Etsuko Moriyama
Etsuko Moriyama
Associate Professor

Ph.D. from Ochanomizu University, Japan
Contact Information
403 Manter Hall
402.472.4979

 

Research Interests


I am interested in bioinformatics, molecular evolution, and molecular population genetics. Owing to many genome projects, almost infinite amount of molecular data is becoming available. They are filled with evolutionary footprints. My interest revolves around mining such information from sequence data, reconstructing the evolutionary process of sequences, genes, and genomes, and applying knowledge we gain from these analyses for protein function prediction and gene mining. Current projects include: 1) development of alignment-free classification methods that can be efficiently and accurately applied to G-protein coupled receptor and other extremely divergent protein superfamily, 2) mining these proteins from diverse genomes, 3) molecular evolutionary analysis of GPCR and other extremely divergent protein superfamily to understand the evolutionary mechanisms of these protein functions, 4) development of sequence simulation methods that incorporate dynamic protein evolution including insertion/deletion, domain structure and shuffling, and 5) improvement of phylogenetic and multiple alignment methods for divergent protein evolution. I am also interested in synonymous codon usage. Although synonymous codon substitutions do not change amino acids, they are not neutral to selection. It makes synonymous codon usage a unique and informative quantity for studying molecular evolution at different levels. One of my goals is to incorporate such information in bioinformatics tools and achieve thorough and multi-dimensional understanding of genomic data.

Publications


Klopffleisch, K., Phan, N., Augustin, K., Bayne, R. S., Booker, K. S., Botella, J. R., Carpita, N. C., Carr, T., Chen, J.-G., Cooke, T. R., Frick-Cheng, A., Friedman, E. J., Fulk, B., Hahn, M. G., Jiang, K., Jorda, L., Kruppe, L., Liu, C., Lorek, J., McCann, M. C., Molina, A., Moriyama, E. N., Mukhtar, M. S., Mudgil, Y., Pattathil, S., Schwarz, J., Seta, S., Tan, M., Temp, U., Trusov, Y., Urano, D., Welter, B., Yang, J., Panstruga, R., Uhrig, J. F. and Jones, A. M. (2011) Arabidopsis G protein interactome reveals connections to cell wall carbohydrates and morphogenesis. Molecular Systems Biology 7: 532.

Anderson, C. L., Strope, C. L., and Moriyama, E. N. (2011) Assessing multiple sequence alignments using visual tools. In Bioinformatics: Trends and Methodologies (ed. Mahdavi, M. A.) InTech (ISBN 978-953-307-282-1)

Anderson, C. L., Strope, C. L. and Moriyama, E. N. (2011) SuiteMSA: Visual tools for multiple sequence alignment comparison and molecular sequence simulation. BMC Bioinformatics 12: 184 (PMCID: 3133551)

Strope, P. K., Nickerson, K. W., Harris, S. D. and Moriyama, E. N. (2011) Molecular evolution of urea amidolyase and urea carboxylase in fungi. BMC Evolutionary Biology 11: 80 (PMCID: 3073912)

Opiyo, S. O., Pardy, R. L., Moriyama, H. and Moriyama, E. N. (2010) Evolution of the Kdo2-lipid A biosynthesis in bacteria. BMC Evolutionary Biology 10: 362 (PMCID: 3087551)

Benson, A. K., Kelly, S. A., Legge, R., Ma, F., Low, S. J., Kim, J., Zhang, M., Oh, P. L., Nehrenberg, D., Hua, K., Kachman, S. D., Moriyama, E. N., Walter, J., Peterson, D. A. and Pomp, D. (2010) Individuality in gut microbiota composition is a complex, polygenic trait shaped by multiple environmental and host genetic factors. Proc Natl Acad Sci USA107: 18933-18938 (PMCID: 2973891)

Moriyama, E. N., Scott, S. D., and Soh, L.-K. (2010) Editorial Int. J. Bioinformatics Research and Applications 6 (Guest Editors for Special Issue: Biotechnology and Bioinformatics Symposium (BIOT-2009))

Prokupek, A. M., Eyun, S.-I., Ko, L., Moriyama, E. N., and Harshman, L. G. (2010) Molecular evolutionary analysis of seminal receptacle sperm storage organ genes of Drosophila melanogaster. Journal of Evolutionary Biology 23: 1386-1398(PMID: 20500366)

Opiyo, S. O. and Moriyama, E. N. (2010) Mining Cytochrome b561 from plant genomes. Int. J. Bioinformatics Research and Applications 6: 209-221 (Special Issue: Biotechnology and Bioinformatics Symposium: BIOT-08) (PMCID: 2846449)

Oh, P. L., Benson, A. K., Peterson, D. A., Patil, P. B., Moriyama, E. N., Roos, S., and Walter, J. (2010) Diversification of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution. ISME Journal 4: 377-387 (PMID: 19924154)

Moriyama, E. N. and Opiyo, S. O. (2010) Bioinformatics of Seven-Transmembrane Receptors in Plant Genomes. Pp. 251-277 in Yalovsky, S., Baluska, F., and Jones, A. eds. Integrated G Proteins Signaling in Plants, Springer-Verlag, Berlin Heidelberg.

