^ Denotes equal contribution. * Denotes corresponding author.

89] Evidence of altered lipid metabolism in adults with down syndrome and Alzheimer’s disease.
Vu M, Gross T, Lott IT, Doran E, Lee JH, Schupf N, Silverman W, Dang L-H, Bansal S, Li Y, Jayatilake M, Spitale RC, Cheema A, Mapstone M, Alzheimer’s Biomarker Consortium-Down Syndrome (ABC-DS)
In Revision

88] Mutually orthogonal bioconjugation of vinyl nucleosides for RNA metabolic labeling.
Gupta M, Singha M, Rasale D, Zhou Z, Bhandari S, Beasley S, Sakr J, Parker S*, Spitale RC*
In Revision

87] The P522R protective variant of PLCG2 promotes the expression of antigen presentation genes by human microglia in Alzheimer mice.
Claes C*, Danhas EP, Jairaman A, Hasselmann J, Chadarevian JP, Shabestari SK, Lim TE, Hidalgo JLS, Cahalan MD, Spitale RC, Blurton-Jones M*, Davtyan H*
In Revision

86] Exploiting endogenous enzymes for cancer cell-selective metabolic labeling of RNA in vivo.
Beasley S, Nguyen K, England W, Tarapre E, Atwood SX, Spitale RC*
In Revision

85] Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq.
Engle KL, Lo H-Y G, Goering R, Li Y, Spitale RC*, Taliaferro M*

84] aPKC drives cilia-independent Hedgehog signaling to maintain basal cell carcinoma growth.
Nguyen TL, Jeon US, Jhumkhawala V, Tan KC, Kumar V, England WE, Spitale RC, Atwood SX*

83] Long-TUC-seq is a robust method for quantification of metabolically labeled full-length isoforms.
Rahmanian S, Balderrama-Gutierrez G, Wyman D, MCgill CS, Nguyen K, Spitale RC*, Mortazavi A.*

82] Transcriptome-wide combinatorial RNA structure probing in living cells.
Chan D^, Feng C^, England W^, Wyman D, Flynn RA, Wang X, Shi, Y, Mortazavi A, Spitale RC*

81] A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification.
Wyman D^, Balderrama-Gutierrez G^, Reese F, Jiang S, Rahmanian S, Zheng W, Williams B, Trout D, England W, Chu S, Spitale RC, Tenner A, Wold B, Mortazavi*

80] Taylor-made production of pyrimidine nucleoside-5'-monophosphate analogues by highly stabilized mutant uracil phosphoribosyltransferase from Toxoplasma gondii.
Acosta J, Nguyen K, Spitale RC, Lucas JF*
Bioresource Technology 2021 In Press

79] Plaque-associated human microglia accumulate lipid droplets in a chimeric model of Alzheimer’s Disease.
Claes C*, Pascal E, Hasselmann J, Chadarevian JP, Shabestari SK, England WE, Lim TE, Silva JL, Spitale RC, Davtyan H, Blurton-Jones M*
Molecular Neurodegeneration 2021 In Press

78] Huntington’s disease mice and human brain tissue exhibit increased G3BP1 granules and TDP43 mislocalization.
Sanchez I, Nguyen T, England W, Lim RG, Vu A, Miramontes R, Byrne LM, Markmiller S, Lau L, Orellana I, Curtis M, Faull RLM, Yeo G, Fowler C, Reidling J, Wild E, Spitale RC, Thompson L*
Journal of Clinical Investigation 2021 In Press

77] Allele-specific RNA knockdown with a biologically stable and catalytically efficient XNAzyme.
Nguyen K^, Wang Y^, England WE, Chaput JC*, Spitale RC*
Journal of the American Chemical Society 2021 In Press
Highlighted by Nature Chemical Biology LINK

76] Chemical methods for measuring RNA expression with metabolic labeling.
Singha M, Spitalny L, Nguyen K, Vandewalle A, Spitale RC*
WIRES RNA 2021 In Press

