Harvard Catalyst Profiles

Contact, publication, and social network information about Harvard faculty and fellows.

Andrea Sarah Foulkes, Sc.D.

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Other Positions
Title
Institution
Department

Research
research activities and funding
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
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  1. OT2HL161841 (FOULKES, ANDREA S) Jun 10, 2021 - Jun 9, 2022
    NIH
    Interactive Data Portals and Robust Analytic Tools to Wrap PASC Cohorts (iDRAW) OTA-21-015A
    Role: Principal Investigator
  2. R01GM127862 (FOULKES, ANDREA S) Apr 1, 2018 - Mar 31, 2022
    NIH
    Methods for integrated analysis of multi-level omics data
    Role: Principal Investigator
  3. R15GM126485 (FOULKES, ANDREA S) Sep 15, 2017 - Aug 31, 2019
    NIH
    Statistical methods for modeling multi-omic data
    Role: Principal Investigator
  4. U01HL123009 (THOMPSON, BOYD TAYLOR) Jun 17, 2014 - Oct 31, 2022
    NIH
    CCC for NHLBI Prevention and Early Treatment of Acute Lung Injury PETAL Network
    Role: Co-Principal Investigator
  5. R01HL107196 (FOULKES, ANDREA S) Feb 3, 2011 - Jan 31, 2018
    NIH
    Methods for high-dimensional data in HIV/CVD research
    Role: Principal Investigator

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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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Cynn E, Li DY, O'Reilly ME, Wang Y, Bashore AC, Jha A, Foulkes AS, Zhang H, Winter H, Maegdefessel L, Yan H, Li M, Ross L, Xue C, Reilly MP. Human Macrophage Long Intergenic Noncoding RNA, SIMALR, Suppresses Inflammatory Macrophage Apoptosis via NTN1 (Netrin-1). Arterioscler Thromb Vasc Biol. 2023 02; 43(2):286-299. PMID: 36546321.
    Citations:    Fields:    Translation:HumansCells
  2. Foulkes AS, Selvaggi C, Shinnick D, Lumish H, Cao T, Thaweethai T, Qian J, Meigs JB, Triant VA, Bassett IV, Reilly MP. Response to Letter to the Editor From Nelson et al: "Understanding the Link Between Obesity and Severe COVID-19 Outcomes: Causal Mediation by Systemic Inflammatory Response". J Clin Endocrinol Metab. 2022 12 17; 108(1):e13. PMID: 36300318; PMCID: PMC9620379.
    Citations:    Fields:    Translation:HumansCells
  3. Maffei C, Gilmore N, Snider SB, Foulkes AS, Bodien YG, Yendiki A, Edlow BL. Automated detection of axonal damage along white matter tracts in acute severe traumatic brain injury. Neuroimage Clin. 2023; 37:103294. PMID: 36529035; PMCID: PMC9792957.
    Citations:    Fields:    
  4. Lubitz SA, Faranesh AZ, Selvaggi C, Atlas SJ, McManus DD, Singer DE, Pagoto S, McConnell MV, Pantelopoulos A, Foulkes AS. Detection of Atrial Fibrillation in a Large Population Using Wearable Devices: The Fitbit Heart Study. Circulation. 2022 11 08; 146(19):1415-1424. PMID: 36148649; PMCID: PMC9640290.
    Citations: 1     Fields:    Translation:Humans
  5. Edlow BL, Bodien YG, Baxter T, Belanger HG, Cali RJ, Deary KB, Fischl B, Foulkes AS, Gilmore N, Greve DN, Hooker JM, Huang SY, Kelemen JN, Kimberly WT, Maffei C, Masood M, Perl DP, Polimeni JR, Rosen BR, Tromly SL, Tseng CJ, Yao EF, Zürcher NR, Mac Donald CL, Dams-O'Connor K. Long-Term Effects of Repeated Blast Exposure in United States Special Operations Forces Personnel: A Pilot Study Protocol. J Neurotrauma. 2022 10; 39(19-20):1391-1407. PMID: 35620901; PMCID: PMC9529318.
    Citations:    Fields:    Translation:Humans
  6. Lumish HS, Kim E, Selvaggi C, Cao T, Gupta A, Foulkes AS, Reilly MP. Biomarkers of Cardiac Injury, Renal Injury, and Inflammation Are Strong Mediators of Sex-Associated Death in COVID-19. Front Cardiovasc Med. 2022; 9:809997. PMID: 35548417; PMCID: PMC9081502.
    Citations: 1     
  7. Curley WH, Bodien YG, Zhou DW, Conte MM, Foulkes AS, Giacino JT, Victor JD, Schiff ND, Edlow BL. Electrophysiological correlates of thalamocortical function in acute severe traumatic brain injury. Cortex. 2022 07; 152:136-152. PMID: 35569326; PMCID: PMC9759728.
