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Items: 1 to 50 of 210

1.

TFutils: Data structures for transcription factor bioinformatics.

Stubbs BJ, Gopaulakrishnan S, Glass K, Pochet N, Everaert C, Raby B, Carey V.

Version 2. F1000Res. 2019 Feb 5 [revised 2019 Jan 1];8:152. doi: 10.12688/f1000research.17976.2. eCollection 2019.

2.

Subtyping COPD using visual and quantitative CT features.

Park J, Hobbs BD, Crapo JD, Make BJ, Regan EA, Humphries S, Carey VJ, Lynch DA, Silverman EK; COPDGene Investigators.

Chest. 2019 Jul 5. pii: S0012-3692(19)31255-3. doi: 10.1016/j.chest.2019.06.015. [Epub ahead of print]

PMID:
31283919
3.

BiocPkgTools: Toolkit for mining the Bioconductor package ecosystem.

Su S, Carey VJ, Shepherd L, Ritchie M, Morgan MT, Davis S.

F1000Res. 2019 May 29;8:752. doi: 10.12688/f1000research.19410.1. eCollection 2019.

4.

deconvSeq: Deconvolution of Cell Mixture Distribution in Sequencing Data.

Du R, Carey V, Weiss S.

Bioinformatics. 2019 May 30. pii: btz444. doi: 10.1093/bioinformatics/btz444. [Epub ahead of print]

PMID:
31147676
5.

Maternal Asthma, Preeclampsia and Risk of Childhood Asthma at Age Six.

Mirzakhani H, Carey VJ, McElrath TF, Hollis BW, O'Connor GT, Zeiger RS, Bacharier L, Litonjua AA, Weiss ST.

Am J Respir Crit Care Med. 2019 May 6. doi: 10.1164/rccm.201901-0081LE. [Epub ahead of print] No abstract available.

PMID:
31059286
6.

Association of the Infant Gut Microbiome With Early Childhood Neurodevelopmental Outcomes: An Ancillary Study to the VDAART Randomized Clinical Trial.

Sordillo JE, Korrick S, Laranjo N, Carey V, Weinstock GM, Gold DR, O'Connor G, Sandel M, Bacharier LB, Beigelman A, Zeiger R, Litonjua AA, Weiss ST.

JAMA Netw Open. 2019 Mar 1;2(3):e190905. doi: 10.1001/jamanetworkopen.2019.0905.

7.

Metabolomics and Communication Skills Development in Children; Evidence from the Ages and Stages Questionnaire.

Kelly RS, Boulin A, Laranjo N, Lee-Sarwar K, Chu SH, Yadama AP, Carey V, Litonjua AA, Lasky-Su J, Weiss ST.

Metabolites. 2019 Mar 5;9(3). pii: E42. doi: 10.3390/metabo9030042.

8.

restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor.

Gopaulakrishnan S, Pollack S, Stubbs BJ, Pagès H, Readey J, Davis S, Waldron L, Morgan M, Carey V.

F1000Res. 2019 Jan 7;8:21. doi: 10.12688/f1000research.17518.1. eCollection 2019.

9.

Targeted expression profiling by RNA-Seq improves detection of cellular dynamics during pregnancy and identifies a role for T cells in term parturition.

Tarca AL, Romero R, Xu Z, Gomez-Lopez N, Erez O, Hsu CD, Hassan SS, Carey VJ.

Sci Rep. 2019 Jan 29;9(1):848. doi: 10.1038/s41598-018-36649-w.

10.

Sex differences in gene expression in response to ischemia in the human left ventricular myocardium.

Stone G, Choi A, Meritxell O, Gorham J, Heydarpour M, Seidman CE, Seidman JG, Aranki SF, Body SC, Carey VJ, Raby BA, Stranger BE, Muehlschlegel JD.

Hum Mol Genet. 2019 May 15;28(10):1682-1693. doi: 10.1093/hmg/ddz014.

PMID:
30649309
11.

Impact of parental asthma, prenatal maternal asthma control, and vitamin D status on risk of asthma and recurrent wheeze in 3-year-old children.

Mirzakhani H, Carey VJ, Zeiger R, Bacharier LB, O'Connor GT, Schatz MX, Laranjo N, Weiss ST, Litonjua AA.

Clin Exp Allergy. 2019 Apr;49(4):419-429. doi: 10.1111/cea.13320. Epub 2019 Jan 3.

PMID:
30461089
12.

A Phase 2, Randomized, Control Trial of Group B Streptococcus (GBS) Type III Capsular Polysaccharide-tetanus Toxoid (GBS III-TT) Vaccine to Prevent Vaginal Colonization With GBS III.

