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Items: 1 to 50 of 109

1.

Kinetic Analysis of Hepatic Metabolism Using Hyperpolarized Dihydroxyacetone.

Kirpich A, Ragavan M, Bankson JA, McIntyre LM, Merritt ME.

J Chem Inf Model. 2019 Jan 28;59(1):605-614. doi: 10.1021/acs.jcim.8b00745. Epub 2019 Jan 15.

PMID:
30602117
2.

A Robust Methodology for Assessing Differential Homeolog Contributions to the Transcriptomes of Allopolyploids.

Boatwright JL, McIntyre LM, Morse AM, Chen S, Yoo MJ, Koh J, Soltis PS, Soltis DE, Barbazuk WB.

Genetics. 2018 Nov;210(3):883-894. doi: 10.1534/genetics.118.301564. Epub 2018 Sep 13.

PMID:
30213855
3.

Event Analysis: Using Transcript Events To Improve Estimates of Abundance in RNA-seq Data.

Newman JRB, Concannon P, Tardaguila M, Conesa A, McIntyre LM.

G3 (Bethesda). 2018 Aug 30;8(9):2923-2940. doi: 10.1534/g3.118.200373.

4.

Analysis of Gene Expression Variance in Schizophrenia Using Structural Equation Modeling.

Igolkina AA, Armoskus C, Newman JRB, Evgrafov OV, McIntyre LM, Nuzhdin SV, Samsonova MG.

Front Mol Neurosci. 2018 Jun 11;11:192. doi: 10.3389/fnmol.2018.00192. eCollection 2018.

5.

The More Dialogue, the Better.

McIntyre LM, Griffen AM, BrintzenhofeSzoc K.

J Hum Lact. 2018 Aug;34(3):584. doi: 10.1177/0890334418778509. Epub 2018 Jun 21. No abstract available.

PMID:
29928826
6.

Variable selection in omics data: A practical evaluation of small sample sizes.

Kirpich A, Ainsworth EA, Wedow JM, Newman JRB, Michailidis G, McIntyre LM.

PLoS One. 2018 Jun 21;13(6):e0197910. doi: 10.1371/journal.pone.0197910. eCollection 2018.

7.

Breast Is Best . . . Except When It's Not.

McIntyre LM, Griffen AM, BrintzenhofeSzoc K.

J Hum Lact. 2018 Aug;34(3):575-580. doi: 10.1177/0890334418774011. Epub 2018 May 22. No abstract available.

PMID:
29787336
8.

SECIMTools: a suite of metabolomics data analysis tools.

Kirpich AS, Ibarra M, Moskalenko O, Fear JM, Gerken J, Mi X, Ashrafi A, Morse AM, McIntyre LM.

BMC Bioinformatics. 2018 Apr 20;19(1):151. doi: 10.1186/s12859-018-2134-1.

9.

Direct Testing for Allele-Specific Expression Differences Between Conditions.

León-Novelo L, Gerken AR, Graze RM, McIntyre LM, Marroni F.

G3 (Bethesda). 2018 Feb 2;8(2):447-460. doi: 10.1534/g3.117.300139.

10.

Elevated ozone reduces photosynthetic carbon gain by accelerating leaf senescence of inbred and hybrid maize in a genotype-specific manner.

Yendrek CR, Erice G, Montes CM, Tomaz T, Sorgini CA, Brown PJ, McIntyre LM, Leakey ADB, Ainsworth EA.

Plant Cell Environ. 2017 Dec;40(12):3088-3100. doi: 10.1111/pce.13075. Epub 2017 Oct 17.

PMID:
29044553
11.

Intergenerational environmental effects: functional signals in offspring transcriptomes and metabolomes after parental jasmonic acid treatment in apomictic dandelion.

Verhoeven KJF, Verbon EH, van Gurp TP, Oplaat C, Ferreira de Carvalho J, Morse AM, Stahl M, Macel M, McIntyre LM.

New Phytol. 2018 Jan;217(2):871-882. doi: 10.1111/nph.14835. Epub 2017 Oct 16.

12.

Disease-specific biases in alternative splicing and tissue-specific dysregulation revealed by multitissue profiling of lymphocyte gene expression in type 1 diabetes.

Newman JRB, Conesa A, Mika M, New FN, Onengut-Gumuscu S, Atkinson MA, Rich SS, McIntyre LM, Concannon P.

Genome Res. 2017 Nov;27(11):1807-1815. doi: 10.1101/gr.217984.116. Epub 2017 Oct 12.

