MOSS LAB PUBLICATIONS

  • Tompkins, V. S., Rouse, W. B., Wang, J., Woodman, M. E., Dow, E. R., Jessop, T. C., & Moss, W. N. (2025). Identification of a conserved RNA structure in the TNFRSF1A 3’UTR: Implications for post-transcriptional regulation. bioRxiv, 2025.06. 18.660452. Cold Spring Harbor Laboratory.

  • Tong, Y., Su, X., Rouse, W., Childs-Disney, J. L., Taghavi, A., Zanon, P. R. A., Kovachka, S., Wang, T., Moss, W. N., & Disney, M. D. (2024). Transcriptome-wide, unbiased profiling of ribonuclease targeting chimeras. Journal of the American Chemical Society, 146(31), 21525-21534. American Chemical Society.

  • Thornhill, E. M., Andrews, R. J., Lozier, Z., Carino, E., Rameix-Welti, M., Éléouët, J., Moss, W. N., & Verhoeven, D. (2024). Analysis Of Respiratory Syncytial Virus Reveals Conserved Rna Secondary Structural Motifs And Impact Viral Lifecycle. bioRxiv, 2024.08. 26.609688. Cold Spring Harbor Laboratory.

  • Rouse, W. B., Tompkins, V. S., O’Leary, C. A., & Moss, W. N. (2024). The RNA secondary structure of androgen receptor-FL and V7 transcripts reveals novel regulatory regions. Nucleic Acids Research, 52(11), 6596-6613. Oxford University Press.

  • Peterson, J. M., Becker, S. T., O’Leary, C. A., Juneja, P., Yang, Y., & Moss, W. N. (2024). Structure of the SARS-CoV-2 frameshift stimulatory element with an upstream multibranch loop. Biochemistry, 63(10), 1287-1296. American Chemical Society.

  • O'Leary, C. A., Eich, T., & Moss, W. N. (2024). Intronic RNA secondary structural information captured for the human MYC pre-mRNA. NAR Genomics and Bioinformatics, 6(4), lqae143. Oxford University Press.

  • Massa, A. L., Chintalapudi, H., Coppenbarger, E. C., Peterson, J. M., Moss, W. N., Frost, H. R., & Leach, S. D. (2024). A common set of structurally distinct endogenous retroviruses predict survival in multiple human tumor types. bioRxiv, 2024.02. 07.579350. Cold Spring Harbor Laboratory.

  • Dhar, D., Mehanovic, S., Moss, W., & Miller, C. L. (2024). Sequences at gene segment termini inclusive of untranslated regions and partial open reading frames play a critical role in mammalian orthoreovirus S gene packaging. PLoS Pathogens, 20(2), e1012037. Public Library of Science.

  • Baliga-Gil, A., Soszynska-Jozwiak, M., Ruszkowska, A., Szczesniak, I., Kierzek, R., Ciechanowska, M., Trybus, M., Jackowiak, P., Peterson, J. M., Moss, W. N., & Kierzek, E. (2024). Targeting sgRNA N secondary structure as a way of inhibiting SARS-CoV-2 replication. Antiviral Research, 228, 105946. Elsevier.

  • Tompkins, V. S., Xue, Z., Peterson, J. M., Rouse, W. B., O’Leary, C. A., & Moss, W. N. (2024). Identification of MYC intron 2 regions that modulate expression. Plos one, 19(1), e0296889. Public Library of Science.

  • Ruddell, B., Hassall, A., Moss, W. N., Sahin, O., Plummer, P. J., Zhang, Q., & Kreuder, A. J. (2023). Direct interaction of small non-coding RNAs CjNC140 and CjNC110 optimizes expression of key pathogenic phenotypes of Campylobacter jejuni. Mbio, 14(4), e00833-23. American Society for Microbiology.

  • Peterson, J. M., O'Leary, C. A., Coppenbarger, E. C., Tompkins, V. S., & Moss, W. N. (2023). Discovery of RNA secondary structural motifs using sequence-ordered thermodynamic stability and comparative sequence analysis. MethodsX, 11, 102275. Elsevier.

