Book chapters, review, and editorials

• Deng L., Kumar J., Rose R., McIntyre W., and Fabris D. “Analyzing RNA post-transcriptional modifications to decipher the epitranscriptomic code” Mass Spectrom. Rev. (2022), https://doi.org/10.1002/mas.21798.
• Fabris D. “Mass spectrometric analysis of nucleic acids” in Nucleic Acids in Chemistry and Biology 4^th Edition, Blackburn and Gait eds., (2022) in press.
• Fabris D. “Ion mobility mass spectrometry of nucleic acids” in Ion Mobility Mass Spectrometry, F. Sobott and A. Ashcroft eds., Royal Society of Chemistry Press (2022) ISBN978-1-83916-166-7.
• Kenderdine T. and Fabris D. “The multifaceted roles of mass spectrometric analysis in nucleic acids drug discovery and development” Mass Spectrom. Rev. (2021) DOI:10.1002/mas.21766.
• van Breemen, R.B., Hathout, Y., and Fabris D. “Catherine Fenselau: a distinguished career dedicated to Biomedical Mass Spectrometry” J. Mass Spectrom. 2020; 55:e4500, February 2020, doi.org/10.1002/jms.4500).
• Fabris D. “MS-based approaches for nucleic acids structural determination” in Nucleic Acids in the Gas Phase, V. Gabelica ed., 253-288 (2014), Springer, Heidelberg, New York, Dordrecht, London (DOI: 10.1007/978-3-642-54842-0).
• Berkenkamp, S., van den Boon, D. and Fabris, D. “Analysis of Nucleic Acids and Practical Implementations in Genomics and Genetics” in MALDI MS: A Practical Guide to Instrumentation, Methods and Applications / 2^nd edition, F. Hillenkamp and J. Peter-Katalinic eds., 169-238 (2014), Wiley-VCH Verlag GmbH & Co kGaA, Weinheim, Germany.
• Hawkins, A. E. and Fabris, D. “RNA Structure Determination by Structural Probing and Mass Spectrometry: MS3D” in RNA 3D structure analysis and prediction, Nucleic Acids and Molecular Biology v. 27, Leontis and E. Westhof, eds, 361-389 (2012), Springer-Verlag, Berlin, Heidelberg (DOI: 10.1007/978-3-642-25740-7_17).
• Fabris D. “Analysis of nucleic acids in the post-genomic era” Anal. Chem. 83, 5810-6 (2011). PubMed PMID: 21651236; PubMed Central PMCID: PMC3432857.
• Fabris D. and Limbach P. A. “Review of the 22nd Sanibel Conference on Mass Spectrometry: From Structural Biology to Drug Discovery: New Roles for Mass Spectrometry of Nucleic Acids,” J. Am. Soc. Mass Spectrom., 7, R1-4 (2010).
• Fabris D. and Yu E. T. “Elucidating the higher-order structure of biopolymers by structural probing and mass spectrometry: MS3D,” Perspective contribution in the J. Mass Spectrom. 45, 841-860 (2010), DOI: 10.1002/jms.1762. PubMed PMID: 20648672; PubMed Central PMCID: PMC3432860.
• Fabris D. “A role for the MS analysis of nucleic acids in the post-genomics age,” Critical Insight contribution in the J. Am. Soc. Mass Spectrom., 21, 1-13 (2010).
• Fabris D., Turner, K. B., Hagan, N. A. “Electrospray ionization – mass spectrometry for the investigation of protein-nucleic acid interactions” in Mass Spectrometry of Nucleosides and Nucleic Acids, Banoub and P. Limbach eds., 303-327 (2010), CRC Press, Taylor and Francis Group, LLC, London, U.K.
• Fabris, D., Marino, J.P., Le Grice, S.F.J. “Revisiting Plus-Strand DNA Synthesis in Retroviruses and Long Terminal Repeat Retrotransposons: Dynamics of Enzyme: Substrate Interactions,” Viruses, 1, 657-677 (2009).
• Fabris D. “Advances in the investigation of the structure-function relationship in nucleic acids and their assemblies,” editorial introducing the homonymous special series of the Biopolymers journal, volume 91(4), iii-iv (2009), John Wiley & Sons, Inc., Hoboken, NJ.
• Fabris, D. “Mass Spectrometric Approaches for the Investigation of Dynamic Processes in Condensed Phase” Mass Spectrom. Rev. 24, 30-54 (2005).
• Fabris D. “Enzyme Kinetics” in The Encyclopedia of Mass Spectrometry, M.L. Gross and R.M. Caprioli eds., Vol. 2, 327-339 (2005), Elsevier Science, Inc., Oxford, U.K..
• Fenselau C., Antoine M., Fabris D., Hathout Y., He T., Zaia J. “A Chemical Mechanism for Inactivation of Anticancer Drugs by Metallothionein” in Metallothionein IV, C.D. Klaassen ed., Birkhäuser-Verlag: Berlin (1999), pp. 577-580.

