Voshall, A. and Moriyama, E. N. (2019) Next-generation transcriptome assembly and analysis: Impact of ploidy, Methods doi: 10.1016/j.ymeth.2019.06.001 (PMCID: 31176772)

Voshall, A. and Moriyama, E. N. (2018) "Chapter 2. Next-generation transcriptome assembly: strategies and performance analysis", in Bioinformatics in the Era of Post Genomics and Big Data (ed. Abdurakhmonov, I). InTech (ISBN 978-1-78923-268-4)

Keel, B. H., Deng, B. and Moriyama, E. N. (2018) MOCASSIN-prot: A multi-objective clustering approach for protein similarity networks. Bioinformatics 34: 1270-1277 (PMID: 29186344) — Supplemental materials —

Voshall, A., Kim, E.-J., Ma, X., Yamasaki, T., Moriyama, E. N., and Cerutti, H. (2017) miRNAs in the alga Chlamydomonas reinhardtii are not phylogenetically conserved and play a limited role in responses to nutrient deprivation. Scientific Reports 7: 5462 (PMCID: 5511227)

Pavlovikj, N., Moriyama, E. N., and Jitender, S. D. (2017) Comparative analysis of alignment tools for nanopore reads. In 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (eds. Hu, X. et al.), pp 169-174.

Wang, H., Eyun, S.-I., Arora, K., Tan, S. Y., Gandra, P., Moriyama, E., Khajuria, C., Jurzenski, J., Li, H., Donahue, M., Narva, K., Siegfried, B. (2017) Patterns of gene expression in western corn rootworm (Diabrotica virgifera virgifera) neonates, challenged with Cry34Ab1, Cry35Ab1 and Cry34/35Ab1, based on next-generation sequencing. Toxins (Basel) 9: 124 (PMCID: 5408198)

DeLong, J. P., Brassil, C. E., Erickson1, E. K., Forbes, V. E., Moriyama, E. N., and Riekhof, W. R. (2017) Breaking the temperature-size rule with dynamic thermal reaction norms and body size oscillations. Evolutionary Ecology Research 18: 293-303

Gradnigo, J. S., Norgren Jr., R. B., and Moriyama, E. N. (2016) Advantages of an improved rhesus macaque genome for evolutionary analyses. PLoS ONE 11: e0167376 (PMCID: 5135103)

Massilamany, C., Akram, M., Loy, J. D., Krishnan, B., Basavalingappa, R. H., Kelly, C., Guda, C., Barletta, R. G., Moriyama, E. N., Smith, T. P., and Reddy, J. (2016) Whole genomic sequence analysis of Bacillus infantis: defining the genetic blueprint of strain NRRL B-14911, an emerging cardiopathogenic microbe. BMC Genomics Supple 7: 511 (PMCID: 5001198)

Gradnigo, J. S., Somerville, G. A., Huether, M. J., Kemmy, R. J., Johnson, C. M., Oliver, M. G., and Moriyama, E. N. (2016) Genome sequence of Streptomyces aureofaciens ATCC 10762. Genome Announcements 4: e00615-e00616 (PMCID: 4919415)

Eyun, S.-I., Moriyama, H., Hoffman, F., and Moriyama, E. N. (2016) Molecular evolution and functional divergence of trace amine-associated receptors. PLoS ONE 11: e0151023 (PMCID: 4786312) — Supplemental materials —

Rodrigues, T. B., Moriyama, E. N., Wang, H., Khajuria, C., and Siegfried, B. D. (2016) Carbon dioxide receptor genes and their expression profile in Diabrotica virgifera virgifera. BMC Res Notes 9: 18 (PMCID: 4706698)

Vellichirammal N. N., Wang, H., Eyun, S.-I., Moriyama, E. N., Coates, B. S., Miller, N. J., and Siegfried, B. D. (2015) Transcriptional analysis of susceptible and resistant European corn borer strains and its response to Cry1F protoxin. BMC Genomics 16: 558 (PMCID: 4518661)

Singh, R., Gradnigo, J., White, D., Lipzen, A., Martin, J., Schackwitz, W., Moriyama, E. N., and Blum, P. (2015) Complete genome sequence of an evolved Thermotoga maritima isolate. Genome Announcements 3: e00557-15 (PMCID: 4447916)