    Citations:    Fields:    Translation:Humans
  8. Foulkes AS, Selvaggi C, Shinnick D, Lumish H, Kim E, Cao T, Thaweethai T, Qian J, Lu F, Yan J, Cheng D, He W, Clerkin KJ, Madhavan MV, Meigs JB, Triant VA, Lubitz SA, Gupta A, Bassett IV, Reilly MP. Understanding the Link Between Obesity and Severe COVID-19 Outcomes: Causal Mediation by Systemic Inflammatory Response. J Clin Endocrinol Metab. 2022 01 18; 107(2):e698-e707. PMID: 34473294; PMCID: PMC8499919.
    Citations: 11     Fields:    Translation:Humans
  9. Cao T, O'Reilly ME, Selvaggi C, Cynn E, Lumish H, Xue C, Jha A, Reilly MP, Foulkes AS. Cis-regulated expression of non-conserved lincRNAs associates with cardiometabolic related traits. J Hum Genet. 2022 May; 67(5):307-310. PMID: 35017681; PMCID: PMC9038657.
    Citations: 1     Fields:    Translation:HumansCells
  10. Selvaggi C, Harrison LJ, Kim E, Reilly MP, Foulkes AS. Signature biomarker states and mortality among hospitalized SARS-CoV-2-infected patients. J Nephrol. 2022 04; 35(3):765-767. PMID: 34989977; PMCID: PMC8733911.
    Citations: 1     Fields:    Translation:HumansCells
  11. Memel ZN, Lee JJ, Foulkes AS, Chung RT, Thaweethai T, Bloom PP. Association of Statins and 28-Day Mortality Rates in Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 Infection. J Infect Dis. 2022 01 05; 225(1):19-29. PMID: 34665852.
    Citations: 10     Fields:    Translation:HumansCellsPHPublic Health
  12. Fischer D, Snider SB, Barra ME, Sanders WR, Rapalino O, Schaefer P, Foulkes AS, Bodien YG, Edlow BL. Disorders of Consciousness Associated With COVID-19: A Prospective Multimodal Study of Recovery and Brain Connectivity. Neurology. 2022 01 18; 98(3):e315-e325. PMID: 34862317; PMCID: PMC8792809.
    Citations: 7     Fields:    Translation:Humans
  13. Khurshid S, Friedman S, Reeder C, Di Achille P, Diamant N, Singh P, Harrington LX, Wang X, Al-Alusi MA, Sarma G, Foulkes AS, Ellinor PT, Anderson CD, Ho JE, Philippakis AA, Batra P, Lubitz SA. ECG-Based Deep Learning and Clinical Risk Factors to Predict Atrial Fibrillation. Circulation. 2022 01 11; 145(2):122-133. PMID: 34743566; PMCID: PMC8748400.
    Citations: 17     Fields:    Translation:Humans
  14. Moschovis PP, Lu M, Hayden D, Yonker LM, Lombay J, Taveras E, Arauz Boudreau A, Triant VA, Foulkes AS, Bassett I, Hibberd PL, Kinane TB. Effect modification by age of the association between obstructive lung diseases, smoking, and COVID-19 severity. BMJ Open Respir Res. 2021 11; 8(1). PMID: 34740944; PMCID: PMC8573665.
    Citations: 1     Translation:HumansCells
  15. Coffey BJ, Threlkeld ZD, Foulkes AS, Bodien YG, Edlow BL. Reemergence of the language network during recovery from severe traumatic brain injury: A pilot functional MRI study. Brain Inj. 2021 11 10; 35(12-13):1552-1562. PMID: 34546806; PMCID: PMC8678186.
    Citations: 1     Fields:    Translation:Humans
  16. Bunnell KM, Thaweethai T, Buckless C, Shinnick DJ, Torriani M, Foulkes AS, Bredella MA. Body composition predictors of outcome in patients with COVID-19. Int J Obes (Lond). 2021 10; 45(10):2238-2243. PMID: 34244597; PMCID: PMC8267764.
    Citations: 13     Fields:    Translation:Humans
  17. Goehler A, Hsu TH, Seiglie JA, Siedner MJ, Lo J, Triant V, Hsu J, Foulkes A, Bassett I, Khorasani R, Wexler DJ, Szolovits P, Meigs JB, Manne-Goehler J. Visceral Adiposity and Severe COVID-19 Disease: Application of an Artificial Intelligence Algorithm to Improve Clinical Risk Prediction. Open Forum Infect Dis. 2021 Jul; 8(7):ofab275. PMID: 34258315; PMCID: PMC8244656.
