Publications

  1. Sun, J., Hwang, P., Sakkas, E.D., Zhou, Y., Perez, L., Dave, I., Kwon, J.B., McMahon, A.E., Wichman, M., Raval, M., Scopino, K., Krizanc, D., Thayer, K.M., and Weir, M.P. (2024). GNN codon adjacency regulates protein translation. BioRxiv 10.1101/2024.03.16.583757

  2. Dalgarno, C., Scopino, K., Raval, M., Nachmanoff, C., Sakkas, E.D., Krizanc, D., Thayer, K.M., and Weir, M.P. (2022). The CAR mRNA-Interaction Surface is a Zipper Extension of the Ribosome A site. International Journal of Molecular Sciences. 2022, 23(3), 1417. https://doi.org/10.3390/ijms23031417

  3. Scopino, K., Dalgarno, C., Nachmanoff, C., Krizanc, D., Thayer, K.M., and Weir, M.P. (2021). Arginine Methylation Regulates Ribosome CAR Function. International Journal of Molecular Sciences. 2021; 22(3):1335. https://doi.org/10.3390/ijms22031335
  4. Barr, W.A., Sheth R.B., Kwon, J., Cho, J., Glickman, J.W., Hart, F., Chatterji, O., Scopino, K., Voelkel-Meiman, K., Krizanc, D., Thayer, K.M. and Weir, M.P. (2020). GCN sensitive protein translation in yeast. PLOS ONE  https://doi.org/10.1371/journal.pone.0233197
  5. Scopino, K., Williams, E., Elsayed, A., Barr, W.A., Krizanc, D., Thayer, K.M., and Weir, M.P. (2020). A Ribosome Interaction Surface Sensitive to mRNA GCN Periodicity. Biomolecules 2020, 10, 849.
  6. Lycette, , B. E., Glickman, J. W., Roth, S. J., Cram, A. E., Kim, T. H., Krizanc, D. and Weir, M. P. (2016)  N-terminal peptide detection with optimized peptide-spectrum matching and streamlined sequence libraries. J. Proteome Res. 10.1021/acs.jproteome.5b00996.
  7.  Lin, M. S., Cherny, J. J., Fournier, C. T., Roth, S. J., Krizanc, D. and Weir, M. P. (2014). Assessment of MS/MS search algorithms with parent-protein profiling. J. Proteome Res. 13 (4), pp 1823–1832.
  8. Fournier, C.T., Cherny, J.C., Truncali, K., Robbins-Pianka, A., Lin, M.S., Krizanc, D. and Weir, M.P. (2012). Amino termini of many yeast proteins map to downstream start codons. J. Proteome Res.  11: 5712-19.
  9. Robbins-Pianka, A., Rice, M.D. and Weir, M.P. (2010). The mRNA landscape at yeast translation initiation sites. Bioinformatics 26: 2651-2655.

    Rank-ordering filter to analyze RNA secondary structure data; see Robbins-Pianka et al. 2010
  10. Weir, M. and Rice, M. (2010). TRII: A Probabilistic Scoring of Drosophila melanogaster Translation Initiation Sites. Eurasip Journal on Bioinformatics and Systems Biology. 2010: 814127.
  11. Stark, A., Lin, M. F., Kheradoiyr, P., Pedersen, J. S. et al. [including Weir, M and Rice, M] (2007). Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450: 219-32.
  12. Weir, M., Eaton, M. and Rice M. (2006). Challenging the spliceosome machine.  Genome Biology 7: R3.
  13. Weir, M. and Rice, M. (2004). Ordered Partitioning reveals extended splice site consensus information. Genomic Research 14, 67-78.
  14. Rice, M., Gladstone, W. Weir M. (2004).  Relational databases: a transparent framework for encouraging biology students to think informatically.  Cell Biology Education 3, 241-252.
  15. Das, T.K., Purkayastha-Mukherjee, C., D’Angelo, J. and Weir, M. (2002). A conserved F-box gene with unusual transcript localization. Development Genes and Evolution 212: 134-140.
  16. Raj, L., Vivekanand, P., Das, T.K., Badam, E., Fernandes, M., Finley, R.L.Jr., Brent. R., Appel, L.F., Hanes, S., and Weir, M. (2000). Targeted localized degradation of Paired protein in Drosophila development. Current Biology 10:1265-1272. (See Nature Cell Biology: News and Views, December, 2000; Pairing Partners)

    Roles of RNA secondary structure in translation initiation; see Robbins-Pianka et al. 2010
  17. Fujioka, M., Jaynes, J. B., Bejsovec, A. M. and Weir, M. (2000). Production of transgenic Drosophila. Methods in Molecular Biology, Vol.136, Developmental Biology Protocols. Vol. 2, pp. 353-364 (R. Tuan and C. Lo, eds.) Humana Press.
  18. Lan, Y., Fujioka, M., Polsgrove, R., Miskiewicz, P., Morrissey, D., Goto, T. and Weir, M. (1998). Plasticity of Drosophila Paired function. Developmental Genetics 23: 45-55.
  19. Miskiewicz, P., Morrissey, D., Lan, Y., Raj, L., Kessler, S., Fujioka, M., Goto, T., and Weir, M. (1996). Both the paired domain and homeodomain are required for in vivo function of Drosophila Paired. Development 122: 2709-2718
  20. Fujioka, M., Miskiewicz, P., Raj, L., Gulledge, A.A., Weir, M., and Goto, T. (1996). Drosophila Paired regulates late even-skipped expression through a composite binding site for the paired domain and the homeodomain. Development 122: 2697-2707.
  21. Cai, J., Lan, Y., Appel, L. F., and Weir, M. (1994). Dissection of the Drosophila Paired Protein: Functional requirements for conserved motifs. Mechanisms of Development 47: 139-150.
  22. Ananthan, J., Morrissey, D., Baler, R., Lan, Y., Weir, M., and Voellmy, R. (1993). Synergistic activation of transcription is mediated by the N-terminal domain of Drosophila fushi tarazu homeoprotein and can occur without DNA binding by the protein Molecular and Cellular Biology 13: 1599-1609.
  23. Morrissey, D., Askew, D., Raj, L., and Weir, M. (1991). Functional dissection of the paired segmentation gene in Drosophila embryos. Genes and Development 5: 1684-1696.
  24. Kamb, A., Weir, M., Rudy, B., Varmus, H. and Kenyon, C. (1989). Identification of genes from pattern formation, tyrosine kinase and potassium channel families by DNA amplification. Proc. Natl. Acad. Sci. USA 12: 4372-4376.
  25. Weir, M. P., and Kornberg, T. (1985). Patterns of engrailed and fushi tarazu transcripts reveal novel intermediate stages in Drosophila segmentation. Nature 318: 433-445.