Journal articles

• McIntyre, W.D.; Nemati, R.; Salehi, M.; Aldrich, C.C.; FitzGibbon, M.; Deng, L.;  Pazos, M.A.;  Rose, R.E.; Toro, B.; Netzband, R.E.; Pager, C.T.; Robinson, I.P.; Bialosuknia, S.M.; Ciota, A.T.; Fabris, D. *; “An Agnostic Framework for the Classification/Identification of Organisms Based on RNA Post-Transcriptional Modifications” Anal. Chem. (2021) 93, 21, 7860-7869, https://doi.org/10.1021/acs.analchem.1c00359
• Sosic, A.*; Göttlich, R.; Fabris, D.; and Gatto, B.; “B-CePs as cross-linking probes for the investigation of RNA higher-order structure” Nucleic Acids Res. (2021) 49, 6660-6672,  https://doi.org/10.1093/nar/gkab468
• Sosic, A.; Olivato, G.; Carraro, C.; Göttlich, R.; Fabris, D.; and Gatto, B.*; “Bis-3-chloropiperidines targeting TAR RNA as a novel strategy to impair the HIV-1 nucleocapsid protein” Molecules (2021), 26, 1874-86, https://doi.org/10.3390/molecules26071874.
• Waldern, J.M. ; Smith, D.; Piazza, C.L.; Bailey, E.J.; Schiraldi, N.J.; Nemati, R.; Fabris, D.; Belfort, M.; Novikova, O.*“Methylation of rRNA as a host defense against rampant group II intron retrotransposition” Mob. DNA (2021), 12:9, https://doi.org/10.1186/s13100-021-00237-z.
• Filandrová, R.; Vališ, K.; Černý, J.; Chmelík, J.; Slavata, L.; Fiala, J.; Rosůlek, M.; Kavan, D.; Man, P.; Chum, T.; Cebecauer, M.; Fabris, D.; Novák, P.*; “Motif orientation matters: structural characterization of TEAD1 recognition of genomic DNA” Structure (2021), 29, 1-12. DOI:10.1016/j.str.2020.11.018
• Endres, L.*; Rose, R.E.; Doyle, F.; Rahn, T.; Lee, B.; Seaman, J.; McIntyre, W.D.; Fabris, D. ; “2’-O-ribose methylation of transfer RNA promotes recovery from oxidative stress in Saccharomyces cerevisiae” PLoS ONE (2020), 15 (2) e0229103. https://doi.org/10.1371/journal.pone.0229103
• Kenderdine, T.; Nemati, R.; Baker, A.; Palmer, M.; Ujma, J.; FitzGibbon, M.; Deng, L.; Royzen, M.; Langridge, J.; Fabris, D.*; “High-Resolution Ion Mobility Spectrometry-Mass Spectrometry of Isomeric/Isobaric Ribonucleotide Variants” J. Mass Spectrom. (2020), 55:e4465, DOI: 10.1002/jms.4465.
• Slavata, L.; Chmelík, J.; Kavan, D.; Filandrová, R.; Fiala, J.; Rosůlek, M.; Mrázek, H.; Kukačka, K.; Vališ, K. ; Man, P.; Miller, M.; McIntyre, W.; Fabris, D.; Novák, P.; “MS-Based Approaches Enable the Structural Characterization of Transcription Factor/DNA Response Element Complex” Biomolecules (2019), 9, 535, DOI: 10.3390/biom9100535.
• Myers, C.A.; D’Esposito, R.J; Fabris, D.; Ranganathan, S.V.; and Chen, A.A.* “CoSIMS: An Optimized Trajectory-Based Collision Simulator for Ion Mobility Spectrometry” J. Phys. Chem. B (2019), 123, 4347-4357, DOI: 10.1021/acs.jpcb.9b01018.
• Carraro, C.; Francke, A.; Sosic, A.; Kohl, F.; Helbing, T.; De Franco, M.; Fabris, D.; Göttlich, R.; and Gatto, B.* “Behind the Mirror: Chirality Tunes the Reactivity and Cytotoxicity of Chloropiperidines as Potential Anticancer Agents” ACS Med. Chem. Lett. (2019), 10, 552-557, DOI: 10.1021/acsmedchemlett.8b00580.
• Kenderdine, T; Xia, Z.; Williams, E.; and Fabris, D.* “Submicrometer Nanospray Emitters Provide New Insights into the Mechanism of Cation Adduction to Anionic Oligonucleotides” Anal. Chem. (2018), 90, 13541-48, DOI: 10.1021/acs.analchem.8b03632.
• Pearson, C. S.; Nemati, R.; Liu, B.; Zhang, J.; Scalabrin, M.; Li, H.; Fabris, D.; Belfort, M.; and Belfort, G.* “Structure of an Engineered Intein Reveals Thiazoline Ring and Provides Mechanistic Insight” Biotech Bioeng. (2018), 116 (4), 709-721, DOI: 10.1002/bit.26875.
• Scalabrin, M; Dixit, S.; Makshood, M. M.; Krzemien, C. E.; and Fabris, D.* “Bifunctional cross-linking approaches for mass spectrometry-based investigation of nucleic acids and protein-nucleic acid assemblies” Methods 44, 64-78 (2018), DOI: 10.1016/j.ymeth.2018.05.001.
