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Keywords
Last Name
Institution

Vincent James Carey, PH.D.

TitleAssociate Professor of Medicine
InstitutionBrigham and Women's Hospital
DepartmentMedicine
AddressBrigham and Women's Hospital
Channing Division of Network Medicine
181 Longwood Ave
Boston MA 02115
Phone617/525-2265
Fax617/731-1541
Other Positions
TitleInstructor in Biostatistics in the School of Public Health
InstitutionHarvard School of Public Health
DepartmentBiostatistics


 Mentoring 
 current student opportunities
Available: 08/01/12, Expires: 07/15/13

Assemble and analyze data from microarray-based and sequencing-based experiments with the objective of developing metrics and preferences for efficiency and accuracy of proposed methods.


 Bibliographic 
 selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Wan ES, Qiu W, Baccarelli A, Carey VJ, Bacherman H, Rennard SI, Agustí A, Anderson WH, Lomas DA, Demeo DL. Systemic steroid exposure is associated with differential methylation in chronic obstructive pulmonary disease. Am J Respir Crit Care Med. 2012 Dec 15; 186(12):1248-55.
    View in: PubMed
  2. Himes BE, Jiang X, Hu R, Wu AC, Lasky-Su JA, Klanderman BJ, Ziniti J, Senter-Sylvia J, Lima JJ, Irvin CG, Peters SP, Meyers DA, Bleecker ER, Kubo M, Tamari M, Nakamura Y, Szefler SJ, Lemanske RF, Zeiger RS, Strunk RC, Martinez FD, Hanrahan JP, Koppelman GH, Postma DS, Nieuwenhuis MA, Vonk JM, Panettieri RA, Markezich A, Israel E, Carey VJ, Tantisira KG, Litonjua AA, Lu Q, Weiss ST. Genome-wide association analysis in asthma subjects identifies SPATS2L as a novel bronchodilator response gene. PLoS Genet. 2012 Jul; 8(7):e1002824.
    View in: PubMed
  3. Anton SD, Gallagher J, Carey VJ, Laranjo N, Cheng J, Champagne CM, Ryan DH, McManus K, Loria CM, Bray GA, Sacks FM, Williamson DA. Diet type and changes in food cravings following weight loss: findings from the POUNDS LOST Trial. Eat Weight Disord. 2012 Jun; 17(2):e101-8.
    View in: PubMed
  4. Wan ES, Qiu W, Baccarelli A, Carey VJ, Bacherman H, Rennard SI, Agusti A, Anderson W, Lomas DA, Demeo DL. Cigarette smoking behaviors and time since quitting are associated with differential DNA methylation across the human genome. Hum Mol Genet. 2012 Jul 1; 21(13):3073-82.
    View in: PubMed
  5. de Souza RJ, Bray GA, Carey VJ, Hall KD, LeBoff MS, Loria CM, Laranjo NM, Sacks FM, Smith SR. Effects of 4 weight-loss diets differing in fat, protein, and carbohydrate on fat mass, lean mass, visceral adipose tissue, and hepatic fat: results from the POUNDS LOST trial. Am J Clin Nutr. 2012 Mar; 95(3):614-25.
    View in: PubMed
  6. Qiu W, Baccarelli A, Carey VJ, Boutaoui N, Bacherman H, Klanderman B, Rennard S, Agusti A, Anderson W, Lomas DA, DeMeo DL. Variable DNA methylation is associated with chronic obstructive pulmonary disease and lung function. Am J Respir Crit Care Med. 2012 Feb 15; 185(4):373-81.
    View in: PubMed
  7. Aschard H, Qiu W, Pasaniuc B, Zaitlen N, Cho MH, Carey V. Combining effects from rare and common genetic variants in an exome-wide association study of sequence data. BMC Proc. 2011; 5 Suppl 9:S44.
    View in: PubMed
  8. Bray GA, Smith SR, DeJonge L, de Souza R, Rood J, Champagne CM, Laranjo N, Carey V, Obarzanek E, Loria CM, Anton SD, Ryan DH, Greenway FL, Williamson D, Sacks FM. Effect of diet composition on energy expenditure during weight loss: the POUNDS LOST Study. Int J Obes (Lond). 2012 Mar; 36(3):448-55.
    View in: PubMed
  9. Carey VJ, Wang YG. Working covariance model selection for generalized estimating equations. Stat Med. 2011 Nov 20; 30(26):3117-24.
    View in: PubMed
  10. Melén E, Kho AT, Sharma S, Gaedigk R, Leeder JS, Mariani TJ, Carey VJ, Weiss ST, Tantisira KG. Expression analysis of asthma candidate genes during human and murine lung development. Respir Res. 2011; 12:86.
    View in: PubMed
  11. King JR, Yogev R, Jean-Philippe P, Graham B, Wiznia A, Britto P, Carey V, Hazra R, Acosta EP. Steady-state pharmacokinetics of tenofovir-based regimens in HIV-infected pediatric patients. Antimicrob Agents Chemother. 2011 Sep; 55(9):4290-4.
    View in: PubMed
  12. Chu JH, Lazarus R, Carey VJ, Raby BA. Quantifying differential gene connectivity between disease states for objective identification of disease-relevant genes. BMC Syst Biol. 2011; 5:89.
    View in: PubMed
  13. Hunninghake GM, Chu JH, Sharma SS, Cho MH, Himes BE, Rogers AJ, Murphy A, Carey VJ, Raby BA. The CD4+ T-cell transcriptome and serum IgE in asthma: IL17RB and the role of sex. BMC Pulm Med. 2011; 11:17.