75] A biologically stable DNAzyme that efficiently silences gene expression in cells.
Wang Y^, Nguyen K^, Spitale RC, Chaput JC*
Nature Chemistry 2021 In Press
Highlighted by Nature Chemistry LINK
Highlighted by Nature Chemical Biology LINK

74] RNA structure probing to characterize RNA-protein interactions on a low abundance pre-mRNA in living cells.
Bubenik JL, Hale M, McConnell O, Wang E, Swanson MS, Spitale RC, Berglund A*
RNA 2020 In Press

73] Identification of novel regulators of dendrite arborization using cell type-specific RNA metabolic labeling.
Aboukilila M, Sami J, Wang J, England W, Spitale RC, Cleary M*
PLoS ONE 2020 In Press

72] A bump-hole strategy for increased stringency of cell-specific metabolic labeling of RNA.
Nguyen K, Kubota M, del Arco J, Feng C, Singha M, Beasley S, Sakr J, Gandhi S, Blurton-Jones M, Fernández Lucas J, Spitale RC*
ACS Chemical Biology 2020 In Press
Chosen as an ACS Editors' Choice Article

71] Chemical approaches to analyzing RNA structure transcriptome-wide.
England WE, Garfio C, Spitale RC*
ChemBioChem 2020 In Press
Chosen as a Very Important Paper

70] Assaying RNA solvent accessibility in living cells with LASER.
Feng C, Spitale RC*
Methods in Enzymology 2020 In Press

69] Structural disruption of exonic stem-loops immediately upstream of the intron regulates mammalian splicing.
Saha K, England W, Biswas T, Fernandez MM, Spitale RC*, Ghosh G*
Nucleic Acids Research 2020 In Press

68] Chromatin remodeling protein HELLS is dispensable for retinal development but important for retinoblastoma tumor initiation and progression.
Zocchi L, Mehta A, Wu SC, Wu J, Gu Y, Wang J, Suh S, Spitale RC, Benavente CA*
Oncogenesis 2020 In Press

67] An optimized chemical-genetic method for cell-specific metabolic labeling of RNA.
Nainar S, Cuthbert B, Lim NM, England WE, Ke K, Sophal K, Quechol R, Mobley D, Goulding CW, Spitale RC*
Nature Methods 2020 In Press

66] Identification of adenosine-to-inosine RNA editing with acrylonitrile reagents.
Li Y^, Gohl M^, Ke K^, Vanderwal C*, Spitale RC*
Organic Letters 2019

65] Functional conservation of lncRNA JPX despite sequence and structural divergence.
Karner H M, Carmona S, Liu Y, Lin B, Efrhard M, Chan D, Baldi P, Spitale RC, Sun S*
Journal of Molecular Biology 2019 In Press

64] Development of a chimeric model to study and manipulate human microglia in vivo.
Hasselmann J, Coburn MA, England W, Figueroa Velez DX, McQuade A, Tu CH, Shabestari SK, Kolahdouzan M, Claes C, Nakayama T, Azevedo R, Coufal NG, Han CZ, Echecerria K, Cummings BJ, Davtyan H, Glass CK, Healy LM, Gandhi SP, Spitale RC, Blurton-Jones M*
Neuron 2019 In Press

63] Expanding the scope of RNA metabolic labeling with vinyl nucleosides and inverse electron-demand Diels-Alder chemistry.
Kubota M^, Nainar S^, Parker S, England W, Furche F, Spitale RC*
ACS Chemical Biology 2019

62] The DNA modification N6-methyl-2’-deoxyadenosine (m6dA) drives activity-induced gene expression and is required for fear extinction.
Li X, Zhao Q, Wei W, Lin Q, Magnan C, Emami MR, Wearick-Silva LE, Viola TW, Marshall PR, Yin J, Madugalle SU, Wang Z, Nainar S, Vågbø CB, Leighton LJ, Zajaczkowski EL, Grassi-Oliveira R, Bjørås M, Baldi PF, Spitale RC, Bredy TW*
Nature Neuroscience 2019

61] Assaying RNA structure with LASER-Seq.
Zinshteyn B*, Chan D, England W, Feng C, Green R, Spitale RC*
Nucleic Acids Research 2019

60] Biochemical methods for analyzing RNA localization: from one to many.
Li Y^, Ke K^, Spitale RC*
Biochemistry (ACS) 2018
Part of a Biochemistry special issue “Regulating the Central Dogma.”

