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Items: 38

1.

Plasma Lipidomics Profiles After a Diet Characterized by Whole Grains Compared to a Diet High in Refined Grains and Added Sugars (FS03-07-19).

Moghadam SD, Navarro S, Shojaie A, Randolph T, Bettcher L, Le C, Hullar M, Kratz M, Neuhouser M, Lampe P, Raftery D, Lampe J.

Curr Dev Nutr. 2019 Jun 13;3(Suppl 1). pii: nzz046.FS03-07-19. doi: 10.1093/cdn/nzz046.FS03-07-19. eCollection 2019 Jun.

2.

Identifiability and estimation of structural vector autoregressive models for subsampled and mixed-frequency time series.

Tank A, Fox EB, Shojaie A.

Biometrika. 2019 Jun;106(2):433-452. doi: 10.1093/biomet/asz007. Epub 2019 Apr 8.

PMID:
31097836
3.

KERNEL-PENALIZED REGRESSION FOR ANALYSIS OF MICROBIOME DATA.

Randolph TW, Zhao S, Copeland W, Hullar M, Shojaie A.

Ann Appl Stat. 2018 Mar;12(1):540-566. doi: 10.1214/17-AOAS1102. Epub 2018 Mar 9.

4.

Gene set analysis methods: a systematic comparison.

Mathur R, Rotroff D, Ma J, Shojaie A, Motsinger-Reif A.

BioData Min. 2018 May 31;11:8. doi: 10.1186/s13040-018-0166-8. eCollection 2018.

5.

Circulating bile acids in healthy adults respond differently to a dietary pattern characterized by whole grains, legumes and fruits and vegetables compared to a diet high in refined grains and added sugars: A randomized, controlled, crossover feeding study.

Ginos BNR, Navarro SL, Schwarz Y, Gu H, Wang D, Randolph TW, Shojaie A, Hullar MAJ, Lampe PD, Kratz M, Neuhouser ML, Raftery D, Lampe JW.

Metabolism. 2018 Jun;83:197-204. doi: 10.1016/j.metabol.2018.02.006. Epub 2018 Feb 17.

6.

Using Twitter for Demographic and Social Science Research: Tools for Data Collection and Processing.

McCormick TH, Lee H, Cesare N, Shojaie A, Spiro ES.

Sociol Methods Res. 2017 Aug;46(3):390-421. doi: 10.1177/0049124115605339. Epub 2015 Oct 9.

7.

Nearly assumptionless screening for the mutually-exciting multivariate Hawkes process.

Chen S, Witten D, Shojaie A.

Electron J Stat. 2017;11(1):1207-1234. doi: 10.1214/17-EJS1251. Epub 2017 Apr 11.

8.

Plasma metabolite abundances are associated with urinary enterolactone excretion in healthy participants on controlled diets.

Miles FL, Navarro SL, Schwarz Y, Gu H, Djukovic D, Randolph TW, Shojaie A, Kratz M, Hullar MAJ, Lampe PD, Neuhouser ML, Raftery D, Lampe JW.

Food Funct. 2017 Sep 20;8(9):3209-3218. doi: 10.1039/c7fo00684e.

9.

Combining Supervised and Unsupervised Learning for Improved miRNA Target Prediction.

Sedaghat N, Fathy M, Modarressi MH, Shojaie A.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Sep-Oct;15(5):1594-1604. doi: 10.1109/TCBB.2017.2727042. Epub 2017 Jul 13.

PMID:
28715336
10.

Exploratory plasma proteomic analysis in a randomized crossover trial of aspirin among healthy men and women.

Wang X, Shojaie A, Zhang Y, Shelley D, Lampe PD, Levy L, Peters U, Potter JD, White E, Lampe JW.

PLoS One. 2017 May 25;12(5):e0178444. doi: 10.1371/journal.pone.0178444. eCollection 2017.

11.

Joint Estimation of Precision Matrices in Heterogeneous Populations.

Saegusa T, Shojaie A.

Electron J Stat. 2016;10(1):1341-1392. doi: 10.1214/16-EJS1137. Epub 2016 May 31.

12.

Transcriptional networks are associated with resistance to Mycobacterium tuberculosis infection.

Seshadri C, Sedaghat N, Campo M, Peterson G, Wells RD, Olson GS, Sherman DR, Stein CM, Mayanja-Kizza H, Shojaie A, Boom WH, Hawn TR; Tuberculosis Research Unit (TBRU).

