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Robert Spitale - Publications

Affiliations: 
Stanford University, Palo Alto, CA 
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56 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Nguyen K, Kubota M, Arco JD, Feng C, Singha M, Beasley S, Sakr J, Gandhi SP, Blurton-Jones M, Fernández Lucas J, Spitale RC. A Bump-Hole Strategy for Increased Stringency of Cell-Specific Metabolic Labeling of RNA. Acs Chemical Biology. PMID 33222436 DOI: 10.1021/acschembio.0c00755  0.56
2019 Karner HM, Webb CH, Carmona S, Liu Y, Lin B, Erhard M, Chan D, Baldi P, Spitale RC, Sun S. Functional Conservation of lncRNA JPX despite Sequence and Structural Divergence. Journal of Molecular Biology. PMID 31518612 DOI: 10.1016/j.jmb.2019.09.002  0.88
2019 Kubota M, Nainar S, Parker SM, England W, Furche F, Spitale RC. Expanding the Scope of RNA Metabolic Labeling with Vinyl Nucleosides and Inverse Electron-Demand Diels-Alder Chemistry. Acs Chemical Biology. PMID 31310712 DOI: 10.1021/acschembio.9b00079  0.56
2018 Beasley S, Nguyen K, Fazio M, Spitale RC. Protected pyrimidine nucleosides for cell-specific metabolic labeling of RNA. Tetrahedron Letters. 59: 3912-3915. PMID 31031425 DOI: 10.1016/j.tetlet.2018.09.040  0.44
2018 Zinshteyn B, Chan D, England W, Feng C, Green R, Spitale RC. Assaying RNA structure with LASER-Seq. Nucleic Acids Research. PMID 30476193 DOI: 10.1093/nar/gky1172  0.88
2018 Zajaczkowski EL, Zhao QY, Zhang ZH, Li X, Wei W, Marshall PR, Leighton LJ, Nainar S, Feng C, Spitale RC, Bredy TW. Bioorthogonal metabolic labelling of nascent RNA in neurons improves the sensitivity of transcriptome-wide profiling. Acs Chemical Neuroscience. PMID 29874042 DOI: 10.1021/acschemneuro.8b00197  0.48
2018 Nguyen K, Aggarwal MB, Feng C, Balderrama G, Fazio M, Mortazavi A, Spitale RC. Spatially-Restricting Bioorthogonal Nucleoside Biosynthesis Enables Selective Metabolic Labeling of the Mitochondrial Transcriptome. Acs Chemical Biology. PMID 29756767 DOI: 10.1021/acschembio.8b00262  0.48
2018 Feng C, Chan D, Joseph J, Muuronen M, Coldren WH, Dai N, Corrêa IR, Furche F, Hadad CM, Spitale RC. Light-activated chemical probing of nucleobase solvent accessibility inside cells. Nature Chemical Biology. 14: 325. PMID 29443971 DOI: 10.1038/nchembio0318-325  0.88
2018 Chan D, Beasley S, Zhen Y, Spitale RC. Facile synthesis and evaluation of a dual-functioning furoyl probe for in-cell SHAPE. Bioorganic & Medicinal Chemistry Letters. PMID 29398542 DOI: 10.1016/j.bmcl.2018.01.042  0.88
2018 Feng C, Chan D, Joseph J, Muuronen M, Coldren WH, Dai N, Corrêa IR, Furche F, Hadad CM, Spitale RC. Light-activated chemical probing of nucleobase solvent accessibility inside cells. Nature Chemical Biology. PMID 29334380 DOI: 10.1038/nchembio.2548  0.88
2017 Chan D, Spitale RC. Defining Functional Structured RNA inside Living Cells. Biochemistry. PMID 29064690 DOI: 10.1021/acs.biochem.7b00816  0.88
2017 Feng C, Chan D, Spitale RC. Assaying RNA Structure Inside Living Cells with SHAPE. Methods in Molecular Biology (Clifton, N.J.). 1648: 247-256. PMID 28766302 DOI: 10.1007/978-1-4939-7204-3_18  0.88
2017 Hida N, Aboukilila MY, Burow DA, Paul R, Greenberg MM, Fazio M, Beasley S, Spitale RC, Cleary MD. EC-tagging allows cell type-specific RNA analysis. Nucleic Acids Research. PMID 28641402 DOI: 10.1093/nar/gkx551  0.44