  • Mirska, B., Woźniak, T., Lorent, D., Ruszkowska, A., Peterson, J. M., Moss, W. N., Mathews, D. H., Kierzek, R., & Kierzek, E. (2023). In vivo secondary structural analysis of Influenza A virus genomic RNA. Cellular and Molecular Life Sciences, 80(5), 136. Springer International Publishing.

  • O'Leary, C. A., Rouse, W. B., Peterson, J. M., Tompkins, V. S., Andrews, R. J., McCown, P. J., & Moss, W. N. (2023). Secondary structural characterization of non-coding RNAs. In Navigating Non-Coding RNA (pp. 175-208). Academic Press.

  • Haltom, J., Trovao, N. S., Guarnieri, J., Vincent, P., Singh, U., Tsoy, S., O’Leary, C. A., Bram, Y., Widjaja, G. A., & Cen, Z. (2023). Sars-cov-2 orphan gene orf10 contributes to more severe covid-19 disease. medRxiv.

  • Tong, Y., Gibaut, Q. M. R., Rouse, W., Childs-Disney, J. L., Suresh, B. M., Abegg, D., Choudhary, S., Akahori, Y., Adibekian, A., & Moss, W. N. (2023). Correction to “Transcriptome-Wide Mapping of Small-Molecule RNA-Binding Sites in Cells Informs an Isoform-Specific Degrader of QSOX1 mRNA”. Journal of the American Chemical Society, 145(16), 9364-9364. American Chemical Society.

  • Tompkins, V. S., Rouse, W. B., O’Leary, C. A., Andrews, R. J., & Moss, W. N. (2022). Analyses of human cancer driver genes uncovers evolutionarily conserved RNA structural elements involved in posttranscriptional control. PLoS One, 17(2), e0264025. Public Library of Science.

  • Soszynska-Jozwiak, M., Ruszkowska, A., Kierzek, R., O’Leary, C. A., Moss, W. N., & Kierzek, E. (2022).Secondary structure of subgenomic RNA M of SARS-CoV-2. Viruses, 14(2), 322. MDPI.

  • Szutkowska, B., Wieczorek, K., Kierzek, R., Zmora, P., Peterson, J. M., Moss, W. N., & Kierzek, E. (2022).Secondary structure of influenza A virus genomic segment 8 RNA folded in a cellular environment. International Journal of Molecular Sciences, 23(5), 2452. MDPI.

  • Rouse, W. B., O’Leary, C. A., Booher, N. J., & Moss, W. N. (2022). Expansion of the RNAStructuromeDB to include secondary structural data spanning the human protein-coding transcriptome. Scientific Reports, 12(1), 14515. Nature Publishing Group UK London.

  • Rouse, W. B., Andrews, R. J., Booher, N. J., Wang, J., Woodman, M. E., Dow, E. R., Jessop, T. C., & Moss, W. N. (2022). Prediction and analysis of functional RNA structures within the integrative genomics viewer. NAR Genomics and Bioinformatics, 4(1), lqab127. Oxford University Press.

  • Rouse, W. B., Gart, J., Peysakhova, L., & Moss, W. N. (2022). Analysis of key genes in Mycobacterium ulcerans reveals conserved RNA structural motifs and regions with apparent pressure to remain unstructured. Frontiers in tropical diseases, 3, 1009362. Frontiers Media SA.

  • Peterson, J. M., O’Leary, C. A., & Moss, W. N. (2022). In silico analysis of local RNA secondary structure in influenza virus A, B and C finds evidence of widespread ordered stability but little evidence of significant covariation. Scientific Reports, 12(1), 310. Nature Publishing Group UK London.

  • O’Leary, C. A., Tompkins, V. S., Rouse, W. B., Nam, G., & Moss, W. N. (2022). Thermodynamic and structural characterization of an EBV infected B-cell lymphoma transcriptome. NAR Genomics and Bioinformatics, 4(4), lqac082. Oxford University Press.

