1. Porman AM, Roberts JT, Chrupcala M, Kennedy M, Williams M, Richer JK, Johnson AM. A single N6-methyladenosine site regulates lncRNA HOTAIR function in breast cancer cells. (2022) PLOS Biology, Nov. 28; 20(11):e3001885. doi: 10.1371/journal.pbio.3001885.
2. Wheeler JR, Whitney ON, Vogler TO, Nguyen ED, Pawlikowski B, Lester E, Cutler A, Elston T, Dalla Betta N, Parker K, Yost K, Vogel H, Rando T, Chang HY, Johnson AM, Parker R, Olwin BB. RNA Binding Proteins Direct Myogenic Cell Fate Decisions. (2022) eLife Jun 13;11:e75844. doi: 10.7554/eLife.75844. PMID: 35695839
3. Balas MM, Hartwick EW, Barrington C, Roberts JT, Wu SK, Bettcher R, Griffin AM, Kieft JS, Johnson AM. (2021) Establishing RNA-RNA interactions remodels lncRNA structure and promotes PRC2 activity. Science Advances  2021 Apr 14;7(16).  doi:10.1126/sciadv.abc9191. PMID: 33853770; PubMed Central PMCID: PMC8046370.
4. Roberts JT, Porman AM, Johnson AM. (2020) Identification of m6A residues at single-nucleotide resolution using eCLIP and an accessible custom analysis pipeline. RNA 27: 527-541. https://www.doi.org/10.1261/rna.078543.120
5. Zukowksi A, Phillips J, Park S, Wu R, Gygi SP, Johnson AM. Proteomic Profiling of Yeast Heterochromatin Connects Direct Physical and Genetic Interactions.Current Genetics.In Press.  PMID: 30310994.
6. Balas MM, Porman AM, Hansen KC, Johnson AM. SILAC-MS profiling of reconstituted human chromatin platforms for the study of transcription and RNA regulation. J. Proteome Research.In Press. PMID: 30192551.
7. Vogler T, Wheeler J, Nguyen E, Hughes M, Lester E, Rao B, Dalla Betta N, Wong P, Whitney O, Shorter J, Eisenberg D, J. Taylor P, Johnson AM, Olwin B, Parker R. Amyloid-like TDP-43 myo-granules associate with sarcomeric RNAs during skeletal muscle formation. Nature. In Press.
8. Nguyen ED, Balas MM, Griffin AM, Roberts JT and Johnson AM.(2018) Global Profiling of hnRNP A2/B1-RNA Binding on Chromatin Highlights LncRNA Interactions. RNA Biology 2018;15(7):901-913.
9. Balas MM and Johnson AM(2018). Exploring the mechanisms behind long noncoding RNAs and cancer. Non-coding RNA Research. 2018 Mar 31;3(3):108-117.
10. Zukowski A and Johnson AM. (2018) The Interplay of Histone H2B Ubiquitination with Budding and Fission Yeast Heterochromatin. Current Genetics Aug;64(4):799-806.
11. Zukowski A, Al-Afaleq NO, Duncan ED, Yao T, Johnson AM. (2017) Recruitment and allosteric stimulation of a histone deubiquitinating enzyme during heterochromatin assembly. J Biol Chem. pii: jbc.RA117.000498. doi: 10.1074/jbc.RA117.000498. [Epub ahead of print] PMID:29288197
12. Liu H, Wang C, Lee S, Deng Y, Wither M, Oh S, Ning F, Dege C, Zhang Q, Liu X, Johnson AM, Zang J, Chen Z, Janknecht R, Hansen K, Marrack P, Li CY, Kappler JW, Hagman J, Zhang G (2017) Clipping of arginine-methylated histone tails by JMJD5 and JMJD7. PNAS 114: E7717-E7726.  PMID: 28847961 PMCID: PMC5604019
13. ​*Meredith EK, *Balas MM, Sindy K, Haislop K, and Johnson AM. (2016) An RNA matchmaker protein regulates the long noncoding RNA HOTAIR. RNA. PMID: 27146324.  * Co-first author
14. Tatavosian R, Zhen CY, Duc HN, Balas MM, Johnson AM, and Ren X. (2015) Distinct Cellular Assembly Stoichiometry of Polycomb Complexes on Chromatin Revealed by Single-Molecule Chromatin Immunoprecipitation Imaging.  J. Biol. Chem. 290(47):28038-54. PMC4653664
15. Johnson A*, Wu R, Peetz M, Gygi SP, Moazed D* (2013) Heterochromatic gene silencing by activator interference and a transcription elongation barrier. J. Biol. Chem. 288: 28771-82. PMC3789973                  *Corresponding Author
16. Wang F, Li G, Mohammad A, Lu C, Currie M, Johnson A, Moazed D (2013) Heterochromatin protein Sir3 induces contacts between the amino terminus of histone H4 and nucleosomal DNA. Proc Natl Acad Sci. 110(21):8495-500. PMC3666683.
17. Johnson A, Li G, Sikorski TW, Buratowski S, Woodcock CL, Moazed D. (2009) Reconstitution of Heterochromatin-Dependent Transcriptional Gene Silencing. Molecular Cell 35: 769-81.
18. Sinha M, Watanabe S, Johnson A, Moazed D, Peterson CL. (2009) Recombinational repair within heterochromatin requires ATP-dependent chromatin remodeling. Cell 138:1109-21.
19. Laurence TA, Kwon Y, Johnson A, Hollars CW, O'Donnell M, Camarero JA, Barsky D. (2008) Motion of a DNA sliding clamp observed by single molecule fluorescence spectroscopy. J. Biol. Chem. 283: 22895-22906.
20. McInerney P, Johnson A, Katz F, O'Donnell M. (2007) Characterization of a Triple DNA Polymerase Replisome. Molecular Cell 27: 527-538.
21. Johnson A, Yao NY, Bowman GD, Kuriyan J, O'Donnell M. (2006) The replication factor C clamp loader requires arginine finger sensors to drive DNA binding and proliferating cell nuclear antigen loading. J. Biol. Chem. 281: 17528-39.
22. Yao NY, Johnson A, Bowman GD, Kuriyan J, O'Donnell M. (2006) Mechanism of proliferating cell nuclear antigen clamp opening by replication factor C. J. Biol. Chem. 281: 17528-39.
23. Johnson A, O’Donnell M. (2005) Cellular DNA Replicases: Components and Dynamics at the Replication Fork.  Ann. Rev. Biochem. Vol. 74: 283-315.
24. Johnson A, O’Donnell M. (2005) DNA Ligase: getting a grip to seal the deal. Curr Biol. 2005 Feb 8;15(3):R90-2.
25. Goedken ER, Levitus M, Johnson A, Bustamante C, O'Donnell M, Kuriyan J. (2004) Fluorescence measurements on the E.coli DNA polymerase clamp loader: implications for conformational changes during ATP and clamp binding. J Mol Biol. 336:1047-59.
26. Snyder AK, Williams CR, Johnson A, O'Donnell M, Bloom LB. (2004) Mechanism of loading the Escherichia coli DNA polymerase III sliding clamp: II. Uncoupling the beta and DNA binding activities of the gamma complex. J Biol Chem. 279:4386-93.
27. Johnson A, O'Donnell M. (2003) Ordered ATP Hydrolysis in the g Complex Clamp Loader AAA+ Machine.  J. Biol. Chem. 278, 14406-14413.