Publications


Google Scholar profile


Under review

  1. Shi Y, Zhang L, Do K, Jenq RJ, Peterson CB. (2024+) CAT: a conditional association test for microbiome data using a leave-out approach. [preprint] [code]

Peer reviewed

Underlining denotes trainees supervised or co-supervised

Statistical methodology

  1. Ren Y, Peterson CB, Vannucci M. (2024+) Bayesian network-guided sparse regression with flexible varying effects. Accepted to Biometrics. [preprint] [code]
  2. Shi Y, Zhang L, Do K, Jenq RR, Peterson CB. (2024) survivalContour: Visualizing predicted survival via colored contour plots. Bioinformatics Advances. 4(1): vbae105. [pdf] [code] [Shiny app]
  3. Ren Y, Osborne N, Peterson CB, DeMaster DM, Ewing-Cobbs L, Vannucci M. (2024) Bayesian varying-effects vector autoregressive models for inference of brain connectivity networks and covariate effects in pediatric traumatic brain injury. Human Brain Mapping. 45(10): e26763. [pdf] [code]
  4. Mishra AK, Mahmud I, Lorenzi PL, Jenq RR, Wargo JA, Ajami NJ, Peterson CB. (2024) TARO: tree-aggregated factor regression for microbiome data integration. Bioinformatics. 40(6): btae321. [pdf] [code]
  5. Qi X, Zhou S, Peterson CB, Wang Y, Fang X, Wang ML, Shen C. (2024) Meta-analysis of censored adverse events. New England Journal of Statistics in Data Science. [pdf] [code]
  6. Peterson CB, Saha S, Do K. (2024) Analysis of microbiome data. Annual Review of Statistics and Its Application. 11. [pdf]
  7. Das P, Peterson CB, Ni Y, Reuben A, Zhang J, Zhang J, Do K, Baladandayuthapani V. (2023) Bayesian hierarchical quantile regression with application to characterizing the immune architecture of lung cancer. Biometrics. 79(3): 2474-2488 [pdf] [code]
  8. Shoemaker K, Ger R, Court LE, Aerts H, Vannucci M, Peterson CB. (2023) Bayesian feature selection for radiomics using reliability metrics. Frontiers in Genetics. 14. Research Topic: Methods for Imaging and Omics Data Science. [pdf] [code]
  9. Shi Y, Zhang L, Do K, Jenq RR, Peterson CB. (2023) Sparse tree-based clustering of microbiome data to characterize microbiome heterogeneity in pancreatic cancer. Journal of the Royal Statistical Society Series C: Applied Statistics. 72(1): 20-36. [pdf] [code]
  10. Wooten ZT, Yu C, Court LE, Peterson CB. (2023) Predictive modeling using shape statistics for interpretable and robust quality assurance of automated contours in radiation treatment planning. Pacific Symposium on Biocomputing 2023. 28: 395-406. [pdf] [code]
  11. Qi X, Zhou S, Wang Y, Peterson CB. (2022) Bayesian sparse modeling to identify high-risk subgroups in meta-analysis of safety data. Research Synthesis Methods. 13(6): 807-820. [pdf] [code]
  12. Das P, De D, Maiti R, Kamal M, Hutcheson KA, Fuller CD, Chakraborty B, Peterson CB. (2022) Estimating the optimal linear combination of predictors using spherically constrained optimization. BMC Bioinformatics. 23(3): 436. [pdf] [code]
  13. Osborne N, Peterson CB, Vannucci M. (2022) Latent network estimation and variable selection for compositional data via variational EM. Journal of Computational and Graphical Statistics. 31(1): 163-175. [pdf] [code]
  14. Zhang L, Shi Y, Do K, Peterson CB†, Jenq RR†. (2021) ProgPermute: Progressive permutation for a dynamic representation of the robustness of microbiome discoveries. BMC Bioinformatics. 22:1-21. †Co-senior authors. [pdf] [code] [Shiny app]
  15. Bogomolov M*, Peterson CB*, Benjamini Y, Sabatti C. (2021) Hypotheses on a tree: new error rates and testing strategies. Biometrika. 108(3): 575-590. *Authors contributed equally. [pdf] [R package]
  16. Zhang L, Shi Y, Jenq RR, Do K, Peterson CB. (2021) Bayesian compositional regression with structured priors for microbiome feature selection. Biometrics. 77(3): 824-838. [pdf] [code]
  17. Ha MJ, Kim J, Galloway-Pena J, Do KA, Peterson CB. (2020) Compositional zero-inflated network estimation for microbiome data. BMC Bioinformatics. 21: 1-20. [pdf] [code]
  18. Shi Y, Zhang L, Do K, Peterson CB†, Jenq RR†. (2020) aPCoA: covariate adjusted principal coordinates analysis. Bioinformatics. 36(13): 4099-4101. †Co-senior authors. [pdf] [R package] [Shiny app]
  19. Peterson CB, Osborne N, Stingo FC, Bourgeat P, Doecke J, Vannucci M. (2020) Bayesian modeling of multiple structural connectivity networks during the progression of Alzheimer's disease. Biometrics. 76(4): 1120-1132. [pdf] [code]
  20. Das P, Peterson CB, Do K, Akbani R, and Baladandayuthapani V. (2020) NExUS: Bayesian simultaneous network estimation across unequal sample sizes. Bioinformatics. 36(3): 798-804. [pdf] [code]
  21. Shaddox E, Peterson CB, Stingo FC, Hanania N, Cruickshank-Quinn C, Kechris K, Bowler R, Vannucci M. (2020) Bayesian inference of networks across multiple sample groups and data types. Biostatistics. 21(3): 561-576. [pdf] [code]
  22. Kim J, Do K, Ha MJ, Peterson CB. (2019) Bayesian inference of hub nodes across multiple networks. Biometrics. 75(1): 172-182. [pdf] [code]
  23. Cremaschi A, Argiento R, Shoemaker K, Peterson CB, Vannucci, M. (2019) Hierarchical normalized completely random measures for robust graphical modeling. Bayesian Analysis. 14(4): 1271-1301. [pdf]
  24. Shaddox E, Stingo F, Peterson CB, Jacobson S, Cruickshank-Quinn C, Kechris K, Bowler R, Vannucci M. (2018) A Bayesian approach for learning gene networks underlying disease severity in COPD. Statistics in Biosciences. 10(1): 59-85. [pdf] [code]
  25. Brzyski D, Peterson CB, Sobczyk P, Candés EJ, Bogdan M, Sabatti C. (2017) Controlling the rate of GWAS false discoveries. Genetics. 205(1):61-75. [pdf]
  26. Peterson CB, Bogomolov M, Benjamini Y, Sabatti C. (2016) TreeQTL: hierarchical error control for eQTL findings. Bioinformatics. 32(16): 2556-2558. [pdf] [R package]
  27. Peterson CB, Bogomolov M, Benjamini Y, Sabatti C. (2016) Many phenotypes without many false discoveries: Error controlling strategies for multi-trait association studies. Genetic Epidemiology. 40(1): 45—56. [pdf]
    See here for more information, including online supplement and implementation details.
  28. Peterson CB, Stingo FC, Vannucci M. (2016) Joint Bayesian variable and graph selection for regression models with network-structured predictors. Statistics in Medicine. 35(7): 1017—1031. [pdf] [code]
  29. Peterson CB, Stingo FC, Vannucci M. (2015) Bayesian inference of multiple Gaussian graphical models. Journal of the American Statistical Association. 110(509): 159—174. [pdf] [code]
  30. Peterson CB, Vannucci M, Karakas C, Choi W, Ma L, Maletic-Savatic M. (2013) Inferring metabolic networks using the Bayesian adaptive graphical lasso with informative priors. Statistics and Its Interface. 6(4): 547—558. [pdf]
  31. Allen GI, Peterson CB, Vannucci M, Maletic-Savatic M. (2013) Regularized partial least squares with an application to NMR spectroscopy. Statistical Analysis and Data Mining. 6(4): 302—314. [pdf]
Statistical applications and collaborations: Microbiome research