PLoS One. 2017 Apr 17;12(4):e0175844. doi: 10.1371/journal.pone.0175844. eCollection 2017.

13.

Network Reconstruction From High-Dimensional Ordinary Differential Equations.

Chen S, Shojaie A, Witten DM.

J Am Stat Assoc. 2017;112(520):1697-1707. doi: 10.1080/01621459.2016.1229197. Epub 2017 Aug 7.

14.

Human Oral Buccal Microbiomes Are Associated with Farmworker Status and Azinphos-Methyl Agricultural Pesticide Exposure.

Stanaway IB, Wallace JC, Shojaie A, Griffith WC, Hong S, Wilder CS, Green FH, Tsai J, Knight M, Workman T, Vigoren EM, McLean JS, Thompson B, Faustman EM.

Appl Environ Microbiol. 2016 Dec 30;83(2). pii: e02149-16. doi: 10.1128/AEM.02149-16. Print 2017 Jan 15.

15.

Network-based pathway enrichment analysis with incomplete network information.

Ma J, Shojaie A, Michailidis G.

Bioinformatics. 2016 Oct 15;32(20):3165-3174. Epub 2016 Jun 29.

16.

Identifying functional cancer-specific miRNA-mRNA interactions in testicular germ cell tumor.

Sedaghat N, Fathy M, Modarressi MH, Shojaie A.

J Theor Biol. 2016 Sep 7;404:82-96. doi: 10.1016/j.jtbi.2016.05.026. Epub 2016 May 25.

17.

Inhibition of the hexosamine biosynthetic pathway promotes castration-resistant prostate cancer.

Kaushik AK, Shojaie A, Panzitt K, Sonavane R, Venghatakrishnan H, Manikkam M, Zaslavsky A, Putluri V, Vasu VT, Zhang Y, Khan AS, Lloyd S, Szafran AT, Dasgupta S, Bader DA, Stossi F, Li H, Samanta S, Cao X, Tsouko E, Huang S, Frigo DE, Chan L, Edwards DP, Kaipparettu BA, Mitsiades N, Weigel NL, Mancini M, McGuire SE, Mehra R, Ittmann MM, Chinnaiyan AM, Putluri N, Palapattu GS, Michailidis G, Sreekumar A.

Nat Commun. 2016 May 19;7:11612. doi: 10.1038/ncomms11612.

18.

Estimation of High-Dimensional Graphical Models Using Regularized Score Matching.

Lin L, Drton M, Shojaie A.

Electron J Stat. 2016;10(1):806-854. doi: 10.1214/16-EJS1126. Epub 2016 Apr 6.

19.

A significance test for graph-constrained estimation.

Zhao S, Shojaie A.

Biometrics. 2016 Jun;72(2):484-93. doi: 10.1111/biom.12418. Epub 2015 Sep 22.

20.

Phenotypic and Molecular Characterization of Plasmid Mediated AmpC among Clinical Isolates of Klebsiella pneumoniae Isolated from Different Hospitals in Tehran.

Azimi L, Erajiyan G, Talebi M, Owlia P, Bina M, Shojaie A, Lari AR.

J Clin Diagn Res. 2015 Apr;9(4):DC01-3. doi: 10.7860/JCDR/2015/11037.5797. Epub 2015 Apr 1.

21.

Lanthanum and zirconium co-doped ZnO nanocomposites: synthesis, characterization and study of photocatalytic activity.

Moafi HF, Zanjanchi MA, Shojaie AF.

J Nanosci Nanotechnol. 2014 Sep;14(9):7139-50.

PMID:
25924382
22.

Antimicrobial susceptibility patterns of the gram-negative bacteria isolated from septicemia in Children's Medical Center, Tehran, Iran.

Rabirad N, Mohammadpoor M, Lari AR, Shojaie A, Bayat R, Alebouyeh M.

J Prev Med Hyg. 2014 Mar;55(1):23-6.

23.

Serial plasma metabolites following hypoxic-ischemic encephalopathy in a nonhuman primate model.

Chun PT, McPherson RJ, Marney LC, Zangeneh SZ, Parsons BA, Shojaie A, Synovec RE, Juul SE.

Dev Neurosci. 2015;37(2):161-71. doi: 10.1159/000370147. Epub 2015 Feb 27.

24.

Selection and estimation for mixed graphical models.

Chen S, Witten DM, Shojaie A.

