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Items: 1 to 50 of 67

1.

Next-generation transcriptome assembly and analysis: Impact of ploidy.

Voshall A, Moriyama EN.

Methods. 2019 Jun 6. pii: S1046-2023(18)30380-3. doi: 10.1016/j.ymeth.2019.06.001. [Epub ahead of print]

PMID:
31176772
2.

MOCASSIN-prot: a multi-objective clustering approach for protein similarity networks.

Keel BN, Deng B, Moriyama EN.

Bioinformatics. 2018 Apr 15;34(8):1270-1277. doi: 10.1093/bioinformatics/btx755.

PMID:
29186344
3.

miRNAs in the alga Chlamydomonas reinhardtii are not phylogenetically conserved and play a limited role in responses to nutrient deprivation.

Voshall A, Kim EJ, Ma X, Yamasaki T, Moriyama EN, Cerutti H.

Sci Rep. 2017 Jul 14;7(1):5462. doi: 10.1038/s41598-017-05561-0.

4.

Advantages of an Improved Rhesus Macaque Genome for Evolutionary Analyses.

Gradnigo JS, Majumdar A, Norgren RB Jr, Moriyama EN.

PLoS One. 2016 Dec 2;11(12):e0167376. doi: 10.1371/journal.pone.0167376. eCollection 2016.

5.

Whole genomic sequence analysis of Bacillus infantis: defining the genetic blueprint of strain NRRL B-14911, an emerging cardiopathogenic microbe.

Massilamany C, Mohammed A, Loy JD, Purvis T, Krishnan B, Basavalingappa RH, Kelley CM, Guda C, Barletta RG, Moriyama EN, Smith TP, Reddy J.

BMC Genomics. 2016 Aug 22;17 Suppl 7:511. doi: 10.1186/s12864-016-2900-2.

6.

Genome Sequence of Streptomyces aureofaciens ATCC Strain 10762.

Gradnigo JS, Somerville GA, Huether MJ, Kemmy RJ, Johnson CM, Oliver MG, Moriyama EN.

Genome Announc. 2016 Jun 23;4(3). pii: e00615-16. doi: 10.1128/genomeA.00615-16.

7.

Molecular Evolution and Functional Divergence of Trace Amine-Associated Receptors.

Eyun SI, Moriyama H, Hoffmann FG, Moriyama EN.

PLoS One. 2016 Mar 10;11(3):e0151023. doi: 10.1371/journal.pone.0151023. eCollection 2016.

8.

Carbon dioxide receptor genes and their expression profile in Diabrotica virgifera virgifera.

Rodrigues TB, Moriyama EN, Wang H, Khajuria C, Siegfried BD.

BMC Res Notes. 2016 Jan 8;9:18. doi: 10.1186/s13104-015-1794-4.

9.

Transcriptional analysis of susceptible and resistant European corn borer strains and their response to Cry1F protoxin.

Nanoth Vellichirammal N, Wang H, Eyun SI, Moriyama EN, Coates BS, Miller NJ, Siegfried BD.

BMC Genomics. 2015 Jul 29;16:558. doi: 10.1186/s12864-015-1751-6.

10.

Identification of AGO3-associated miRNAs and computational prediction of their targets in the green alga Chlamydomonas reinhardtii.

Voshall A, Kim EJ, Ma X, Moriyama EN, Cerutti H.

Genetics. 2015 May;200(1):105-21. doi: 10.1534/genetics.115.174797. Epub 2015 Mar 13.

11.

De novo assembly of the common marmoset transcriptome from NextGen mRNA sequences.

Maudhoo MD, Ren D, Gradnigo JS, Gibbs RM, Lubker AC, Moriyama EN, French JA, Norgren RB Jr.

Gigascience. 2014 Sep 19;3:14. doi: 10.1186/2047-217X-3-14. eCollection 2014.

12.

Molecular evolution of glycoside hydrolase genes in the Western corn rootworm (Diabrotica virgifera virgifera).

Eyun SI, Wang H, Pauchet Y, Ffrench-Constant RH, Benson AK, Valencia-Jiménez A, Moriyama EN, Siegfried BD.

PLoS One. 2014 Apr 9;9(4):e94052. doi: 10.1371/journal.pone.0094052. eCollection 2014. Erratum in: PLoS One. 2014;9(7):e102818.

13.

Comparative studies of differential gene calling using RNA-Seq data.

Zheng X, Moriyama EN.

BMC Bioinformatics. 2013;14 Suppl 13:S7. doi: 10.1186/1471-2105-14-S13-S7. Epub 2013 Oct 1.

14.

Reductive evolution and the loss of PDC/PAS domains from the genus Staphylococcus.

Shah N, Gaupp R, Moriyama H, Eskridge KM, Moriyama EN, Somerville GA.