    Citations: 6     
  18. Lau ES, McNeill JN, Paniagua SM, Liu EE, Wang JK, Bassett IV, Selvaggi CA, Lubitz SA, Foulkes AS, Ho JE. Sex differences in inflammatory markers in patients hospitalized with COVID-19 infection: Insights from the MGH COVID-19 patient registry. PLoS One. 2021; 16(4):e0250774. PMID: 33909684.
    Citations: 17     Fields:    Translation:HumansCells
  19. Lubitz SA, Faranesh AZ, Atlas SJ, McManus DD, Singer DE, Pagoto S, Pantelopoulos A, Foulkes AS. Rationale and design of a large population study to validate software for the assessment of atrial fibrillation from data acquired by a consumer tracker or smartwatch: The Fitbit heart study. Am Heart J. 2021 08; 238:16-26. PMID: 33865810.
    Citations: 21     Fields:    Translation:HumansCTClinical Trials
  20. Memel ZN, Lee JJ, Foulkes AS, Chung RT, Thaweethai T, Bloom PP. Statins Are Associated with Improved 28-day Mortality in Patients Hospitalized with SARS-CoV-2 Infection. medRxiv. 2021 Apr 06. PMID: 33851192; PMCID: PMC8043489.
    Citations:    
  21. McNeill JN, Lau ES, Paniagua SM, Liu EE, Wang JK, Bassett IV, Selvaggi CA, Lubitz SA, Foulkes AS, Ho JE. The role of obesity in inflammatory markers in COVID-19 patients. Obes Res Clin Pract. 2021 Jan-Feb; 15(1):96-99. PMID: 33390322; PMCID: PMC7833898.
    Citations: 13     Fields:    Translation:HumansCells
  22. Bassett IV, Triant VA, Bunda BA, Selvaggi CA, Shinnick DJ, He W, Lu F, Porneala BC, Cao T, Lubitz SA, Meigs JB, Hsu J, Foulkes AS. Massachusetts general hospital Covid-19 registry reveals two distinct populations of hospitalized patients by race and ethnicity. PLoS One. 2020; 15(12):e0244270. PMID: 33351826; PMCID: PMC7755195.
    Citations: 16     Fields:    Translation:HumansCells
  23. Snider SB, Bodien YG, Frau-Pascual A, Bianciardi M, Foulkes AS, Edlow BL. Ascending arousal network connectivity during recovery from traumatic coma. Neuroimage Clin. 2020; 28:102503. PMID: 33395992.
    Citations: 10     Fields:    Translation:Humans
  24. Foulkes AS, Selvaggi C, Cao T, O'Reilly ME, Cynn E, Ma P, Lumish H, Xue C, Reilly MP. Nonconserved Long Intergenic Noncoding RNAs Associate With Complex Cardiometabolic Disease Traits. Arterioscler Thromb Vasc Biol. 2021 01; 41(1):501-511. PMID: 33176448.
    Citations: 4     Fields:    Translation:Humans
  25. Robinson LB, Fu X, Bassett IV, Triant VA, Foulkes AS, Zhang Y, Camargo CA, Blumenthal KG. COVID-19 severity in hospitalized patients with asthma: A matched cohort study. J Allergy Clin Immunol Pract. 2021 01; 9(1):497-500. PMID: 33164794.
    Citations: 16     Fields:    Translation:HumansCells
  26. Stone JH, Frigault MJ, Serling-Boyd NJ, Fernandes AD, Harvey L, Foulkes AS, Horick NK, Healy BC, Shah R, Bensaci AM, Woolley AE, Nikiforow S, Lin N, Sagar M, Schrager H, Huckins DS, Axelrod M, Pincus MD, Fleisher J, Sacks CA, Dougan M, North CM, Halvorsen YD, Thurber TK, Dagher Z, Scherer A, Wallwork RS, Kim AY, Schoenfeld S, Sen P, Neilan TG, Perugino CA, Unizony SH, Collier DS, Matza MA, Yinh JM, Bowman KA, Meyerowitz E, Zafar A, Drobni ZD, Bolster MB, Kohler M, D'Silva KM, Dau J, Lockwood MM, Cubbison C, Weber BN, Mansour MK. Efficacy of Tocilizumab in Patients Hospitalized with Covid-19. N Engl J Med. 2020 12 10; 383(24):2333-2344. PMID: 33085857; PMCID: PMC7646626.
    Citations: 653     Fields:    Translation:Humans
  27. Gu X, Tadesse MG, Foulkes AS, Ma Y, Balasubramanian R. Bayesian variable selection for high dimensional predictors and self-reported outcomes. BMC Med Inform Decis Mak. 2020 09 07; 20(1):212. PMID: 32894123.