Biometrika. 2015 Mar;102(1):47-64. Epub 2014 Dec 24.

25.

The cluster graphical lasso for improved estimation of Gaussian graphical models.

Tan KM, Witten D, Shojaie A.

Comput Stat Data Anal. 2015 May;85:23-36.

26.

Comparative study of computational methods for reconstructing genetic networks of cancer-related pathways.

Sedaghat N, Saegusa T, Randolph T, Shojaie A.

Cancer Inform. 2014 Sep 21;13(Suppl 2):55-66. doi: 10.4137/CIN.S13781. eCollection 2014. Review.

27.

Graph Estimation with Joint Additive Models.

Voorman A, Shojaie A, Witten D.

Biometrika. 2014 Mar 1;101(1):85-101.

28.

The Cluster Elastic Net for High-Dimensional Regression With Unknown Variable Grouping.

Witten DM, Shojaie A, Zhang F.

Technometrics. 2014 Feb 20;56(1):112-122.

29.

Inferring regulatory networks by combining perturbation screens and steady state gene expression profiles.

Shojaie A, Jauhiainen A, Kallitsis M, Michailidis G.

PLoS One. 2014 Feb 28;9(2):e82393. doi: 10.1371/journal.pone.0082393. eCollection 2014.

30.

Metabolomic profiling identifies biochemical pathways associated with castration-resistant prostate cancer.

Kaushik AK, Vareed SK, Basu S, Putluri V, Putluri N, Panzitt K, Brennan CA, Chinnaiyan AM, Vergara IA, Erho N, Weigel NL, Mitsiades N, Shojaie A, Palapattu G, Michailidis G, Sreekumar A.

J Proteome Res. 2014 Feb 7;13(2):1088-100. doi: 10.1021/pr401106h. Epub 2013 Dec 31.

31.

Using random walks to identify cancer-associated modules in expression data.

Petrochilos D, Shojaie A, Gennari J, Abernethy N.

BioData Min. 2013 Oct 15;6(1):17. doi: 10.1186/1756-0381-6-17.

32.

Inter-individual differences in response to dietary intervention: integrating omics platforms towards personalised dietary recommendations.

Lampe JW, Navarro SL, Hullar MA, Shojaie A.

Proc Nutr Soc. 2013 May;72(2):207-18. doi: 10.1017/S0029665113000025. Epub 2013 Feb 6.

33.

Metabolomic profiling reveals potential markers and bioprocesses altered in bladder cancer progression.

Putluri N, Shojaie A, Vasu VT, Vareed SK, Nalluri S, Putluri V, Thangjam GS, Panzitt K, Tallman CT, Butler C, Sana TR, Fischer SM, Sica G, Brat DJ, Shi H, Palapattu GS, Lotan Y, Weizer AZ, Terris MK, Shariat SF, Michailidis G, Sreekumar A.

Cancer Res. 2011 Dec 15;71(24):7376-86. doi: 10.1158/0008-5472.CAN-11-1154. Epub 2011 Oct 11.

34.

Metabolomic profiling reveals a role for androgen in activating amino acid metabolism and methylation in prostate cancer cells.

Putluri N, Shojaie A, Vasu VT, Nalluri S, Vareed SK, Putluri V, Vivekanandan-Giri A, Byun J, Pennathur S, Sana TR, Fischer SM, Palapattu GS, Creighton CJ, Michailidis G, Sreekumar A.

PLoS One. 2011;6(7):e21417. doi: 10.1371/journal.pone.0021417. Epub 2011 Jul 18.

35.

Discovering graphical Granger causality using the truncating lasso penalty.

Shojaie A, Michailidis G.

Bioinformatics. 2010 Sep 15;26(18):i517-23. doi: 10.1093/bioinformatics/btq377.

36.

Penalized likelihood methods for estimation of sparse high-dimensional directed acyclic graphs.

Shojaie A, Michailidis G.

Biometrika. 2010 Sep;97(3):519-538. Epub 2010 Jul 9.

37.

Network enrichment analysis in complex experiments.

Shojaie A, Michailidis G.

Stat Appl Genet Mol Biol. 2010;9:Article22. doi: 10.2202/1544-6115.1483. Epub 2010 May 22.

38.

Analysis of gene sets based on the underlying regulatory network.

Shojaie A, Michailidis G.

J Comput Biol. 2009 Mar;16(3):407-26. doi: 10.1089/cmb.2008.0081.

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