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Items: 1 to 20 of 90

1.

Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens.

Deschamps S, Mudge J, Cameron C, Ramaraj T, Anand A, Fengler K, Hayes K, Llaca V, Jones TJ, May G.

Sci Rep. 2016 Jun 28;6:28625. doi: 10.1038/srep28625.

PMID:
27350167
2.

Novel Meiotic miRNAs and Indications for a Role of PhasiRNAs in Meiosis.

Dukowic-Schulze S, Sundararajan A, Ramaraj T, Kianian S, Pawlowski WP, Mudge J, Chen C.

Front Plant Sci. 2016 Jun 2;7:762. doi: 10.3389/fpls.2016.00762. eCollection 2016.

3.

Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.

Wright JC, Mudge J, Weisser H, Barzine MP, Gonzalez JM, Brazma A, Choudhary JS, Harrow J.

Nat Commun. 2016 Jun 2;7:11778. doi: 10.1038/ncomms11778.

PMID:
27250503
4.

The combined influence of two agricultural contaminants on natural communities of phytoplankton and zooplankton.

Baker LF, Mudge JF, Thompson DG, Houlahan JE, Kidd KA.

Ecotoxicology. 2016 Jul;25(5):1021-32. doi: 10.1007/s10646-016-1659-1. Epub 2016 Apr 25.

PMID:
27112456
5.

Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes.

Suh A, Witt CC, Menger J, Sadanandan KR, Podsiadlowski L, Gerth M, Weigert A, McGuire JA, Mudge J, Edwards SV, Rheindt FE.

Nat Commun. 2016 Apr 21;7:11396. doi: 10.1038/ncomms11396.

6.

The plant-specific protein FEHLSTART controls male meiotic entry, initializing meiotic synchronization in Arabidopsis.

Li J, Dukowic-Schulze S, Lindquist IE, Farmer AD, Kelly B, Li T, Smith AG, Retzel EF, Mudge J, Chen C.

Plant J. 2015 Nov;84(4):659-71. doi: 10.1111/tpj.13026. Epub 2015 Oct 22.

PMID:
26382719
7.

Creating reference gene annotation for the mouse C57BL6/J genome assembly.

Mudge JM, Harrow J.

Mamm Genome. 2015 Oct;26(9-10):366-78. doi: 10.1007/s00335-015-9583-x. Epub 2015 Jul 18.

8.

Monte Carlo-based distance analysis using unit mass resolution ICP-MS data for shellfish site of origin verification.

Mudge JF, Engel ME, Ryan CN, Klein DM.

Integr Environ Assess Manag. 2015 Jul;11(3):515-6. doi: 10.1002/ieam.1648. No abstract available.

PMID:
26119767
9.

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.

Frankish A, Uszczynska B, Ritchie GR, Gonzalez JM, Pervouchine D, Petryszak R, Mudge JM, Fonseca N, Brazma A, Guigo R, Harrow J.

BMC Genomics. 2015;16 Suppl 8:S2. doi: 10.1186/1471-2164-16-S8-S2. Epub 2015 Jun 18.

10.

Polarimetric characterization of birefringent filter components.

Mudge J, Mitchell K, Tarbell T.

Appl Opt. 2015 Jan 10;54(2):259-65. doi: 10.1364/AO.54.000259.

PMID:
25967624
11.

Comparative genome analysis of non-toxigenic non-O1 versus toxigenic O1 Vibrio cholerae.

Mukherjee M, Kakarla P, Kumar S, Gonzalez E, Floyd JT, Inupakutika M, Devireddy AR, Tirrell SR, Bruns M, He G, Lindquist IE, Sundararajan A, Schilkey FD, Mudge J, Varela MF.

Genom Discov. 2014;2(1):1-15.

12.

Next-generation transcriptome sequencing, SNP discovery and validation in four market classes of peanut, Arachis hypogaea L.

Chopra R, Burow G, Farmer A, Mudge J, Simpson CE, Wilkins TA, Baring MR, Puppala N, Chamberlin KD, Burow MD.

Mol Genet Genomics. 2015 Jun;290(3):1169-80. doi: 10.1007/s00438-014-0976-4. Epub 2015 Feb 7.

PMID:
25663138
13.

Comparisons of de novo transcriptome assemblers in diploid and polyploid species using peanut (Arachis spp.) RNA-Seq data.

Chopra R, Burow G, Farmer A, Mudge J, Simpson CE, Burow MD.

PLoS One. 2014 Dec 31;9(12):e115055. doi: 10.1371/journal.pone.0115055. eCollection 2014.

14.

Draft Genome Sequences of Vancomycin-Susceptible Staphylococcus aureus Related to Heterogeneous Vancomycin-Intermediate S. aureus.

Ramaraj T, Matyi SA, Sundararajan A, Lindquist IE, Devitt NP, Schilkey FD, Lamichhane-Khadka R, Hoyt PR, Mudge J, Gustafson JE.

Genome Announc. 2014 Oct 9;2(5). pii: e01033-14. doi: 10.1128/genomeA.01033-14.

15.

In situ calibration of tunable filters: Lyot and Michelson.

Mudge J, Tarbell T.

Appl Opt. 2014 Aug 1;53(22):4978-86. doi: 10.1364/AO.53.004978.

PMID:
25090330
16.

Draft Genomes of Heterogeneous Vancomycin-Intermediate Staphylococcus aureus Strain MM66 and MM66 Derivatives with Altered Vancomycin Resistance Levels.

Matyi SA, Ramaraj T, Sundararajan A, Lindquist IE, Devitt NP, Schilkey FD, Lamichhane-Khadka R, Hoyt PR, Mudge J, Gustafson JE.

Genome Announc. 2014 Jul 10;2(4). pii: e00688-14. doi: 10.1128/genomeA.00688-14.

17.

The direct and indirect effects of a glyphosate-based herbicide and nutrients on Chironomidae (Diptera) emerging from small wetlands.

Baker LF, Mudge JF, Houlahan JE, Thompson DG, Kidd KA.

Environ Toxicol Chem. 2014 Sep;33(9):2076-85. doi: 10.1002/etc.2657. Epub 2014 Aug 7.

PMID:
24899169
18.

SNP markers identify widely distributed clonal lineages of Phytophthora colocasiae in Vietnam, Hawaii and Hainan Island, China.

Shrestha S, Hu J, Fryxell RT, Mudge J, Lamour K.

Mycologia. 2014 Jul-Aug;106(4):676-85. doi: 10.3852/13-165. Epub 2014 Jun 3.

19.

The transcriptome landscape of early maize meiosis.

Dukowic-Schulze S, Sundararajan A, Mudge J, Ramaraj T, Farmer AD, Wang M, Sun Q, Pillardy J, Kianian S, Retzel EF, Pawlowski WP, Chen C.

BMC Plant Biol. 2014 May 3;14:118. doi: 10.1186/1471-2229-14-118.

20.

Improved Hybrid Genome Assemblies of Two Strains of Bacteroides xylanisolvens, SD_CC_1b and SD_CC_2a, Obtained Using Illumina and 454 Sequencing Technologies.

Ramaraj T, Sundararajan A, Schilkey FD, Delvecchio VG, Donlon M, Ziemer C, Mudge J.

Genome Announc. 2014 Apr 3;2(2). pii: e00237-14. doi: 10.1128/genomeA.00237-14.

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