Publications for the McIntyre Lab (Full)
Gonzalo M, Holland JB, Vyn TJ, and McIntyre LM (2009) Direct Mapping Of Density Response In a Population of B73 x Mo17 Recombinant Inbred Lines of Maize (Zea Mays L.). Heredity in press.
Morse AM, Whetten R, Dubos C, Campbell MM. (2009) Post-translational modification of an R2R3-MYB transcription factor by a MAP Kinase during xylem development. New Phytologist. 183: 1001-1013.
Ramirez-Carvajal GA, Morse AM, Dervinis C, Davis JM. (2009) The cytokinin type-B response regulator PtRR13 is a negative regulator of adventitious root development in Populus. Plant Physiology. 150:759-771.
Main BJ, Bickel RD, McIntyre LM, Graze RM, Calabrase PP and Nuzhdin SV (2009) Allele-specific expression assays using Solexa. BMC Genomics 10:422.
Telonis-Scott M, Hallas R, McKechnie SW, Wee CW, and Hoffmann AA (2009) Selection for cold resistance alters gene transcript levels in Drosophila melanogaster. Journal of Insect Physiology 55: 549-555.
Graze RM, McIntyre LM, Main BJ, Wayne ML, and Nuzhdin SV (2009) Regulatory divergence in Drosophila melanogaster and D. simulans, a genome-wide analysis of allele-specific expression.Genetics Genetics 183: 547-561.
Nuzhdin SV, Brisson JA, Pickering A, Wayne ML, Harshman L G, and McIntyre LM (2009) Natural genetic variation in transcriptome reflects network structure inferred with major effect mutations: insulin TOR and associated phenotypes in Drosophila melanogaster. BMC Genomics 10:124.
Engelkes T, Morrien E, Verhoeven KJF, Bezemer TM, Biere A, Harvey JA, McIntyre LM, Tamis WLM, and van der Putten WH (2008) Successful range-expanding plants experience less above-ground and below-ground enemy impact. Nature 456:946-948.
Telonis-Scott M, Kopp A, Wayne ML, Nuzhdin SV, and McIntyre LM. (2008) Sex-specific Splicing in Drosophila: Widespread Occurrence, Tissue-specificity, and Evolutionary Conservation. Genetics 181:421-434.
Fung RWM, Gonzalo M, Fekete C, Kovacs LG, He Y, Marsh E, McIntyre LM, Schachtman DP and Qin W (2008) Powdery Mildew Induces Defense-Oriented Reprogramming of the Transcriptome in a Susceptible but not in a Resistant. Grapevine Plant Physiology. 146: 236-249.
Fowler VG, Nelson CL, McIntyre LM, Kreiswirth BN, Monk A, Archer GL, Federspiel J, Naidich S, Remortel B, Rude T, Brown P, Reller LB, Corey GR, and Gill SR (2007) Potential Associations between Hematogenous Complications and Bacterial Genotype in Staphylococcus aureus. Journal of Infectious Diseases 196:738-47.
Graze RM, Barmina O, Tufts D, Naderi E, Harmon KL, Persianinova M, and Nuzhdin SV (2007) New candidate genes for sex comb divergence between Drosophila mauritiana and Drosophila simulans. Genetics, 176: 2561–2576.
Gonzalo M, Vyn T, Holland JB, and McIntyre LM (2007) Mapping reciprocal effects and interactions with plant density stress in Zae mays L. Heredity 99:14-30.
Kopp A, Barmina O, Hamilton AM, Higgins LA, McIntyre LM, and Jones C (2008)Evolution of gene expression in the Drosophila olfactory system. Molecular Biology and Evolution 25:1081-1092.
Slotte T, Holm K, McIntyre LM, Lagercrantz U, and Lascoux M. (2007) Differential expression of genes important for adaptation in Capsella bursa-pastoris/ (Brassicaceae). Plant Physiology. 145:160-173.
Wayne ML, Telonis-Scott M, Bono LM, Harshman L, Kopp A, Nuzhdin, SV, and McIntyre LM (2007) Simpler mode of inheritance of transcriptional variation in male Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America. 104: 18577-18582.
Gonzalo M, Vyn TJ, Holland JB, and McIntyre LM (2006) Mapping density response in maize: a direct approach for testing genotype and treatment interactions. Genetics. 173: 331-48.