    View in: PubMed
  14. Sharma S, Murphy A, Howrylak J, Himes B, Cho MH, Chu JH, Hunninghake GM, Fuhlbrigge A, Klanderman B, Ziniti J, Senter-Sylvia J, Liu A, Szefler SJ, Strunk R, Castro M, Hansel NN, Diette GB, Vonakis BM, Adkinson NF, Carey VJ, Raby BA. The impact of self-identified race on epidemiologic studies of gene expression. Genet Epidemiol. 2011 Feb; 35(2):93-101.
    View in: PubMed
  15. Millán Núñez-Cortés J, Montoya JP, Salas XP, Hernández Mijares A, Carey VJ, Hermans MP, Sacks FM, Fruchart JC. [The REALIST (REsiduAl risk, LIpids and Standard Therapies) study: an analysis of residual risk attributable to lipid profile in acute coronary syndrome]. Endocrinol Nutr. 2011 Jan; 58(1):38-47.
    View in: PubMed
  16. Murphy A, Chu JH, Xu M, Carey VJ, Lazarus R, Liu A, Szefler SJ, Strunk R, Demuth K, Castro M, Hansel NN, Diette GB, Vonakis BM, Adkinson NF, Klanderman BJ, Senter-Sylvia J, Ziniti J, Lange C, Pastinen T, Raby BA. Mapping of numerous disease-associated expression polymorphisms in primary peripheral blood CD4+ lymphocytes. Hum Mol Genet. 2010 Dec 1; 19(23):4745-57.
    View in: PubMed
  17. Furtado JD, Campos H, Sumner AE, Appel LJ, Carey VJ, Sacks FM. Dietary interventions that lower lipoproteins containing apolipoprotein C-III are more effective in whites than in blacks: results of the OmniHeart trial. Am J Clin Nutr. 2010 Oct; 92(4):714-22.
    View in: PubMed
  18. Troy EB, Carey VJ, Kasper DL, Comstock LE. Orientations of the Bacteroides fragilis capsular polysaccharide biosynthesis locus promoters during symbiosis and infection. J Bacteriol. 2010 Nov; 192(21):5832-6.
    View in: PubMed
  19. Sacks FM, Carey VJ, Fruchart JC. Combination lipid therapy in type 2 diabetes. N Engl J Med. 2010 Aug 12; 363(7):692-4; author reply 694-5.
    View in: PubMed
  20. Carey VJ, Bishop L, Laranjo N, Harshfield BJ, Kwiat C, Sacks FM. Contribution of high plasma triglycerides and low high-density lipoprotein cholesterol to residual risk of coronary heart disease after establishment of low-density lipoprotein cholesterol control. Am J Cardiol. 2010 Sep 15; 106(6):757-63.
    View in: PubMed
  21. Williamson DA, Anton SD, Han H, Champagne CM, Allen R, Leblanc E, Ryan DH, Rood J, McManus K, Laranjo N, Carey VJ, Loria CM, Bray GA, Sacks FM. Early behavioral adherence predicts short and long-term weight loss in the POUNDS LOST study. J Behav Med. 2010 Aug; 33(4):305-14.
    View in: PubMed
  22. Sharma S, Tantisira K, Carey V, Murphy AJ, Lasky-Su J, Celedón JC, Lazarus R, Klanderman B, Rogers A, Soto-Quirós M, Avila L, Mariani T, Gaedigk R, Leeder S, Torday J, Warburton D, Raby B, Weiss ST. A role for Wnt signaling genes in the pathogenesis of impaired lung function in asthma. Am J Respir Crit Care Med. 2010 Feb 15; 181(4):328-36.
    View in: PubMed
  23. Williamson DA, Anton SD, Han H, Champagne CM, Allen R, LeBlanc E, Ryan DH, McManus K, Laranjo N, Carey VJ, Loria CM, Bray GA, Sacks FM. Adherence is a multi-dimensional construct in the POUNDS LOST trial. J Behav Med. 2010 Feb; 33(1):35-46.
    View in: PubMed
  24. Kho AT, Bhattacharya S, Tantisira KG, Carey VJ, Gaedigk R, Leeder JS, Kohane IS, Weiss ST, Mariani TJ. Transcriptomic analysis of human lung development. Am J Respir Crit Care Med. 2010 Jan 1; 181(1):54-63.
    View in: PubMed
  25. Shiu C, Cunningham CK, Greenough T, Muresan P, Sanchez-Merino V, Carey V, Jackson JB, Ziemniak C, Fox L, Belzer M, Ray SC, Luzuriaga K, Persaud D. Identification of ongoing human immunodeficiency virus type 1 (HIV-1) replication in residual viremia during recombinant HIV-1 poxvirus immunizations in patients with clinically undetectable viral loads on durable suppressive highly active antiretroviral therapy. J Virol. 2009 Oct; 83(19):9731-42.
    View in: PubMed
  26. Du R, Tantisira K, Carey V, Bhattacharya S, Metje S, Kho AT, Klanderman BJ, Gaedigk R, Lazarus R, Mariani TJ, Leeder JS, Weiss ST. Platform dependence of inference on gene-wise and gene-set involvement in human lung development. BMC Bioinformatics. 2009; 10:189.
    View in: PubMed
  27. Chu JH, Weiss ST, Carey VJ, Raby BA. A graphical model approach for inferring large-scale networks integrating gene expression and genetic polymorphism. BMC Syst Biol. 2009; 3:55.