Strope, C. L., Abel, K., Scott, S. D., and Moriyama, E. N. (2009) Biological sequence simulation for testing complex evolutionary hypotheses: indel-Seq-Gen version 2.0. Mol Biol Evol 26: 2581-2593 (PMCID: 2760465)

Lu, G., Wang, Z., Jones, A. M., and Moriyama, E. N. (2009) 7TMRmine: A Web server for hierarchical mining of 7TMR proteins. BMC Genomics 10: 275 (PMCID: 2718930)

Martínez, I., Wallace, G., Zhang, C., Legge, R., Benson, A. K., Carr, T. P., Moriyama, E. N., and Walter, J. (2009) Dietary modulation of the gut microbial-host metabolic interplay in a hamster model for hypercholesterolemia. Applied and Environmental Microbiology 75: 4175-4184 (PMCID: 2698331)

Opiyo, S. O. and Moriyama, E. N. (2009) Mining the Arabidopsis and rice genomes for cyclophilin protein families. Int. J. Bioinformatics Research and Applications 5: 295-309 (PMCID: 2697455)

Prokupek, A., Hoffmann, F., Eyun, S. I., Moriyama, E., Zhou, M. and Harshman, L. (2008) Expressed sequence tag analysis of Drosophila spermatheca genes: protein evolution and identity. Evolution 62: 2936-2947 (PMID: 18752616)

Veerappan, C. S., Avramova, Z. and Moriyama, E. N. (2008) Evolution of SET-domain protein families in the unicellular and multicellular Ascomycota fungi. BMC Evolutionary Biology 8: 190 (PMCID: 2474616)

Vicario, S., Moriyama, E. N. and Powell, J. R. (2007) Codon usage in twelve species of Drosophila. BMC Evolutionary Biology 7: 226 (PMCID: 2213667)

Johnston, C. A., Temple, B. R., Chen, J.-G., Gao, Y., Moriyama, E. N., Jones, A. M., Siderovski, D. P. and Willard, F. S. (2007) Comment on "A G protein-coupled receptor is a plasma membrane receptor for the plant hormone abscisic acid". Science 318: 914 (PMID: 17991845)

Strope, P. K. and Moriyama, E. N. (2007) Simple alignment-free methods for protein classification: a case study from G-protein coupled receptors. Genomics 89: 602-612 (PMID: 17336495)

Xia, X., Huang, H., Carullo, M., Betran, E., and Moriyama, E. N. (2007) Conflict between translation initiation and elongation in vertebrate mitochondrial genomes. PLoS ONE 2: e227 (PMCID: 1794132)

Strope, C. L., Scott, S. D. and Moriyama, E. N. (2007) indel-Seq-Gen: a new protein family simulator incorporating domains, motifs, and indels. Mol Biol Evol 24: 640-649 (PMID: 17158778)

Opiyo, S. O. and Moriyama, E. N. (2007) Protein family classification with partial least squares. J Proteome Res 6: 846-853 (PMID: 17269741)

Moriyama, E. N., Strope, P. K., Opiyo, S. O., Chen, Z. and Jones, A. M. (2006) Mining the Arabidopsis thaliana genome for highly-divergent seven transmembrane receptors. Genome Biology 7: R96 (PMCID: 1794564)

Lu, G., Jiang, L., Kotalik, R. M., Rowley, T. W., Zhang, L., Chen, X. J., and Moriyama, E. N. (2006) GenomeBlast: a web tool for small genome comparison. BMC Bioinformatics 7: S18 (PMCID: 1780113)

Moriyama, E. N. and J. Kim. (2005) Protein family classification with discriminant function analysis. Pp. 121-132 in Gustafson, J. P., Shoemaker, R. and Snape, J. W. eds. Genome Exploitation: Data Mining the Genome. Springer, New York.

Simbahan, J., Kurth, E., Schelert, J., Moriyama, E. N., Jovanovich, S. and Blum, P. (2005) Community analysis of a mercury hotspring support domain-specific forms of 3 mercuric reductase. Appl Environ Microbiol 71: 8836-8845 (PMCID: 1317467)

Lu, G. and E. N. Moriyama (2004) Vector NTI, a balanced all-in-one sequence analysis suite. Briefings in Bioinformatics 5: 1-11 (PMID: 15606974)

Sainz, A. C., L. V. Mauro, E. N. Moriyama, and B. A. García (2004) Phylogeny of triatomine vectors of Trypanosoma cruzisuggested by mitochondrial DNA sequences. Genetica 121: 229-240 (PMID: 15521421)

Powell, J. R., E. Sezzi, E. N. Moriyama, J. M. Gleason and A. Caccone (2003) Analysis of a shift in codon usage inDrosophila. J Mol Evol, 57: S214-S225 (PMID: 15008418)

Dorer, D.R., J. A. Rudnick, E. N. Moriyama and A. C. Christensen (2003) A family of genes clustered at the Triplo-lethal locus of Drosophila melanogaster has an unusual evolutionary history and significant synteny with Anopheles gambiae.Genetics, 165: 613-621 (PMCID: 1462804)

Moriyama, E. N. (2003) Codon Usage. in Cooper, D. N. ed. Nature Encyclopedia of the Human Genome. Nature Publishing Group, Macmillan Publishers Ltd, London.

García, B. A., E. N. Moriyama and J. R. Powell (2001) Mitochondrial DNA sequences of Triatomines (Hemiptera: Reduviidae): Phylogenetic relationships. J Med Entomol 38: 675-683 (PMID: 11580040)

Kim, J., E. N. Moriyama, C. G. Warr, P. J. Clyne and J. R. Carlson (2000) Identification of novel multi-transmembrane proteins from genomic databases using quasi-periodic structural properties. Bioinformatics 16: 767-775 (PMID: 11108699)