McCarthy, S., Gradnigo, J., Johnson, T., Payne, S., Lipzen, A., Martin, J., Schackwitz, W., Moriyama, E. N., and Blum, P. (2015) Complete genome sequence of Sulfolobus solfataricus strain 98/2 and evolved derivatives. Genome Announcements 3: e00549-15 (PMCID: 4447912)

Voshall, A., Kim, E.-J., Ma, X., Moriyama, E. N., and Cerutti, H. (2015) Identification of AGO3 associated miRNAs and computational prediction of their targets in the green alga Chlamydomonas reinhardtii. Genetics 200: 105-121 (PMCID: 4423357)

Maudhoo, M. D., Ren, D. Gradnigo, J. S., Gibbs, R. M., Lubker, A. C., Moriyama, E. N., French, J. A., and Norgren Jr, .R. B. (2014) De novo assembly of the common marmoset transcriptome from NextGen mRNA sequences. GigaScience 3: 14 (PMCID: 4169894)

Eyun, S.-I., Wang, H., Pauchet, Y., Ffrench-Constant, R.H., Benson, A.K., Valencia-Jiménez, A., Moriyama, E.N., and Siegfried, B.D. (2014) Molecular evolution of glycoside hydrolase genes in the western corn rootworm (Diabrotica virgifera virgifera). PLoS One 9: e94052 (PMCID: 3981738) — Supplemental materials —

Yamasaki, T., Voshall, A., Kim, E.-J., Moriyama, E. N., Cerutti, H., and Ohama T. (2013) Complementarity to a miRNA seed region is sufficient to induce moderate repression of a target transcript in the unicellular green alga Chlamydomonas reinhardtii. The Plant Journal 76: 1045-1056 (PMID: 24127635)

Zheng, X. and Moriyama, E. N. (2013) Comparative studies of differential gene calling using RNA-Seq data. BMC Bioinformatics 14: S7 (PMCID: 3891352)

Shah, N., Gaupp, R., Moriyama, H., Eskridge, K. M., Moriyama, E. N.*, and Somerville, G. A.* (2013) Reductive evolution and the loss of PDC/PAS domains from the genus Staphylococcus. BMC Genomics 14: 524 (PMCID: 3284338)

Deng, B., Hinds, B., Zheng, X., and Moriyama, E. N. (2013) Bioinformatic game theory and its application to biological affinity networks. Applied Mathematics 4: 92-108.

Ma, X., Kim, E.-J., Kook, I., Ma, F., Voshall, A., Moriyama, E. N., and Cerutti, H. (2013) Small interfering RNA-mediated translation repression alters ribosome sensitivity to inhibition by cycloheximide in Chlamydomonas reinhardtii. Plant Cell 25: 985-998 (PMCID: 3634701)

Wilson, R. A., Fernandez, J., Quispe, C. F., Gradnigo, J., Seng, A., Moriyama, E. N., and Wright, J. D. (2012) Towards defining nutrient conditions encountered by the rice blast fungus during host infection. PLoS ONE 7: e47392 (PMCID: 3468542)

Shah, N., Dorer, D. R., Moriyama, E. N., and Christensen, A. C. (2012) Evolution of a large, conserved and syntenic gene family in insects. G3: Genes, Genomes, Genetics 2: 313-319 (PMCID: 3284338) — Supplemental materials —

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 (PMCID: 3202803) — AGIdb: Arabidopsis G-signaling Interactome Database —

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) — Supplemental files —

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) — SuiteMSA website —

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 USA 107: 18933-18938 (Published online before print October 11, 2010, doi: 10.1073/pnas.1007028107) (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) — the project home page —

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) — Supplementary tables — (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 (Advanced Access published in 11/2009; doi: 10.1038/ismej.2009.123) (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 (Advanced Access published in 08/2009; doi: 10.1093/molbev/msp174) (PMCID: 2760465) — indel-Seq-Gen website —

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) — 7TMRmine website —

Martínez, I., Wallace, G., Zhang, C., Legge, R., Benson, A. K., Carr, T. P., Moriyama, E. N., and Walter, J. (2009) Diet-induced metabolic improvements in a hamster model of hypercholesterolemia are strongly linked to alterations of the gut microbiota. 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 (Special Issue: Biotechnology and Bioinformatics Symposium (BIOT-07)) (PMCID: 2697455) — Supplementary tables —

