Philip S. Boonstra

philbXumichYedu, where X= @ and Y= .
Twitter: @psboonstra
GitHub: psboonstra
Cross Validated: psboonstra
Research Associate Professor,
Dept. of Biostatistics, University of Michigan


Curriculum Vitae

Main   Education   Teaching   Research   Software   Clinical Trials


Google scholar

Research Interests
My goal for any statistical analysis is to get the most out of the data, thus my research interests focus on shrinkage estimation, model selection, and sharing strength betwen multiple heterogenous datasets. The underlying theme in all of my work -- methodological and applied -- is to connect new and/or complex statistical methodology with the scientific problem at hand. Some of my other specific research interests include Publications (Published / Accepted)
  1. Saran R , Hedgeman E, Plantinga L, Burrows NR, Gillespie BW , Young EW , Coresh J , Pavkov M , Williams D, and Powe NR, for the CKD Surveillance Team (2010). "Establishing a National Chronic Kidney Disease Surveillance System for the United States" Clinical Journal of the American Society of Nephrology 5, 152-161
  2. Boonstra PS, Gruber SB, Raymond VM, Huang SC, Timshel S, Nilbert M, and Mukherjee B (2010). "A review of statistical methods for testing genetic anticipation: Looking for an answer in Lynch syndrome" Genetic Epidemiology 34, 756-768
  3.   Accepted Version The definitive version is available at onlinelibrary.wiley.com
      R Code
  4. Boonstra PS, Mukherjee B, Taylor JMG, Nilbert M, Moreno V, and Gruber SB (2011). "Bayesian modeling for genetic anticipation in presence of mutational heterogeneity: A case-study in hereditary non-polyposis colorectal cancer (Lynch syndrome)" Biometrics 67, 1627-1637
  5.   Accepted Version The definitive version is available at onlinelibrary.wiley.com. There is a typo in the definition of the Brier Score on the top of page 14. The argument to the estimated survivor function should be "t".
  6. Boonstra PS, Taylor JMG, and Mukherjee B (2013). "Incorporating auxiliary information for improved prediction in high dimensional datasets: An ensemble of shrinkage approaches" Biostatistics 14, 259-272
  7.   Accepted Version The definitive version is available at oxfordjournals.org
      Accepted Version (Supplementary Materials)
  8. Boonstra PS, Mukherjee B, and Taylor JMG (2013). "Bayesian shrinkage methods for partially observed high-dimensional data" Annals of Applied Statistics 7, 2272-2292
  9.   Accepted Version The definitive version is available at projecteuclid.org/euclid.aoas
      R/C Code For Data Analysis
  10. Boonstra PS*, Bondarenko I*, Park SK, Vokonas PS, and Mukherjee B (2014). "Propensity score-based diagnostics for categorical response regression models" Statistics in Medicine 33, 455-469 *Equal contribution authors
  11.   Accepted Version The definitive version is available at onlinelibrary.wiley.com
  12. Stenzel SL, Ahn J, Boonstra PS, Gruber SB, and Mukherjee B (2014). "The impact of exposure biased sampling designs on detection of gene-environment interactions in case-control studies with potential exposure misclassification" European Journal of Epidemiology 30, 413-423
  13. Boonstra PS, Shen JC, Taylor JMG, Braun TM, Griffith KA, Daignault S, Kalemkerian GP, Lawrence TS, and Schipper MJ (2015). "A statistical evaluation of dose expansion cohorts in phase I clinical trials" Journal of the National Cancer Institute 107, dju429.
  14.   Definitive version
  15. Boonstra PS, Mukherjee B, and Taylor JMG (2015). "A small-sample choice of the tuning parameter in ridge regression" Statistica Sinica 25, 1185-1206
  16.   Accepted Version The definitive version is available at www3.stat.sinica.edu.tw/statistica/
      Accepted Version (Supplementary Materials)
      R Code For Simulation Study
  17. Boonstra PS, Taylor JMG, and Mukherjee B (2015). "Adaptive shrinkage via the hyperpenalized EM algorithm" Statistics in Biosciences 7, 417-431
  18.   Accepted Version
  19. Boonstra PS, Mukherjee B, Gruber SB, Ahn J, Schmit SL, and Chatterjee N (2016). "Tests for gene-environment interactions and joint effects with exposure misclassification" American Journal of Epidemiology 183, 237-247
  20.   Accepted Version
      Accepted Version (Supplementary Materials)
      R Code For Simulation Study