59] Protected pyrimidine nucleosides for cell-specific metabolic labeling of RNA.
Beasley S, Nguyen K, Fazio M, Spitale RC*
Tetrahedron Letters 2018 In Press

58] Bioorthogonal metabolic labelling of nascent RNA in neurons improves the sensitivity of transcriptome-wide profiling.
Zajaczkowski E, Zhao Q-Y, Zhang Z, Li X, Wei W, Marshall P, Leighton L, Nainar S, Feng C, Spitale RC*, Bredy T*
ACS Chemical Neuroscience 2018 In Press

57] Spatially-restricting bioorthogonal nucleoside biosynthesis enables selective metabolic labeling of the mitochondrial transcriptome.
Nguyen K, Aggarwal M, Feng C, Balderrama G, Fazio M, Mortazavi A, Spitale RC*
ACS Chemical Biology 2018 In Press

56] Improved analysis of RNA localization by spatially-restricted oxidation of RNA-protein complexes.
Li Y, Aggarwal MB, Nguyen K, Ke K, Spitale RC*
Biochemistry (ACS) 2018 In Press
Highlighted in the Biochemistry "News Flash"

55] Facile synthesis and evaluation of a dual-functioning furoyl probe for in-cell SHAPE.
Chan D^, Beasley S^, Zhen Y, Spitale RC*
Bioorganic & Medicinal Chemistry Letters 2018 In Press

54] Light-activated chemical probing of nucleobase solvent accessibility inside cells.
Feng C^, Chan D^, Joseph J, Muuronen M, Coldren WH, Dai N, Correa IR, Furche F, Hadad C, Spitale RC*
Nature Chemical Biology 2018 In Press
Highlighted in "News & Views" at Nature Chemical Biology
Highlighted in "Methods in Brief" at Nature Methods

53] Defining functional structured RNA inside living cells.
Chan D & Spitale RC*
Biochemistry (ACS) 2017 In Press

52] Assaying RNA localization in situ with spatially-restricted nucleobase oxidation.
Li Y, Aggarwal MB, Nguyen K, Ke K, Spitale RC*
ACS Chemical Biology 2017 In Press

51] Experience-dependent neural plasticity, learning, and memory in the era of epitranscriptomics.
Leighton LJ, Ke K, Zajaczkowski E, Edmunds J, Spitale RC, Bredy TW*
Genes, Brain and Behaviour 2017 In Press

50] Assaying RNA structure inside living cells with SHAPE.
Feng C, Chan D, Spitale RC*
Methods in Molecular Biology 2017 1648:247-256

49] High-throughput aptamer discovery through Apta-Seq and its application to genomic SELEX of human ATP aptamers.
Abdelsayed M, Ho B, Vu M, Spitale RC, Luptak A*
ACS Chemical Biology 2017 12(8):2149-2156.

48] EC-tagging allows cell type-specific RNA analysis.
Hida N, Aboukilila M, Burow D, Paul R, Greenberg M, Fazio M, Beasley S, Spitale RC, Cleary M*
Nucleic Acids Research 2017 45(15):e138.

47] Temporal labeling of nascent RNA using photo-click chemistry in live cells.
Nainar S, Kubota M, McNitt C, Tran C, Popik V, Spitale RC*
Journal of the American Chemical Society 2017 139(24):8090-8093.