McIntyre LM, Bono LM, Genissel A, Westerman R, Junk D, Telonis-Scott M, Harshman L, Wayne ML, Kopp A, and Nuzhdin SV (2006) Sex Specific expression of alternative transcripts in Drosophila. Genome Biology 7: R79.
Spurlock DM, McDaneld TG, and McIntyre LM (2006) Changes in skeletal muscle gene expression following clenbuterol administration. BMC Genetics 7: 320.
Subramanyam S, Sardesai N, Puthoff DP, Meyer JM, Gonzalo M, and Williams CE (2006) Expression of two defense-response genes, Hfr-1 and Wci-1, under biotic and abiotic stresses in wheat. Plant Science 170: 90-103.
Verhoeven KJ, Jannink JL, and McIntyre LM (2006) Using mating designs to uncover QTL and the genetic architecture of complex traits. Heredity. 96: 139-49.
Barmina O, Gonzalo M, McIntyre LM, and Kopp A (2005) Sex- and segment-specific modulation of gene expression profiles in Drosophila. Dev Biol. 288: 528-44.
Coffman CJ, Doerge RW, Simonsen KL, Nichols KM, Duarte CK, Wolfinger RD, and McIntyre LM (2005) Model selection in binary trait locus mapping. Genetics. 170: 1281-97.
Coffman CJ, Wayne ML, Nuzhdin SV, Higgins LA, and McIntyre LM (2005) Identification of co-regulated transcripts affecting male body size in Drosophila. Genome Biol. 6: R53.
Hammes UZ, Schachtman DP, Berg RH, Nielsen E, Koch W, McIntyre LM, and Taylor CG (2005) Nematode-induced changes of transporter gene expression in Arabidopsis roots. Mol Plant Microbe Interact. 18: 1247-57.
Telonis-Scott M, McIntyre LM, and Wayne ML (2005) Genetic architecture of two fitness-related traits in Drosophila melanogaster: ovariole number and thorax length. Genetica. 125: 211-22.
Verhoeven K, Simonsen K, and McIntyre LM (2005) Implementing false discovery rate control: increasing your power. Oikos 108: 643-647.
Wayne ML, Pan YJ, Nuzhdin SV, and McIntyre LM (2004) Additivity and trans-acting effects on gene expression in male Drosophila simulans. Genetics. 168: 1413-20.
Fowler VG Jr, Sakoulas G, McIntyre LM, Meka VG, Arbeit RD, Cabell CH, Stryjewski ME, Eliopoulos GM, Reller LB, Corey GR, Jones T, Lucindo N, Yeaman MR, and Bayer AS (2004) Persistent bacteremia due to methicillin-resistant Staphylococcus aureus infection is associated with agr dysfunction and low-level in vitro resistance to thrombin-induced platelet microbicidal protein. J Infect Dis. 190: 1140-9.
Nuzhdin SV, Wayne ML, Harmon KL, and McIntyre LM (2004) Common pattern of evolution of gene expression level and protein sequence in Drosophila. Mol Biol Evol. 21: 1308-17.
Pirttila AM, McIntyre LM, Payne GA, and Woloshuk CP (2004) Expression profile analysis of wild-type and fcc1 mutant strains of Fusarium verticillioides during fumonisin biosynthesis. Fungal Genet Biol. 41: 647-56.
Li H, Singh AK, McIntyre LM, and Sherman LA (2004) Differential gene expression in response to hydrogen peroxide and the putative PerR regulon of Synechocystis sp. strain PCC 6803. J Bacteriol. 186: 3331-45.
Pedra JH, McIntyre LM, Scharf ME, and Pittendrigh BR (2004) Genome-wide transcription profile of field- and laboratory-selected dichlorodiphenyltrichloroethane (DDT)-resistant Drosophila. Proc Natl Acad Sci U S A. 101: 7034-9.
Simonsen KL, and McIntyre LM (2004) Using alpha wisely: improving power to detect multiple QTL. Stat Appl Genet Mol Biol. 3: Article1.
Kopp, A., Graze, R.M., Xu, S., Carroll SB, and Nuzhdin SV (2003) Quantitative Trait Loci Responsible for Variation in Sexually Dimorphic Traits in Drosophila melanogaster. Genetics, 163, 771-787.