  • Kauffmann, A. D., Kennedy, S. D., Moss, W. N., Kierzek, E., Kierzek, R., & Turner, D. H. (2022). Nuclear magnetic resonance reveals a two hairpin equilibrium near the 3′-splice site of influenza A segment 7 mRNA that can be shifted by oligonucleotides. RNA, 28(4), 508-522. Cold Spring Harbor Lab.

  • Singh, N. N., O'Leary, C. A., Eich, T., Moss, W. N., & Singh, R. N. (2022). Structural context of a critical exon of spinal muscular atrophy gene. Frontiers in Molecular Biosciences, 9, 928581. Frontiers Media SA.

  • Andrews, R. J., Rouse, W. B., O’Leary, C. A., Booher, N. J., & Moss, W. N. (2022). ScanFold 2.0: a rapid approach for identifying potential structured RNA targets in genomes and transcriptomes. PeerJ, 10, e14361. PeerJ Inc.

  • Pawlica, P., Yario, T. A., White, S., Wang, J., Moss, W. N., Hui, P., Vinetz, J. M., & Steitz, J. A. (2021). SARS-CoV-2 expresses a microRNA-like small RNA able to selectively repress host genes. Proceedings of the National Academy of Sciences, 118(52), e2116668118. National Academy of Sciences.

  • Soszynska-Jozwiak, M., Pszczola, M., Piasecka, J., Peterson, J. M., Moss, W. N., Taras-Goslinska, K., Kierzek, R., & Kierzek, E. (2021). Universal and strain specific structure features of segment 8 genomic RNA of influenza A virus—application of 4-thiouridine photocrosslinking. Journal of Biological Chemistry, 297(6). Elsevier.

  • Michalak, P., Piasecka, J., Szutkowska, B., Kierzek, R., Biala, E., Moss, W. N., & Kierzek, E. (2021).Conserved structural motifs of two distant IAV subtypes in genomic segment 5 RNA. Viruses, 13(3), 525. MDPI.

  • Dooley, S. K., Baken, E. K., Moss, W. N., Howe, A., & Young, J. K. (2021). Identification and evolution of Cas9 tracrRNAs. The CRISPR Journal, 4(3), 438-447. Mary Ann Liebert, Inc.

  • Andrews, R. J., O’Leary, C. A., Tompkins, V. S., Peterson, J. M., Haniff, H. S., Williams, C., Disney, M. D., & Moss, W. N. (2021). A map of the SARS-CoV-2 RNA structurome. NAR genomics and bioinformatics, 3(2), lqab043. Oxford University Press.

  • Zhang, P., Park, H. J., Zhang, J., Junn, E., Andrews, R. J., Velagapudi, S. P., Abegg, D., Vishnu, K., Costales, M. G., Childs-Disney, J. L., & Moss, W. N., et al. (2020). Translation of the intrinsically disordered protein α-synuclein is inhibited by a small molecule targeting its structured mRNA. Proceedings of the National Academy of Sciences, 117(3), 1457-1467. National Academies Press.

  • Ursu, A., Childs-Disney, J. L., Andrews, R. J., O’Leary, C. A., Meyer, S. M., Angelbello, A. J., Moss, W. N., & Disney, M. D. (2020). Design of small molecules targeting RNA structure from sequence. Chemical Society Reviews, 49(20), 7252-7270. Royal Society of Chemistry.

  • Pavlovic Djuranovic, S., Erath, J., Andrews, R. J., Bayguinov, P. O., Chung, J. J., Chalker, D. L., Fitzpatrick, J. A. J., Moss, W. N., Szczesny, P., & Djuranovic, S. (2020). Plasmodium falciparum translational machinery condones polyadenosine repeats. Elife, 9, e57799. eLife Sciences Publications, Ltd.

  • Moss, L. I., Tompkins, V. S., & Moss, W. N. (2020). Differential expression analysis comparing EBV uninfected to infected human cell lines identifies induced non-micro small non-coding RNAs. Non-coding RNA Research, 5(1), 32-36. Elsevier.

  • Haniff, H. S., Tong, Y., Liu, X., Chen, J. L., Suresh, B. M., Andrews, R. J., Peterson, J. M., O’Leary, C. A., Benhamou, R. I., Moss, W. N., & Disney, M. D. (2020). Targeting the SARS-CoV-2 RNA genome with small molecule binders and ribonuclease targeting chimera (RIBOTAC) degraders. ACS Central Science, 6(10), 1713-1721. American Chemical Society.