    Citations:    Fields:    Translation:Humans
  28. Seiglie J, Platt J, Cromer SJ, Bunda B, Foulkes AS, Bassett IV, Hsu J, Meigs JB, Leong A, Putman MS, Triant VA, Wexler DJ, Manne-Goehler J. Diabetes as a Risk Factor for Poor Early Outcomes in Patients Hospitalized With COVID-19. Diabetes Care. 2020 12; 43(12):2938-2944. PMID: 32847827.
    Citations: 44     Fields:    Translation:HumansCells
  29. Edlow BL, Barra ME, Zhou DW, Foulkes AS, Snider SB, Threlkeld ZD, Chakravarty S, Kirsch JE, Chan ST, Meisler SL, Bleck TP, Fins JJ, Giacino JT, Hochberg LR, Solt K, Brown EN, Bodien YG. Personalized Connectome Mapping to Guide Targeted Therapy and Promote Recovery of Consciousness in the Intensive Care Unit. Neurocrit Care. 2020 10; 33(2):364-375. PMID: 32794142; PMCID: PMC8336723.
    Citations: 17     Fields:    Translation:HumansCTClinical Trials
  30. Foulkes AS, Balasubramanian R, Qian J, Reilly MP. Non-random sampling leads to biased estimates of transcriptome association. Sci Rep. 2020 04 10; 10(1):6193. PMID: 32277087.
    Citations:    Fields:    Translation:HumansCells
  31. Abdulhaqq SA, Martinez M, Kang G, Rodriguez IV, Nichols SM, Beaumont D, Joseph J, Azzoni L, Yin X, Wise M, Weiner D, Liu Q, Foulkes A, Münch J, Kirchhoff F, Coutifaris C, Tomaras GD, Sariol C, Marx PA, Li Q, Kraiselburd EN, Montaner LJ. Repeated semen exposure decreases cervicovaginal SIVmac251 infection in rhesus macaques. Nat Commun. 2019 08 21; 10(1):3753. PMID: 31434895.
    Citations: 2     Fields:    Translation:HumansAnimalsCells
  32. Ray EL, Qian J, Brecha R, Reilly MP, Foulkes AS. Stochastic imputation for integrated transcriptome association analysis of a longitudinally measured trait. Stat Methods Med Res. 2020 04; 29(4):1167-1180. PMID: 31172883; PMCID: PMC8848832.
    Citations: 2     Fields:    Translation:Cells
  33. Pencina MJ, Parikh CR, Kimmel PL, Cook NR, Coresh J, Feldman HI, Foulkes A, Gimotty PA, Hsu CY, Lemley K, Song P, Wilkins K, Gossett DR, Xie Y, Star RA. Statistical methods for building better biomarkers of chronic kidney disease. Stat Med. 2019 05 20; 38(11):1903-1917. PMID: 30663113.
    Citations: 5     Fields:    Translation:Humans
  34. Qian J, Ray E, Brecha RL, Reilly MP, Foulkes AS. A likelihood-based approach to transcriptome association analysis. Stat Med. 2019 04 15; 38(8):1357-1373. PMID: 30515859.
    Citations: 3     Fields:    Translation:Humans
  35. 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. Deep RNA Sequencing Uncovers a Repertoire of Human Macrophage Long Intergenic Noncoding RNAs Modulated by Macrophage Activation and Associated With Cardiometabolic Diseases. J Am Heart Assoc. 2017 Nov 13; 6(11). PMID: 29133519.
    Citations: 24     Fields:    Translation:HumansCells
  36. Qian J, Nunez S, Kim S, Reilly MP, Foulkes AS. A score test for genetic class-level association with nonlinear biomarker trajectories. Stat Med. 2017 Aug 30; 36(19):3075-3091. PMID: 28543585.
    Citations: 2     Fields:    Translation:Humans
  37. Chen S, Nunez S, Reilly MP, Foulkes AS. Bayesian variable selection for post-analytic interrogation of susceptibility loci. Biometrics. 2017 06; 73(2):603-614. PMID: 27858978.
    Citations: 1     Fields:    Translation:Humans
  38. Ballantyne RL, Zhang X, Nuñez S, Xue C, Zhao W, Reed E, Salaheen D, Foulkes AS, Li M, Reilly MP. Genome-wide interrogation reveals hundreds of long intergenic noncoding RNAs that associate with cardiometabolic traits. Hum Mol Genet. 2016 07 15; 25(14):3125-3141. PMID: 27288454; PMCID: PMC5181595.
    Citations: 24     Fields:    Translation:HumansCells
  39. 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. Transcriptome-Wide Analysis Reveals Modulation of Human Macrophage Inflammatory Phenotype Through Alternative Splicing. Arterioscler Thromb Vasc Biol. 2016 07; 36(7):1434-47. PMID: 27230130; PMCID: PMC4919157.
