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Ali Shojaie, Ph.D. - Publications

Affiliations: 
2010 University of Michigan, Ann Arbor, Ann Arbor, MI 
Area:
Statistics, Biostatistics Biology, Bioinformatics Biology
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36 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Jin K, Wilson KA, Beck JN, Nelson CS, Brownridge GW, Harrison BR, Djukovic D, Raftery D, Brem RB, Yu S, Drton M, Shojaie A, Kapahi P, Promislow D. Genetic and metabolomic architecture of variation in diet restriction-mediated lifespan extension in Drosophila. Plos Genetics. 16: e1008835. PMID 32644988 DOI: 10.1371/Journal.Pgen.1008835  0.339
2020 Shojaie A. Differential network analysis: A statistical perspective Wiley Interdisciplinary Reviews: Computational Statistics. DOI: 10.1002/Wics.1508  0.34
2019 Ma J, Shojaie A, Michailidis G. A comparative study of topology-based pathway enrichment analysis methods. Bmc Bioinformatics. 20: 546. PMID 31684881 DOI: 10.1186/S12859-019-3146-1  0.582
2019 Haris A, Shojaie A, Simon N. Nonparametric regression with adaptive truncation via a convex hierarchical penalty. Biometrika. 106: 87-107. PMID 31427821 DOI: 10.1093/Biomet/Asy056  0.336
2019 Tank A, Fox EB, Shojaie A. Identifiability and estimation of structural vector autoregressive models for subsampled and mixed-frequency time series. Biometrika. 106: 433-452. PMID 31097836 DOI: 10.1093/Biomet/Asz007  0.316
2018 Randolph TW, Zhao S, Copeland W, Hullar M, Shojaie A. KERNEL-PENALIZED REGRESSION FOR ANALYSIS OF MICROBIOME DATA. The Annals of Applied Statistics. 12: 540-566. PMID 30224943 DOI: 10.1214/17-Aoas1102  0.393
2018 Mathur R, Rotroff D, Ma J, Shojaie A, Motsinger-Reif A. Gene set analysis methods: a systematic comparison. Biodata Mining. 11: 8. PMID 29881462 DOI: 10.1186/S13040-018-0166-8  0.35
2017 Chen S, Shojaie A, Witten DM. Network Reconstruction From High-Dimensional Ordinary Differential Equations. Journal of the American Statistical Association. 112: 1697-1707. PMID 29618851 DOI: 10.1080/01621459.2016.1229197  0.386
2017 Wang X, Shojaie A, Zhang Y, Shelley D, Lampe PD, Levy L, Peters U, Potter JD, White E, Lampe JW. Exploratory plasma proteomic analysis in a randomized crossover trial of aspirin among healthy men and women. Plos One. 12: e0178444. PMID 28542447 DOI: 10.1371/Journal.Pone.0178444  0.303
2017 Zhang Y, Linder MH, Shojaie A, Ouyang Z, Shen R, Baggerly KA, Baladandayuthapani V, Zhao H. Dissecting Pathway Disturbances Using Network Topology and Multi-platform Genomics Data Statistics in Biosciences. 10: 86-106. DOI: 10.1007/S12561-017-9193-0  0.391
2016 Lin L, Drton M, Shojaie A. Estimation of High-Dimensional Graphical Models Using Regularized Score Matching. Electronic Journal of Statistics. 10: 806-854. PMID 28638498 DOI: 10.1214/16-Ejs1126  0.355
2016 Saegusa T, Shojaie A. Joint Estimation of Precision Matrices in Heterogeneous Populations. Electronic Journal of Statistics. 10: 1341-1392. PMID 28473876 DOI: 10.1214/16-Ejs1137  0.364
2016 Ma J, Shojaie A, Michailidis G. Network-based pathway enrichment analysis with incomplete network information. Bioinformatics (Oxford, England). PMID 27357170 DOI: 10.1093/Bioinformatics/Btw410  0.578
2016 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, et al. Inhibition of the hexosamine biosynthetic pathway promotes castration-resistant prostate cancer. Nature Communications. 7: 11612. PMID 27194471 DOI: 10.1038/Ncomms11612  0.544
2016 Kaushik AK, Shojaie A, Panzitt K, Sonavane R, Venghatakrishnan H, Manikkam M, Zaslavsky A, Putluri V, Vasu V, Zhang Y, Khan A, Lloyd S, Szafran A, Dasgupta S, Bader D, et al. Abstract 1056: Inhibition of hexose monophosphate pathway promotes castration resistant prostate cancer Cancer Research. 76: 1056-1056. DOI: 10.1158/1538-7445.Am2016-1056  0.305
2015 Basu S, Shojaie A, Michailidis G. Network Granger Causality with Inherent Grouping Structure. Journal of Machine Learning Research : Jmlr. 16: 417-453. PMID 34267606  0.52
2015 Chen S, Witten DM, Shojaie A. Selection and estimation for mixed graphical models. Biometrika. 102: 47-64. PMID 27625437 DOI: 10.1093/Biomet/Asu051  0.311
2015 Zhao S, Shojaie A. A significance test for graph-constrained estimation. Biometrics. PMID 26393533 DOI: 10.1111/Biom.12418  0.332