  • Benhamou, R. I., Angelbello, A. J., Andrews, R. J., Wang, E. T., Moss, W. N., & Disney, M. D. (2020).Structure-specific cleavage of an RNA repeat expansion with a dimeric small molecule is advantageous over sequence-specific recognition by an oligonucleotide. ACS chemical biology, 15(2), 485-493. American Chemical Society.

  • Andrews, R. J., Baber, L., & Moss, W. N. (2020). Mapping the RNA structural landscape of viral genomes. Methods, 183, 57-67. Elsevier.

  • Andrews, R. J., O’Leary, C. A., & Moss, W. N. (2020). A survey of RNA secondary structural propensity encoded within human herpesvirus genomes: global comparisons and local motifs. PeerJ, 8, e9882. PeerJ Inc.

  • Ungerleider, N. A., Jain, V., Wang, Y., Maness, N. J., Blair, R. V., Alvarez, X., Midkiff, C., Kolson, D., Bai, S., Roberts, C., & Moss, W. N. (2019). Comparative analysis of gammaherpesvirus circular RNA repertoires: conserved and unique viral circular RNAs. Journal of virology, 93(6), 10.1128/jvi. 01952-18. American Society for Microbiology.

  • Tompkins, V. S., Valverde, D. P., & Moss, W. N. (2019). Human regulatory proteins associate with non-coding RNAs from the EBV IR1 region. BMC research notes, 11(1), 139. BioMed Central London.

  • O’Leary, C. A., Andrews, R. J., Tompkins, V. S., Chen, J. L., Childs-Disney, J. L., Disney, M. D., & Moss, W. N. (2019). RNA structural analysis of the MYC mRNA reveals conserved motifs that affect gene expression. PLoS One, 14(6), e0213758. Public Library of Science.

  • Michalak, P., Soszynska-Jozwiak, M., Biala, E., Moss, W. N., Kesy, J., Szutkowska, B., Lenartowicz, E., Kierzek, R., & Kierzek, E. (2019). Secondary structure of the segment 5 genomic RNA of influenza A virus and its application for designing antisense oligonucleotides. Scientific reports, 9(1), 3801. Nature Publishing Group UK London.

  • Kumarasinghe, N., & Moss, W. N. (2019). Analysis of a structured intronic region of the LMP2 pre-mRNA from EBV reveals associations with human regulatory proteins and nuclear actin. BMC Research Notes, 12(1), 33. BioMed Central London.

  • Chen, J. L., Moss, W. N., Spencer, A., Zhang, P., Childs-Disney, J. L., & Disney, M. D. (2019). The RNA encoding the microtubule-associated protein tau has extensive structure that affects its biology. PLoS One, 14(7), e0219210. Public Library of Science.

  • Andrews, R. J., & Moss, W. N. (2019). Computational approaches for the discovery of splicing regulatory RNA structures. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, 1862(11-12), 194380. Elsevier.

  • Angelbello, A. J., Rzuczek, S. G., Mckee, K. K., Chen, J. L., Olafson, H., Cameron, M. D., Moss, W. N., Wang, E. T., & Disney, M. D. (2019). Precise small-molecule cleavage of an r (CUG) repeat expansion in a myotonic dystrophy mouse model. Proceedings of the National Academy of Sciences, 116(16), 7799-7804. National Academies Press.

  • Moss, W., O'Leary, C., & Andrews, R. (2019). Folding the druggable RNA structurome. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 257. AMER CHEMICAL SOC.

  • O’Leary, C. A., Andrews, R. J., Tompkins, V. S., Chen, J. L., Childs-Disney, J. L., Disney, M. D., & Moss, W. N. (2019). Scans of the MYC mRNA reveal multiple stable secondary structures—including a 3′ UTR motif, conserved across vertebrates, that can affect gene expression. bioRxiv, 564864. Cold Spring Harbor Laboratory.