  21. Boonstra PS, Taylor JMG, Smolska-Ciszewska B, Behrendt K, Dworzecki T, Gawkowska-Suwinska M, Bialas B, and Suwinski R (2016). "Alpha/beta (α/β) ratio for prostate cancer derived from external beam radiotherapy and brachytherapy boost" The British Journal of Radiology 89, 20150957
  22. Krauss JC, Boonstra PS, Vantsevich A, and Friedman CP (2016). "Is the problem list in the eye of the beholder?: An exploration of consistency across physicians" Journal of the American Medical Informatics Association 23, 859-865
  23. Barbaro RP, Boonstra PS, Paden ML, Folafoluwa OO, Roberts LA, Annich GM, Bartlett RH, Moler F, and Davis MM (2016). "Development and validation of pediatric risk estimate score for children using extracorporeal respiratory Support (Ped-RESCUERS)" Intensive Care Medicine 42, 879-888
  24. Boonstra PS, Taylor JMG and Mukherjee B (2016). "Increasing efficiency for estimating treatment-biomarker interactions with historical data" Statistical Methods in Medical Research 25, 2959-2971.
  25.   Accepted Version The definitive version is available at smm.sagepub.com
  26. Polk A, Lu Y, Wang T, Seymour E, Bailey NG, Singer JW, Boonstra PS, Lim MS, Malek S, and Wilcox RA (2017). "Colony-stimulating Factor-1 Receptor is required for nurse-like cell survival in chronic lymphocytic leukemia" Clinical Cancer Research 22, 6118-6128
  27. Boonstra PS, Braun TM, Taylor JMG, Kidwell KM, Bellile EL , Daignault S, Zhao L, Griffith KA, Lawrence TS, Kalemkerian GP, and Schipper MJ (2017). "Statistical controversies in clinical research: building the bridge to phase II-efficacy estimation in dose-expansion cohorts" Annals of Oncology 28, 1427-1435
  28.   R Code for Simulation Study
      Published Version
  29. Soni PD*, Boonstra PS*, Schipper MJ, Bazzi L, Dess RT, Matuszak MM, Kong F, Hayman JA, Ten Haken RK, Lawrence TS, Kalemkerian GP, and Jolly S (2017). "Lower incidence of esophagitis in the elderly undergoing definitive radiation therapy for lung cancer" Journal of Thoracic Oncology 12, 539-546 *Equal contribution authors
  30. Moyer JS, Flynn S, Boonstra PS, Kraft C, Chinn S, Baker SR, Schwartz JL, Bichakjian, CK, Fullen D, Durham AB, Lowe L, and Johnson TM (2017). "Efficacy of staged excision with permanent section margin control for cutaneous head and neck melanoma" JAMA Dermatology 153, 282-288
  31. DaSilva AF, Nascimento TD, Jassar H, Heffernan J, Toback RL, Lucas S, DosSantos MF, Bellile EL, Boonstra PS , Taylor JMG, Casey KL, Koeppe RA, Smith YR, Zubieta J (2017). "Dopamine D2/D3 imbalance during migraine attack and allodynia in vivo" Neurology 88, 1634-1641
  32. Barbaro RP, Boonstra PS, Moler FW, Davis MM, and Prosser LA (2017). "Hospital-level variation in inpatient cost among children receiving extracorporeal membrane oxygenation" Perfusion 153, 282-288
  33. Hawkins PG*, Boonstra PS*, Hobson ST, Hearn JWD, Hayman JA, Ten Haken RK, Matuszak MM, Stanton P, Kalemkerian GP, Ramnath N, Lawrence TS, Schipper MJ, Kong F, and Jolly S (2017). "Radiation-induced lung toxicity in non-small-cell lung cancer: Understanding the interactions of clinical factors and cytokines with the dose-toxicity relationship" Radiotherapy and Oncology 125, 66-72 *Equal contribution authors
  34. von Salome J, Boonstra PS, Karimi M, Silander G, Stenmark-Askmalm M, Gebre-Medhin S, Aravidis C, Nilbert M, Lindblom A, and Lagerstedt-Robinson K (2017). "Genetic anticipation in Swedish Lynch syndrome families" PLOS Genetics 13, e1007012
  35.   Published version
  36. Grivas PD, Devata S, Khoriaty R, Boonstra PS, Ruch J, McDonnell K, Hernandez LA, Wilfong J, Smerage J, Ison MG, Eisenberg JNS, Silveira M, Cooney KA, and Worden FP (2017). "Low-cost intervention to increase influenza vaccination rates at a comprehensive cancer center" Journal of Cancer Education 32, 871-877
  37. Boonstra PS*, Polk A*, Brown N, Hristov AC, Bailey NG, Kaminski MS, Phillips T, Devata S, Mayer T, and Wilcox RA (2017). "A single center phase II study of ixazomib in patients with relapsed or refractory cutaneous or peripheral T-cell lymphomas" American Journal of Hematology 92, 1287-1294 *Equal contribution authors
  38. Hawkins PG*, Boonstra PS*, Hobson ST, Hayman JA, Ten Haken RK, Matuszak MM, Stanton P, Kalemkerian GP, Lawrence TS, Schipper MJ, and Jolly S (2018). "Prediction of radiation esophagitis in non-small cell lung cancer using clinical factors, dosimetric parameters, and pretreatment cytokine levels" Translational Oncology 11, 102-108 *Equal contribution authors