Hillier SL, Ferrieri P, Edwards MS, Ewell M, Ferris D, Fine P, Carey V, Meyn L, Hoagland D, Kasper DL, Paoletti LC, Hill H, Baker CJ.

Clin Infect Dis. 2019 May 30;68(12):2079-2086. doi: 10.1093/cid/ciy838.

PMID:
30281066
13.

Impact of Preeclampsia on the Relationship between Maternal Asthma and Offspring Asthma. An Observation from the VDAART Clinical Trial.

Mirzakhani H, Carey VJ, McElrath TF, Qiu W, Hollis BW, O'Connor GT, Zeiger RS, Bacharier L, Litonjua AA, Weiss ST.

Am J Respir Crit Care Med. 2019 Jan 1;199(1):32-42. doi: 10.1164/rccm.201804-0770OC.

PMID:
30153046
14.

Expression network analysis reveals cord blood vitamin D-associated genes affecting risk of early life wheeze.

Mirzakhani H, Al-Garawi AA, Carey VJ, Qiu W, Litonjua AA, Weiss ST.

Thorax. 2019 Feb;74(2):200-202. doi: 10.1136/thoraxjnl-2018-211962. Epub 2018 Jul 18.

PMID:
30021811
15.

Role of local CpG DNA methylation in mediating the 17q21 asthma susceptibility gasdermin B (GSDMB)/ORMDL sphingolipid biosynthesis regulator 3 (ORMDL3) expression quantitative trait locus.

Kothari PH, Qiu W, Croteau-Chonka DC, Martinez FD, Liu AH, Lemanske RF Jr, Ober C, Krishnan JA, Nicolae DL, Barnes KC, London SJ, Barraza-Villarreal A, White SR, Naureckas ET, Millstein J, Gauderman WJ, Gilliland FD, Carey VJ, Weiss ST, Raby BA; Asthma BioRepository for Integrative Genomic Exploration (Asthma BRIDGE) Consortium.

J Allergy Clin Immunol. 2018 Jun;141(6):2282-2286.e6. doi: 10.1016/j.jaci.2017.11.057. Epub 2018 Jan 31. No abstract available.

16.

Water Wicking and Droplet Spreading on Randomly Structured Thin Nanoporous Layers.

Wemp CK, Carey VP.

Langmuir. 2017 Dec 19;33(50):14513-14525. doi: 10.1021/acs.langmuir.7b03687. Epub 2017 Dec 6.

PMID:
29155595
17.

Software for the Integration of Multiomics Experiments in Bioconductor.

Ramos M, Schiffer L, Re A, Azhar R, Basunia A, Rodriguez C, Chan T, Chapman P, Davis SR, Gomez-Cabrero D, Culhane AC, Haibe-Kains B, Hansen KD, Kodali H, Louis MS, Mer AS, Riester M, Morgan M, Carey V, Waldron L.

Cancer Res. 2017 Nov 1;77(21):e39-e42. doi: 10.1158/0008-5472.CAN-17-0344.

18.

Multiband absorbers for the long-wave infrared regime.

Carey VA, Mirotznik MS.

Appl Opt. 2017 Oct 20;56(30):8403-8413. doi: 10.1364/AO.56.008403.

PMID:
29091619
19.

Concomitant nevirapine impacts pharmacokinetic exposure to the antimalarial artemether-lumefantrine in African children.

Huang L, Carey V, Lindsey JC, Marzan F, Gingrich D, Graham B, Barlow-Mosha L, Ssemambo PK, Kamthunzi P, Nachman S, Parikh S, Aweeka FT; IMPAACT P1079 protocol team.

PLoS One. 2017 Oct 24;12(10):e0186589. doi: 10.1371/journal.pone.0186589. eCollection 2017.

20.

Cavity-based aluminum nanohole arrays with tunable infrared resonances.

Debbrecht B, McElhiney M, Carey V, Cullen C, Mirotznik MS, DeLacy BG.

Opt Express. 2017 Oct 2;25(20):24501-24511. doi: 10.1364/OE.25.024501.

PMID:
29041394
21.

Time Course of Change in Blood Pressure From Sodium Reduction and the DASH Diet.

Juraschek SP, Woodward M, Sacks FM, Carey VJ, Miller ER 3rd, Appel LJ.

Hypertension. 2017 Nov;70(5):923-929. doi: 10.1161/HYPERTENSIONAHA.117.10017.

22.

The Association of Maternal Asthma and Early Pregnancy Vitamin D with Risk of Preeclampsia: An Observation From Vitamin D Antenatal Asthma Reduction Trial (VDAART).