13.

Reliable Detection of Herpes Simplex Virus Sequence Variation by High-Throughput Resequencing.

Morse AM, Calabro KR, Fear JM, Bloom DC, McIntyre LM.

Viruses. 2017 Aug 16;9(8). pii: E226. doi: 10.3390/v9080226.

14.

UBASH3A Mediates Risk for Type 1 Diabetes Through Inhibition of T-Cell Receptor-Induced NF-κB Signaling.

Ge Y, Paisie TK, Newman JRB, McIntyre LM, Concannon P.

Diabetes. 2017 Jul;66(7):2033-2043. doi: 10.2337/db16-1023. Epub 2017 Jun 12.

15.

Back to the Future: Multiparent Populations Provide the Key to Unlocking the Genetic Basis of Complex Traits.

de Koning DJ, McIntyre LM.

G3 (Bethesda). 2017 Jun 7;7(6):1617-1618. doi: 10.1534/g3.117.042846. No abstract available.

16.

Back to the Future: Multiparent Populations Provide the Key to Unlocking the Genetic Basis of Complex Traits.

de Koning DJ, McIntyre LM.

Genetics. 2017 Jun;206(2):527-529. doi: 10.1534/genetics.117.203265. No abstract available.

17.

A comprehensive analysis of myocardial substrate preference emphasizes the need for a synchronized fluxomic/metabolomic research design.

Ragavan M, Kirpich A, Fu X, Burgess SC, McIntyre LM, Merritt ME.

Am J Physiol Heart Circ Physiol. 2017 Jun 1;312(6):H1215-H1223. doi: 10.1152/ajpheart.00016.2017. Epub 2017 Apr 14.

18.

Presence of arachidonoyl-carnitine is associated with adverse cardiometabolic responses in hypertensive patients treated with atenolol.

Weng L, Gong Y, Culver J, Gardell SJ, Petucci C, Morse AM, Frye RF, Turner ST, Chapman A, Boerwinkle E, Gums J, Beitelshees AL, Borum PR, Johnson JA, Garrett TJ, McIntyre LM, Cooper-DeHoff RM.

Metabolomics. 2016 Oct;12(10). pii: 160. doi: 10.1007/s11306-016-1098-2. Epub 2016 Sep 15.

19.

SHH Protein Variance in the Limb Bud Is Constrained by Feedback Regulation and Correlates with Altered Digit Patterning.

Zhang R, Lee C, Lawson LY, Svete LJ, McIntyre LM, Harfe BD.

G3 (Bethesda). 2017 Mar 10;7(3):851-858. doi: 10.1534/g3.116.033019.

20.

High-Throughput Phenotyping of Maize Leaf Physiological and Biochemical Traits Using Hyperspectral Reflectance.

Yendrek CR, Tomaz T, Montes CM, Cao Y, Morse AM, Brown PJ, McIntyre LM, Leakey AD, Ainsworth EA.

Plant Physiol. 2017 Jan;173(1):614-626. doi: 10.1104/pp.16.01447. Epub 2016 Nov 15.

21.

Neurons That Underlie Drosophila melanogaster Reproductive Behaviors: Detection of a Large Male-Bias in Gene Expression in fruitless-Expressing Neurons.

Newell NR, New FN, Dalton JE, McIntyre LM, Arbeitman MN.

G3 (Bethesda). 2016 Aug 9;6(8):2455-65. doi: 10.1534/g3.115.019265.

22.

Buffering of Genetic Regulatory Networks in Drosophila melanogaster.

Fear JM, León-Novelo LG, Morse AM, Gerken AR, Van Lehmann K, Tower J, Nuzhdin SV, McIntyre LM.

Genetics. 2016 Jul;203(3):1177-90. doi: 10.1534/genetics.116.188797. Epub 2016 May 18.

23.

RNA-seq analysis of impact of PNN on gene expression and alternative splicing in corneal epithelial cells.

Akin D, Newman JR, McIntyre LM, Sugrue SP.

Mol Vis. 2016 Jan 16;22:40-60. eCollection 2016.

24.

The Wright stuff: reimagining path analysis reveals novel components of the sex determination hierarchy in Drosophila melanogaster.

Fear JM, Arbeitman MN, Salomon MP, Dalton JE, Tower J, Nuzhdin SV, McIntyre LM.

BMC Syst Biol. 2015 Sep 4;9:53. doi: 10.1186/s12918-015-0200-0.

25.

