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Stochastic imputation for integrated transcriptome association analysis of a longitudinally measured trait.

Ray EL, Qian J, Brecha R, Reilly MP, Foulkes AS.

Stat Methods Med Res. 2019 Jun 7:962280219852720. doi: 10.1177/0962280219852720. [Epub ahead of print]


A likelihood-based approach to transcriptome association analysis.

Qian J, Ray E, Brecha RL, Reilly MP, Foulkes AS.

Stat Med. 2019 Apr 15;38(8):1357-1373. doi: 10.1002/sim.8040. Epub 2018 Dec 4.


Deep RNA Sequencing Uncovers a Repertoire of Human Macrophage Long Intergenic Noncoding RNAs Modulated by Macrophage Activation and Associated With Cardiometabolic Diseases.

Zhang H, Xue C, Wang Y, Shi J, Zhang X, Li W, Nunez S, Foulkes AS, Lin J, Hinkle CC, Yang W, Morrisey EE, Rader DJ, Li M, Reilly MP.

J Am Heart Assoc. 2017 Nov 13;6(11). pii: e007431. doi: 10.1161/JAHA.117.007431.


A score test for genetic class-level association with nonlinear biomarker trajectories.

Qian J, Nunez S, Kim S, Reilly MP, Foulkes AS.

Stat Med. 2017 Aug 30;36(19):3075-3091. doi: 10.1002/sim.7314. Epub 2017 May 23.


Bayesian variable selection for post-analytic interrogation of susceptibility loci.

Chen S, Nunez S, Reilly MP, Foulkes AS.

Biometrics. 2017 Jun;73(2):603-614. doi: 10.1111/biom.12620. Epub 2016 Nov 17.


Genome-wide interrogation reveals hundreds of long intergenic noncoding RNAs that associate with cardiometabolic traits.

Ballantyne RL, Zhang X, Nuñez S, Xue C, Zhao W, Reed E, Salaheen D, Foulkes AS, Li M, Reilly MP.

Hum Mol Genet. 2016 Jul 15;25(14):3125-3141. Epub 2016 Jun 10.


Transcriptome-Wide Analysis Reveals Modulation of Human Macrophage Inflammatory Phenotype Through Alternative Splicing.

Lin J, Hu Y, Nunez S, Foulkes AS, Cieply B, Xue C, Gerelus M, Li W, Zhang H, Rader DJ, Musunuru K, Li M, Reilly MP.

Arterioscler Thromb Vasc Biol. 2016 Jul;36(7):1434-47. doi: 10.1161/ATVBAHA.116.307573. Epub 2016 May 26. Erratum in: Arterioscler Thromb Vasc Biol. 2016 Nov;36(11):e96.


A Simple Test of Class-Level Genetic Association Can Reveal Novel Cardiometabolic Trait Loci.

Qian J, Nunez S, Reed E, Reilly MP, Foulkes AS.

PLoS One. 2016 Feb 9;11(2):e0148218. doi: 10.1371/journal.pone.0148218. eCollection 2016.


HIV-1-negative female sex workers sustain high cervical IFNɛ, low immune activation, and low expression of HIV-1-required host genes.

Abdulhaqq SA, Zorrilla C, Kang G, Yin X, Tamayo V, Seaton KE, Joseph J, Garced S, Tomaras GD, Linn KA, Foulkes AS, Azzoni L, VerMilyea M, Coutifaris C, Kossenkov AV, Showe L, Kraiselburd EN, Li Q, Montaner LJ.

Mucosal Immunol. 2016 Jul;9(4):1027-38. doi: 10.1038/mi.2015.116. Epub 2015 Nov 11.


A guide to genome-wide association analysis and post-analytic interrogation.

Reed E, Nunez S, Kulp D, Qian J, Reilly MP, Foulkes AS.

Stat Med. 2015 Dec 10;34(28):3769-92. doi: 10.1002/sim.6605. Epub 2015 Sep 6.


Serum Fractalkine (CX3CL1) and Cardiovascular Outcomes and Diabetes: Findings From the Chronic Renal Insufficiency Cohort (CRIC) Study.

Shah R, Matthews GJ, Shah RY, McLaughlin C, Chen J, Wolman M, Master SR, Chai B, Xie D, Rader DJ, Raj DS, Mehta NN, Budoff M, Fischer MJ, Go AS, Townsend RR, He J, Kusek JW, Feldman HI, Foulkes AS, Reilly MP; CRIC Study Investigators.

Am J Kidney Dis. 2015 Aug;66(2):266-73. doi: 10.1053/j.ajkd.2015.01.021. Epub 2015 Mar 17.


Higher plasma CXCL12 levels predict incident myocardial infarction and death in chronic kidney disease: findings from the Chronic Renal Insufficiency Cohort study.