46] Photo-controlled cell-specific metabolic labeling of RNA.
Feng C^, Li Y^, Spitale RC*
Organic & Biomolecular Chemistry 2017 15(24):5117-5120

45] Initial in vitro functional characterization of serum exosomal microRNAs from patients with metastatic basal cell carcinoma.
Chang J, Tran DC, Zhu GA, Li R, Whitson R, Kim YH, Gupta A, Afshari A, Antes T, Spitale RC*, Chang ALS*
British Journal of Dermatology 2017 In Press

44] Comparative analysis reveals furoyl in vivo SHAPE reagents form stable ribosyl ester adducts.
Chan D, Feng C, Zhen Y, Flynn RA, Spitale RC*
Biochemistry (ACS) 2017 56(13):1811-1814

43] MotifMap-RNA: A comprehensive map of RBP binding sites.
Yu L, Sun S, Wood M, Bredy TW, Spitale RC*, Baldi P*
Bioinformatics 2017 33(13):2029-2031.

[ MotifMap-RNA Web Server ]

42] Measuring RNA structure transcriptome-wide with icSHAPE.
Chan D, Feng C, Spitale RC*
Methods 2017 120:85-90

41] Cell-selective bioorthogonal metabolic labeling of RNA.
Nguyen K^, Fazio M^, Kubota M, Feng C, Nainar S, Li X, Atwood SX, Bredy TW, Spitale RC*
Journal of the American Chemical Society 2017 139(6):2148-2151

40] Novel gene expression profile of women with intrinsic skin youthfulness by whole-transcriptome sequencing.
Xu J, Spitale RC, Guan LL, Flynn RA, Torre EA, Li R, Raber I, Qu K, Kern D, Knaggs HE, Chang HY, Chang ALS*
PLoS ONE 2016 9;11(11).

39] Evolving insights into the qualitative nature of RNA and its functional diversity in the brain.
Nainar S, Marshall P, Spitale RC*, Bredy T*
Nature Neuroscience 2016 19(10):1292-8.

38] Metabolic incorporation of azide functionality into cellular RNA.
Nainar S, Beasley S, Fazio M, Kubota M, Spitale RC*
ChemBioChem 2016 17(22):2149-2152.

37] Chemical tools for dissecting the role of lncRNAs in epigenetic regulation.
Nainar S, Feng C, Spitale RC*
ACS Chemical Biology 2016 11(8):2091-100.

36] Defining the identity of mouse embryonic dermal fibroblasts.
Budnick I, Hamburg-Shields E, Chen D, Torre E, Jarrell A, Akhtar-Zaidi B, Cordovan O, Spitale RC, Scacheri P, Atit R*
Genesis 2016 54(8):415-30.

35] The CDKN2A/p16INK4a 5'UTR sequence and translational regulation: impact of novel variants predisposing to melanoma.
Andreotti V, Bisio A, Bressac de-Paillerets B, Harland M, Cabaret O, Newton-Bishop J, Pastorino L, Bruno W, Bertorelli R, De Sactis V, Menin C, Fronza G, Queirolo P, Spitale RC, Bianchi-Scarra G, Inga A*, Ghiorzo P.*
Pigment Cell & Melanoma Research 2016 29(2):210-21.

34] Progress and challenges for chemical probing of RNA structure inside living cells.
Kubota M, Tran C, Spitale RC*
Nature Chemical Biology 2015 11(12):933-41.

33] The 5'-untranslated region of p16INK4a melanoma tumor suppressor acts as a cellular IRES, controls mRNA translation during hypoxic stress, and is a target of YBX1.
Bisio A, Latorre E, Ghiorzo P, Spitale RC, Provenzani A*, Inga A*
Oncotarget 2015 6(37):39980-94.

32] The emerging functions of regulatory RNA species in skin biology.
Beasley S, Pilkus M, Spitale RC*, Petersen I*
Experimental Dermatology 2015 24(11):827-8.