Mirzakhani H, Carey VJ, McElrath TF, Laranjo N, O'Connor G, Iverson RE, Lee-Parritz A, Strunk RC, Bacharier LB, Macones GA, Zeiger RS, Schatz M, Hollis BW, Litonjua AA, Weiss ST.

J Allergy Clin Immunol Pract. 2018 Mar - Apr;6(2):600-608.e2. doi: 10.1016/j.jaip.2017.07.018. Epub 2017 Sep 8.

23.

Alcohol consumption and breast tumor gene expression.

Wang J, Heng YJ, Eliassen AH, Tamimi RM, Hazra A, Carey VJ, Ambrosone CB, de Andrade VP, Brufsky A, Couch FJ, King TA, Modugno F, Vachon CM, Hunter DJ, Beck AH, Hankinson SE.

Breast Cancer Res. 2017 Sep 12;19(1):108. doi: 10.1186/s13058-017-0901-y.

24.

Decline in CD4 T lymphocytes with monotherapy bridging strategy for non-adherent adolescents living with HIV infection: Results of the IMPAACT P1094 randomized trial.

Agwu AL, Warshaw MG, McFarland EJ, Siberry GK, Melvin AJ, Wiznia AA, Fairlie L, Boyd S, Harding P, Spiegel HML, Abrams EJ, Carey VJ; P1094 Study Team.

PLoS One. 2017 Jun 12;12(6):e0178075. doi: 10.1371/journal.pone.0178075. eCollection 2017.

25.

Integration of metabolomic and transcriptomic networks in pregnant women reveals biological pathways and predictive signatures associated with preeclampsia.

Kelly RS, Croteau-Chonka DC, Dahlin A, Mirzakhani H, Wu AC, Wan ES, McGeachie MJ, Qiu W, Sordillo JE, Al-Garawi A, Gray KJ, McElrath TF, Carey VJ, Clish CB, Litonjua AA, Weiss ST, Lasky-Su JA.

Metabolomics. 2017 Jan;13(1). pii: 7. doi: 10.1007/s11306-016-1149-8. Epub 2016 Dec 12.

26.

Vitamin D supplementation during pregnancy: Effect on the neonatal immune system in a randomized controlled trial.

Hornsby E, Pfeffer PE, Laranjo N, Cruikshank W, Tuzova M, Litonjua AA, Weiss ST, Carey VJ, O'Connor G, Hawrylowicz C.

J Allergy Clin Immunol. 2018 Jan;141(1):269-278.e1. doi: 10.1016/j.jaci.2017.02.039. Epub 2017 May 26.

27.

Vitamin D supplementation in pregnancy, prenatal 25(OH)D levels, race, and subsequent asthma or recurrent wheeze in offspring: Secondary analyses from the Vitamin D Antenatal Asthma Reduction Trial.

Wolsk HM, Harshfield BJ, Laranjo N, Carey VJ, O'Connor G, Sandel M, Strunk RC, Bacharier LB, Zeiger RS, Schatz M, Hollis BW, Weiss ST, Litonjua AA.

J Allergy Clin Immunol. 2017 Nov;140(5):1423-1429.e5. doi: 10.1016/j.jaci.2017.01.013. Epub 2017 Mar 9.

PMID:
28285844
28.

Expression Quantitative Trait loci (QTL) in tumor adjacent normal breast tissue and breast tumor tissue.

Quiroz-Zárate A, Harshfield BJ, Hu R, Knoblauch N, Beck AH, Hankinson SE, Carey V, Tamimi RM, Hunter DJ, Quackenbush J, Hazra A.

PLoS One. 2017 Feb 2;12(2):e0170181. doi: 10.1371/journal.pone.0170181. eCollection 2017.

29.

The interaction between equipoise and logistics in clinical trials: A case study.

Warshaw MG, Carey VJ, McFarland EJ, Dawson L, Abrams E, Melvin A, Fairlie L, Spiegel H, Jay J, Agwu AL; IMPAACT P1094 Team.

Clin Trials. 2017 Jun;14(3):314-318. doi: 10.1177/1740774517690734. Epub 2017 Jan 31.

30.

Effect of type and amount of dietary carbohydrate on biomarkers of glucose homeostasis and C reactive protein in overweight or obese adults: results from the OmniCarb trial.

Juraschek SP, Miller ER 3rd, Selvin E, Carey VJ, Appel LJ, Christenson RH, Sacks FM.

BMJ Open Diabetes Res Care. 2016 Nov 14;4(1):e000276. eCollection 2016.

31.

Early pregnancy vitamin D status and risk of preeclampsia.