• Sosic, A.; Saccone, I.; Carraro, C.; Kenderdine, T.; Gamba, E.; Caliendo, G.; Corvino, A.; Fiorino, F.; DiVaio, P.; Magli, E.; Perissutti, E.; Santagada, V.; Severino, B.; Spada, V.; Fabris, D.; Frecentese, F.; Gatto, B.* “Non-Natural Linker Configuration in 2,6-Dipeptidyl-Anthraquinones Enhances the Inhibition of TAR RNA Binding/Annealing Activities by HIV-1 NC and Tat Proteins” Bioconjugate Chem. 29(7), 2195-2207 (2018), DOI: 10.1021/acs.bioconjchem.8b00104.
• McIntyre, W; Netzband, R.; Bonenfant, G.; Biegel, J.M.; Miller, C.; Fuchs, G.; Henderson, E.; Arra, M.; Canki, M.; Fabris, D.* and Pager, C.T.* “Positive-sense RNA viruses reveal the complexity and dynamics of the cellular and viral epitranscriptomes during infection” Nucleic Acids Res. 46(11), 5776-5791 (2018), journal cover, DOI: 10.1093/nar/gky029.
• Wang, R.; Ranganathan, S.V.; Haruehanroe ngra, P.; Mao, S.; Scalabrin, M.; Fabris, D.; Chen, A.; Liu, H.; Hassan, A.E.A.; Gan, J.; and Sheng, J.* “Construction and structure studies of DNA-bipyridine complexes as versatile scaffolds for site-specific incorporation of metal ions into DNA” J. Biomol. Struct. Dyn. 22, 1-11 (2018), DOI: 10.1080/07391102.2018.1441071.
• Gamba, E.; Mori, M.; Kovalenko, L.; Giannini, A.; Sosic, A.; Saladini, F.; Fabris, D.; Mély, Y.; Gatto, B.; and Botta, M.* “Identification of novel 2-benzoxazolinone derivatives with specific inhibitory activity against the HIV-1 nucleocapsid protein” Eur. J. Med Chem. 145, 154-164 (2017), DOI:10.1016/j.ejmech.2017.12.073.
• Sosic, A.; Zuravka, I.; Schmitt, N.-K.; Miola, A.; Göttlich, R.; Fabris, D.; and Gatto, B. “Direct and Topoisomerase II mediated DNA damage by Bis-3-chloropiperidines: the importance of being an earnest G” Chem. Med. Chem. 12(17), 1471-1479 (2017), DOI: 10.1002/cmdc.201700368.
• Vangaveti, S.; D’Esposito, R. J.; Lippens, J. L.; Fabris, D.; and Ranganathan, S. V.* “A coarse-grained model for assisting the investigation of structure and dynamics of large nucleic acids by Ion Mobility Spectrometry Mass Spectrometry” Phys. Chem. Chem. Phys. 19(23), 14937-14946 (2017), DOI: 10.1039/c7cp00717e.
• Spell, S.R.; Mangrum, J.B.; Peterson, E.J.; Fabris, D.; Ptak, R.; and Farrell N.P.* “Au(iii) compounds as HIV nucleocapsid protein (NCp7)-nucleic acid antagonists” Chem Commun. (Camb) 53(1), 91-94 (2016), DOI: 10.1039/c6cc07970a.
• Garabedian, A.; Butcher, D.; Lippens, J.L.; Miksovska, J.; Chapagain, P.; Fabris, D.; Ridgeway, M.; Park, M.; and Fernandez-Lima, F.* “Structures of the kinetically trapped i-motif DNA intermediates” Phys. Chem. Chem. Phys. 18(38), 266691-26702 (2016), DOI: 10.1039/c6cp04418b.
• Lippens, J.L.; Ranganathan, S.V.; D’Esposito, R.J.; and Fabris, D.* “Modular calibrant sets for the structural analysis of nucleic acids by ion mobility spectrometry mass spectrometry” Analyst 141, 4084-99 (2016), DOI: 10.1039/C6AN00453A.
• Rose, R.E.; Pazos, M.A. II; Curcio, J.; and Fabris, D. “Global profiling of RNA post-transcriptional modifications as an effective tool for investigating the epitranscriptomics of stress response” Mol. Cell. Proteomics 15(3), 932-44 (2016) DOI: 10.1074/mcp.M115.054718.
• Xue, J.; Manigrasso, M.; Scalabrin, M.; Rai, V.; Reverdatto, S.; Burz, D.S.; Fabris, D.; Schmidt, A.M.; Shekhtman, A.* “Change in the Molecula Dimension of a RAGE-ligand complex triggers RAGE signalling” Structure 24, 1509-1522 (2016), DOI: 10.1016/j.str.2016.06.021.
• Frecentese, F.;  Sosic, A.; Saccone, I.; Gamba, E.; Link, K.; Miola, A.; Cappellini, M.; Cattelan, M.G.; Severino, B.; Fiorino, F.; Magli, E.; Corvino, A.; Perissutti, E.; Fabris, D.; Gatto, B.; Caliendo, G.; Santagada, V.* “Synthesis and in vitro screening of new series of 2,6-dipeptidyl-anthraquinones: influence of side chain length on HIV-1 nucleocapsid inhibition” J. Med. Chem. 59(5), 1914-24 (2016) DOI: 10.1021/acs.jmedchem.5b01494.