2015 Tan KM, Witten D, Shojaie A. The cluster graphical lasso for improved estimation of Gaussian graphical models. Computational Statistics & Data Analysis. 85: 23-36. PMID 25642008 DOI: 10.1016/J.Csda.2014.11.015  0.302
2015 Basu S, Shojaie A, Michailidis G. Network Granger causality with inherent grouping structure Journal of Machine Learning Research. 16: 417-453.  0.452
2014 Sedaghat N, Saegusa T, Randolph T, Shojaie A. Comparative study of computational methods for reconstructing genetic networks of cancer-related pathways. Cancer Informatics. 13: 55-66. PMID 25288880 DOI: 10.4137/Cin.S13781  0.388
2014 Voorman A, Shojaie A, Witten D. Graph Estimation with Joint Additive Models. Biometrika. 101: 85-101. PMID 25013234 DOI: 10.1093/Biomet/Ast053  0.355
2014 Shojaie A, Jauhiainen A, Kallitsis M, Michailidis G. Inferring regulatory networks by combining perturbation screens and steady state gene expression profiles. Plos One. 9: e82393. PMID 24586224 DOI: 10.1371/Journal.Pone.0082393  0.58
2014 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, et al. Metabolomic profiling identifies biochemical pathways associated with castration-resistant prostate cancer. Journal of Proteome Research. 13: 1088-100. PMID 24359151 DOI: 10.1021/Pr401106H  0.575
2013 Petrochilos D, Shojaie A, Gennari J, Abernethy N. Using random walks to identify cancer-associated modules in expression data. Biodata Mining. 6: 17. PMID 24128261 DOI: 10.1186/1756-0381-6-17  0.401
2013 Panzitt K, Shojaie A, Putluri N, Basu S, Putluri V, Samanta S, Ittmann M, Vergara I, Michailidis G, Palapattu G, Sreekumar A. Abstract 5387: Integrative analysis of transcriptomic and metabolomic data reveals a critical role for aminosugar metabolism in prostate cancer. Cancer Research. 73: 5387-5387. DOI: 10.1158/1538-7445.Am2013-5387  0.544
2012 Shojaie A, Basu S, Michailidis G. Adaptive Thresholding for Reconstructing Regulatory Networks from Time-Course Gene Expression Data Statistics in Biosciences. 4: 66-83. DOI: 10.1007/S12561-011-9050-5  0.586
2011 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, et al. Metabolomic profiling reveals potential markers and bioprocesses altered in bladder cancer progression. Cancer Research. 71: 7376-86. PMID 21990318 DOI: 10.1158/0008-5472.Can-11-1154  0.528
2011 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. Metabolomic profiling reveals a role for androgen in activating amino acid metabolism and methylation in prostate cancer cells. Plos One. 6: e21417. PMID 21789170 DOI: 10.1371/Journal.Pone.0021417  0.533
2011 Shojaie A, Jauhiainen A, Kallatsis M, Michailidis G. Reconstructing gene regulatory networks by integrating perturbation screens and steady-state gene expression profiles F1000research. 2. DOI: 10.7490/F1000Research.2103.1  0.341
2010 Shojaie A, Michailidis G. Penalized likelihood methods for estimation of sparse high-dimensional directed acyclic graphs. Biometrika. 97: 519-538. PMID 22434937 DOI: 10.1093/Biomet/Asq038  0.531
2010 Shojaie A, Michailidis G. Discovering graphical Granger causality using the truncating lasso penalty. Bioinformatics (Oxford, England). 26: i517-23. PMID 20823316 DOI: 10.1093/Bioinformatics/Btq377  0.579
2010 Shojaie A, Michailidis G. Network enrichment analysis in complex experiments. Statistical Applications in Genetics and Molecular Biology. 9: Article22. PMID 20597848 DOI: 10.2202/1544-6115.1483  0.597
2010 Putluri N, Vasu VT, Shojaie A, Thangjam GS, Vareed SK, Putluri V, Butler C, Giri JG, Park MA, Ponnala R, Sana TR, Fischer SM, Sica G, Brat DJ, Shi H, et al. Abstract A52: Metabolomic profiling reveals impaired xenobiotic metabolism in bladder cancer Cancer Epidemiology, Biomarkers & Prevention. 19. DOI: 10.1158/1055-9965.Disp-10-A52  0.537
2010 Shojaie A, Michailidis G. Penalized principal component regression on graphs for analysis of subnetworks Advances in Neural Information Processing Systems 23: 24th Annual Conference On Neural Information Processing Systems 2010, Nips 2010.  0.53
2009 Shojaie A, Michailidis G. Analysis of gene sets based on the underlying regulatory network. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 407-26. PMID 19254181 DOI: 10.1089/Cmb.2008.0081  0.588
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