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Items: 31


The Komodo dragon (Varanus komodoensis) genome and identification of innate immunity genes and clusters.

van Hoek ML, Prickett MD, Settlage RE, Kang L, Michalak P, Vliet KA, Bishop BM.

BMC Genomics. 2019 Aug 30;20(1):684. doi: 10.1186/s12864-019-6029-y.


Novel roles for scleraxis in regulating adult tenocyte function.

Nichols AEC, Settlage RE, Werre SR, Dahlgren LA.

BMC Cell Biol. 2018 Aug 7;19(1):14. doi: 10.1186/s12860-018-0166-z.


Fusobacterium Genomics Using MinION and Illumina Sequencing Enables Genome Completion and Correction.

Todd SM, Settlage RE, Lahmers KK, Slade DJ.

mSphere. 2018 Jul 5;3(4). pii: e00269-18. doi: 10.1128/mSphere.00269-18.


RNA-Seq Analysis of Developing Pecan (Carya illinoinensis) Embryos Reveals Parallel Expression Patterns among Allergen and Lipid Metabolism Genes.

Mattison CP, Rai R, Settlage RE, Hinchliffe DJ, Madison C, Bland JM, Brashear S, Graham CJ, Tarver MR, Florane C, Bechtel PJ.

J Agric Food Chem. 2017 Feb 22;65(7):1443-1455. doi: 10.1021/acs.jafc.6b04199. Epub 2017 Feb 13.


Targeted capture enrichment and sequencing identifies extensive nucleotide variation in the turkey MHC-B.

Reed KM, Mendoza KM, Settlage RE.

Immunogenetics. 2016 Mar;68(3):219-29. doi: 10.1007/s00251-015-0893-7. Epub 2016 Jan 5.


Molt-dependent transcriptomic analysis of cement proteins in the barnacle Amphibalanus amphitrite.

Wang Z, Leary DH, Liu J, Settlage RE, Fears KP, North SH, Mostaghim A, Essock-Burns T, Haynes SE, Wahl KJ, Spillmann CM.

BMC Genomics. 2015 Oct 24;16:859. doi: 10.1186/s12864-015-2076-1.


Cutting Edge: Plasmacytoid Dendritic Cells in Late-Stage Lupus Mice Defective in Producing IFN-α.

Liao X, Li S, Settlage RE, Sun S, Ren J, Reihl AM, Zhang H, Karyala SV, Reilly CM, Ahmed SA, Luo XM.

J Immunol. 2015 Nov 15;195(10):4578-82. doi: 10.4049/jimmunol.1501157. Epub 2015 Oct 7.


High Resolution Discovery Proteomics Reveals Candidate Disease Progression Markers of Alzheimer's Disease in Human Cerebrospinal Fluid.

Hendrickson RC, Lee AY, Song Q, Liaw A, Wiener M, Paweletz CP, Seeburger JL, Li J, Meng F, Deyanova EG, Mazur MT, Settlage RE, Zhao X, Southwick K, Du Y, Holder D, Sachs JR, Laterza OF, Dallob A, Chappell DL, Snyder K, Modur V, King E, Joachim C, Bondarenko AY, Shearman M, Soper KA, Smith AD, Potter WZ, Koblan KS, Sachs AB, Yates NA.

PLoS One. 2015 Aug 13;10(8):e0135365. doi: 10.1371/journal.pone.0135365. eCollection 2015.


Alterations of a Cellular Cholesterol Metabolism Network Are a Molecular Feature of Obesity-Related Type 2 Diabetes and Cardiovascular Disease.

Ding J, Reynolds LM, Zeller T, Müller C, Lohman K, Nicklas BJ, Kritchevsky SB, Huang Z, de la Fuente A, Soranzo N, Settlage RE, Chuang CC, Howard T, Xu N, Goodarzi MO, Chen YD, Rotter JI, Siscovick DS, Parks JS, Murphy S, Jacobs DR Jr, Post W, Tracy RP, Wild PS, Blankenberg S, Hoeschele I, Herrington D, McCall CE, Liu Y.

Diabetes. 2015 Oct;64(10):3464-74. doi: 10.2337/db14-1314. Epub 2015 Jul 7.


Modulation of the spleen transcriptome in domestic turkey (Meleagris gallopavo) in response to aflatoxin B1 and probiotics.