• Murray, B.; Sorci, M.; Rosenthal, J.; Lippens, J.; Isaacson, D.; Das, P.; Fabris, D.; Li, S.; Belfort, G.* “A2T and A2V Aβ peptides exhibit different aggregation kinetics, primary nucleation, morphology, structure and LTP inhibition” Proteins: Struct. Funct. and Bioinf. 4(4), 488-500 (2016), journal cover, DOI: 10.1002/prot.24995.
• Ribaudo, G.; Scalabrin, M.; Pavan, V.; Fabris, D.; Zagotto, G.* “Constrained bisanthrene derivatives as G-quadruplex binders” ARKIVOC, 3, 145-160 (2016).
• Lippens, J.L.; Mangrum, J.B.; McIntyre, W.; Redick, B.; and Fabris, D.* “A simple heated-capillary modification improves the analysis of non-covalent complexes by Z-spray electrospray ionization” Rapid Comm. Mass Spectrom. 30, 773-783 (2016), DOI: 10.1002/rcm.7490.
• Sosic, A.; Sinigaglia, L.; Cappellini, M.; Carli, I.; Parolin, C.; Zagotto, G.; Sabatino, G.; Rivero, P.; Fabris, D.; and Gatto, B. “Mechanisms of HIV-1 nucleocapsid protein inhibition by lysyl-peptidyl-anthraquinone conjugates” Bioconjugate Chem. 27(1), 247-56 (2016), DOI 10.1021/acs.bioconjchem.5b00627.
• Tosoni, E.; Frasson, I.; Scalabrin, M.; Perrone, P.; Butovskaya, E.; Nadai, M.; Palù, G.; Fabris, D.; Richter, S.* “Nucleolin stabilizes G-quadruplex structures folded by the LTR promoter and silences HIV-1 viral transcription” Nucleic Acids Res. 43(18), 8884-97 (2015), DOI:10.1093/nar/gkv897.
• Rose, R. E.; Quinn, R.; Sayre, J. L.; and Fabris, D.* “Profiling ribonucleotide modifications at full-transcriptome level: a step towards MS-based epitranscriptomics” RNA, 21, 1-14 (2015), DOI:10.1261/rna.049429.114.
• Sosic, A.; Cappellini, M.; Sinigaglia, L.; Jacquet, R.; Deffieux, D.; Fabris, D.; Quideau, S.; Gatto, B.* “Polyphenolic C-glucosidic ellagitannins present in oak-aged wine inhibit HIV-1 nucleocapsid protein” Tetrahedron, 71, 3020-3026 (2015). DOI:10.1016/j.tet.2015.01.035.
• Asare-Okai, P. N.; Agustin, E.; Fabris, D.; Royzen, M.* “Site-specific fluorescence labelling of RNA using bio-orthogonal reaction of trans-cyclooctene and tetrazine” Chem Commun., 50 (58), 7844 -7847 (2014).
• Scalabrin, M.; Siu, Y.; Asare-Okai, P. N.; Fabris, D.* “Structure-specific ribonucleases for MS-based elucidation of higher-order RNA structure” J. Am. Soc. Mass Spectrom., 25 (7), 1136–45 (2014), DOI: 10.1007/s13361-014-0911-2.
• Quinn, R.; Basanta-Sanchez, M.; Rose, R. E.; Fabris, D.* “Direct infusion analysis of nucleotide mixtures of very similar or identical elemental composition” J. Mass Spectrom. 48 (6), 703–712 (2013), DOI: 10.1002/jms.3207. PubMed PMID: 23722961; PubMed Central PMCID: PMC3767442.
• Stephenson, W.; Asare-Okai, P. N.; Chen, A.; Keller, S.; Santiago, R.; Tenenbaum, S.; Garcia, A. E.; Fabris, D.*; Li, P.T.X.* “The essential role of stacking adenines in a two-base-pair RNA kissing complex” J. Amer. Chem. Soc. 135 (15), 5602–5611 (2013), DOI: 10.1021/ja310820h. PubMed PMID: 23517345; PubMed Central PMCID: PMC3664431.
• Doria, F.; Nadai, M.; Folini, M.; Scalabrin, M.; Germani, L; Sattin, G.; Mella, M.; Palumbo, M.; Zaffaroni, N.; Fabris, D.; Freccero, M.; and Richter, S.* “Targeting Loop Adenines in G-Quadruplex by a Selective Oxirane” Chem. Eur. J. 19, 78-82 (2012), DOI: 10.1002/chem.201203097. PubMed PMID: 23212868; PubMed Central PMCID: PMC3863998.
• Fabris, D.*; Kellersberger, K.A.; Wilhide, J.A. “Higher-order structure of nucleic acids in the gas-phase: Top-down analysis of base-pairing interactions” Int. J. Mass Spectrom. 312, 155-162 (2012). PubMed PMID: 24027423; PubMed Central PMCID: PMC3767431.