Jin T, Bokarewa M, McIntyre LM, Tarkowski A, Corey GR, Reller LB, and Fowler VG (2003) Fatal Outcome Of Bacteremic Patients Caused By Infection With Staphylokinase Deficient Staphylococcus aureus. JMM. 52: 919-923.
Lahner B, Gong J, Mahmoudian M, Smith EL, Abid KB, Rogers EE, Guerinot ML, Harper JF, Ward JM, McIntyre L, Schroeder JI, and Salt DE (2003) Genomic scale profiling of nutrient and trace elements in Arabidopsis thaliana. Nat Biotechnol. 21(10): 1215-21.
Coffman CJ, Doerge RW, Wayne ML, and McIntyre LM (2003) Intersection tests for single marker QTL analysis can be more powerful than two marker QTL analysis. BMC Genet. 4: 10.
Singh AK, McIntyre LM, and Sherman LA (2003) Microarray analysis of the genome-wide response to iron deficiency and iron reconstitution in the cyanobacterium Synechocystis sp. PCC 6803. Plant Physiol. 132: 1825-39.
Oddone EZ, Horner RD, Johnston DC, Stechuchak K, McIntyre L, Ward A, Alley LG, Whittle J, Kroupa L, and Taylor J (2002) Carotid endarterectomy and race: do clinical indications and patient preferences account for differences? Stroke. 33: 2936-43.
Wayne ML, and McIntyre LM (2002) Combining mapping and arraying: An approach to candidate gene identification. Proc Natl Acad Sci U S A. 99: 14903-6.
Moody DE, Zou Z, and McIntyre L (2002) Cross-species hybridisation of pig RNA to human nylon microarrays. BMC Genomics. 3: 27.
Moody D, Fadlia B, Singh A, Shah S, and McIntyre LM (2002) Quantitative Comparison of Image Analysis Software. DNA Press 155-166.
Vermerris W, Thompson KJ, and McIntyre LM (2002) The maize Brown midrib1 locus affects cell wall composition and plant development in a dose-dependent manner. Heredity. 88: 450-7.
Bepler G, Gautam A, McIntyre LM, Beck AF, Chervinsky DS, Kim YC, Pitterle DM, and Hyland A (2002) Prognostic significance of molecular genetic aberrations on chromosome segment 11p15.5 in non-small-cell lung cancer. J Clin Oncol. 20: 1353-60.
Vermerris W, Thompson KJ, McIntyre LM, and Axtell JD (2002) Evidence for an evolutionarily conserved interaction between cell wall biosynthesis and flowering in maize and sorghum. BMC Evol Biol. 2: 2.
Rosenberg CK, Cummings TJ, Saunders AM, Widico C, McIntyre LM, and Hulette CM (2001) Dementia with Lewy bodies and Alzheimer's disease. Acta Neuropathol (Berl). 102: 621-6.
McIntyre LM, Coffman CJ, and Doerge RW (2001) Detection and localization of a single binary trait locus in experimental populations. Genet Res. 78: 79-92.
Hoenig H, Hoff J, McIntyre L, and Branch LG (2001) The self-reported functional measure: Predictive validity for health care utilization in multiple sclerosis and spinal cord injury. Arch Phys Med Rehabil. 82: 613-8.
McIntyre LM, O'Briant KC, McBride CM, and Bepler G (2001) Rater agreement and utility of the mutagen-induced chromosome damage assay. Anticancer Res. 21: 605-9.
Peck BM, Asch DA, Goold SD, Roter DL, Ubel PA, McIntyre LM, Abbott KH, Hoff JA, Koropchak CM, and Tulsky JA (2001) Measuring patient expectations: does the instrument affect satisfaction or expectations? Med Care. 39: 100-8.
Fowler VG Jr, McIntyre LM, Yeaman MR, Peterson GE, Barth Reller L, Corey GR, Wray D, and Bayer AS (2000) In vitro resistance to thrombin-induced platelet microbicidal protein in isolates of Staphylococcus aureus from endocarditis patients correlates with an intravascular device source. J Infect Dis. 182: 1251-4.
Oberg AL, Ferguson JA, McIntyre LM, and Horner RD (2000) Incidence of stroke and season of the year: evidence of an association. Am J Epidemiol. 152: 558-64.