  39. Ma V, Boonstra PS, Menghrajani K, Perkins C, Gowin KL, Mesa R, Gotlib JR, and Talpaz M (2018). "Treatment with JAK inhibitors in myelofibrosis patients nullifies the prognostic impact of unfavorable cytogenetics" Clinical Lymphoma, Myeloma, and Leukemia 18, e201-e210
  40. Owen DR, Boonstra PS, Viglianti B, Balter J, Schipper MJ, Jackson W, ElNaqa I, Jolly S, Ten Haken RK, and Matuszak MM (2018). "Modeling patient-specific dose-function response using SPECT/CT to personalize prediction of radiation-induced lung toxicity" International Journal of Radiation Oncology · Biology · Physics 102, 1265-1275
  41.   Published version
  42. Barbaro RP, Boonstra PS, Kuo KW, Selewski DT, Bailly DK, Stone CL, Chow CY, Annich GM, Moler FW, and Paden ML (2019). "Evaluating mortality risk adjustment among children receiving extracorporeal support for respiratory failure" ASAIO Journal 65, 277-284
  43.   Published version
  44. Boonstra PS, Barbaro RP, and Sen A (2019). "Default priors for the intercept parameter in logistic regressions" Computational Statistics & Data Analysis 133, 245-256
  45.   Published version
      Authors' version
      (Supplementary Materials)
      Software
  46. Menghrajani K*, Boonstra PS*, Perkins C, Gowin KL, Weber A, Mesa R, Gotlib JR, Wang L, Singer JW, and Talpaz M (2019). "Predictive models for splenic response to JAK-inhibitor therapy in patients with myelofibrosis" Leukemia & Lymphoma 60, 1036-1042 *Equal contribution authors
  47.   Published version
  48. Geer M*, Roberts E*#, Shango M, Till B, Smith S, Abbas H, Hill B, Kaplan J, Barr PM, Caimi PF, Stephens DM, Lin E, Herrera AF, Rosenbaum E, Amengual K, Boonstra PS, Devata S, Wilcox RA, Kaminski M, and Phillips T (2019). "Multicenter retrospective study of intravascular DLBCL treated at academic institutions within the United States" British Journal of Haematology 186, 255-262 *Equal contribution authors #Biostatistics graduate student mentee
  49. Boonstra PS and Barbaro RP (2019). "Incorporating historical models with adaptive Bayesian updates" Biostatistics
  50.   Advance access version
      Authors' version
      (Supplementary Materials)
      Software
  51. Chase EC# and Boonstra PS (2019) "Accounting for established predictors with the multi-step elastic net" Statistics in Medicine 38, 4534-4544 #Biostatistics graduate student mentee
  52.   Published version
  53. Little RJA, West BT, Boonstra PS and Hu J (2019). "Measures of the degree of departure from ignorable sample selection" Journal of Survey Statistics and Methodology
  54.   Advance access version
  55. Ahmed A, Merrill J, Alsawah F, Bockenstedt P, Campagnaro E, Devata S, Gitlin S, Kaminski M, Cusick A, Phillips T, Sood S, Talpaz M, Quiery A, Boonstra PS, and Wilcox RA (2019). "Ruxolitinib as a Targeted Therapy in Adult Patients with Secondary HLH" Lancet Oncology
  56.   Advance access version
  57. Andridge R, West BT, Little RJA, Boonstra PS, and Alvarado-Leiton F (2019). "Indices of non-ignorable selection bias for proportions estimated from non-probability samples" In press at Journal of the Royal Statistical Society: Series B
  58. Hanks JE, Kovatch KJ, Ali SA, Roberts E#, Durham AB, Smith JD, Bradford CR, Malloy KM, Boonstra PS, and McLean SA (2019). "Long-term outcomes, prognostic value, and accuracy of sentinel lymph node biopsy in head and neck melanoma" In press at Otolaryngology-Head and Neck Surgery #Biostatistics graduate student mentee
  59. Bankhead A, McMaster T, Boonstra PS, and Palmbos PL (2019). "Isoform-specific TP63 expression is linked with distinct clinical outcomes in bladder cancer" In press at EBioMedicine
  60. Boonstra PS and Krauss JC "Inferring a consensus problem list using penalized multistage models for ordered data" In press at Annals of Applied Statistics
  61.   Authors' version
      Software
  62. Salami SS, Tosoian JJ, Srinivas N, Jones, Jr TA, Brockman S, Elkhoury FF, Bazzi S, Plouffe KR, Sumida L, Siddiqui J, Liu CJ, Kunju LP, Morgan TM, Natarajan S, Boonstra PS, Tomlins SA, Udager AM, Sisk, Jr AE, Marks LS, and and Palapattu GS "Molecular Dissection of Grade Progression in Men on Active Surveillance for Prostate Cancer" In press at European Urology
Publications (Under Review)