• Cantara, W. A.; Crain, P. F.; Rozenski, J.; McCloskey, J. A.; Harris, K. A.; Zhang, X.; Vendeix, F. A. P.; Fabris, D.; Agris, P. F.* “The RNA modification database, RNAMDB: 2011 update” Nucleic Acids Res. 39(suppl 1), D195-D201 (2011). DOI: 10.1093/nar/gkq1028. Epub 2010 Nov 10. PubMed PMID: 21071406; PubMed Central PMCID: PMC3013656.
• Turner, K. B.; Yi-Brunozzi, H. Y.; Brinson, R. G.; Marino, J. P.; Fabris, D.*; and Le Grice, S. F. J.* “SHAMS – combining chemical modification of RNA with mass spectrometry to examine polypurine tract-containing RNA/DNA hybrids” RNA 15, 1605-1613 (2009). DOI: 10.1261/rna.1615409. Epub 2009 Jun 17. PubMed PMID: 19535461; PubMed Central PMCID: PMC2714758.
• Brinson, R. G.; Turner, K. B.; Yi-Brunozzi, H. Y.; Le Grice, S. F. J.; Fabris, D.; and Marino, J. P. “Probing anomalous structural features in polypurine tract-containing RNA:DNA hybrids with neomycin B” Biochemistry 48, 6988-6997 (2009). DOI: 10.1021/bi900357j. PubMed PMID: 19449839; PubMed Central PMCID: PMC2802280.
• Ramos, I., Fernandez E., Fabris D., and Good, T. “Kinetic study of β-amyloid residue accessibility by reductive alkylation and mass spectrometry” Biotech Bioeng. 104, 181-192 (2009). DOI: 1002/bit.22367. PubMed PMID: 19418563; PubMed Central PMCID: PMC2716430.
• Gapeev, A.; Berton, A.; Fabris, D. “Current-controlled nanospray ionization mass spectrometry” J. Am. Soc. Mass Spectrom. 20, 1334-1341 (2009). DOI: 10.1016/j.jasms.2009.03.007. Epub 2009 Mar 14. PubMed PMID: 19359196.
• Turner, K. B.; Kohlway, A. S.; Hagan, N. A.; Fabris, D. “Non-covalent probes for the investigation of structure and dynamics of protein-nucleic acid assemblies: the case of NC-mediated dimerization of genomic RNA in HIV-1” invited contribution to Biopolymers 91, 283-296 (2009). DOI: 10.1002/bip.21107. PubMed PMID: 18946871; PubMed Central PMCID: PMC2776628.
• Yu, E. T.; Hawkins, A.; Kuntz, I. D.; Rahn, L. A.; Rothfuss, A.; Sale, K; Young, M. M.; Yang, C. L.; Pancerella, C. M.; Fabris, D. “The collaboratory for MS3D: a new cyberinfrastructure for the structural elucidation of biological macromolecules and their assemblies using mass spectrometry-based approaches” Proteome Res. 7, 4848-4857 (2008). DOI: 10.1021/pr800443f. PubMed PMID: 18817429; PubMed Central PMCID: PMC2677910.
• Turner, K. B.; Monti, S.; Fabris, D. “Like polarity ion/ion reactions enable the investigation of specific metal interactions in nucleic acids and their non-covalent assemblies” J. Am. Chem. Soc. 30, 13353-13363 (2008). DOI: 10.1021/ja8045734. Epub 2008 Sep 12. PubMed PMID: 18785739; PubMed Central PMCID: PMC2654192.
• Legiewicz, M.; Badorrek, C.; Turner, C. B.; Fabris, D.; Hamm, T; Rekosh, D.; Hammarskjöld, M.-L.; Le Grice, S. F. J. “Resistance to RevM10 inhibition reflects a conformational switch in the HIV-1 Rev response element” Proc. Natl. Acad. Sci. U.S.A. 105, 1365-14370 (2008). DOI: 10.1073/pnas.0804461105. Epub 2008 Sep 5. PubMed PMID: 18776047; PubMed Central PMCID: PMC2567145.
• Holland, R.; Hawkins, A. E.; Eggler, A.; Mesecar, A.; Fabris, D.; Fishbein, J. C. “Prospective Type 1 and Type 2 Disulfides of Keap1 Protein” Chem. Res. Toxicol. 21, 2051-2060 (2008). DOI: 10.1021/tx800226m. Epub 2008 Aug 26. PubMed PMID: 18729328.
• Yu, E. T.; Hawkins, A.; Eaton, J.; Fabris, D. “MS3D structural elucidation of the HIV-1 packaging signal” Proc. Natl. Acad. Sci. U.S.A. 105, 12248-12253 (2008). DOI: 10.1073/pnas.0800509105. Epub 2008 Aug 19. PubMed PMID: 18713870; PubMed Central PMCID: PMC2527897.
• Zhang, Q.; Crosland, E.; Fabris, D. “Nested Arg-specific bifunctional crosslinkers for MS-based structural analysis of proteins and protein assemblies” invited contribution to Anal. Chim. Acta 627, 117-128 (2008). DOI: 10.1016/j.aca.2008.05.074. Epub 2008 Jun 5. PubMed PMID: 18790135; PubMed Central PMCID: PMC2677909.
