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 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 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
  3. 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
    4.   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".
  4. 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
    5.   Accepted Version The definitive version is available at oxfordjournals.org
      Accepted Version (Supplementary Materials)
  5. Boonstra PS, Mukherjee B, and Taylor JMG (2013) "Bayesian shrinkage methods for partially observed high-dimensional data" Annals of Applied Statistics 7, 2272-2292
    6.   Accepted Version The definitive version is available at projecteuclid.org/euclid.aoas
      R/C Code For Data Analysis
  6. 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
    7.   Accepted Version The definitive version is available at onlinelibrary.wiley.com
  7. 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
  8. 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.
    9.   Definitive version
  9. Boonstra PS, Mukherjee B, and Taylor JMG (2015) "A small-sample choice of the tuning parameter in ridge regression" Statistica Sinica 25, 1185-1206
    10.   Accepted Version The definitive version is available at www3.stat.sinica.edu.tw/statistica/
      Accepted Version (Supplementary Materials)
      R Code For Simulation Study
  10. Boonstra PS, Taylor JMG, and Mukherjee B (2015) "Adaptive shrinkage via the hyperpenalized EM algorithm" Statistics in Biosciences 7, 417-431
    11.   Accepted Version
  11. 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
    12.   Accepted Version
      Accepted Version (Supplementary Materials)
      R Code For Simulation Study
  12. 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
  13. 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
  14. 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
  15. 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.
    16.   Accepted Version The definitive version is available at smm.sagepub.com
  16. 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
  17. 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
    18.   R Code for Simulation Study
      Published Version
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
    24.   Published version
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
    29.   Published version
  29. 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
    30.   Published version
  30. Boonstra PS, Barbaro RP, and Sen A (2019) "Default priors for the intercept parameter in logistic regressions" Computational Statistics & Data Analysis 133, 245-256
    31.   Published version
      Authors' version
      (Supplementary Materials)
      Software
  31. 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
    32.   Published version
  32. 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
  33. 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
    34.   Published version
  34. 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" Journal of the Royal Statistical Society: Series C 68, 1465-1483
    35.   Published version
  35. 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 6, e630-e637
    36.   Published version
  36. Boonstra PS and Barbaro RP (2020) "Incorporating historical models with adaptive Bayesian updates" Biostatistics 21, e47-e64
    37.   Published version
      Authors' version
      (Supplementary Materials)
      Software
  37. 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" Otolaryngology-Head and Neck Surgery 162, 520-529 #Biostatistics graduate student mentee
  38. Bankhead A, McMaster T, Boonstra PS, and Palmbos PL (2020) "Isoform-specific TP63 expression is linked with distinct clinical outcomes in bladder cancer" EBioMedicine 51, 102561
    39.   Published version
  39. Baker LH, Boonstra PS, Reinke D, Peregrine-Antalis E, Zebrack B, and Weinberg RL (2020) "Preliminary findings from a prospective cohort study at a high-risk cancer survivorship clinic" Journal of Cancer Metastasis and Treatment 6, 24
    40.   Published version
  40. Boonstra PS and Krauss JC (2020) "Inferring a consensus problem list using penalized multistage models for ordered data" Annals of Applied Statistics 14, 1557-1580
    41.   Published version
      Authors' version
      Software
  41. Barbaro RP*, MacLaren G*, Boonstra PS, Iwashyna TJ, Slutsky AS, Fan E, Paden ML, Ogino MT, Bartlett RH, Tonna J, Hyslop R, Fanning JJ, Rycus PT, Hyer S, Agerstrand C, Hryniewicz K, Diaz R, Lorusso R, Combes A, Brodie D, for the Extracorporeal Life Support Organization (2020) "Extracorporeal membrane oxygenation support in COVID-19: The registry report from the Extracorporeal Life Support Organization" The Lancet 396, 1071-1078 *Equal contribution authors
    42.   Published version
  42. Little RJA, West BT, Boonstra PS and Hu J (2020) "Measures of the degree of departure from ignorable sample selection" Journal of Survey Statistics and Methodology 8, 932-964
    43.   Published version
  43. Boonstra PS, Ahmed A, Merrill SA, and Wilcox RA (2021) "Ruxolitinib in adult patients with secondary hemophagocytic lymphohistiocytosis" American Journal of Hematology 96, E103-E105
    44.   Published version
  44. Owen DR, Sun Y, Boonstra PS, McFarlane M, Viglianti BL, Balter JM, El Naqa I, Schipper MJ, Schonewolf CA, Ten Haken RK, Kong FM, Jolly S, and Matuszak MM (2021) "Investigating the SPECT dose-function metrics associated with radiation-induced lung toxicity risk in non-small cell lung cancer patients undergoing radiation therapy" Advances in Radiation Oncology 6, 100666
    45.   Published version
  45. 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 Palapattu GS (2021) "Serial molecular profiling of low-grade prostate cancer to assess tumor upgrading: A longitudinal cohort study" (2021) European Urology 79, 456-465
    46.   Published version
  46. Boonstra PS, Braun TM, and Chase EC (2021) "A modular framework for seamless oncology trials" Clinical Trials 18, 303-313
    47.   Published version
      Authors' version
      Software
  47. Delaney PG, Eisner ZJ, Thullah AH, Muller B, Gan J, Timbo A, Kamara S, Sandy K, Boonstra PS, Scott JW, and Raghavendran K (2021) "Evaluating a novel Prehospital Emergency Trauma Care Assessment Tool (PETCAT) for low- and middle-income countries: Lay first responders expand prehospital care in Sierra Leone" World Journal of Surgery 45, 2370-2377
    48.   Published version
  48. Boonstra PS, Little RJA, West BT, Andridge RR, and Alvarado-Leiton F (2021) "A simulation study of diagnostics for bias in non-probability samples" Journal of Official Statistics 37, 751-769
    49.   Published version
      Authors' version
      Software
  49. West BT, Little RJA, Andridge RR, Boonstra PS, Ware EB, Pandit A, and Alvarado-Leiton F (2021) "Assessing selection bias in regression coefficients estimated from nonprobability samples with applications to genetics and demographic surveys" Annals of Applied Statistics 15, 1556-1581
    50.   Published version
  50. Barbaro RP, MacLaren G, Boonstra PS , Agerstrand CL, Combes A, Brodie D, for the Extracorporeal Life Support Organization (2021) "Extracorporeal Membrane Oxygenation for COVID-19: Evolving outcomes from an international registry" In press at The Lancet
    51.   Early access version
Publications (Under Review)
Last updated: 30 Sep 2021