    View in: PubMed
  28. Lawrence M, Gentleman R, Carey V. rtracklayer: an R package for interfacing with genome browsers. Bioinformatics. 2009 Jul 15; 25(14):1841-2.
    View in: PubMed
  29. Kim WJ, Silverman EK, Hoffman E, Criner GJ, Mosenifar Z, Sciurba FC, Make BJ, Carey V, Estépar RS, Diaz A, Reilly JJ, Martinez FJ, Washko GR. CT metrics of airway disease and emphysema in severe COPD. Chest. 2009 Aug; 136(2):396-404.
    View in: PubMed
  30. Carey VJ, Davis AR, Lawrence MF, Gentleman R, Raby BA. Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x. Bioinformatics. 2009 Jun 1; 25(11):1447-8.
    View in: PubMed
  31. Sacks FM, Bray GA, Carey VJ, Smith SR, Ryan DH, Anton SD, McManus K, Champagne CM, Bishop LM, Laranjo N, Leboff MS, Rood JC, de Jonge L, Greenway FL, Loria CM, Obarzanek E, Williamson DA. Comparison of weight-loss diets with different compositions of fat, protein, and carbohydrates. N Engl J Med. 2009 Feb 26; 360(9):859-73.
    View in: PubMed
  32. King JR, Acosta EP, Yogev R, Wiznia A, Kraimer J, Graham B, Carey V, Britto P, Jean-Philippe P, Moye J, Watson D. Steady-state pharmacokinetics of lopinavir/ritonavir in combination with efavirenz in human immunodeficiency virus-infected pediatric patients. Pediatr Infect Dis J. 2009 Feb; 28(2):159-61.
    View in: PubMed
  33. Carey VJ, Gentleman R. Interpreting genetics of gene expression: integrative architecture in Bioconductor. Pac Symp Biocomput. 2009; 380-90.
    View in: PubMed
  34. Foudi A, Hochedlinger K, Van Buren D, Schindler JW, Jaenisch R, Carey V, Hock H. Analysis of histone 2B-GFP retention reveals slowly cycling hematopoietic stem cells. Nat Biotechnol. 2009 Jan; 27(1):84-90.
    View in: PubMed
  35. Baron MJ, Wong SL, Nybakken K, Carey VJ, Madoff LC. Host glycosaminoglycan confers susceptibility to bacterial infection in Drosophila melanogaster. Infect Immun. 2009 Feb; 77(2):860-6.
    View in: PubMed
  36. Asare AL, Gao Z, Carey VJ, Wang R, Seyfert-Margolis V. Power enhancement via multivariate outlier testing with gene expression arrays. Bioinformatics. 2009 Jan 1; 25(1):48-53.
    View in: PubMed
  37. Borenshtein D, Fry RC, Groff EB, Nambiar PR, Carey VJ, Fox JG, Schauer DB. Diarrhea as a cause of mortality in a mouse model of infectious colitis. Genome Biol. 2008; 9(8):R122.
    View in: PubMed
  38. Foreman MG, DeMeo DL, Hersh CP, Carey VJ, Fan VS, Reilly JJ, Shapiro SD, Silverman EK. Polymorphic variation in surfactant protein B is associated with COPD exacerbations. Eur Respir J. 2008 Oct; 32(4):938-44.
    View in: PubMed
  39. Furtado JD, Campos H, Appel LJ, Miller ER, Laranjo N, Carey VJ, Sacks FM. Effect of protein, unsaturated fat, and carbohydrate intakes on plasma apolipoprotein B and VLDL and LDL containing apolipoprotein C-III: results from the OmniHeart Trial. Am J Clin Nutr. 2008 Jun; 87(6):1623-30.
    View in: PubMed
  40. Fuhlbrigge A, Carey VJ, Finkelstein JA, Lozano P, Inui TS, Weiss KB. Are performance measures based on automated medical records valid for physician/practice profiling of asthma care? Med Care. 2008 Jun; 46(6):620-6.
    View in: PubMed
  41. Ben-Porath I, Thomson MW, Carey VJ, Ge R, Bell GW, Regev A, Weinberg RA. An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors. Nat Genet. 2008 May; 40(5):499-507.
    View in: PubMed
  42. Carey VJ, Gentry J, Sarkar R, Gentleman D, Ramaswamy S. SGDI: system for genomic data integration. Pac Symp Biocomput. 2008; 141-52.
    View in: PubMed
  43. Tishler PV, Carey VJ. Can comparison of MZ- and DZ-twin concordance rates be used invariably to estimate heritability? Twin Res Hum Genet. 2007 Oct; 10(5):712-7.
    View in: PubMed
  44. Huber W, Carey VJ, Long L, Falcon S, Gentleman R. Graphs in molecular biology. BMC Bioinformatics. 2007; 8 Suppl 6:S8.
    View in: PubMed
  45. Tarca AL, Carey VJ, Chen XW, Romero R, Draghici S. Machine learning and its applications to biology. PLoS Comput Biol. 2007 Jun; 3(6):e116.
    View in: PubMed
  46. Vincent Carey, A Weinberg, S Pahwa, A Kovacs, S Burchett, and ACTG 366 Study Group. Prognostic Value of 3-Color Flow Cytometry in Advanced Pediatric HIV Disease. CROI 2007: 14th Conference on Retroviruses and Opportunistic Infections. 2007; 14.