• Turner, K. B.; Brinson, R. G.; Yi-Brunozzi, H. Y.; Rausch, J. W.; Miller, J. T. Le Grice, S. F. J.; Marino, J. P.; Fabris, D. “Structural probing of the HIV-1 Polypurine Tract RNA:DNA Hybrid using Classic Nucleic Acid Ligands” Nucleic Acids Res. 36, 2799-2810 (2008). DOI: 10.1093/nar/gkn129. Epub 2008 Apr 9. PubMed PMID: 18400780; PubMed Central PMCID; PMC2377446.
• Stephen, A. G.; Datta, S. A. K.; Worthy, K. M.; Bindu, L.;  Fivash, M.J.; Turner, K. B.; Fabris, D.; Rein, A.; Fisher, R.J. “Measuring the binding stoichiometry of HIV-1 Gag to very-low-density oligonucleotide surfaces using plasmon resonance spectroscopy” J. Biomol. Tech. 18, 259-266 (2007). PubMed PMID: 17916799; PubMed Central PMCID: PMC2062552.
• Turner, K. B.; Hagan, N. A.; Fabris, D. “Understanding the isomerization of the HIV-1 dimerization initiation domain by the nucleocapsid protein” J. Mol. Biol. 369, 812-828 (2007). DOI: 10.1016/j.jmb.2007.03.065.
• Fabris, D.; Chaudhari, P.; Hagan, N. A.; Turner, K. B. “Functional Investigations of Retroviral Protein-RNA Complexes by Nanospray-FTICR Mass Spectrometry” Eur. J. Mass Spectrom. 13, 29-33 (2007). PubMed PMID: 17878535.
• Hagan, N. A. and Fabris, D. “Dissecting the protein-RNA and RNA-RNA interactions in the nucleocapsid-mediated dimerization and isomerization of HIV-1 stemloop 1” J. Mol. Biol. 365, 396-410 (2007). DOI: 10.1016/j.jmb.2006.09.081
• Zhang, Q.; Yu, E. T.; Kellersberger, K. A.; Crosland, E.; Fabris, D. “Toward building a database of bifunctional probes for the MS3D investigation of nucleic acids structures” invited contribution to J. Am. Soc. Mass Spectrom. 17, 1570-1581 (2006). Epub 2006 Jul 27. PubMed PMID: 16875836.
• Turner, K. B.; Hagan, N. A.; Kohlway, A.; Fabris, D. “Mapping noncovalent ligand binding to stemloop domains of the HIV-1 packaging signal by tandem mass spectrometry” invited contribution to J. Am. Soc. Mass Spectrom. 17, 1401-1411 (2006), journal cover. Epub 2006 Jul 26. PubMed PMID: 16872834.
• Turner, K. B.; Hagan, N. A.; Fabris, D. “Inhibitory effects of archetypical nucleic acid ligands on the interactions of HIV-1 nucleocapsid protein with elements of Psi-RNA” Nucleic Acids Res. 34, 1305-1316 (2006). DOI: 10.1093/nar/gkl004.
• Fisher, R.J.; Fivash, M.J.; Stephen, A.G.; Hagan, N.A.; Shenoy, S.R.; Medaglia, M.V.; Smith, L.R.; Worthy, K.M.; Simpson, J.T.; Shoemaker, R.; McNitt, K.L.; Johnson, D.J.; Hixson, C.V.; Gorelick, R.J.; Fabris, D.; Henderson, L.E.; Rein, A. “Complex interactions of HIV-1 nucleocapsid protein with oligonucleotides” Nucleic Acids Res. 34, 472-484 (2006). Print 2006. Erratum in: Nucleic Acids Res. 2006;34(3):1082. DOI: 10.1093/nar/gkj442.
• Rait, V. K.; Zhang, Q.; Fabris, D.; Mason, J. T.; O’Leary, T. J. “Conversions of formaldehyde-modified 2´-deoxyadenosine 5´-monophosphate in conditions modeling formalin-fixed tissue dehydration” Histochem. Cytochem. 54, 301-310 (2006). Epub 2005 Aug 22. PubMed PMID: 16116034; PubMed Central PMCID: PMC1783762.
• Akinsiku, O.; Yu, E.T.; Fabris, D. “Mass spectrometric investigation of protein alkylation by the RNA footprinting probe kethoxal” J. Mass Spectrom. 40, 1372-1381 (2005). PubMed PMID: 16237662.
• Vanderver, A.; Schiffmann, R.; Timmons, M.; Kellersberger, K. A.; Fabris, D.; Hoffman, E. P.; Maletkovic, J.; Hathout, Y. “Decreased asialoferritin in cerebrospinal fluid of patients with childhood-onset ataxia and central nervous system hypomyelination/vanishing white matter disease” Clin. Chem. 51, 2031-2042 (2005). Epub 2005 Sep 9. PubMed PMID: 16155092.
• Richter, S.; Fabris, D.; Moro, S.; Palumbo, M. “Dissecting the reactivity of clerocidin towards common buffer systems by means of selected drug analogues” Chem. Res. Toxicol. 18, 35-40 (2005). PubMed PMID: 15651847.