    Citations: 23     Fields:    Translation:HumansCells
  40. Qian J, Nunez S, Reed E, Reilly MP, Foulkes AS. A Simple Test of Class-Level Genetic Association Can Reveal Novel Cardiometabolic Trait Loci. PLoS One. 2016; 11(2):e0148218. PMID: 26859766.
    Citations: 5     Fields:    Translation:Humans
  41. 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. HIV-1-negative female sex workers sustain high cervical IFN?, low immune activation, and low expression of HIV-1-required host genes. Mucosal Immunol. 2016 07; 9(4):1027-38. PMID: 26555708; PMCID: PMC4864149.
    Citations: 16     Fields:    Translation:HumansCells
  42. Reed E, Nunez S, Kulp D, Qian J, Reilly MP, Foulkes AS. A guide to genome-wide association analysis and post-analytic interrogation. Stat Med. 2015 Dec 10; 34(28):3769-92. PMID: 26343929.
    Citations: 36     Fields:    Translation:Humans
  43. Papasavvas E, Foulkes A, Yin X, Joseph J, Ross B, Azzoni L, Kostman JR, Mounzer K, Shull J, Montaner LJ. Plasmacytoid dendritic cell and functional HIV Gag p55-specific T cells before treatment interruption can inform set-point plasma HIV viral load after treatment interruption in chronically suppressed HIV-1(+) patients. Immunology. 2015 Jul; 145(3):380-90. PMID: 25684333.
    Citations: 8     Fields:    Translation:HumansCells
  44. 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. Serum Fractalkine (CX3CL1) and Cardiovascular Outcomes and Diabetes: Findings From the Chronic Renal Insufficiency Cohort (CRIC) Study. Am J Kidney Dis. 2015 Aug; 66(2):266-73. PMID: 25795074; PMCID: PMC4516570.
    Citations: 15     Fields:    Translation:Humans
  45. 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. 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. J Acquir Immune Defic Syndr. 2014 Apr 01; 65(4):405-13. PMID: 24226059; PMCID: PMC3943721.
    Citations: 7     Fields:    Translation:AnimalsCells
  46. 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. Higher plasma CXCL12 levels predict incident myocardial infarction and death in chronic kidney disease: findings from the Chronic Renal Insufficiency Cohort study. Eur Heart J. 2014 Aug 14; 35(31):2115-22. PMID: 24306482.
    Citations: 21     Fields:    Translation:Humans
  47. Haile CN, Murrough JW, Iosifescu DV, Chang LC, Al Jurdi RK, Foulkes A, Iqbal S, Mahoney JJ, De La Garza R, Charney DS, Newton TF, Mathew SJ. Plasma brain derived neurotrophic factor (BDNF) and response to ketamine in treatment-resistant depression. Int J Neuropsychopharmacol. 2014 Feb; 17(2):331-6. PMID: 24103211.
    Citations: 87     Fields:    Translation:Humans
  48. 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, Saleheen D, Feldman HI, Rader DJ, Foulkes AS, Reilly MP. Candidate gene association study of coronary artery calcification in chronic kidney disease: findings from the CRIC study (Chronic Renal Insufficiency Cohort). J Am Coll Cardiol. 2013 Aug 27; 62(9):789-98. PMID: 23727086; PMCID: PMC3953823.
    Citations: 18     Fields:    Translation:Humans
  49. 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. 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. J Infect Dis. 2013 Jul 15; 208(2):363. PMID: 23570845.
    Citations: 3     Fields:    Translation:HumansCells
  50. Foulkes AS, Matthews GJ, Das U, Ferguson JF, Lin R, Reilly MP. Mixed modeling of meta-analysis P-values (MixMAP) suggests multiple novel gene loci for low density lipoprotein cholesterol. PLoS One. 2013; 8(2):e54812. PMID: 23405096.
    Citations: 3     Fields:    Translation:Humans
  51. 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. Concurrent measures of total and integrated HIV DNA monitor reservoirs and ongoing replication in eradication trials. AIDS. 2012 Nov 28; 26(18):2295-306. PMID: 23014521; PMCID: PMC4692807.
    Citations: 60     Fields:    Translation:HumansCells
  52. 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. Pegylated Interferon alfa-2a monotherapy results in suppression of HIV type 1 replication and decreased cell-associated HIV DNA integration. J Infect Dis. 2013 Jan 15; 207(2):213-22. PMID: 23105144; PMCID: PMC3532820.