  • Ungerleider, N., Concha, M., Lin, Z., Roberts, C., Wang, X., Cao, S., Baddoo, M., Moss, W. N., Yu, Y., & Seddon, M. (2018). The epstein barr virus circRNAome. PLoS pathogens, 14(8), e1007206. Public Library of Science.

  • Moss, W. N. (2018). The ensemble diversity of non-coding RNA structure is lower than random sequence. Non-coding RNA Research, 3(3), 100-107. Elsevier.

  • Moss, W. N. (2018). RNA2DMut: a web tool for the design and analysis of RNA structure mutations. Rna, 24(3), 273-286. Cold Spring Harbor Lab.

  • Kumarasinghe, N., & Moss, W. N. (2018). Analysis of a structured intronic region of the LMP2 pre-mRNA from EBV reveals associations with human regulatory proteins. bioRxiv, 405977. Cold Spring Harbor Laboratory.

  • Djuranovic, S. P., Erath, J., Andrews, R. J., Bayguinov, P. O., Chung, J. J., Chalker, D. L., Fitzpatrick, J. A. J., Moss, W. N., Szczesny, P., & Djuranovic, S. (2018). PolyA tracks and poly-lysine repeats are the Achilles heel of Plasmodium falciparum. bioRxiv, 420109. Cold Spring Harbor Laboratory.

  • Andrews, R. J., Roche, J., & Moss, W. N. (2018). ScanFold: an approach for genome-wide discovery of local RNA structural elements—applications to Zika virus and HIV. PeerJ, 6, e6136. PeerJ Inc.

  • Andrews, R. J., Roche, J., & Moss, W. N. (2018). Genome-wide discovery of local RNA structural elements in Zika virus. PeerJ Preprints.

  • Soszynska-Jozwiak, M., Michalak, P., Moss, W. N., Kierzek, R., Kesy, J., & Kierzek, E. (2017). Influenza virus segment 5 (+) RNA-secondary structure and new targets for antiviral strategies. Scientific Reports, 7(1), 15041. Nature Publishing Group UK London.

  • Andrews, R. J., Baber, L., & Moss, W. N. (2017). RNAStructuromeDB: A genome-wide database for RNA structural inference. Scientific Reports, 7(1), 17269. Nature Publishing Group UK London.

  • Alahari, S. K., Gregory, B. D., Polacek, N., Almeida, M., Gupta, A., Riley, K. J., Atianand, M. K., Gupta, S. K. S., Baluska, G., Hagiwara, K., & Moss, W. N. (2017). Acknowledgement to Reviewers of Non-Coding RNA in 2016.

  • Tycowski, K. T., Guo, Y. E., Lee, N., Moss, W. N., Vallery, T. K., Xie, M., & Steitz, J. A. (2016). Viral noncoding RNAs: more surprises. Genes & development, 29(6), 567-584. Cold Spring Harbor Lab.

  • Soszynska-Jozwiak, M., Ruszkowska, A., Kierzek, R., & Kierzek, E. (2016). Secondary structure model of the naked segment 7 influenza A virus genomic RNA. Biochemical Journal, 473(23), 4327-4348. Portland Press Ltd.

  • Pawlica, P., Moss, W. N., & Steitz, J. A. (2016). Host miRNA degradation by Herpesvirus saimiri small nuclear RNA requires an unstructured interacting region. Rna, 22(8), 1181-1189. Cold Spring Harbor Lab.

  • Lenartowicz, E., Kesy, J., Ruszkowska, A., Soszynska-Jozwiak, M., Michalak, P., Moss, W. N., Turner, D. H., Kierzek, R., & Kierzek, E. (2016). Self-folding of naked segment 8 genomic RNA of influenza A virus. PloS one, 11(2), e0148281. Public Library of Science.

  • Steitz, J. A., Lee, N., Moss, W. N., Yario, T. A., Vilborg, A., Passarelli, M. C., & Tycowski, K. T. (2016).Abstract IA14: Noncoding RNAs of viral and cellular origin: Links to oncogenesis. Cancer Research, 76(6_Supplement), IA14-IA14. The American Association for Cancer Research.