  47. VJ Carey, BJ Harshfield. 2007.
  48. Carey VJ, Morgan M, Falcon S, Lazarus R, Gentleman R. GGtools: analysis of genetics of gene expression in bioconductor. Bioinformatics. 2007 Feb 15; 23(4):522-3.
    View in: PubMed
  49. Bilban M, Heintel D, Scharl T, Woelfel T, Auer MM, Porpaczy E, Kainz B, Kröber A, Carey VJ, Shehata M, Zielinski C, Pickl W, Stilgenbauer S, Gaiger A, Wagner O, Jäger U. Deregulated expression of fat and muscle genes in B-cell chronic lymphocytic leukemia with high lipoprotein lipase expression. Leukemia. 2006 Jun; 20(6):1080-8.
    View in: PubMed
  50. Hufnagel M, Carey VJ, Baldassarri L, Reinert RR, Huebner J. Distribution of four capsular serotypes of Enterococcus faecalis among clinical isolates from different geographical origins and infection sites. Infection. 2006 Feb; 34(1):22-5.
    View in: PubMed
  51. VJ Carey. GGtools: software for genetics of gene expression. 2006.
  52. Reimers M, Carey VJ. Bioconductor: an open source framework for bioinformatics and computational biology. Methods Enzymol. 2006; 411:119-34.
    View in: PubMed
  53. Finkelstein JA, Lozano P, Fuhlbrigge AL, Carey VJ, Inui TS, Soumerai SB, Sullivan SD, Wagner EH, Weiss ST, Weiss KB. Practice-level effects of interventions to improve asthma care in primary care settings: the Pediatric Asthma Care Patient Outcomes Research Team. Health Serv Res. 2005 Dec; 40(6 Pt 1):1737-57.
    View in: PubMed
  54. Appel LJ, Sacks FM, Carey VJ, Obarzanek E, Swain JF, Miller ER, Conlin PR, Erlinger TP, Rosner BA, Laranjo NM, Charleston J, McCarron P, Bishop LM. Effects of protein, monounsaturated fat, and carbohydrate intake on blood pressure and serum lipids: results of the OmniHeart randomized trial. JAMA. 2005 Nov 16; 294(19):2455-64.
    View in: PubMed
  55. Gentleman RC, Carey VJ. Visualization and annotation of genomic experiments. Dunn MJ, Jorde LB, Little PFR, Subramaniam S, Editors. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 2005.
  56. Cohen ND, Carey VJ, Donahue JG, Seahorn JL, Brown SE, Riddle TW. Temporality of early-term abortions associated with mare reproductive loss syndrome in horses. Am J Vet Res. 2005 Oct; 66(10):1792-7.
    View in: PubMed
  57. Bricker AL, Carey VJ, Wessels MR. Role of NADase in virulence in experimental invasive group A streptococcal infection. Infect Immun. 2005 Oct; 73(10):6562-6.
    View in: PubMed
  58. Kovacs A, Montepiedra G, Carey V, Pahwa S, Weinberg A, Frenkel L, Capparelli E, Mofenson L, Smith E, McIntosh K, Burchett SK. Immune reconstitution after receipt of highly active antiretroviral therapy in children with advanced or progressive HIV disease and complete or partial viral load response. J Infect Dis. 2005 Jul 15; 192(2):296-302.
    View in: PubMed
  59. Orimo A, Gupta PB, Sgroi DC, Arenzana-Seisdedos F, Delaunay T, Naeem R, Carey VJ, Richardson AL, Weinberg RA. Stromal fibroblasts present in invasive human breast carcinomas promote tumor growth and angiogenesis through elevated SDF-1/CXCL12 secretion. Cell. 2005 May 6; 121(3):335-48.
    View in: PubMed
  60. Fuhlbrigge AL, Carey VJ, Finkelstein JA, Lozano P, Inui TS, Weiss ST, Weiss KB. Validity of the HEDIS criteria to identify children with persistent asthma and sustained high utilization. Am J Manag Care. 2005 May; 11(5):325-30.
    View in: PubMed
  61. Carey VJ, Pahwa S, Weinberg A. Reliability of CD4 quantitation in human immunodeficiency virus-positive children: implications for definition of immunologic response to highly active antiretroviral therapy. Clin Diagn Lab Immunol. 2005 May; 12(5):640-3.
    View in: PubMed
  62. Sullivan SD, Lee TA, Blough DK, Finkelstein JA, Lozano P, Inui TS, Fuhlbrigge AL, Carey VJ, Wagner E, Weiss KB. A multisite randomized trial of the effects of physician education and organizational change in chronic asthma care: cost-effectiveness analysis of the Pediatric Asthma Care Patient Outcomes Research Team II (PAC-PORT II). Arch Pediatr Adolesc Med. 2005 May; 159(5):428-34.
    View in: PubMed
  63. Carey VJ, Gentleman RC, Huber W, Gentry J. Bioconductor software for graphs. Gentleman RC, Carey VJ, Huber W, Irizarry RA, Dudoit S, editors. Bioinformatics and Computational Biology Solutions Using R and Bioconductor. 2005; 347-68.
  64. Huber W, Gentleman RC, Carey VJ. Graphs. Gentleman RC, Carey VJ, Huber W, Irizarry RA, Dudoit S, editors. Bioinformatics and Computational Biology Solutions Using R and Bioconductor. 2005; 337-46.