    Citations: 128     Fields:    Translation:HumansCells
  53. Azzoni L, Foulkes AS, Firnhaber C, Yin X, Xiang ZQ, Li Y, Stevens W, Gross R, Ertl HC, Sanne I, Montaner LJ. Antiretroviral therapy interruptions result in loss of protective humoral immunity to neoantigens in HIV-infected individuals. AIDS. 2012 Jul 17; 26(11):1355-62. PMID: 22516873; PMCID: PMC3548620.
    Citations: 2     Fields:    Translation:HumansCells
  54. 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. Prioritizing CD4 count monitoring in response to ART in resource-constrained settings: a retrospective application of prediction-based classification. PLoS Med. 2012; 9(4):e1001207. PMID: 22529752.
    Citations: 5     Fields:    Translation:HumansCells
  55. Conradie F, Foulkes AS, Ive P, Yin X, Roussos K, Glencross DK, Lawrie D, Stevens W, Montaner LJ, Sanne I, Azzoni L. Natural killer cell activation distinguishes Mycobacterium tuberculosis-mediated immune reconstitution syndrome from chronic HIV and HIV/MTB coinfection. J Acquir Immune Defic Syndr. 2011 Nov 01; 58(3):309-18. PMID: 21826013; PMCID: PMC3196770.
    Citations: 27     Fields:    Translation:HumansCells
  56. Papasavvas E, Azzoni L, Foulkes A, Violari A, Cotton MF, Pistilli M, Reynolds G, Yin X, Glencross DK, Stevens WS, McIntyre JA, Montaner LJ. Increased microbial translocation in = 180 days old perinatally human immunodeficiency virus-positive infants as compared with human immunodeficiency virus-exposed uninfected infants of similar age. Pediatr Infect Dis J. 2011 Oct; 30(10):877-82. PMID: 21552185.
    Citations: 24     Fields:    Translation:HumansCells
  57. Eliot M, Ferguson J, Reilly MP, Foulkes AS. Ridge regression for longitudinal biomarker data. Int J Biostat. 2011; 7(1):Article 37. PMID: 22049265.
    Citations: 1     Fields:    Translation:Humans
  58. Liu Y, Foulkes AS. Latent variable modeling paradigms for genotype-trait association studies. Biom J. 2011 Sep; 53(5):838-54. PMID: 21887796.
    Citations: 1     Fields:    Translation:HumansCells
  59. Azzoni L, Foulkes AS, Firnhaber C, Yin X, Crowther NJ, Glencross D, Lawrie D, Stevens W, Papasavvas E, Sanne I, Montaner LJ. Metabolic and anthropometric parameters contribute to ART-mediated CD4+ T cell recovery in HIV-1-infected individuals: an observational study. J Int AIDS Soc. 2011 Jul 29; 14:37. PMID: 21801351; PMCID: PMC3163506.
    Citations: 6     Fields:    Translation:HumansCells
  60. 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. Randomized trial of time-limited interruptions of protease inhibitor-based antiretroviral therapy (ART) vs. continuous therapy for HIV-1 infection. PLoS One. 2011; 6(6):e21450. PMID: 21738668.
    Citations: 4     Fields:    Translation:Cells
  61. Au K, Lin R, Foulkes AS. Mixture modelling as an exploratory framework for genotype-trait associations. J R Stat Soc Ser C Appl Stat. 2011 05; 60(3):355-375. PMID: 22368304.
    Citations: 1     
  62. Foulkes AS, Au K. R statistical tools for gene discovery. Methods Mol Biol. 2011; 760:73-90. PMID: 21779991.
    Citations:    Fields:    
  63. 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. Association between HIV replication and serum leptin levels: an observational study of a cohort of HIV-1-infected South African women. J Int AIDS Soc. 2010 Sep 07; 13:33. PMID: 20822522; PMCID: PMC2941743.
    Citations: 9     Fields:    Translation:HumansCells
  64. Foulkes AS, Azzoni L, Li X, Johnson MA, Smith C, Mounzer K, Montaner LJ. Prediction based classification for longitudinal biomarkers. Ann Appl Stat. 2010 Sep; 4(3):1476-1497. PMID: 21274424.
    Citations: 8     
  65. Eliot M, Azzoni L, Firnhaber C, Stevens W, Glencross DK, Sanne I, Montaner LJ, Foulkes AS. Tree-Based Methods for Discovery of Association between Flow Cytometry Data and Clinical Endpoints. Adv Bioinformatics. 2009; 2009:235320. PMID: 20145719.
    Citations: 1     
  66. Li X, Thomas BN, Rich SM, Ecker D, Tumwine JK, Foulkes AS. Estimating and testing haplotype-trait associations in non-diploid populations. J R Stat Soc Ser C Appl Stat. 2009 12; 58(5):663-678. PMID: 20011038.