2017 Feng C, Li Y, Spitale RC. Photo-controlled cell-specific metabolic labeling of RNA. Organic & Biomolecular Chemistry. PMID 28569333 DOI: 10.1039/c7ob01009e  0.48
2017 Nainar S, Kubota M, McNitt CD, Tran C, Popik VV, Spitale RC. Temporal Labeling of Nascent RNA Using Photo-click Chemistry in Live Cells. Journal of the American Chemical Society. PMID 28562039 DOI: 10.1021/jacs.7b03121  0.56
2017 Chan D, Feng C, Spitale RC. Measuring RNA Structure Transcriptome-Wide with icSHAPE. Methods (San Diego, Calif.). PMID 28336307 DOI: 10.1016/j.ymeth.2017.02.010  0.88
2017 Liu Y, Sun S, Bredy T, Wood M, Spitale RC, Baldi P. MotifMap-RNA: a genome-wide map of RBP binding sites. Bioinformatics (Oxford, England). PMID 28334276 DOI: 10.1093/bioinformatics/btx087  0.32
2017 Chan D, Feng C, Zhen Y, Flynn R, Spitale RC. Comparative Analysis Reveals Furoyl In Vivo SHAPE Rea-gents Form Stable Ribosyl Ester Adducts. Biochemistry. PMID 28319368 DOI: 10.1021/acs.biochem.7b00128  0.88
2017 Nguyen K, Fazio M, Kubota M, Nainar S, Feng C, Li X, Atwood SX, Bredy T, Spitale RC. Cell-Selective Bioorthogonal Metabolic Labeling of RNA. Journal of the American Chemical Society. PMID 28139910 DOI: 10.1021/jacs.6b11401  0.56
2016 Xu J, Spitale RC, Guan L, Flynn RA, Torre EA, Li R, Raber I, Qu K, Kern D, Knaggs HE, Chang HY, Chang AL. Novel Gene Expression Profile of Women with Intrinsic Skin Youthfulness by Whole Transcriptome Sequencing. Plos One. 11: e0165913. PMID 27829007 DOI: 10.1371/journal.pone.0165913  0.36
2016 Nainar S, Marshall PR, Tyler CR, Spitale RC, Bredy TW. Evolving insights into RNA modifications and their functional diversity in the brain. Nature Neuroscience. 19: 1292-8. PMID 27669990 DOI: 10.1038/nn.4378  0.56
2016 Nainar S, Beasley S, Fazio M, Kubota M, Dai N, Corrêa IR, Spitale R. Metabolic Incorporation of Azide Functionality into Cellular RNA. Chembiochem : a European Journal of Chemical Biology. PMID 27595557 DOI: 10.1002/cbic.201600300  0.56
2016 Nainar S, Feng C, Spitale RC. Chemical tools for dissecting the role of lncRNAs in epigenetic regulation. Acs Chemical Biology. PMID 27267401 DOI: 10.1021/acschembio.6b00366  0.56
2016 Arda HE, Li L, Tsai J, Torre EA, Rosli Y, Peiris H, Spitale RC, Dai C, Gu X, Qu K, Wang P, Wang J, Grompe M, Scharfmann R, Snyder MS, et al. Age-Dependent Pancreatic Gene Regulation Reveals Mechanisms Governing Human β Cell Function. Cell Metabolism. PMID 27133132 DOI: 10.1016/j.cmet.2016.04.002  0.56
2016 Flynn RA, Zhang QC, Spitale RC, Lee B, Mumbach MR, Chang HY. Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE. Nature Protocols. 11: 273-90. PMID 26766114 DOI: 10.1038/nprot.2016.011  0.56
2015 Andreotti V, Bisio A, Bressac-de Paillerets B, Harland M, Cabaret O, Newton-Bishop J, Pastorino L, Bruno W, Bertorelli R, De Sanctis V, Provenzani A, Menin C, Fronza G, Queirolo P, Spitale RC, et al. The CDKN2A/p16(INK) (4a) 5'UTR sequence and translational regulation: impact of novel variants predisposing to melanoma. Pigment Cell & Melanoma Research. PMID 26581427 DOI: 10.1111/pcmr.12444  0.56
2015 Kubota M, Tran C, Spitale RC. Progress and challenges for chemical probing of RNA structure inside living cells. Nature Chemical Biology. 11: 933-41. PMID 26575240 DOI: 10.1038/nchembio.1958  0.56
