2013.
`6. Strack, R.L. and Jaffrey, S.R. “Using RNA Mimics of GFP to Image RNA Dynamics in
`Mammalian Cells” in Fluorescence Microscopy: Super-Resolution and other Novel
`Techniques, Elsevier Press, 2014.
`7. Jaffrey, S.R. “Nitric Oxide, Donors, & Inhibitors,” Basic and Clinical Pharmacology, 13th ed.
`Ed. Bertram G. Katzung. McGraw-Hill (New York, NY), 2015.
`8. Jaffrey, S.R. “Nitric Oxide, Donors, & Inhibitors,” Basic and Clinical Pharmacology, 14th ed.
`Ed. Bertram G. Katzung. McGraw-Hill (New York, NY), 2018.
`
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`
`
`Patents
`
`10
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`

`

`
`1. “CAPON: a protein associated with neuronal nitric oxide synthase,” S. H. Snyder, S. R. Jaffrey.
`Patent No. US 6,103,872. Issued, Aug. 15, 2000, Filed Jan. 22, 1998.
`2. “Protein inhibitor of neuronal nitric oxide synthase,” S. H. Snyder, S. R. Jaffrey. Patent No. US
`6,168,926. Issued, Jan. 2, 2001, Filed Dec. 23, 1998.
`3. “Method for assaying Protein Nitrosylation,” S. H. Snyder, S. R. Jaffrey, C. D. Ferris, H.
`Erdjument-Bromage, P. Tempst. Patent No. US 7,001,738. Issued, Feb. 21, 2006, Filed Dec.
`27, 2004.
`4. “Mass spectrometry-based identification of proteins,” S. R. Jaffrey. Patent No. US 7,674,766
`B2, Issued Mar. 9, 2010.
`5. “RNA sequences that induce fluorescence of small molecule fluorophores,” S. R. Jaffrey, R. L.
`Strack, G. Filonov, W. Song. Patent No. US 9,664,676, Issued May 30, 2017.
`6. “Methods for expressing proteins in axons,” Jaffrey, S.R. and Hengst, U.
`PCT/US2009/000118. Priority date: 11-Jan-2008, International filing date: 09-Jan-2009.
`7. “Antibodies for ubiquitinated proteins,” G. Xu and S. R. Jaffrey. Application number:
`12/455,496, Publication number: US 2009/0317409 A1. Filed Jan. 2, 2009.
`8. “Coupled recognition/detection system for in vivo and in vitro use,” S. R. Jaffrey and J. S.
`Paige. PCT US1024622. March 4, 2010.
`9. “Novel methods for RNA detection and quantification,” S. R. Jaffrey and J. S. Paige. U.S.
`Patent No. 9,868,781. Issued Jan 16, 2018.
`10. “Methods and kit for characterizing the modified base of a transcriptome,” S. R. Jaffrey, Kate
`D. Meyer, and Christopher Mason. Publication No. WO2013123481. Aug 22, 2013.
`11. “Use of nicotinamide riboside to treat hearing loss,” K.D. Brown, A.A. Sauve, S. R. Jaffrey.
`U.S. Patent No. 9,861,651. Issued Jan 9, 2018.
`
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`
`Invited Lectures
`Keynote Speaker, 2021 Gordon