Mirzakhani H, Litonjua AA, McElrath TF, O'Connor G, Lee-Parritz A, Iverson R, Macones G, Strunk RC, Bacharier LB, Zeiger R, Hollis BW, Handy DE, Sharma A, Laranjo N, Carey V, Qiu W, Santolini M, Liu S, Chhabra D, Enquobahrie DA, Williams MA, Loscalzo J, Weiss ST.

J Clin Invest. 2016 Dec 1;126(12):4702-4715. doi: 10.1172/JCI89031. Epub 2016 Nov 14.

32.

Factors influencing the infant gut microbiome at age 3-6 months: Findings from the ethnically diverse Vitamin D Antenatal Asthma Reduction Trial (VDAART).

Sordillo JE, Zhou Y, McGeachie MJ, Ziniti J, Lange N, Laranjo N, Savage JR, Carey V, O'Connor G, Sandel M, Strunk R, Bacharier L, Zeiger R, Weiss ST, Weinstock G, Gold DR, Litonjua AA.

J Allergy Clin Immunol. 2017 Feb;139(2):482-491.e14. doi: 10.1016/j.jaci.2016.08.045. Epub 2016 Oct 13.

33.

The Role of Vitamin D in the Transcriptional Program of Human Pregnancy.

Al-Garawi A, Carey VJ, Chhabra D, Mirzakhani H, Morrow J, Lasky-Su J, Qiu W, Laranjo N, Litonjua AA, Weiss ST.

PLoS One. 2016 Oct 6;11(10):e0163832. doi: 10.1371/journal.pone.0163832. eCollection 2016.

34.

Pharmacokinetics of Unboosted Atazanavir in Treatment-experienced HIV-infected Children, Adolescents and Young Adults.

Cressey TR, Hazra R, Wiznia A, Foca M, Jean-Philippe P, Graham B, King JR, Britto P, Carey VJ, Acosta EP, Yogev R; IMPAACT P1058A Team.

Pediatr Infect Dis J. 2016 Dec;35(12):1333-1335.

35.

Gene Expression Profiling in Blood Provides Reproducible Molecular Insights into Asthma Control.

Croteau-Chonka DC, Qiu W, Martinez FD, Strunk RC, Lemanske RF Jr, Liu AH, Gilliland FD, Millstein J, Gauderman WJ, Ober C, Krishnan JA, White SR, Naureckas ET, Nicolae DL, Barnes KC, London SJ, Barraza-Villarreal A, Carey VJ, Weiss ST, Raby BA; Asthma BioRepository for Integrative Genomic Exploration (Asthma BRIDGE) Consortium.

Am J Respir Crit Care Med. 2017 Jan 15;195(2):179-188. doi: 10.1164/rccm.201601-0107OC.

36.

Clinical trial data access: Opening doors with TrialShare.

Asare AL, Carey VJ, Rotrosen D, Nepom GT.

J Allergy Clin Immunol. 2016 Sep;138(3):724-726. doi: 10.1016/j.jaci.2016.05.034. Epub 2016 Jul 12. No abstract available.

PMID:
27474121
37.

Universality of human microbial dynamics.

Bashan A, Gibson TE, Friedman J, Carey VJ, Weiss ST, Hohmann EL, Liu YY.

Nature. 2016 Jun 9;534(7606):259-62. doi: 10.1038/nature18301.

38.

Pharmacokinetics of Once-Daily Darunavir/Ritonavir With and Without Etravirine in Human Immunodeficiency Virus-Infected Children, Adolescents, and Young Adults.

Larson KB, Cressey TR, Yogev R, Wiznia A, Hazra R, Jean-Philippe P, Graham B, Gonzalez A, Britto P, Carey VJ, Acosta EP; International Maternal Pediatric and Adolescent AIDS Clinical Trial Protocol P1058A Team.

J Pediatric Infect Dis Soc. 2016 Jun;5(2):131-7. doi: 10.1093/jpids/piu142. Epub 2015 Jan 28.

39.

Rilpivirine Pharmacokinetics Without and With Darunavir/Ritonavir Once Daily in Adolescents and Young Adults.

Foca M, Yogev R, Wiznia A, Hazra R, Jean-Philippe P, Graham B, Britto P, Carey VJ, King J, Acosta EP, Cressey TR; IMPAACT P1058A Team.

Pediatr Infect Dis J. 2016 Sep;35(9):e271-4. doi: 10.1097/INF.0000000000001214.

40.

Pharmacokinetics of Darunavir/Ritonavir With Etravirine Both Twice Daily in Human Immunodeficiency Virus-Infected Adolescents and Young Adults.