  65. Carey VJ, Bishop L, Charleston J, Conlin P, Erlinger T, Laranjo N, McCarron P, Miller E, Rosner B, Swain J, Sacks FM, Appel LJ. Rationale and design of the Optimal Macro-Nutrient Intake Heart Trial to Prevent Heart Disease (OMNI-Heart). Clin Trials. 2005; 2(6):529-37.
    View in: PubMed
  66. Carey VJ, Temple Lang D, Gentry J, Zhang J, Gentleman RC. Querying on-line resources. Gentleman RC, Carey VJ, Huber W, Irizarry RA, Dudoit S, editors. Bioinformatics and Computational Biology Solutions Using R and Bioconductor. 2005; 135-46.
  67. Gentleman RC, Carey VJ, Zhang J. Meta-data resources and tools in Bioconductor. Gentleman RC, Carey VJ, Huber W, Irizarry RA, Dudoit S, editors. Bioinformatics and Computational Biology Solutions Using R and Bioconductor. 2005; 111-34.
  68. Gentleman R, Scholtens D, Ding B, Carey VJ, Huber W. Case studies using graphs on biological data. Gentleman R, Carey VJ, Huber W, Irizarry RA, Dudoit S, editors. Bioinformatics and Computational Biology Solutions Using R and Bioconductor. 2005; 363-93.
  69. Gentleman RC, Carey VJ, Huber W, Irizarry RA, Dudoit S, editors. Bioinformatics and Computational Biology Solutions with R and Bioconductor. 2005.
  70. Carey VJ. Machine learning concepts and tools for statistical genomics. Gentleman RC, Carey VJ, Huber W, Irizarry RA, Dudoit S, editors. Bioinformatics and Computational Biology Solutions Using R and Bioconductor. 2005; 273-92.
  71. Hersh CP, DeMeo DL, Al-Ansari E, Carey VJ, Reilly JJ, Ginns LC, Silverman EK. Predictors of survival in severe, early onset COPD. Chest. 2004 Nov; 126(5):1443-51.
    View in: PubMed
  72. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004; 5(10):R80.
    View in: PubMed
  73. Lozano P, Finkelstein JA, Carey VJ, Wagner EH, Inui TS, Fuhlbrigge AL, Soumerai SB, Sullivan SD, Weiss ST, Weiss KB. A multisite randomized trial of the effects of physician education and organizational change in chronic-asthma care: health outcomes of the Pediatric Asthma Care Patient Outcomes Research Team II Study. Arch Pediatr Adolesc Med. 2004 Sep; 158(9):875-83.
    View in: PubMed
  74. Carey VJ, Gentry J, Whalen E, Gentleman R. Network structures and algorithms in Bioconductor. Bioinformatics. 2005 Jan 1; 21(1):135-6.
    View in: PubMed
  75. Durinck S, Allemeersch J, Carey VJ, Moreau Y, De Moor B. Importing MAGE-ML format microarray data into BioConductor. Bioinformatics. 2004 Dec 12; 20(18):3641-2.
    View in: PubMed
  76. Weinberg A, Pahwa S, Oyomopito R, Carey VJ, Zimmer B, Mofenson L, Kovacs A, Burchett SK. Antimicrobial-specific cell-mediated immune reconstitution in children with advanced human immunodeficiency virus infection receiving highly active antiretroviral therapy. Clin Infect Dis. 2004 Jul 1; 39(1):107-14.
    View in: PubMed
  77. Tang ML, Tang NS, Carey VJ. Confidence interval for rate ratio in a 2 x 2 table with structural zero: an application in assessing false-negative rate ratio when combining two diagnostic tests. Biometrics. 2004 Jun; 60(2):550-5; discussion 555.
    View in: PubMed
  78. Fuhlbrigge A, Carey VJ, Adams RJ, Finkelstein JA, Lozano P, Weiss ST, Weiss KB. Evaluation of asthma prescription measures and health system performance based on emergency department utilization. Med Care. 2004 May; 42(5):465-71.
    View in: PubMed
  79. DeMeo DL, Carey VJ, Chapman HA, Reilly JJ, Ginns LC, Speizer FE, Weiss ST, Silverman EK. Familial aggregation of FEF(25-75) and FEF(25-75)/FVC in families with severe, early onset COPD. Thorax. 2004 May; 59(5):396-400.
    View in: PubMed
  80. Carey VJ, Yong FH, Frenkel LM, McKinney RM. Growth velocity assessment in paediatric AIDS: smoothing, penalized quantile regression and the definition of growth failure. Stat Med. 2004 Feb 15; 23(3):509-26.
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  81. Krueger WA, Krueger-Rameck S, Koch S, Carey V, Pier GB, Huebner J. Assessment of the role of antibiotics and enterococcal virulence factors in a mouse model of extraintestinal translocation. Crit Care Med. 2004 Feb; 32(2):467-71.
    View in: PubMed
  82. Jess Mar, Robert Gentleman, Vince Carey. MLInterfaces: Interfaces to R machine learning procedures for high-throughput data structures. 2004.
  83. Wang YG, Carey VJ. Unbiased estimating equations from working correlation models for irregularly timed repeated measures. J Amer Stat Assoc. 2004; 99:845-53.
  84. Seahorn JL, Slovis NM, Reimer JM, Carey VJ, Donahue JG, Cohen ND. Case-control study of factors associated with fibrinous pericarditis among horses in central Kentucky during spring 2001. J Am Vet Med Assoc. 2003 Sep 15; 223(6):832-8.