    Citations: 2     
  67. Mehta N, Trzmielina S, Nonyane BA, Eliot MN, Lin R, Foulkes AS, McNeal K, Ammann A, Eulalievyolo V, Sullivan JL, Luzuriaga K, Somasundaran M. Low-cost HIV-1 diagnosis and quantification in dried blood spots by real time PCR. PLoS One. 2009 Jun 05; 4(6):e5819. PMID: 19503790.
    Citations: 16     Fields:    Translation:HumansCells
  68. 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. Circulating monocytes in HIV-1-infected viremic subjects exhibit an antiapoptosis gene signature and virus- and host-mediated apoptosis resistance. J Immunol. 2009 Apr 01; 182(7):4459-70. PMID: 19299747; PMCID: PMC2776064.
    Citations: 53     Fields:    Translation:HumansCells
  69. Papasavvas E, Foulkes A, Li X, Kostman JR, Mounzer KC, Montaner LJ. Evidence of a decrease in CD4 recovery once back on antiretroviral therapy after sequential > or =6 weeks antiretroviral therapy interruptions. J Acquir Immune Defic Syndr. 2009 Mar 01; 50(3):334-5. PMID: 19242262; PMCID: PMC2726754.
    Citations: 1     Fields:    Translation:Humans
  70. Nonyane BA, Foulkes AS. Application of two machine learning algorithms to genetic association studies in the presence of covariates. BMC Genet. 2008 Nov 14; 9:71. PMID: 19014573.
    Citations: 8     Fields:    Translation:Humans
  71. Gross R, Aplenc R, Tenhave T, Foulkes AS, Thakur R, Mosepele M, Barrett JS, Flexner C, Strom BL, Bisson G. Slow efavirenz metabolism genotype is common in Botswana. J Acquir Immune Defic Syndr. 2008 Nov 01; 49(3):336-7. PMID: 18978480; PMCID: PMC5070462.
    Citations: 21     Fields:    Translation:Humans
  72. Foulkes AS, Yucel R, Reilly MP. Mixed modeling and multiple imputation for unobservable genotype clusters. Stat Med. 2008 Jul 10; 27(15):2784-801. PMID: 17893946.
    Citations: 7     Fields:    
  73. Foulkes AS, Yucel R, Li X. A likelihood-based approach to mixed modeling with ambiguity in cluster identifiers. Biostatistics. 2008 Oct; 9(4):635-57. PMID: 18343883; PMCID: PMC2536727.
    Citations: 7     Fields:    Translation:HumansCells
  74. DeMichele A, Gimotty P, Botbyl J, Aplenc R, Colligon T, Foulkes AS, Rebbeck TR. In response to "Drug metabolizing enzyme polymorphisms predict clinical outcome in a node-positive breast cancer cohort". J Clin Oncol. 2007 Dec 10; 25(35):5675-7. PMID: 18065748.
    Citations: 6     Fields:    Translation:Humans
  75. Li X, Foulkes AS, Yucel RM, Rich SM. An expectation maximization approach to estimate malaria haplotype frequencies in multiply infected children. Stat Appl Genet Mol Biol. 2007; 6:Article33. PMID: 18052916.
    Citations: 12     Fields:    Translation:HumansAnimals
  76. 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. Baseline viral load and immune activation determine the extent of reconstitution of innate immune effectors in HIV-1-infected subjects undergoing antiretroviral treatment. J Immunol. 2007 Aug 15; 179(4):2642-50. PMID: 17675528.
    Citations: 40     Fields:    Translation:HumansCellsCTClinical Trials
  77. Stone J, Foulkes A, Adamson K, Stevenson L, Al-Shahi Salman R. Thyrotoxicosis presenting with headache. Cephalalgia. 2007 Jun; 27(6):561-2. PMID: 17598793.
    Citations: 3     Fields:    Translation:Humans
  78. Azzoni L, Chehimi J, Zhou L, Foulkes AS, June R, Maino VC, Landay A, Rinaldo C, Jacobson LP, Montaner LJ. Early and delayed benefits of HIV-1 suppression: timeline of recovery of innate immunity effector cells. AIDS. 2007 Jan 30; 21(3):293-305. PMID: 17255736.
    Citations: 16     Fields:    Translation:HumansCells
  79. Foulkes AS, DeGruttola VG. A resampling-based approach to multiple testing with uncertainty in phase. Int J Biostat. 2007; 3(1):Article 2. PMID: 22550644.
    Citations: 1     Fields:    Translation:HumansCells
  80. Nonyane BA, Foulkes AS. Multiple imputation and random forests (MIRF) for unobservable, high-dimensional data. Int J Biostat. 2007; 3(1):Article 12. PMID: 22550652.