31] Merging chemistry and genomics to gain a holistic perspective on RNA structure.
Kubota M, Chan D, Spitale RC*
Bioessays 2015 37(10):1129-38.
This article was chosen as an "Issue Highlight" by Bioessays
Highlighted by Chemistry Views

30] Assessment of the genetic basis of rosacea by genome-wide association study.
Chang AL*, Raber I, Xu J, Li R, Spitale RC, Chen J, Kiefer AK, Tian C, Eriksson NK, Hinds DA, Tung JY.
Journal of Investigative Dermatology 2015 135(6):1548-55.

29] Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics.
Liberman JA , Suddala KC, Aytenfisu A , Chan D, Belashov I, Salim M, Mathews DH , Spitale RC , Walter NG, Wedekind JE*
Proceedings of the National Academy of Sciences 2015

28] Technologies to probe functions and mechanisms of long noncoding RNAs.
Chu C, Spitale RC*, Chang HY*
Nature Structural & Molecular Biology 2015 22(1):29-35.

27] Molecular targets of aspirin and cancer prevention.
Alfonso L, Ai G, Spitale RC, Bhat GJ*
British Journal of Cancer 2014 111(1):61-7.

Papers from the Rob Spitale (University of Rochester and Stanford University)

26] The genetic architecture of age-dependent human pancreatic cell maturation.
Arda HE, Tsai J, Li L, Torre EA, Rosli Y, Spitale RC, Dai C, Qu K, Wang P, Wang J, Grompe M, Scharfmann R, Snyder MS, Bottino R, Powers A, Chang HY, Kim S*
Cell Metabolism 2016 23(5):909-20.

25] icSHAPE: transcriptome-wide interrogation of RNA secondary structure in living cells.
Flynn RA, Zhang QC, Spitale RC, Lee B, Mumbach M, Chang HY*
Nature Protocols 2015 11(2):273-90

24] Assessment of the genetic basis of rosacea by genome-wide association study.
Chang AL, Raber I, Xu J, Li R, Spitale RC, Chen J, Kiefer AK, Tian C, Eriksson NK, Hinds DA, Tung JY.
Journal of Investigative Dermatology 2015 135(6):1548-55.

23] Technologies to probe functions and mechanisms of long noncoding RNAs.
Chu C, Spitale RC*, Chang HY*
Nature Structural & Molecular Biology 2015 22(1):29-35.

22] Dynamic landscape of RNA structures in vivo reveals principles of post-transcriptional regulation.
Spitale RC, Flynn RA, Zhang QC, Crisalli P, Jung J-W, Kuchelmeister H, Torre EA, Batista PJ, Kool ET, Chang HY
Nature 2015 519(7544):486-90.
Highlight in Nature Reviews Genetics
Highlight in Nature Methods

21] Dissecting non-coding and pathogen RNA-protein interactomes.
Flynn RA, Martin LR, Spitale RC, Sarnow P, Sagan S, & Chang HY
RNA 2015 (1):135-43.
Highlight in Nature Reviews Genetics

20] RNA helicase DDX21 coordinates transcription and noncoding RNA processing of the ribosomal pathway.
Calo-Velazquez E, Flynn RA, Martin L, Spitale RC, Chang HY, Wysocka J
Nature 2014 Nov 24. doi: 10.1038/nature13923.

19] RNA structural analysis by evolving SHAPE chemistry.
Spitale RC, Flynn RA, Torre EA, Kool ET, Chang HY
WIRES RNA 2014 Nov-Dec;5(6):867-81

18] Landscape and variation of RNA secondary structure across the human transcriptome.
Wan Y, Qu K, Zhang QC, Flynn RA, Manor O, Ouyang Z, Zhang J, Spitale RC, Snyder MP, Segal E, Chang HY.
Nature 2014 Jan 30;505(7485):706-9.
Link to paper

17] Tandem stem-loops in roX RNAs act together to mediate X chromosome dosage compensation in Drosophila.
Ilik IA, Quinn JJ, Georgiev P, Tavares-Cadete F, Maticzka D, Toscano S, Wan Y, Spitale RC, Luscombe N, Backofen R, Chang HY, Akhtar A.
Molecular Cell 2013 Jul 25;51(2):156-73.
Highlight in Molecular Cell