A flexible Bayesian method for detecting allelic imbalance in RNA-seq data.

León-Novelo LG, McIntyre LM, Fear JM, Graze RM.

BMC Genomics. 2014 Oct 23;15:920. doi: 10.1186/1471-2164-15-920.

26.

GENETICS and G3: community-driven science, community-driven journals.

de Koning DJ, McIntyre LM.

G3 (Bethesda). 2014 Sep 18;4(9):1567-8. doi: 10.1534/g3.114.013680. No abstract available.

27.

A systems biology approach identified different regulatory networks targeted by KSHV miR-K12-11 in B cells and endothelial cells.

Yang Y, Boss IW, McIntyre LM, Renne R.

BMC Genomics. 2014 Aug 8;15:668. doi: 10.1186/1471-2164-15-668.

28.

LANA binds to multiple active viral and cellular promoters and associates with the H3K4methyltransferase hSET1 complex.

Hu J, Yang Y, Turner PC, Jain V, McIntyre LM, Renne R.

PLoS Pathog. 2014 Jul 17;10(7):e1004240. doi: 10.1371/journal.ppat.1004240. eCollection 2014 Jul.

29.

What the X has to do with it: differences in regulatory variability between the sexes in Drosophila simulans.

Graze RM, McIntyre LM, Morse AM, Boyd BM, Nuzhdin SV, Wayne ML.

Genome Biol Evol. 2014 Apr;6(4):818-29. doi: 10.1093/gbe/evu060.

30.

Leveraging biological replicates to improve analysis in ChIP-seq experiments.

Yang Y, Fear J, Hu J, Haecker I, Zhou L, Renne R, Bloom D, McIntyre LM.

Comput Struct Biotechnol J. 2014 Jan 31;9:e201401002. doi: 10.5936/csbj.201401002. eCollection 2014.

31.

Consistent errors in first strand cDNA due to random hexamer mispriming.

van Gurp TP, McIntyre LM, Verhoeven KJ.

PLoS One. 2013 Dec 30;8(12):e85583. doi: 10.1371/journal.pone.0085583. eCollection 2013.

32.

Male-specific Fruitless isoforms have different regulatory roles conferred by distinct zinc finger DNA binding domains.

Dalton JE, Fear JM, Knott S, Baker BS, McIntyre LM, Arbeitman MN.

BMC Genomics. 2013 Sep 27;14:659. doi: 10.1186/1471-2164-14-659.

33.

Plants know where it hurts: root and shoot jasmonic acid induction elicit differential responses in Brassica oleracea.

Tytgat TO, Verhoeven KJ, Jansen JJ, Raaijmakers CE, Bakx-Schotman T, McIntyre LM, van der Putten WH, Biere A, van Dam NM.

PLoS One. 2013 Jun 11;8(6):e65502. doi: 10.1371/journal.pone.0065502. Print 2013. Erratum in: PLoS One. 2013;8(10). doi:10.1371/annotation/4574edb2-15bd-4689-bf84-b947ebe81ed2.

34.

Purification of transcripts and metabolites from Drosophila heads.

Jensen K, Sanchez-Garcia J, Williams C, Khare S, Mathur K, Graze RM, Hahn DA, McIntyre LM, Rincon-Limas DE, Fernandez-Funez P.

J Vis Exp. 2013 Mar 15;(73):e50245. doi: 10.3791/50245.

35.

Ago HITS-CLIP expands understanding of Kaposi's sarcoma-associated herpesvirus miRNA function in primary effusion lymphomas.

Haecker I, Gay LA, Yang Y, Hu J, Morse AM, McIntyre LM, Renne R.

PLoS Pathog. 2012;8(8):e1002884. doi: 10.1371/journal.ppat.1002884. Epub 2012 Aug 23. Erratum in: PLoS Pathog. 2013 Mar;9(3). doi: 10.1371/annotation/bb6f7450-8506-41c3-8519-020df8b382b9.

36.

Genotype-phenotype mapping in a post-GWAS world.

Nuzhdin SV, Friesen ML, McIntyre LM.

Trends Genet. 2012 Sep;28(9):421-6. doi: 10.1016/j.tig.2012.06.003. Epub 2012 Jul 18.

37.

Genetic variation in the Yolk protein expression network of Drosophila melanogaster: sex-biased negative correlations with longevity.

Tarone AM, McIntyre LM, Harshman LG, Nuzhdin SV.

Heredity (Edinb). 2012 Oct;109(4):226-34. doi: 10.1038/hdy.2012.34. Epub 2012 Jul 4.