    View in: PubMed
  85. Cohen ND, Carey VJ, Donahue JG, Seahorn JL, Harrison LR. Descriptive epidemiology of late-term abortions associated with the mare reproductive loss syndrome in central Kentucky. J Vet Diagn Invest. 2003 May; 15(3):295-7.
    View in: PubMed
  86. Stewart SA, Ben-Porath I, Carey VJ, O'Connor BF, Hahn WC, Weinberg RA. Erosion of the telomeric single-strand overhang at replicative senescence. Nat Genet. 2003 Apr; 33(4):492-6.
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  87. Coleman FT, Mueschenborn S, Meluleni G, Ray C, Carey VJ, Vargas SO, Cannon CL, Ausubel FM, Pier GB. Hypersusceptibility of cystic fibrosis mice to chronic Pseudomonas aeruginosa oropharyngeal colonization and lung infection. Proc Natl Acad Sci U S A. 2003 Feb 18; 100(4):1949-54.
    View in: PubMed
  88. Cohen ND, Donahue JG, Carey VJ, Seahorn JL, Piercy D, Donahoe JK, Williams DM, Brown SE, Riddle TW. Case-control study of early-term abortions (early fetal losses) associated with mare reproductive loss syndrome in central Kentucky. J Am Vet Med Assoc. 2003 Jan 15; 222(2):210-7.
    View in: PubMed
  89. Cohen ND, Carey VJ, Donahue JG, Seahorn JL, Donahoe JK, Williams DM, Harrison LR. Case-control study of late-term abortions associated with mare reproductive loss syndrome in central Kentucky. J Am Vet Med Assoc. 2003 Jan 15; 222(2):199-209.
    View in: PubMed
  90. Gentleman RC, Carey VJ. Bioconductor: software and development strategies for statistical genomics. Parmigiani G, Garrett E, Irizarry R, Zeger S, editors. The analysis of gene expression data: Methods and software. 2003; 46-72.
  91. Carey VJ. Ontology concepts and tools for statistical genomics. J Multivariate Analysis. 2003; 90:213-28.
  92. Zhang J, Carey V, Gentleman R. An extensible application for assembling annotation for genomic data. Bioinformatics. 2003 Jan; 19(1):155-6.
    View in: PubMed
  93. Wang YG, Carey VJ. Working correlation structure misspecification, estimation and covariate design: implications for GEE performance. Biometrika. 2003; 90:29-42.
  94. Gaughan DM, Hughes MD, Seage GR, Selwyn PA, Carey VJ, Gortmaker SL, Oleske JM. The prevalence of pain in pediatric human immunodeficiency virus/acquired immunodeficiency syndrome as reported by participants in the Pediatric Late Outcomes Study (PACTG 219). Pediatrics. 2002 Jun; 109(6):1144-52.
    View in: PubMed
  95. Donahue JG, Chan KA, Andrade SE, Beck A, Boles M, Buist DS, Carey VJ, Chandler JM, Chase GA, Ettinger B, Fishman P, Goodman M, Guess HA, Gurwitz JH, LaCroix AZ, Levin TR, Platt R. Gastric and duodenal safety of daily alendronate. Arch Intern Med. 2002 Apr 22; 162(8):936-42.
    View in: PubMed
  96. Tishler PV, Carey VJ, Reed T, Fabsitz RR. The role of genotype in determining the effects of cigarette smoking on pulmonary function. Genet Epidemiol. 2002 Mar; 22(3):272-82.
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  97. van Breukelen F, Carey V. Ubiquitin conjugate dynamics in the gut and liver of hibernating ground squirrels. J Comp Physiol B. 2002 Apr; 172(3):269-73.
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  98. Wright RJ, Cohen S, Carey V, Weiss ST, Gold DR. Parental stress as a predictor of wheezing in infancy: a prospective birth-cohort study. Am J Respir Crit Care Med. 2002 Feb 1; 165(3):358-65.
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  99. Naugler WE, Yong FH, Carey VJ, Dragavon JA, Coombs RW, Frenkel LM. T69D/N pol mutation, human immunodeficiency virus type 1 RNA levels, and syncytium-inducing phenotype are associated with CD4 cell depletion during didanosine therapy. J Infect Dis. 2002 Feb 15; 185(4):448-55.
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  100. R. Gentleman, V. Carey, M. Morgan, S. Falcon. Biobase: foundational structures and functions for Bioconductor. 2002.
  101. Puopolo KM, Hollingshead SK, Carey VJ, Madoff LC. Tandem repeat deletion in the alpha C protein of group B streptococcus is recA independent. Infect Immun. 2001 Aug; 69(8):5037-45.
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  102. Coyne MJ, Tzianabos AO, Mallory BC, Carey VJ, Kasper DL, Comstock LE. Polysaccharide biosynthesis locus required for virulence of Bacteroides fragilis. Infect Immun. 2001 Jul; 69(7):4342-50.
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  103. Carey VJ, Baker CJ, Platt R. Bayesian inference on protective antibody levels using case-control data. Biometrics. 2001 Mar; 57(1):135-42.
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  104. Carey VJ, Rosner BA. Analysis of longitudinally observed irregularly timed multivariate outcomes: regression with focus on cross-component correlation. Stat Med. 2001 Jan 15; 20(1):21-31.
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  105. Carey VJ. GEE solvers: case studies in DSC design and implementation. Proceedings of the 2d International Workshop on Distributed Statistical Computing. 2001; 1-14.