16] Control of somatic tissue differentiation by the long non-coding RNA TINCR.
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.
Nature 2013 Jan 10;493(7431):231-5.
Highlight in F1000 Prime

15] RNA SHAPE analysis in living cells.
Spitale RC, Crisalli P, Flynn RA, Torre EA, Kool ET, Chang HY.
Nature Chemical Biology 2013 Jan;9(1):18-20.
Highlight in Nature Methods
Highlight in F1000
Highlight in Biotechniques

14] Differential effects of dietary supplements on metabolomic profile of smokers versus non-smokers.
Spitale RC, Cheng MY, Chun KA, Gorell ES, Munoz CA, Kern DG, Wood SM, Knaggs HE, Wulff J, Beebe KD, Chang AL.
Genome Medicine 2012 Feb 23;4(2):14.

13] Understanding the transcriptome through RNA structure.
Wan Y, Kertesz M, Spitale RC, Segal E, Chang HY.
Nature Reviews Genetics 2011 Aug 18;12(9):641-55.

12] RNA templating the epigenome: long noncoding RNAs as molecular scaffolds.
Spitale RC, Tsai MC, Chang HY.
Epigenetics 2011 May;6(5):539-43.

11] Long intergenic noncoding RNAs: new links in cancer progression.
Tsai MC, Spitale RC, Chang HY.
Cancer Research 2011 Jan 1;71(1):3-7.

10] Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation.
Guo M, Spitale RC, Volpini R, Krucinska J, Cristalli G, Carey PR, Wedekind JE.
Journal of the American Chemical Society 2009 Sep 16;131(36):12908-9.
Cited as a "Science and Technology Highlight" by C&E News

9] Single-atom imino substitutions at A9 and A10 reveal distinct effects on the fold and function of the hairpin ribozyme catalytic core.
Spitale RC, Volpini R, Mungillo MV, Krucinska J, Cristalli G, Wedekind JE.
Biochemistry (ACS) 2009 Aug 25;48(33):7777-9.
Chosen as a "Hot Paper" by Biochemistry

8] Exploring ribozyme conformational changes with X-ray crystallography.
Spitale RC, Wedekind JE.
Methods 2009 Oct;49(2):87-100.

7] Identification of an imino group indispensable for cleavage by a small ribozyme.
Spitale RC, Volpini R, Heller MG, Krucinska J, Cristalli G, Wedekind JE.
Journal of the American Chemical Society 2009 May 6;131(17):6093-5.

6] The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain.
Spitale RC, Torelli AT, Krucinska J, Bandarian V, Wedekind JE.
Journal of Biological Chemistry 2009 Apr 24;284(17):11012-6.
Highlited in JBC as the "Paper of the Week"
Rob Spitale and Andrew Torelli Highlight

5] Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme.
Torelli AT, Spitale RC, Krucinska J, Wedekind JE.
Biohemical and Biophysical Research Communications 2008 Jun 20;371(1):154-8.

4] Efficient syntheses of 5'-deoxy-5'-fluoroguanosine and -inosine.
Spitale RC, Heller MG, Pelly AJ, Wedekind JE.
Journal of Organic Chemistry 2007 Oct 26;72(22):8551-4.

3] A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme.
MacElrevey C, Spitale RC, Krucinska J, Wedekind JE.
Acta Crystallogr D Biol Crystallogr. 2007 Jul;63(Pt 7):812-25.

2] Single Step Synthesis of Functional Organic Receptors via a Tri-directional Minisci Reaction.
Palde PB, McNaughton BR, Ross NT, Gareiss PC, Mace CR, Spitale RC, Miller, BL
Synthesis 2007(15): 2287-2290

1] Improved and Highly Versatile Synthesis of 5-Aryltropones.
Potenziano J, Spitale RC, Janik, ME
Synthetic Communications 2005 35:15, 2005-2016