  1. Hayase E, Hayase T, Mukherjee A, …, Peled JU, van den Brink MR, Peterson CB, …, Jenq RR. (2024) Bacteroides ovatus alleviates dysbiotic microbiota-induced intestinal graft-versus-host disease. Cell Host & Microbe.
  2. Glitza IC, Seo YD, Spencer CN, Wortman JR, …, Peterson CB, et al. (2024) Randomized placebo-controlled, biomarker-stratified phase Ib microbiome modulation in melanoma: impact of antibiotic preconditioning on microbiome and immunity. Cancer Discovery. 14(7): 1161-1175.
  3. Zhang L, San Valentin EM, John TM, Jenq RR, Do K, Hanna EY, Peterson CB†, Reyes-Gibby CC†. (2024) Influence of oral microbiome on longitudinal patterns of oral mucositis severity in patients with squamous cell carcinoma of the head and neck. Cancer. 130(1): 150-161. †Co-corresponding authors.
  4. Witt RG, Cass SH, Tran T, Damania A, Nelson EE, …, Peterson CB, et al. (2023) Gut microbiome in patients with early-stage and late-stage melanoma. JAMA Dermatology. 59(10): 1076-1084.
  5. Button JE, Cosetta CM, Reens AL, Brooker SL, Rowan-Nash AD, …, Peterson CB, Koh AY, Rechtman DJ, Jenq RR, McKenzie GJ. (2023) Precision modulation of dysbiotic adult microbiomes with a human-milk-derived synbiotic reshapes gut microbial composition and metabolites. Cell Host & Microbe. 31(9): 1523-1538.
  6. Francisco DM, Zhang L, Jiang Y, Olvera A, Adachi J, Guevara EY, Aitken SL, Garey KW, Peterson CB, et al. (2023) Risk factors associated with severe Clostridioides difficile infection in patients with cancer. Infectious Diseases and Therapy. 12(1): 209-225.
  7. Schwabkey Z, Wiesnoski DH, Chang C, Tsai W, Pham D, …, Peterson CB, Do KA, Zhang L, Shi Y, …, Jenq RR. (2022) Diet-derived metabolites and mucus link the gut microbiome to fever after cytotoxic cancer treatment. Science Translational Medicine. 14(671): eabo3445.
  8. Schmiester M, Maier R, Riedel R, Durek P, Frentsch M, Kolling S, Mashreghi MF, Jenq R, Zhang L, Peterson CB, Bullinger L, Chang H, Na I. (2022) Flow cytometry can reliably capture gut microbial composition in healthy adults as well as dysbiosis dynamics in patients with aggressive B-cell non-Hodgkin lymphoma. Gut Microbes. 14(1): 2081475.
  9. Franklin S, Aitken SL, Shi Y, Sahasrabhojane PV, Robinson S, Peterson CB, et al. (2022) Oral and stool microbiome coalescence and its association with antibiotic exposure in acute leukemia patients. Frontiers in Cellular and Infection Microbiology. 12: 848580.
  10. Shi Y, Zhang L, Peterson CB†, Do K†, Jenq RR†. (2022) Performance determinants of unsupervised clustering methods for microbiome data. Microbiome. 10(25):1-12. †Authors contributed equally.
  11. Spencer CN, McQuade JL, Gopalakrishnan V, McCulloch JA, Vetizou M, Cogdill AP, Khan MA, Zhang X, White MG, Peterson CB, Wong MC, et al. (2021) Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response. Science. 374(6575): 1632-1640.
  12. Hajjar J, Mendoza T, Zhang L, Fu S, Piha-Paul SA, Hong DS, Janku F, Karp DD, Ballhausen A, Gong J, Zarifa A, Peterson CB, et al. (2021) Associations between the gut microbiome and fatigue in cancer patients. Scientific Reports. 11: 5847.
  13. Reyes-Gibby CC, Wang J, Zhang L, Peterson CB, Do KA, et al. (2020) Oral microbiome and onset of oral mucositis in patients with squamous cell carcinoma of the head and neck. Cancer. 126(23): 5124-5136.
  14. Robinson S, Peterson CB, Sahasrabhojane P, Ajami NJ, Shelburne SA, Kontoyiannis DP, Galloway-Pena JR. (2020) Observational cohort study of oral mycobiome and interkingdom interactions over the course of induction therapy for leukemia. mSphere. 5(2): e00048-20.
  15. Galloway-Pena JR, Shi Y, Peterson CB, Sahasrabhojane PV, Gopalakrishnan V, Brumlow CE, et al. (2020) Gut microbiome signatures are predictive of infectious risk following induction therapy for acute myeloid leukemia. Clinical Infectious Diseases. 71(1): 63-71.
  16. Riquelme E, Zhang Y, Zhang L, Maria M, Michelle Z, Dong W, …, Peterson CB, et al. (2019) Tumor microbiome diversity and composition influence pancreatic cancer outcomes. Cell. 178(4): 795-806.e12.
  17. Galloway-Pena JR, Peterson CB, Malik F, Sahasrabhojane PV, Shah DP, Brumlow CE, et al. (2019) Fecal microbiome, metabolites, and stem cell transplant outcomes: a single-center pilot study. Open Forum Infectious Diseases. 6(5).
  18. Jiang Z, Jenq RR, Ajami NJ, Petrosino JF, Alexander AA, Ke S, Iqbal T, DuPont AW, Muldrew K, Shi Y, Peterson CB, Do K, DuPont HL. (2018) Safety and preliminary efficacy of orally administered lyophilized fecal microbiota product compared with frozen product given by enema for recurrent clostridium difficile infection: a randomized clinical trial. PLoS ONE. 13(11): e0205064.
Statistical applications and collaborations: Medical physics