  106. Litonjua AA, Carey VJ, Burge HA, Weiss ST, Gold DR. Exposure to cockroach allergen in the home is associated with incident doctor-diagnosed asthma and recurrent wheezing. J Allergy Clin Immunol. 2001 Jan; 107(1):41-7.
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  107. Carey VJ. Literate statistical programming: concepts and tools. Chance. 2001; 14:46-50.
  108. Silverman EK, Weiss ST, Drazen JM, Chapman HA, Carey V, Campbell EJ, Denish P, Silverman RA, Celedon JC, Reilly JJ, Ginns LC, Speizer FE. Gender-related differences in severe, early-onset chronic obstructive pulmonary disease. Am J Respir Crit Care Med. 2000 Dec; 162(6):2152-8.
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  109. Baker CJ, Paoletti LC, Rench MA, Guttormsen HK, Carey VJ, Hickman ME, Kasper DL. Use of capsular polysaccharide-tetanus toxoid conjugate vaccine for type II group B Streptococcus in healthy women. J Infect Dis. 2000 Oct; 182(4):1129-38.
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  110. Stevens RC, Rodman JH, Yong FH, Carey V, Knupp CA, Frenkel LM. Effect of food and pharmacokinetic variability on didanosine systemic exposure in HIV-infected children. Pediatric AIDS Clinical Trials Group Protocol 144 Study Team. AIDS Res Hum Retroviruses. 2000 Mar 20; 16(5):415-21.
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  111. Kalka-Moll WM, Tzianabos AO, Wang Y, Carey VJ, Finberg RW, Onderdonk AB, Kasper DL. Effect of molecular size on the ability of zwitterionic polysaccharides to stimulate cellular immunity. J Immunol. 2000 Jan 15; 164(2):719-24.
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  112. Litonjua AA, Carey VJ, Weiss ST, Gold DR. Race, socioeconomic factors, and area of residence are associated with asthma prevalence. Pediatr Pulmonol. 1999 Dec; 28(6):394-401.
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  113. Celedon JC, Speizer FE, Drazen JM, Weiss ST, Campbell EJ, Carey VJ, Reilly JJ, Ginns L, Silverman EK. Bronchodilator responsiveness and serum total IgE levels in families of probands with severe early-onset COPD. Eur Respir J. 1999 Nov; 14(5):1009-14.
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  114. Cohen ND, Mundy GD, Peloso JG, Carey VJ, Amend NK. Results of physical inspection before races and race-related characteristics and their association with musculoskeletal injuries in Thoroughbreds during races. J Am Vet Med Assoc. 1999 Sep 1; 215(5):654-61.
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  115. Gold DR, Burge HA, Carey V, Milton DK, Platts-Mills T, Weiss ST. Predictors of repeated wheeze in the first year of life: the relative roles of cockroach, birth weight, acute lower respiratory illness, and maternal smoking. Am J Respir Crit Care Med. 1999 Jul; 160(1):227-36.
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  116. Carey VJ. An approach to heteroskedastic modeling. Statistical Modeling. 1999; 142-9.
  117. Rexrode KM, Carey VJ, Hennekens CH, Walters EE, Colditz GA, Stampfer MJ, Willett WC, Manson JE. Abdominal adiposity and coronary heart disease in women. JAMA. 1998 Dec 2; 280(21):1843-8.
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  118. Thakker M, Park JS, Carey V, Lee JC. Staphylococcus aureus serotype 5 capsular polysaccharide is antiphagocytic and enhances bacterial virulence in a murine bacteremia model. Infect Immun. 1998 Nov; 66(11):5183-9.
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  119. Ashbaugh CD, Warren HB, Carey VJ, Wessels MR. Molecular analysis of the role of the group A streptococcal cysteine protease, hyaluronic acid capsule, and M protein in a murine model of human invasive soft-tissue infection. J Clin Invest. 1998 Aug 1; 102(3):550-60.
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  120. Carey VJ, Yong FH, Frenkel LM, McKinney RE. Pediatric AIDS prognosis using somatic growth velocity. AIDS. 1998 Jul 30; 12(11):1361-9.
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  121. Litonjua AA, Carey VJ, Burge HA, Weiss ST, Gold DR. Parental history and the risk for childhood asthma. Does mother confer more risk than father? Am J Respir Crit Care Med. 1998 Jul; 158(1):176-81.
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  122. Albert CM, Hennekens CH, O'Donnell CJ, Ajani UA, Carey VJ, Willett WC, Ruskin JN, Manson JE. Fish consumption and risk of sudden cardiac death. JAMA. 1998 Jan 7; 279(1):23-8.
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  123. Gravekamp C, Kasper DL, Michel JL, Kling DE, Carey V, Madoff LC. Immunogenicity and protective efficacy of the alpha C protein of group B streptococci are inversely related to the number of repeats. Infect Immun. 1997 Dec; 65(12):5216-21.
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  124. Beckett WS, Pace PA, Sferlazza SJ, Carey VJ, Weiss ST. Annual variability in methacholine responsiveness in nonasthmatic working adults. Eur Respir J. 1997 Nov; 10(11):2515-21.
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  125. Solomon CG, Willett WC, Carey VJ, Rich-Edwards J, Hunter DJ, Colditz GA, Stampfer MJ, Speizer FE, Spiegelman D, Manson JE. A prospective study of pregravid determinants of gestational diabetes mellitus. JAMA. 1997 Oct 1; 278(13):1078-83.