Mehta NN, Matthews GJ, Krishnamoorthy P, Shah R, McLaughlin C, Patel P, Budoff M, Chen J, Wolman M, Go A, He J, Kanetsky PA, Master SR, Rader DJ, Raj D, Gadegbeku CA, Shah R, Schreiber M, Fischer MJ, Townsend RR, Kusek J, Feldman HI, Foulkes AS, Reilly MP; Chronic Renal Insufficiency Cohort (CRIC) Study Investigators.

Eur Heart J. 2014 Aug 14;35(31):2115-22. doi: 10.1093/eurheartj/eht481. Epub 2013 Dec 4.


Serial cervicovaginal exposures with replication-deficient SIVsm induce higher dendritic cell (pDC) and CD4+ T-cell infiltrates not associated with prevention but a more severe SIVmac251 infection of rhesus macaques.

Abdulhaqq SA, Martinez MI, Kang G, Foulkes AS, Rodriguez IV, Nichols SM, Hunter M, Sariol CA, Ruiz LA, Ross BN, Yin X, Speicher DW, Haase AT, Marx PA, Li Q, Kraiselburd EN, Montaner LJ.

J Acquir Immune Defic Syndr. 2014 Apr 1;65(4):405-13. doi: 10.1097/QAI.0000000000000047.


Candidate gene association study of coronary artery calcification in chronic kidney disease: findings from the CRIC study (Chronic Renal Insufficiency Cohort).

Ferguson JF, Matthews GJ, Townsend RR, Raj DS, Kanetsky PA, Budoff M, Fischer MJ, Rosas SE, Kanthety R, Rahman M, Master SR, Qasim A, Li M, Mehta NN, Shen H, Mitchell BD, O'Connell JR, Shuldiner AR, Ho WK, Young R, Rasheed A, Danesh J, He J, Kusek JW, Ojo AO, Flack J, Go AS, Gadegbeku CA, Wright JT Jr, Saleheen D, Feldman HI, Rader DJ, Foulkes AS, Reilly MP; CRIC Study Principal Investigators.

J Am Coll Cardiol. 2013 Aug 27;62(9):789-98. doi: 10.1016/j.jacc.2013.01.103. Epub 2013 May 30.


Improved treatment for primary HIV infection by interferon-alfa therapy? Does HCV treatment in HIV/HCV coinfected patients help us to test this hypothesis? Reply to zur Wiesch and van Lunzen.

Azzoni L, Foulkes AS, Papasavvas E, Mexas AM, Lynn KM, Mounzer K, Tebas P, Jacobson JM, Frank I, O'Doherty U, Kostman J, Montaner LJ.

J Infect Dis. 2013 Jul 15;208(2):363. doi: 10.1093/infdis/jit160. Epub 2013 Apr 9. No abstract available.


Mixed modeling of meta-analysis P-values (MixMAP) suggests multiple novel gene loci for low density lipoprotein cholesterol.

Foulkes AS, Matthews GJ, Das U, Ferguson JF, Lin R, Reilly MP.

PLoS One. 2013;8(2):e54812. doi: 10.1371/journal.pone.0054812. Epub 2013 Feb 6.


Pegylated Interferon alfa-2a monotherapy results in suppression of HIV type 1 replication and decreased cell-associated HIV DNA integration.

Azzoni L, Foulkes AS, Papasavvas E, Mexas AM, Lynn KM, Mounzer K, Tebas P, Jacobson JM, Frank I, Busch MP, Deeks SG, Carrington M, O'Doherty U, Kostman J, Montaner LJ.

J Infect Dis. 2013 Jan 15;207(2):213-22. doi: 10.1093/infdis/jis663. Epub 2012 Oct 26.


Concurrent measures of total and integrated HIV DNA monitor reservoirs and ongoing replication in eradication trials.

Mexas AM, Graf EH, Pace MJ, Yu JJ, Papasavvas E, Azzoni L, Busch MP, Di Mascio M, Foulkes AS, Migueles SA, Montaner LJ, O'Doherty U.

AIDS. 2012 Nov 28;26(18):2295-306. doi: 10.1097/QAD.0b013e32835a5c2f.


Prioritizing CD4 count monitoring in response to ART in resource-constrained settings: a retrospective application of prediction-based classification.

Azzoni L, Foulkes AS, Liu Y, Li X, Johnson M, Smith C, Kamarulzaman AB, Montaner J, Mounzer K, Saag M, Cahn P, Cesar C, Krolewiecki A, Sanne I, Montaner LJ.

PLoS Med. 2012;9(4):e1001207. doi: 10.1371/journal.pmed.1001207. Epub 2012 Apr 17.