BMC Genomics. 2013 Jul 31;14:524. doi: 10.1186/1471-2164-14-524.

15.

Evolution of a large, conserved, and syntenic gene family in insects.

Shah N, Dorer DR, Moriyama EN, Christensen AC.

G3 (Bethesda). 2012 Feb;2(2):313-9. doi: 10.1534/g3.111.001412. Epub 2012 Feb 1.

16.

Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesis.

Klopffleisch K, Phan N, Augustin K, Bayne RS, Booker KS, Botella JR, Carpita NC, Carr T, Chen JG, Cooke TR, Frick-Cheng A, Friedman EJ, Fulk B, Hahn MG, Jiang K, Jorda L, Kruppe L, Liu C, Lorek J, McCann MC, Molina A, Moriyama EN, Mukhtar MS, Mudgil Y, Pattathil S, Schwarz J, Seta S, Tan M, Temp U, Trusov Y, Urano D, Welter B, Yang J, Panstruga R, Uhrig JF, Jones AM.

Mol Syst Biol. 2011 Sep 27;7:532. doi: 10.1038/msb.2011.66.

17.

SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation.

Anderson CL, Strope CL, Moriyama EN.

BMC Bioinformatics. 2011 May 21;12:184. doi: 10.1186/1471-2105-12-184.

18.

Molecular evolution of urea amidolyase and urea carboxylase in fungi.

Strope PK, Nickerson KW, Harris SD, Moriyama EN.

BMC Evol Biol. 2011 Mar 29;11:80. doi: 10.1186/1471-2148-11-80.

19.

Evolution of the Kdo2-lipid A biosynthesis in bacteria.

Opiyo SO, Pardy RL, Moriyama H, Moriyama EN.

BMC Evol Biol. 2010 Nov 24;10:362. doi: 10.1186/1471-2148-10-362.

20.

Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors.

Benson AK, Kelly SA, Legge R, Ma F, Low SJ, Kim J, Zhang M, Oh PL, Nehrenberg D, Hua K, Kachman SD, Moriyama EN, Walter J, Peterson DA, Pomp D.

Proc Natl Acad Sci U S A. 2010 Nov 2;107(44):18933-8. doi: 10.1073/pnas.1007028107. Epub 2010 Oct 11.

21.

Molecular evolutionary analysis of seminal receptacle sperm storage organ genes of Drosophila melanogaster.

Prokupek AM, Eyun SI, Ko L, Moriyama EN, Harshman LG.

J Evol Biol. 2010 Jul;23(7):1386-98. doi: 10.1111/j.1420-9101.2010.01998.x. Epub 2010 May 24.

22.

Mining Cytochrome b561 proteins from plant genomes.

Opiyo SO, Moriyama EN.

Int J Bioinform Res Appl. 2010;6(2):209-21.

23.

Diversification of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution.

Oh PL, Benson AK, Peterson DA, Patil PB, Moriyama EN, Roos S, Walter J.

ISME J. 2010 Mar;4(3):377-87. doi: 10.1038/ismej.2009.123. Epub 2009 Nov 19.

PMID:
19924154
24.

Biological sequence simulation for testing complex evolutionary hypotheses: indel-Seq-Gen version 2.0.

Strope CL, Abel K, Scott SD, Moriyama EN.

Mol Biol Evol. 2009 Nov;26(11):2581-93. doi: 10.1093/molbev/msp174. Epub 2009 Aug 3.

25.

7TMRmine: a Web server for hierarchical mining of 7TMR proteins.

Lu G, Wang Z, Jones AM, Moriyama EN.

BMC Genomics. 2009 Jun 19;10:275. doi: 10.1186/1471-2164-10-275.

26.

Mining the Arabidopsis and rice genomes for cyclophilin protein families.

Opiyo SO, Moriyama EN.

Int J Bioinform Res Appl. 2009;5(3):295-309.

27.

Diet-induced metabolic improvements in a hamster model of hypercholesterolemia are strongly linked to alterations of the gut microbiota.

Martínez I, Wallace G, Zhang C, Legge R, Benson AK, Carr TP, Moriyama EN, Walter J.

Appl Environ Microbiol. 2009 Jun;75(12):4175-84. doi: 10.1128/AEM.00380-09. Epub 2009 May 1.

28.

Evolution of SET-domain protein families in the unicellular and multicellular Ascomycota fungi.

Veerappan CS, Avramova Z, Moriyama EN.

BMC Evol Biol. 2008 Jul 1;8:190. doi: 10.1186/1471-2148-8-190.

29.

Codon usage in twelve species of Drosophila.

Vicario S, Moriyama EN, Powell JR.

BMC Evol Biol. 2007 Nov 15;7:226.