2015 Spitale RC, Flynn RA, Zhang QC, Crisalli P, Lee B, Jung JW, Kuchelmeister HY, Batista PJ, Torre EA, Kool ET, Chang HY. Erratum: Structural imprints in vivo decode RNA regulatory mechanisms. Nature. PMID 26416736 DOI: 10.1038/nature15717  0.36
2015 Beasley SM, Plikus MV, Spitale RC, Pedersen IM. The emerging functions of regulatory RNA species in skin biology. Experimental Dermatology. 24: 827-8. PMID 26309056 DOI: 10.1111/exd.12850  0.56
2015 Kubota M, Chan D, Spitale RC. RNA structure: Merging chemistry and genomics for a holistic perspective. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 37: 1129-38. PMID 26288173 DOI: 10.1002/bies.201300146  0.88
2015 Liberman JA, Suddala KC, Aytenfisu A, Chan D, Belashov IA, Salim M, Mathews DH, Spitale RC, Walter NG, Wedekind JE. Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics. Proceedings of the National Academy of Sciences of the United States of America. PMID 26106162 DOI: 10.1073/pnas.1503955112  0.56
2015 Spitale RC, Flynn RA, Zhang QC, Crisalli P, Lee B, Jung JW, Kuchelmeister HY, Batista PJ, Torre EA, Kool ET, Chang HY. Structural imprints in vivo decode RNA regulatory mechanisms. Nature. 519: 486-90. PMID 25799993 DOI: 10.1038/nature14263  0.56
2015 Chang AL, Raber I, Xu J, Li R, Spitale R, Chen J, Kiefer AK, Tian C, Eriksson NK, Hinds DA, Tung JY. Assessment of the genetic basis of rosacea by genome-wide association study. The Journal of Investigative Dermatology. 135: 1548-55. PMID 25695682 DOI: 10.1038/jid.2015.53  0.56
2015 Chu C, Spitale RC, Chang HY. Technologies to probe functions and mechanisms of long noncoding RNAs. Nature Structural & Molecular Biology. 22: 29-35. PMID 25565030 DOI: 10.1038/nsmb.2921  0.56
2015 Calo E, Flynn RA, Martin L, Spitale RC, Chang HY, Wysocka J. RNA helicase DDX21 coordinates transcription and ribosomal RNA processing. Nature. 518: 249-53. PMID 25470060 DOI: 10.1038/nature13923  0.56
2015 Flynn RA, Martin L, Spitale RC, Do BT, Sagan SM, Zarnegar B, Qu K, Khavari PA, Quake SR, Sarnow P, Chang HY. Dissecting noncoding and pathogen RNA-protein interactomes. Rna (New York, N.Y.). 21: 135-43. PMID 25411354 DOI: 10.1261/rna.047803.114  0.56
2015 Kubota M, Chan D, Spitale RC. RNA structure: Merging chemistry and genomics for a holistic perspective Bioessays. DOI: 10.1002/bies.201300146  0.56
2014 Spitale RC, Flynn RA, Torre EA, Kool ET, Chang HY. RNA structural analysis by evolving SHAPE chemistry. Wiley Interdisciplinary Reviews. Rna. 5: 867-81. PMID 25132067 DOI: 10.1002/wrna.1253  0.56
2014 Wan Y, Qu K, Zhang QC, Flynn RA, Manor O, Ouyang Z, Zhang J, Spitale RC, Snyder MP, Segal E, Chang HY. Landscape and variation of RNA secondary structure across the human transcriptome. Nature. 505: 706-9. PMID 24476892 DOI: 10.1038/nature12946  0.56
2013 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. Tandem stem-loops in roX RNAs act together to mediate X chromosome dosage compensation in Drosophila. Molecular Cell. 51: 156-73. PMID 23870142 DOI: 10.1016/j.molcel.2013.07.001  0.56
2013 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, et al. Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature. 493: 231-5. PMID 23201690 DOI: 10.1038/nature11661  0.56
2013 Spitale RC, Crisalli P, Flynn RA, Torre EA, Kool ET, Chang HY. RNA SHAPE analysis in living cells. Nature Chemical Biology. 9: 18-20. PMID 23178934 DOI: 10.1038/nchembio.1131  0.56