Antiretroviral therapy interruptions result in loss of protective humoral immunity to neoantigens in HIV-infected individuals.

Azzoni L, Foulkes AS, Firnhaber C, Yin X, Xiang ZQ, Li Y, Stevens W, Gross R, Ertl HC, Sanne I, Montaner LJ.

AIDS. 2012 Jul 17;26(11):1355-62. doi: 10.1097/QAD.0b013e328354648e.


Mixture modelling as an exploratory framework for genotype-trait associations.

Au K, Lin R, Foulkes AS.

J R Stat Soc Ser C Appl Stat. 2011 May;60(3):355-375.


Ridge regression for longitudinal biomarker data.

Eliot M, Ferguson J, Reilly MP, Foulkes AS.

Int J Biostat. 2011;7(1):Article 37. doi: 10.2202/1557-4679.1353. Epub 2011 Sep 27.


Latent variable modeling paradigms for genotype-trait association studies.

Liu Y, Foulkes AS.

Biom J. 2011 Sep;53(5):838-54. doi: 10.1002/bimj.201000218.


Natural killer cell activation distinguishes Mycobacterium tuberculosis-mediated immune reconstitution syndrome from chronic HIV and HIV/MTB coinfection.

Conradie F, Foulkes AS, Ive P, Yin X, Roussos K, Glencross DK, Lawrie D, Stevens W, Montaner LJ, Sanne I, Azzoni L.

J Acquir Immune Defic Syndr. 2011 Nov 1;58(3):309-18. doi: 10.1097/QAI.0b013e31822e0d15.


Metabolic and anthropometric parameters contribute to ART-mediated CD4+ T cell recovery in HIV-1-infected individuals: an observational study.

Azzoni L, Foulkes AS, Firnhaber C, Yin X, Crowther NJ, Glencross D, Lawrie D, Stevens W, Papasavvas E, Sanne I, Montaner LJ.

J Int AIDS Soc. 2011 Jul 29;14:37. doi: 10.1186/1758-2652-14-37.


R statistical tools for gene discovery.

Foulkes AS, Au K.

Methods Mol Biol. 2011;760:73-90. doi: 10.1007/978-1-61779-176-5_5.


Randomized trial of time-limited interruptions of protease inhibitor-based antiretroviral therapy (ART) vs. continuous therapy for HIV-1 infection.

Firnhaber C, Azzoni L, Foulkes AS, Gross R, Yin X, Van Amsterdam D, Schulze D, Glencross DK, Stevens W, Hunt G, Morris L, Fox L, Sanne I, Montaner LJ.

PLoS One. 2011;6(6):e21450. doi: 10.1371/journal.pone.0021450. Epub 2011 Jun 28.


Prediction based classification for longitudinal biomarkers.

Foulkes AS, Azzoni L, Li X, Johnson MA, Smith C, Mounzer K, Montaner LJ.

Ann Appl Stat. 2010 Sep;4(3):1476-1497.


Association between HIV replication and serum leptin levels: an observational study of a cohort of HIV-1-infected South African women.

Azzoni L, Crowther NJ, Firnhaber C, Foulkes AS, Yin X, Glencross D, Gross R, Kaplan MD, Papasavvas E, Schulze D, Stevens W, van der Merwe T, Waisberg R, Sanne I, Montaner LJ.

J Int AIDS Soc. 2010 Sep 7;13:33. doi: 10.1186/1758-2652-13-33.


Tree-Based Methods for Discovery of Association between Flow Cytometry Data and Clinical Endpoints.

Eliot M, Azzoni L, Firnhaber C, Stevens W, Glencross DK, Sanne I, Montaner LJ, Foulkes AS.

Adv Bioinformatics. 2009;2009:235320. doi: 10.1155/2009/235320. Epub 2010 Jan 21.


Estimating and testing haplotype-trait associations in non-diploid populations.

Li X, Thomas BN, Rich SM, Ecker D, Tumwine JK, Foulkes AS.

J R Stat Soc Ser C Appl Stat. 2009 Dec;58(5):663-678.


Low-cost HIV-1 diagnosis and quantification in dried blood spots by real time PCR.

Mehta N, Trzmielina S, Nonyane BA, Eliot MN, Lin R, Foulkes AS, McNeal K, Ammann A, Eulalievyolo V, Sullivan JL, Luzuriaga K, Somasundaran M.

PLoS One. 2009 Jun 5;4(6):e5819. doi: 10.1371/journal.pone.0005819.


Circulating monocytes in HIV-1-infected viremic subjects exhibit an antiapoptosis gene signature and virus- and host-mediated apoptosis resistance.