    Citations: 3     Fields:    Translation:HumansCells
  81. Sathiyaseelan J, Goenka R, Parent M, Benson RM, Murphy EA, Fernandes DM, Foulkes AS, Baldwin CL. Treatment of Brucella-susceptible mice with IL-12 increases primary and secondary immunity. Cell Immunol. 2006 Sep; 243(1):1-9. PMID: 17184756.
    Citations: 23     Fields:    Translation:AnimalsCells
  82. Foulkes AS, Wohl DA, Frank I, Puleo E, Restine S, Wolfe ML, Dube MP, Tebas P, Reilly MP. Associations among race/ethnicity, ApoC-III genotypes, and lipids in HIV-1-infected individuals on antiretroviral therapy. PLoS Med. 2006 Mar; 3(3):e52. PMID: 16417409; PMCID: PMC1334223.
    Citations: 38     Fields:    Translation:HumansCells
  83. Papasavvas E, Kostman JR, Thiel B, Pistilli M, Mackiewicz A, Foulkes A, Gross R, Jordan KA, Nixon DF, Grant R, Poulin JF, McCune JM, Mounzer K, Montaner LJ. HIV-1-specific CD4+ T cell responses in chronically HIV-1 infected blippers on antiretroviral therapy in relation to viral replication following treatment interruption. J Clin Immunol. 2006 Jan; 26(1):40-54. PMID: 16418802.
    Citations: 11     Fields:    Translation:HumansCells
  84. DeMichele A, Aplenc R, Botbyl J, Colligan T, Wray L, Klein-Cabral M, Foulkes A, Gimotty P, Glick J, Weber B, Stadtmauer E, Rebbeck TR. Drug-metabolizing enzyme polymorphisms predict clinical outcome in a node-positive breast cancer cohort. J Clin Oncol. 2005 Aug 20; 23(24):5552-9. PMID: 16110016.
    Citations: 15     Fields:    Translation:Humans
  85. Reilly MP, Foulkes AS, Wolfe ML, Rader DJ. Higher order lipase gene association with plasma triglycerides. J Lipid Res. 2005 Sep; 46(9):1914-22. PMID: 15961789.
    Citations: 4     Fields:    Translation:Humans
  86. Zhao JX, Foulkes AS, George EI. Exploratory Bayesian model selection for serial genetics data. Biometrics. 2005 Jun; 61(2):591-9. PMID: 16011709.
    Citations: 3     Fields:    Translation:HumansCells
  87. Foulkes AS, Reilly M, Zhou L, Wolfe M, Rader DJ. Mixed modelling to characterize genotype-phenotype associations. Stat Med. 2005 Mar 15; 24(5):775-89. PMID: 15696502.
    Citations: 9     Fields:    Translation:Humans
  88. Papasavvas E, Kostman JR, Mounzer K, Grant RM, Gross R, Gallo C, Azzoni L, Foulkes A, Thiel B, Pistilli M, Mackiewicz A, Shull J, Montaner LJ. Randomized, controlled trial of therapy interruption in chronic HIV-1 infection. PLoS Med. 2004 Dec; 1(3):e64. PMID: 15630469; PMCID: PMC539050.
    Citations: 37     Fields:    Translation:HumansCells
  89. De Gruttola V, Foulkes AS. Validation and discovery in Markov models of genetics data. Stat Appl Genet Mol Biol. 2004; 3:Article38. PMID: 16646818.
    Citations: 1     Fields:    
  90. Bastone L, Reilly M, Rader DJ, Foulkes AS. MDR and PRP: a comparison of methods for high-order genotype-phenotype associations. Hum Hered. 2004; 58(2):82-92. PMID: 15711088.
    Citations: 21     Fields:    Translation:Humans
  91. Foulkes AS, DeGruttola V. Characterizing classes of antiretroviral drugs by genotype. Stat Med. 2003 Aug 30; 22(16):2637-55. PMID: 12898549.
    Citations: 2     Fields:    Translation:HumansCells
  92. Foulkes AS, De GV. Characterizing the relationship between HIV-1 genotype and phenotype: prediction-based classification. Biometrics. 2002 Mar; 58(1):145-56. PMID: 11890310.
    Citations: 10     Fields:    Translation:HumansCells
  93. Sevin AD, DeGruttola V, Nijhuis M, Schapiro JM, Foulkes AS, Para MF, Boucher CA. Methods for investigation of the relationship between drug-susceptibility phenotype and human immunodeficiency virus type 1 genotype with applications to AIDS clinical trials group 333. J Infect Dis. 2000 Jul; 182(1):59-67. PMID: 10882582.
    Citations: 19     Fields:    Translation:HumansCellsCTClinical Trials
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.