McIntyre LM, Martin ER, Simonsen KL, and Kaplan NL (2000) Circumventing multiple testing: a multilocus Monte Carlo approach to testing for association. Genet Epidemiol. 19: 18-29.
McBride CM, Halabi S, Bepler G, Lyna P, McIntyre L, Lipkus I, Albright J, and O'Briant K (2000) Maximizing the motivational impact of feedback of lung cancer susceptibility on smokers' desire to quit. J Health Commun. 5: 229-41.
Steinhauser KE, Clipp EC, McNeilly M, Christakis NA, McIntyre LM, and Tulsky JA (2000) In search of a good death: observations of patients, families, and providers. Ann Intern Med. 132: 825-32.
Bosworth HB, Parsey KS, Butterfield MI, McIntyre LM, Oddone EZ, Stechuchak KM, and Bastian LA (2000) Racial variation in wanting and obtaining mental health services among women veterans in a primary care clinic. J Natl Med Assoc. 92: 231-6.
Denmark-Wahnefried W, Schildkraut JM, Thompson D, Lesko SM, McIntyre L, Schwingl P, Paulson DF, Robertson CN, Anderson EE, and Walther PJ (2000) Early onset baldness and prostate cancer risk. Cancer Epidemiol Biomarkers Prev. 9: 325-8.
Hoenig H, McIntyre L, Hoff J, Samsa G, and Branch LG (1999) Disability fingerprints: patterns of disability in spinal cord injury and multiple sclerosis differ. J Gerontol A Biol Sci Med Sci. 54: M613-20.
Johnston EM, McIntyre LM, Hoff JA, and Bepler G (1999) The effect of orchiectomy on lung cancer survival. Anticancer Res. 19: 5567-70.
Vermerris W, and McIntyre LM (1999) Time to flowering in brown midrib mutants of maize: an alternative approach to the analysis of developmental traits. Heredity. 83: 171-8.
Oddone EZ, Horner RD, Sloane R, McIntyre L, Ward A, Whittle J, Passman LJ, Kroupa L, Heaney R, Diem S, and Matchar D (1999) Race, presenting signs and symptoms, use of carotid artery imaging, and appropriateness of carotid endarterectomy. Stroke. 30: 1350-6.
Hoenig H, Branch LG, McIntyre L, Hoff J, and Horner RD (1999) The validity in persons with spinal cord injury of a self-reported functional measure derived from the functional independence measure. Spine. 24: 539-43; discussion 543-4.
McIntyre LM, Butterfield MI, Nanda K, Parsey K, Stechuchak KM, McChesney AW, Koons C, and Bastian LA (1999) Validation of a Trauma Questionnaire in veteran women. J Gen Intern Med. 14: 186-9.
Hulette CM, Welsh-Bohmer KA, Murray MG, Saunders AM, Mash DC, and McIntyre LM (1998) Neuropathological and neuropsychological changes in "normal" aging: evidence for preclinical Alzheimer disease in cognitively normal individuals. J Neuropathol Exp Neurol. 57: 1168-74.
Butterfield M, McIntyre LM, Stechuchak K, Nanda K, and Bastian L (1998) Mental disorder symptoms in veteran women: Impact of physical and sexual assault. J. Am. Med. Women's Assoc. 53: 198-200.
Hoenig H, McIntyre L, Sloane R, Branch LG, Truncali A, and Horner RD (1998) The reliability of a self-reported measure of disease, impairment, and function in persons with spinal cord dysfunction. Arch Phys Med Rehabil. 79: 378-87.
Oddone EZ, Horner RD, Diers T, Lipscomb J, McIntyre L, Cauffman C, Whittle J, Passman LJ, Kroupa L, Heaney R, and Matchar D (1998) Understanding racial variation in the use of carotid endarterectomy: the role of aversion to surgery. J Natl Med Assoc. 90: 25-33.
McIntyre LM, and Weir BS (1997) Hardy-Weinberg testing for continuous data. Genetics. 147: 1965-75.
Butterfield M, Bastian L, McIntyre LM, Koons C, Vollmer M, and Burns B (1996) Screening for mental disorder symptoms and a history of sexual trauma and battering among women using primary health care services. J. Clinical Outcomes Management 3: 55-61.
McIntyre LM (1994) Using cigarette data for an introduction to multiple regression. Journal of Statistics Education 2.