Giri MS, Nebozyhn M, Raymond A, Gekonge B, Hancock A, Creer S, Nicols C, Yousef M, Foulkes AS, Mounzer K, Shull J, Silvestri G, Kostman J, Collman RG, Showe L, Montaner LJ.

J Immunol. 2009 Apr 1;182(7):4459-70. doi: 10.4049/jimmunol.0801450.


Application of two machine learning algorithms to genetic association studies in the presence of covariates.

Nonyane BA, Foulkes AS.

BMC Genet. 2008 Nov 14;9:71. doi: 10.1186/1471-2156-9-71.


Slow efavirenz metabolism genotype is common in Botswana.

Gross R, Aplenc R, Tenhave T, Foulkes AS, Thakur R, Mosepele M, Barrett JS, Flexner C, Strom BL, Bisson G.

J Acquir Immune Defic Syndr. 2008 Nov 1;49(3):336-7. doi: 10.1097/QAI.0b013e31817c1ed0. No abstract available.


A likelihood-based approach to mixed modeling with ambiguity in cluster identifiers.

Foulkes AS, Yucel R, Li X.

Biostatistics. 2008 Oct;9(4):635-57. doi: 10.1093/biostatistics/kxm055. Epub 2008 Mar 14.


In response to "Drug metabolizing enzyme polymorphisms predict clinical outcome in a node-positive breast cancer cohort".

DeMichele A, Gimotty P, Botbyl J, Aplenc R, Colligon T, Foulkes AS, Rebbeck TR.

J Clin Oncol. 2007 Dec 10;25(35):5675-7. No abstract available.


An expectation maximization approach to estimate malaria haplotype frequencies in multiply infected children.

Li X, Foulkes AS, Yucel RM, Rich SM.

Stat Appl Genet Mol Biol. 2007;6:Article33. Epub 2007 Nov 19.


Mixed modeling and multiple imputation for unobservable genotype clusters.

Foulkes AS, Yucel R, Reilly MP.

Stat Med. 2008 Jul 10;27(15):2784-801.


Baseline viral load and immune activation determine the extent of reconstitution of innate immune effectors in HIV-1-infected subjects undergoing antiretroviral treatment.

Chehimi J, Azzoni L, Farabaugh M, Creer SA, Tomescu C, Hancock A, Mackiewicz A, D'Alessandro L, Ghanekar S, Foulkes AS, Mounzer K, Kostman J, Montaner LJ.

J Immunol. 2007 Aug 15;179(4):2642-50.


Early and delayed benefits of HIV-1 suppression: timeline of recovery of innate immunity effector cells.

Azzoni L, Chehimi J, Zhou L, Foulkes AS, June R, Maino VC, Landay A, Rinaldo C, Jacobson LP, Montaner LJ.

AIDS. 2007 Jan 30;21(3):293-305.


Multiple imputation and random forests (MIRF) for unobservable, high-dimensional data.

Nonyane BA, Foulkes AS.

Int J Biostat. 2007;3(1):Article 12.


A resampling-based approach to multiple testing with uncertainty in phase.

Foulkes AS, DeGruttola VG.

Int J Biostat. 2007;3(1):Article 2.


Treatment of Brucella-susceptible mice with IL-12 increases primary and secondary immunity.

Sathiyaseelan J, Goenka R, Parent M, Benson RM, Murphy EA, Fernandes DM, Foulkes AS, Baldwin CL.

Cell Immunol. 2006 Sep;243(1):1-9. Epub 2006 Dec 20.


Validation and discovery in Markov models of genetics data.

De Gruttola V, Foulkes AS.

Stat Appl Genet Mol Biol. 2004;3:Article38. Epub 2004 Dec 27.


Associations among race/ethnicity, ApoC-III genotypes, and lipids in HIV-1-infected individuals on antiretroviral therapy.

Foulkes AS, Wohl DA, Frank I, Puleo E, Restine S, Wolfe ML, Dube MP, Tebas P, Reilly MP.

PLoS Med. 2006 Mar;3(3):e52.


Exploratory Bayesian model selection for serial genetics data.

Zhao JX, Foulkes AS, George EI.

Biometrics. 2005 Jun;61(2):591-9.


Higher order lipase gene association with plasma triglycerides.

Reilly MP, Foulkes AS, Wolfe ML, Rader DJ.

J Lipid Res. 2005 Sep;46(9):1914-22. Epub 2005 Jun 16.


MDR and PRP: a comparison of methods for high-order genotype-phenotype associations.

Bastone L, Reilly M, Rader DJ, Foulkes AS.

Hum Hered. 2004;58(2):82-92.


Mixed modelling to characterize genotype-phenotype associations.

Foulkes AS, Reilly M, Zhou L, Wolfe M, Rader DJ.

Stat Med. 2005 Mar 15;24(5):775-89.


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