Monson MS, Settlage RE, Mendoza KM, Rawal S, El-Nezami HS, Coulombe RA, Reed KM.

Immunogenetics. 2015 Mar;67(3):163-78. doi: 10.1007/s00251-014-0825-y. Epub 2015 Jan 20.


Response of the hepatic transcriptome to aflatoxin B1 in domestic turkey (Meleagris gallopavo).

Monson MS, Settlage RE, McMahon KW, Mendoza KM, Rawal S, El-Nezami HS, Coulombe RA, Reed KM.

PLoS One. 2014 Jun 30;9(6):e100930. doi: 10.1371/journal.pone.0100930. eCollection 2014.


Next-generation sequencing strategies for characterizing the turkey genome.

Dalloul RA, Zimin AV, Settlage RE, Kim S, Reed KM.

Poult Sci. 2014 Feb;93(2):479-84. doi: 10.3382/ps.2013-03560.


Discretized Gaussian mixture for genotyping of microsatellite loci containing homopolymer runs.

Tae H, Kim DY, McCormick J, Settlage RE, Garner HR.

Bioinformatics. 2014 Mar 1;30(5):652-9. doi: 10.1093/bioinformatics/btt595. Epub 2013 Oct 17.


Characterizing the Genetic Basis for Nicotine Induced Cancer Development: A Transcriptome Sequencing Study.

Bavarva JH, Tae H, Settlage RE, Garner HR.

PLoS One. 2013 Jun 18;8(6):e67252. doi: 10.1371/journal.pone.0067252. Print 2013.


ReviSTER: an automated pipeline to revise misaligned reads to simple tandem repeats.

Tae H, McMahon KW, Settlage RE, Bavarva JH, Garner HR.

Bioinformatics. 2013 Jul 15;29(14):1734-41. doi: 10.1093/bioinformatics/btt277. Epub 2013 May 15.


Improved variation calling via an iterative backbone remapping and local assembly method for bacterial genomes.

Tae H, Settlage RE, Shallom S, Bavarva JH, Preston D, Hawkins GN, Adams LG, Garner HR.

Genomics. 2012 Nov;100(5):271-6. doi: 10.1016/j.ygeno.2012.07.015. Epub 2012 Aug 10.


Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropis gaditana.

Radakovits R, Jinkerson RE, Fuerstenberg SI, Tae H, Settlage RE, Boore JL, Posewitz MC.

Nat Commun. 2012 Feb 21;3:686. doi: 10.1038/ncomms1688. Erratum in: Nat Commun. 2013;4. doi:10.1038/ncomms3356.


The ABRF Proteomics Research Group studies: educational exercises for qualitative and quantitative proteomic analyses.

Friedman DB, Andacht TM, Bunger MK, Chien AS, Hawke DH, Krijgsveld J, Lane WS, Lilley KS, MacCoss MJ, Moritz RL, Settlage RE, Sherman NE, Weintraub ST, Witkowska HE, Yates NA, Turck CW.

Proteomics. 2011 Apr;11(8):1371-81. doi: 10.1002/pmic.201000736. Epub 2011 Mar 11.


Application of an end-to-end biomarker discovery platform to identify target engagement markers in cerebrospinal fluid by high resolution differential mass spectrometry.

Paweletz CP, Wiener MC, Bondarenko AY, Yates NA, Song Q, Liaw A, Lee AY, Hunt BT, Henle ES, Meng F, Sleph HF, Holahan M, Sankaranarayanan S, Simon AJ, Settlage RE, Sachs JR, Shearman M, Sachs AB, Cook JJ, Hendrickson RC.

J Proteome Res. 2010 Mar 5;9(3):1392-401. doi: 10.1021/pr900925d.


Quantitative analysis of histone deacetylase-1 selective histone modifications by differential mass spectrometry.

Lee AY, Paweletz CP, Pollock RM, Settlage RE, Cruz JC, Secrist JP, Miller TA, Stanton MG, Kral AM, Ozerova ND, Meng F, Yates NA, Richon V, Hendrickson RC.

J Proteome Res. 2008 Dec;7(12):5177-86. doi: 10.1021/pr800510p.