30.

Comment on "A G protein coupled receptor is a plasma membrane receptor for the plant hormone abscisic acid".

Johnston CA, Temple BR, Chen JG, Gao Y, Moriyama EN, Jones AM, Siderovski DP, Willard FS.

Science. 2007 Nov 9;318(5852):914; author reply 914.

31.

Simple alignment-free methods for protein classification: a case study from G-protein-coupled receptors.

Strope PK, Moriyama EN.

Genomics. 2007 May;89(5):602-12. Epub 2007 Mar 2.

32.

Conflict between translation initiation and elongation in vertebrate mitochondrial genomes.

Xia X, Huang H, Carullo M, Betrán E, Moriyama EN.

PLoS One. 2007 Feb 21;2(2):e227.

33.

Protein family classification with partial least squares.

Opiyo SO, Moriyama EN.

J Proteome Res. 2007 Feb;6(2):846-53.

PMID:
17269741
34.

GenomeBlast: a web tool for small genome comparison.

Lu G, Jiang L, Helikar RM, Rowley TW, Zhang L, Chen X, Moriyama EN.

BMC Bioinformatics. 2006 Dec 12;7 Suppl 4:S18.

35.

indel-Seq-Gen: a new protein family simulator incorporating domains, motifs, and indels.

Strope CL, Scott SD, Moriyama EN.

Mol Biol Evol. 2007 Mar;24(3):640-9. Epub 2006 Dec 8.

PMID:
17158778
36.

Mining the Arabidopsis thaliana genome for highly-divergent seven transmembrane receptors.

Moriyama EN, Strope PK, Opiyo SO, Chen Z, Jones AM.

Genome Biol. 2006;7(10):R96. Epub 2006 Oct 25.

37.

Vector NTI, a balanced all-in-one sequence analysis suite.

Lu G, Moriyama EN.

Brief Bioinform. 2004 Dec;5(4):378-88.

PMID:
15606974
38.

Phylogeny of triatomine vectors of Trypanosoma cruzi suggested by mitochondrial DNA sequences.

Sainz AC, Mauro LV, Moriyama EN, García BA.

Genetica. 2004 Jul;121(3):229-40.

PMID:
15521421
39.

Analysis of a shift in codon usage in Drosophila.

Powell JR, Sezzi E, Moriyama EN, Gleason JM, Caccone A.

J Mol Evol. 2003;57 Suppl 1:S214-25.

PMID:
15008418
41.

Mitochondrial DNA sequences of triatomines (Hemiptera: Reduviidae): phylogenetic relationships.

García BA, Moriyama EN, Powell JR.

J Med Entomol. 2001 Sep;38(5):675-83.

PMID:
11580040
42.

Identification of novel multi-transmembrane proteins from genomic databases using quasi-periodic structural properties.

Kim J, Moriyama EN, Warr CG, Clyne PJ, Carlson JR.

Bioinformatics. 2000 Sep;16(9):767-75.

PMID:
11108699
43.

Characterization of the soluble guanylyl cyclase beta-subunit gene in the mosquito Anopheles gambiae.

Caccone A, García BA, Mathiopoulos KD, Min GS, Moriyama EN, Powell JR.

Insect Mol Biol. 1999 Feb;8(1):23-30.

PMID:
9927171
44.
45.

Genome size and intron size in Drosophila.

Moriyama EN, Petrov DA, Hartl DL.

Mol Biol Evol. 1998 Jun;15(6):770-3. No abstract available.

PMID:
9615458
46.

Codon usage bias and tRNA abundance in Drosophila.

Moriyama EN, Powell JR.

J Mol Evol. 1997 Nov;45(5):514-23.

PMID:
9342399
47.

Synonymous substitution rates in Drosophila: mitochondrial versus nuclear genes.

Moriyama EN, Powell JR.

J Mol Evol. 1997 Oct;45(4):378-91.

PMID:
9321417
48.

Evolution of codon usage bias in Drosophila.

Powell JR, Moriyama EN.

Proc Natl Acad Sci U S A. 1997 Jul 22;94(15):7784-90.

49.

MITOCHONDRIAL DNA PHYLOGENIES FOR THE DROSOPHILA OBSCURA GROUP.

Gleason JM, Caccone A, Moriyama EN, White KP, Powell JR.

Evolution. 1997 Apr;51(2):433-440. doi: 10.1111/j.1558-5646.1997.tb02430.x.

PMID:
28565356
50.

A molecular phylogeny for the Drosophila melanogaster subgroup and the problem of polymorphism data.

Caccone A, Moriyama EN, Gleason JM, Nigro L, Powell JR.

Mol Biol Evol. 1996 Nov;13(9):1224-32.

PMID:
8896375

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