• Yu, E. T.; Zhang, Q.; Fabris, D. “Untying the FIV frameshifting pseudoknot structure by MS3D” J. Mol. Biol. 345, 69-80 (2005). PubMed PMID: 15567411. doi: 10.1016/j.jmb.2004.10.014.
• Kellersberger, K. A.; Yu, E. T.; Merenbloom, S. I.; Fabris, D. “Atmospheric Pressure MALDI-FTMS of Normal and Chemically Modified RNA” J. Am. Soc. Mass Spectrom. 16, 199-207 (2005). PubMed PMID: 15694770.
• Richter, S.; Menegazzo, I.; Fabris, D.; Palumbo, M. “Concerted bis-alkylating reactivity of clerocidin towards unpaired cytosine residues in DNA” Nucleic Acids Res. 32, 5658-5667 (2004). PubMed PMID: 15494453.
• Maddaford, S. P.; Motamed, M.; Turner, K. B.; Choi, M. S. K.; Ramnauth, J.; Rakhit, S.; Hudgins, R. R.; Fabris, D.; Johnson, P. E. “Identification of a novel non-carbohydrate molecule that binds to the ribosomal A-site RNA” Med. Chem. Lett. 14, 5987-5990 (2004). PubMed PMID: 15546714.
• Yu, E. T.; Fabris, D. “Toward Multiplexing the Application of Solvent Accessibility Probes for the Investigation of RNA 3D Structures by Electrospray Ionization-Fourier transform ion cyclotron mass spectrometry” Biochem. 344, 356-366, (2004). PMID: 15494143. doi: 10.1016/j.ab.2004.07.034
• Kellersberger, K. A.; Tan, P.; Laiko, V. V.; Doroshenko, V. M.; Fabris, D. “Atmospheric Pressure MALDI / Fourier transform ion cyclotron mass spectrometry” Anal. Chem. 76, 3930-3934 (2004). PubMed PMID: 15253626.
• Kellersberger, K. A.; Yu, E.; Kruppa, G. H.; Young, M. M.; Fabris, D. “Top-down characterization of nucleic acids modified by structural probes using high-resolution tandem mass spectrometry and automated data interpretation” Anal. Chem. 76, 2438-2445 (2004). PubMed PMID: 15117181.
• Richter, S.; Fabris, D.; Binaschi, M.; Gatto, B.; Capranico, G.; Palumbo, M. “Effects of Common Buffer Systems on Drug Activity: the Case of Clerocidin” Chem.Res. Toxicol. 17, 492-501 (2004). PubMed PMID: 15089091.
• Gelhaus, S.; LaCourse, W.R.; Hagan, N.; Amarasinghe, G.; Fabris, D. “Rapid Purification of RNA Stem Loops” Nucleic Acids Res. 31, e135 (2003). PubMed PMID: 14576335; PubMed Central PMCID: PMC275492.
• Hagan, N.; Fabris, D. “Direct Mass Spectrometric Analysis of the Stoichiometry and Binding Affinity of the Complexes between Nucleocapsid Protein and RNA Stem-Loops of the HIV-1 Psi-Recognition Element” Biochemistry 42, 10736-10745 (2003). DOI: 10.1021/bi0348922.
• Richter, S.; Gatto, B.; Fabris, D.; Takao, K.-i.; Kobayashi, S.; Palumbo, M. “Clerocidin Alkylates DNA through its Epoxide Function: Evidence for a Fine Tuned Mechanism of Action” Nucleic Acids Res. 31, 5149-5156 (2003). PubMed PMID: 12930966; PubMed Central PMCID: PMC212796.
• Yu, E.; Fabris, D. “Direct probing of RNA structures and RNA-protein interactions in the HIV-1 packaging signal by chemical modification and electrospray Fourier transform mass spectrometry” J. Mol. Biol. 330, 211-223 (2003). PubMed PMID: 12823962. doi: 10.1016/s0022-2836(03)00589-8
• Zhang, Q., Hamilton, D., Creighton, D., Ganem, B., Fabris, D. “Alkylation of DNA by the Anti-Tumor Drug COMC” Org. Lett. 4, 1459-62 (2002). PubMed Central PMCID: 11975603.
• Cai, M., Shi, X., Sidorov, V., Fabris, D., Lam, Y.-F., Davis, J.T. “Cation-Directed Self-Assembly of Lipophilic Nucleosides: The Cation’s Central Role in the Structure and Dynamics of a Hydrogen-Bonded Assembly” Tetrahedron 58, 661-671 (2002).
• Hathout Y., Fabris D., Fenselau C. “Stoichiometry in Zinc Ion Transfer from Metallothionein to a Zinc-Finger Peptide” J. Mass Spectrom. Ion Proc. 204, 1-6 (2001).
• Fabris, D. “Steady-State Kinetics of Ricin A-Chain Reaction with the Sarcin/Ricin Loop and with HIV-1 Psi-RNA Hairpins Evaluated by Electrospray Ionization Mass Spectrometry” J. Am. Chem. Soc. 122, 8779-8780 (2000).
• He, T., Wei, D., Fabris, D., Fenselau, C. “Intracellular Sequestration of Anti-Tumor Drugs by Metallothionein” Cell Mol. Biol. (Noisy-le-grand) 46, 383-92 (2000).