2012 Spitale RC, Cheng MY, Chun KA, Gorell ES, Munoz CA, Kern DG, Wood SM, Knaggs HE, Wulff J, Beebe KD, Chang AL. Differential effects of dietary supplements on metabolomic profile of smokers versus non-smokers. Genome Medicine. 4: 14. PMID 22360970 DOI: 10.1186/gm313  0.56
2011 Wan Y, Kertesz M, Spitale RC, Segal E, Chang HY. Understanding the transcriptome through RNA structure. Nature Reviews. Genetics. 12: 641-55. PMID 21850044 DOI: 10.1038/nrg3049  0.56
2011 Spitale RC, Tsai MC, Chang HY. RNA templating the epigenome: long noncoding RNAs as molecular scaffolds. Epigenetics : Official Journal of the Dna Methylation Society. 6: 539-43. PMID 21393997 DOI: 10.4161/epi.6.5.15221  0.56
2011 Tsai MC, Spitale RC, Chang HY. Long intergenic noncoding RNAs: new links in cancer progression. Cancer Research. 71: 3-7. PMID 21199792 DOI: 10.1158/0008-5472.CAN-10-2483  0.56
2010 Guo M, Spitale RC, Volpini R, Krucinska J, Cristalli G, Carey PR, Wedekind JE. Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a pre-catalytic conformation Aip Conference Proceedings. 1267: 627-628. DOI: 10.1063/1.3482715  0.56
2009 Guo M, Spitale RC, Volpini R, Krucinska J, Cristalli G, Carey PR, Wedekind JE. Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation. Journal of the American Chemical Society. 131: 12908-9. PMID 19702306 DOI: 10.1021/ja9060883  0.56
2009 Spitale RC, Volpini R, Mungillo MV, Krucinska J, Cristalli G, Wedekind JE. Single-atom imino substitutions at A9 and A10 reveal distinct effects on the fold and function of the hairpin ribozyme catalytic core. Biochemistry. 48: 7777-9. PMID 19634899 DOI: 10.1021/bi9011622  0.56
2009 Spitale RC, Wedekind JE. Exploring ribozyme conformational changes with X-ray crystallography. Methods (San Diego, Calif.). 49: 87-100. PMID 19559088 DOI: 10.1016/j.ymeth.2009.06.003  0.56
2009 Spitale RC, Volpini R, Heller MG, Krucinska J, Cristalli G, Wedekind JE. Identification of an imino group indispensable for cleavage by a small ribozyme. Journal of the American Chemical Society. 131: 6093-5. PMID 19354216 DOI: 10.1021/ja900450h  0.56
2009 Spitale RC, Torelli AT, Krucinska J, Bandarian V, Wedekind JE. The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain. The Journal of Biological Chemistry. 284: 11012-6. PMID 19261617 DOI: 10.1074/jbc.C900024200  0.56
2008 Torelli AT, Spitale RC, Krucinska J, Wedekind JE. Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme. Biochemical and Biophysical Research Communications. 371: 154-8. PMID 18423397 DOI: 10.1016/j.bbrc.2008.04.036  0.56
2007 Spitale RC, Heller MG, Pelly AJ, Wedekind JE. Efficient syntheses of 5'-deoxy-5'-fluoroguanosine and -inosine. The Journal of Organic Chemistry. 72: 8551-4. PMID 17902696 DOI: 10.1021/jo7015778  0.56
2007 MacElrevey C, Spitale RC, Krucinska J, Wedekind JE. A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme. Acta Crystallographica. Section D, Biological Crystallography. 63: 812-25. PMID 17582172 DOI: 10.1107/S090744490702464X  0.56
2007 Palde PB, McNaughton BR, Ross NT, Gareiss PC, Mace CR, Spitale RC, Miller BL. Single-step synthesis of functional organic receptors via a tridirectional minisci reaction Synthesis. 2287-2290. DOI: 10.1055/s-2007-983792  0.56
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