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  126. Lee JC, Park JS, Shepherd SE, Carey V, Fattom A. Protective efficacy of antibodies to the Staphylococcus aureus type 5 capsular polysaccharide in a modified model of endocarditis in rats. Infect Immun. 1997 Oct; 65(10):4146-51.
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  127. Carey VJ. Using hypertext and the Internet for structure and management of observational studies. Stat Med. 1997 Aug 15; 16(15):1667-82.
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  128. Carey VJ, Walters EE, Colditz GA, Solomon CG, Willett WC, Rosner BA, Speizer FE, Manson JE. Body fat distribution and risk of non-insulin-dependent diabetes mellitus in women. The Nurses' Health Study. Am J Epidemiol. 1997 Apr 1; 145(7):614-9.
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  129. Kasper DL, Paoletti LC, Wessels MR, Guttormsen HK, Carey VJ, Jennings HJ, Baker CJ. Immune response to type III group B streptococcal polysaccharide-tetanus toxoid conjugate vaccine. J Clin Invest. 1996 Nov 15; 98(10):2308-14.
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  130. Hanrahan JP, Brown RW, Carey VJ, Castile RG, Speizer FE, Tager IB. Passive respiratory mechanics in healthy infants. Effects of growth, gender, and smoking. Am J Respir Crit Care Med. 1996 Sep; 154(3 Pt 1):670-80.
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  131. David MM, Hanrahan JP, Carey V, Speizer FE, Tager IB. Respiratory symptoms in urban Hispanic and non-Hispanic white women. Am J Respir Crit Care Med. 1996 Apr; 153(4 Pt 1):1285-91.
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  132. Carey VJ, Weiss ST, Tager IB, Leeder SR, Speizer FE. Airways responsiveness, wheeze onset, and recurrent asthma episodes in young adolescents. The East Boston Childhood Respiratory Disease Cohort. Am J Respir Crit Care Med. 1996 Jan; 153(1):356-61.
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  133. Katz J, Carey VJ, Zeger SL, Sommer A. Estimation of design effects and diarrhea clustering within households and villages. Am J Epidemiol. 1993 Dec 1; 138(11):994-1006.
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  134. Galai N, Muñoz A, Chen K, Carey VJ, Chmiel J, Zhou SY. Tracking of markers and onset of disease among HIV-1 seroconverters. Stat Med. 1993 Nov 30; 12(22):2133-45.
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  135. Carey V, Vimpani G, Taylor R. Childhood injury mortality in New South Wales: geographical and socio-economic variations. J Paediatr Child Health. 1993 Apr; 29(2):136-40.
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  136. Wax Y, Galai N, Carey V, Simchen E. Cox regression models for intermediate events, with discharge from hospital as an example. Epidemiology. 1993 Mar; 4(2):120-7.
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  137. Carey V, Zeger S, Diggle P. Modelling multivariate binary data with alternating logistic regressions. Biometrika. 1993; 80(3):517-526.
  138. Carey VJ. Regression analysis for large binary clusters. 1993.
  139. Hoover D, Munoz A, Carey V, Taylor J, Van Raden M, Chmiel J, Kingsley L. Using events from dropouts in nonparametric survival function estimation with application to incubation of AIDS. J Am Stat Assoc. 1993; 88:37-43.
  140. Muñoz A, Carey V, Schouten JP, Segal M, Rosner B. A parametric family of correlation structures for the analysis of longitudinal data. Biometrics. 1992 Sep; 48(3):733-42.
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  141. Muñoz A, Carey V, Taylor JM, Chmiel JS, Kingsley L, Van Raden M, Hoover DR. Estimation of time since exposure for a prevalent cohort. Stat Med. 1992 May; 11(7):939-52.
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  142. Carey V. S-plus and C routines for the solution of generalized estimating equations. 1992.
  143. Hoover DR, Muñoz A, Carey V, Odaka N, Taylor JM, Chmiel JS, Armstrong J, Vermund SH. The unseen sample in cohort studies: estimation of its size and effect. Multicenter AIDS Cohort Study. Stat Med. 1991 Dec; 10(12):1993-2003.
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  144. Hoover DR, Muñoz A, Carey V, Chmiel JS, Taylor JM, Margolick JB, Kingsley L, Vermund SH. Estimating the 1978-1990 and future spread of human immunodeficiency virus type 1 in subgroups of homosexual men. Am J Epidemiol. 1991 Nov 15; 134(10):1190-205.
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  145. Margolick JB, Carey V, Muñoz A, Polk BF, Giorgi JV, Bauer KD, Kaslow R, Rinaldo C. Development of antibodies to HIV-1 is associated with an increase in circulating CD3+CD4-CD8- lymphocytes. Clin Immunol Immunopathol. 1989 Jun; 51(3):348-61.
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  146. Muñoz A, Carey V, Saah AJ, Phair JP, Kingsley LA, Fahey JL, Ginzburg HM, Polk BF. Predictors of decline in CD4 lymphocytes in a cohort of homosexual men infected with human immunodeficiency virus. J Acquir Immune Defic Syndr. 1988; 1(4):396-404.
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  147. Muñoz A, Rosner B, Carey V. Regression analysis in the presence of heterogeneous intraclass correlations. Biometrics. 1986 Sep; 42(3):653-8.
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  148. Tager IB, Muñoz A, Rosner B, Weiss ST, Carey V, Speizer FE. Effect of cigarette smoking on the pulmonary function of children and adolescents. Am Rev Respir Dis. 1985 May; 131(5):752-9.
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