• Cai, M., Marlow, A.L., Fettinger, J.C., Fabris, D., Haverlock, T.J., Moyer, B.A., Davis J. “Binding Cesium Ions with Nucleosides: Templated Self-Assembly of Isoguanosine Pentamers” Angew. Chem. Int. Ed. 39, 1283-85 (2000).
• Hua, S., Fabris, D., Inesi G. “Characterization of Calcium, Nucleotide, Phosphate and Vanadate Bound States by Derivatization of Sarcoplasmic Reticulum ATPase with ThioGloI” J. 77, 2217-2225 (1999).
• Fabris D., Hathout Y., Fenselau C. “Investigation of Zinc Chelation in Zinc-Finger Arrays by Electrospray Mass Spectrometry” Inorg. Chem. 38, 1322 -1325 (1999).
• Fabris D., Fenselau C. “Characterization of Allosteric Insulin Hexamers by Electrospray Ionization Mass Spectrometry” Anal. Chem. 71, 384-387 (1999).
• Wei, D., Fabris D., Fenselau C. “Covalent Sequestration Phosphoramide Mustard by Metallothionein: an In-Vitro Study” Drug Metab. Disp. 27, 786-91 (1999).
• Zaia J., Fabris D., Karpel R., Wei D., Fenselau C. “Monitoring Metal Ion Flux in Reactions of Metallothionein and Drug-Modified Metallothionein by Electrospray Mass Spectrometry” Protein Sci. 7, 2398-2404 (1998), DOI: 10.1002/pro.5560071117.
• He T., Fabris D., Fenselau C. “Identification of Thymosin Proteins in Human Bladder Tumor Cells by Mass Spectrometry and Data Base Searching” Mass Spectrom. Soc. Jpn. 46, 97-102 (1998).
• Antoine M., Fabris D., Fenselau C. “Covalent Sequestration of the Nitrogen Mustard Mechlorethamine by Metallothionein” Drug Metab. Disp. 26, 921-926 (1998).
• Fabris D., Zaia J., Hathout Y., Fenselau C. “Retention of Thiol Protons in Two Classes of Protein Zinc Coordination Centers” J. Am. Chem. Soc. 118, 12242-12243 (1996).
• Hathout Y., Fabris D., Han S.M., Fenselau C., Sowder R.C. II, Henderson L.E. “Characterization of Intermediates in the Oxidation of Zinc Fingers in the HIV-1 Nucleocapsid Protein P7” Drug Metab. Disp. 24, 1395-1400 (1996).
• Hathout Y., Ellis,T. ,Fabris D., Fenselau C. “Cross-Linking of Human Placenta π-class Glutathione-S-Transferase Dimer by Chlorambucil” Chem. Res. Toxicol. 9, 1044-49 (1996).
• Zaia J., Jiang L., Han S.M., Tabb J.R., Wu Z., Fabris D., Fenselau C. “A Binding Site for Chlorambucil on Metallothionein” Biochemistry 35, 2830-2835 (1996).
• Fabris D., Vestling M.M., Cordero M.M., Doroshenko, V.M., Cotter R.J., Fenselau C. “Sequencing Electroblotted Proteins by Tandem Mass Spectrometry” Rapid Commun. Mass Spectrom. 9, 1051-1055 (1995).
• Fabris D., Wu Z., Fenselau C. “Massive Cluster Impact Ionization on a Four Sector Tandem Mass Spectrometer” J. Mass Spectrom. 30, 140-143 (1995).
• Davis J.T., Tirumala S., Jenssen J.R., Fabris D. “Isoguanosine-K⁺ Tetramers” J. Org. Chem. 60, 4167-4176 (1995).
• Kaltashov, I. A., Fabris, D., Fenselau, C. C. “Assessment of Gas Phase Basicities of Protonated Peptides by the Kinetic Method” J. Phys. Chem. 99, 10046-10051 (1995).
• Fabris D., Kelly M., Wu Z., Fenselau C. “Collision Energy Effects on the Collision-induced Dissociation of Multiply Charged Melittin” Rapid Commun. Mass Spectrom. 8, 791-795 (1994).
• Tobin G. J., Sowder R. C. II, Fabris D., Hu M., Battles J. K., Fenselau C., Henderson L. E., Gonda A. M. “Amino Acid Sequence Analysis of the Proteolytic Cleavage Products of the BIV Gag Precursor Polypeptide” J. Virol. 68, 7620-7627 (1994).
• Fabris D., Kelly M., Murphy C., Wu Z., Fenselau C. “High Energy CID of Multiply Charged Polypeptides Produced by Electrospray” J. Am. Soc. Mass Spectrom. 4, 652-661 (1993).
• Fabris D., Traldi P., Benassi C.A., Pastore S., Bettero A., Rossato P. “Mass Spectrometric Approaches in the Characterization of the Decomposition Products of Dowicil 200” Biol. Mass Spectrom. 20, 361-366 (1991).

Patent

Patent # 11,339,441,  filed on May 12, 2016, awarded on May 24, 2022

Rose and Fabris D.“Profiling chemically modified DNA/RNA units for disease and cancer diagnosis.”