Differential mass spectrometry of rat plasma reveals proteins that are responsive to 17beta-estradiol and a selective estrogen receptor modulator PPT.

Zhao X, Deyanova EG, Lubbers LS, Zafian P, Li JJ, Liaw A, Song Q, Du Y, Settlage RE, Hickey GJ, Yates NA, Hendrickson RC.

J Proteome Res. 2008 Oct;7(10):4373-83. doi: 10.1021/pr800309z. Epub 2008 Sep 12.


Identification of the surfactant protein A receptor 210 as the unconventional myosin 18A.

Yang CH, Szeliga J, Jordan J, Faske S, Sever-Chroneos Z, Dorsett B, Christian RE, Settlage RE, Shabanowitz J, Hunt DF, Whitsett JA, Chroneos ZC.

J Biol Chem. 2005 Oct 14;280(41):34447-57. Epub 2005 Aug 8.


Proteomic characterization of messenger ribonucleoprotein complexes bound to nontranslated or translated poly(A) mRNAs in the rat cerebral cortex.

Angenstein F, Evans AM, Ling SC, Settlage RE, Ficarro S, Carrero-Martinez FA, Shabanowitz J, Hunt DF, Greenough WT.

J Biol Chem. 2005 Feb 25;280(8):6496-503. Epub 2004 Dec 13.


Preventing the spontaneous modification of an HLA-A2-restricted peptide at an N-terminal glutamine or an internal cysteine residue enhances peptide antigenicity.

Thompson LW, Hogan KT, Caldwell JA, Pierce RA, Hendrickson RC, Deacon DH, Settlage RE, Brinckerhoff LH, Engelhard VH, Shabanowitz J, Hunt DF, Slingluff CL Jr.

J Immunother. 2004 May-Jun;27(3):177-83.


A receptor for activated C kinase is part of messenger ribonucleoprotein complexes associated with polyA-mRNAs in neurons.

Angenstein F, Evans AM, Settlage RE, Moran ST, Ling SC, Klintsova AY, Shabanowitz J, Hunt DF, Greenough WT.

J Neurosci. 2002 Oct 15;22(20):8827-37.


A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis.

Dragon F, Gallagher JE, Compagnone-Post PA, Mitchell BM, Porwancher KA, Wehner KA, Wormsley S, Settlage RE, Shabanowitz J, Osheim Y, Beyer AL, Hunt DF, Baserga SJ.

Nature. 2002 Jun 27;417(6892):967-70. Epub 2002 Jun 9.


Androgen receptor phosphorylation. Regulation and identification of the phosphorylation sites.

Gioeli D, Ficarro SB, Kwiek JJ, Aaronson D, Hancock M, Catling AD, White FM, Christian RE, Settlage RE, Shabanowitz J, Hunt DF, Weber MJ.

J Biol Chem. 2002 Aug 9;277(32):29304-14. Epub 2002 May 15.


Chloroplast PNPase exists as a homo-multimer enzyme complex that is distinct from the Escherichia coli degradosome.

Baginsky S, Shteiman-Kotler A, Liveanu V, Yehudai-Resheff S, Bellaoui M, Settlage RE, Shabanowitz J, Hunt DF, Schuster G, Gruissem W.

RNA. 2001 Oct;7(10):1464-75.


A myosin I isoform in the nucleus.

Pestic-Dragovich L, Stojiljkovic L, Philimonenko AA, Nowak G, Ke Y, Settlage RE, Shabanowitz J, Hunt DF, Hozak P, de Lanerolle P.

Science. 2000 Oct 13;290(5490):337-41.


Immunodominance among EBV-derived epitopes restricted by HLA-B27 does not correlate with epitope abundance in EBV-transformed B-lymphoblastoid cell lines.

Crotzer VL, Christian RE, Brooks JM, Shabanowitz J, Settlage RE, Marto JA, White FM, Rickinson AB, Hunt DF, Engelhard VH.

J Immunol. 2000 Jun 15;164(12):6120-9.


Biochemical identification of a mutated human melanoma antigen recognized by CD4(+) T cells.

Pieper R, Christian RE, Gonzales MI, Nishimura MI, Gupta G, Settlage RE, Shabanowitz J, Rosenberg SA, Hunt DF, Topalian SL.

J Exp Med. 1999 Mar 1;189(5):757-66.

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