38.

The chemical interactions underlying tomato flavor preferences.

Tieman D, Bliss P, McIntyre LM, Blandon-Ubeda A, Bies D, Odabasi AZ, Rodríguez GR, van der Knaap E, Taylor MG, Goulet C, Mageroy MH, Snyder DJ, Colquhoun T, Moskowitz H, Clark DG, Sims C, Bartoshuk L, Klee HJ.

Curr Biol. 2012 Jun 5;22(11):1035-9. doi: 10.1016/j.cub.2012.04.016. Epub 2012 May 24.

39.

Facilitating discovery: the role of society journals in collaborative science.

McIntyre LM, de Koning DJ.

G3 (Bethesda). 2012 Feb;2(2):151-2. doi: 10.1534/g3.111.001859. Epub 2012 Feb 1. No abstract available.

40.

Partitioning transcript variation in Drosophila: abundance, isoforms, and alleles.

Yang Y, Graze RM, Walts BM, Lopez CM, Baker HV, Wayne ML, Nuzhdin SV, McIntyre LM.

G3 (Bethesda). 2011 Nov;1(6):427-36. doi: 10.1534/g3.111.000596. Epub 2011 Nov 1.

41.

The pathology associated with visceral toxicosis of catfish.

Khoo LH, Goodwin AE, Wise DJ, Holmes WE, Hanson LA, Steadman JM, McIntyre LM, Gaunt PS.

J Vet Diagn Invest. 2011 Nov;23(6):1217-21. doi: 10.1177/1040638711425577.

PMID:
22362805
42.

Facilitating discovery: the role of Society Journals in collaborative science.

McIntyre LM, de Koning DJ.

Genetics. 2012 Feb;190(2):285-6. doi: 10.1534/genetics.111.137935. No abstract available.

43.

Allelic imbalance in Drosophila hybrid heads: exons, isoforms, and evolution.

Graze RM, Novelo LL, Amin V, Fear JM, Casella G, Nuzhdin SV, McIntyre LM.

Mol Biol Evol. 2012 Jun;29(6):1521-32. doi: 10.1093/molbev/msr318. Epub 2012 Jan 7.

44.

Generalized shrinkage F-like statistics for testing an interaction term in gene expression analysis in the presence of heteroscedasticity.

Yang J, Casella G, McIntyre LM.

BMC Bioinformatics. 2011 Nov 1;12:427. doi: 10.1186/1471-2105-12-427.

45.

Polymorphisms in fibronectin binding protein A of Staphylococcus aureus are associated with infection of cardiovascular devices.

Lower SK, Lamlertthon S, Casillas-Ituarte NN, Lins RD, Yongsunthon R, Taylor ES, DiBartola AC, Edmonson C, McIntyre LM, Reller LB, Que YA, Ros R, Lower BH, Fowler VG Jr.

Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18372-7. doi: 10.1073/pnas.1109071108. Epub 2011 Oct 24.

46.

RNA-seq: technical variability and sampling.

McIntyre LM, Lopiano KK, Morse AM, Amin V, Oberg AL, Young LJ, Nuzhdin SV.

BMC Genomics. 2011 Jun 6;12:293. doi: 10.1186/1471-2164-12-293.

47.

Potential associations between severity of infection and the presence of virulence-associated genes in clinical strains of Staphylococcus aureus.

Gill SR, McIntyre LM, Nelson CL, Remortel B, Rude T, Reller LB, Fowler VG Jr.

PLoS One. 2011 Apr 26;6(4):e18673. doi: 10.1371/journal.pone.0018673.

48.

Expression of defense genes in Drosophila evolves under a different selective regime from expression of other genes.

Wayne ML, Pienaar J, Telonis-Scott M, Sylvestre LS, Nuzhdin SV, McIntyre LM.

Evolution. 2011 Apr;65(4):1068-78. doi: 10.1111/j.1558-5646.2010.01197.x. Epub 2010 Dec 22.

49.

Transcriptional network structure has little effect on the rate of regulatory evolution in yeast.

Kopp A, McIntyre LM.

Mol Biol Evol. 2012 Aug;29(8):1899-905. doi: 10.1093/molbev/msq283. Epub 2010 Oct 21.

50.

Epistasis: obstacle or advantage for mapping complex traits?

Verhoeven KJ, Casella G, McIntyre LM.

PLoS One. 2010 Aug 26;5(8):e12264. doi: 10.1371/journal.pone.0012264.

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