Cressey TR, Yogev R, Wiznia A, Hazra R, Jean-Philippe P, Graham B, Gonzalez A, Britto P, Carey VJ, Fletcher CV, Acosta EP; IMPAACT P1058A Team.

J Pediatric Infect Dis Soc. 2017 Sep 1;6(3):294-296. doi: 10.1093/jpids/piw017.

41.

Effect of Prenatal Supplementation With Vitamin D on Asthma or Recurrent Wheezing in Offspring by Age 3 Years: The VDAART Randomized Clinical Trial.

Litonjua AA, Carey VJ, Laranjo N, Harshfield BJ, McElrath TF, O'Connor GT, Sandel M, Iverson RE Jr, Lee-Paritz A, Strunk RC, Bacharier LB, Macones GA, Zeiger RS, Schatz M, Hollis BW, Hornsby E, Hawrylowicz C, Wu AC, Weiss ST.

JAMA. 2016 Jan 26;315(4):362-70. doi: 10.1001/jama.2015.18589.

PMID:
26813209
42.

Lung VITAL: Rationale, design, and baseline characteristics of an ancillary study evaluating the effects of vitamin D and/or marine omega-3 fatty acid supplements on acute exacerbations of chronic respiratory disease, asthma control, pneumonia and lung function in adults.

Gold DR, Litonjua AA, Carey VJ, Manson JE, Buring JE, Lee IM, Gordon D, Walter J, Friedenberg G, Hankinson JL, Copeland T, Luttmann-Gibson H.

Contemp Clin Trials. 2016 Mar;47:185-95. doi: 10.1016/j.cct.2016.01.003. Epub 2016 Jan 16.

43.

A POSTERIORI ERROR ANALYSIS OF TWO STAGE COMPUTATION METHODS WITH APPLICATION TO EFFICIENT DISCRETIZATION AND THE PARAREAL ALGORITHM.

Chaudhry JH, Estep D, Tavener S, Carey V, Sandelin J.

SIAM J Numer Anal. 2016;54(5):2974-3002. doi: 10.1137/16M1079014. Epub 2016 Oct 4.

44.

Age, Sexual Dimorphism, and Disease Associations in the Developing Human Fetal Lung Transcriptome.

Kho AT, Chhabra D, Sharma S, Qiu W, Carey VJ, Gaedigk R, Vyhlidal CA, Leeder JS, Tantisira KG, Weiss ST.

Am J Respir Cell Mol Biol. 2016 Jun;54(6):814-21. doi: 10.1165/rcmb.2015-0326OC.

45.

Expression Quantitative Trait Loci Information Improves Predictive Modeling of Disease Relevance of Non-Coding Genetic Variation.

Croteau-Chonka DC, Rogers AJ, Raj T, McGeachie MJ, Qiu W, Ziniti JP, Stubbs BJ, Liang L, Martinez FD, Strunk RC, Lemanske RF Jr, Liu AH, Stranger BE, Carey VJ, Raby BA.

PLoS One. 2015 Oct 16;10(10):e0140758. doi: 10.1371/journal.pone.0140758. eCollection 2015. Review.

46.

Public data and open source tools for multi-assay genomic investigation of disease.

Kannan L, Ramos M, Re A, El-Hachem N, Safikhani Z, Gendoo DM, Davis S, Gomez-Cabrero D, Castelo R, Hansen KD, Carey VJ, Morgan M, Culhane AC, Haibe-Kains B, Waldron L.

Brief Bioinform. 2016 Jul;17(4):603-15. doi: 10.1093/bib/bbv080. Epub 2015 Oct 12. Review.

47.

Low vs high glycemic index diet--reply.

Sacks FM, Appel LJ, Carey VJ.

JAMA. 2015 Apr 7;313(13):1372-3. doi: 10.1001/jama.2015.2081. No abstract available.

PMID:
25849187
48.

Orchestrating high-throughput genomic analysis with Bioconductor.

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M.

Nat Methods. 2015 Feb;12(2):115-21. doi: 10.1038/nmeth.3252. Review.

49.

Prevention of rare diseases: how revolutionary techniques can help vulnerable individuals-the example of serogroup B meningococcal infection.

McIntosh ED, Carey V, Toneatto D, Dull P, Wassil J.

Ther Adv Vaccines. 2015 Jan;3(1):13-23. doi: 10.1177/2051013614557477. Review.

50.

The Bioconductor channel in F1000Research.

Huber W, Carey V, Davis S, Hansen KD, Morgan M.

Version 2. F1000Res. 2015 Jul 10 [revised 2016 Jan 1];4:217. doi: 10.12688/f1000research.6758.2. eCollection 2015.

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