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

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 (doi:10.1186/1471-2148-8-190) (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 (doi: 10.1016/j.ygeno.2007.01.008) (PMID: 17336495)
— Supplementary data (Figure, Tables, Datasets used) —

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 (doi:10.1371/journal.pone.0000227) (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 (Advanced Access published in 12/2006; doi: 10.1093/molbev/msl195) (PMID: 17158778) — Preprint PDF file, Supplementary files, indel-Seq-Gen Web site —

Opiyo, S. O. and Moriyama, E. N. (2007) Protein family classification with partial least squares. J Proteome Res 6: 846-853 (Web released in 12/2006, doi: 10.1021/pr060534k) (PMID: 17269741) — Supplementary Tables —

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) — Supplementary Materials —

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) — GenomeBlast web —

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. (preprint PDF file)

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 cruzi suggested 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 in Drosophila. 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. (preprint PDF file)

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)

Caccone, A., B. A. García, K. D. Mathiopoulos, G.-S. Min, E. N. Moriyama and J. R. Powell (1999) Characterization of the soluble guanylyl cyclase b-subunit gene in the mosquito Anopheles gambiae. Insect Mol Biol 8: 23-30 (PMID: 9927171)

Moriyama, E. N., D. A. Petrov and D. L. Hartl (1998) Genome size and intron size in Drosophila. Mol Biol Evol 15: 770-773 (PMID: 9615458)

Moriyama, E. N. and J. R. Powell (1998) Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli. Nucleic Acids Res 26: 3188-3193 (PMCID: 147681)

Moriyama, E. N. and J. R. Powell (1998) Scientific Correspondence. Nucleic Acids Res 26: 4540 (PMCID: 147868)

Moriyama, E. N. and J. R. Powell (1997) Codon usage bias and tRNA abundance in Drosophila. J Mol Evol 45: 514-523 (PMID: 9342399)

Moriyama, E. N. and J. R. Powell (1997) Synonymous substitution rates of Drosophila: mitochondrial versus nuclear genes. J Mol Evol 45: 378-391 (PMID: 9321417)

Powell, J. R. and E. N. Moriyama (1997) Evolution of codon usage bias in Drosophila. Proc Natl Acad Sci USA 94: 7784-7790 (PMCID: 33704)

Gleason, J. M., A. Caccone, E. N. Moriyama, K. P. White and J. R. Powell (1997) Mitochondrial DNA phylogenies for the Drosophila obscura group. Evolution 51: 433-440.

Moriyama, E. N. and J. R. Powell (1996) Intraspecific nuclear DNA variation in Drosophila. Mol Biol Evol 13: 261-277 (PMID: 8583899)

Caccone, A., E. N. Moriyama, J. M. Gleason, L. Nigro and J. R. Powell (1996) A molecular phylogeny for the Drosophila melanogaster subgroup and the problem of polymorphism data. Mol Biol Evol 13: 1224-1232 (PMID: 8896375)

Nurminsky, D. I., E. N. Moriyama, E. R. Lozovskaya and D. L. Hartl (1996) Molecular phylogeny and genome evolution in the Drosophila virilis species group: duplications of the alcohol dehydrogenase gene. Mol Biol Evol 13: 132-149 (PMID: 8583887)

Fushitani, K., K. Higashiyama, E. N. Moriyama, K. Imai and K. Hosokawa (1996) The amino acid sequences of two a chains of hemoglobins from Komodo dragon Varanus komodoensis and phylogenetic relationships of amniotes. Mol Biol Evol 13: 1039-1043 (PMID: 8752011)

Lohe, A. R., E. N. Moriyama, D.-A. Lidholm and D. L. Hartl (1995) Horizontal transmission, vertical inactivation, and stochastic loss of Mariner-like transposable elements. Mol Biol Evol 12: 62-72 (PMID: 7877497)

Hartl, D. L., E. N. Moriyama and S. A. Sawyer (1994) Selection intensity for codon bias. Genetics 138: 227-234 (PMCID: 1206133)

Moriyama, E. N. and D. L. Hartl (1993) Codon usage bias and base composition of nuclear genes in Drosophila. Genetics 135: 847-858 (PMCID: 1205521)

(last updated: June 27, 2019)

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