  1. McCoy K, Marisetty S, Tan D, Jensen CT, Siewerdsen JH, Peterson CB, Ahmad M. (2024) Automatic vessel attenuation measurement for quality control of contrast‐enhanced CT: Validation on the portal vein. Medical Physics. 51:(9): 5954-5964.
  2. Leone AO, Mohamed AS, Fuller CD, Peterson CB, Garden AS, Lee A, Mayo LL, Moreno AC, Reddy JP, Hoffman K, Niedzielski JS, Court LE, Whitaker TJ. (2024) A visualization and radiation treatment plan quality scoring method for triage in a population-based context. Advances in Radiation Oncology. 9(8): 101533.
  3. Taylor PA, Hartzell S, Mirandola A, Ciocca M, Magro G, Alvarez P, Peterson CB, Peeler CR, Koay EJ, Howell RM, Kry SF. (2024) OSLD nanoDot characterization for carbon radiotherapy dosimetry. Physics in Medicine & Biology. 69(11): 115001.
  4. Taylor PA, Mirandola A, Ciocca M, Hartzell S, Vai A, Alvarez P, Howell RM, Koay EJ, Peeler CR, Peterson CB, Kry SF. (2024) Technical note: Radiological clinical equivalence for phantom materials in carbon ion therapy. Medical Physics. 51(7): 5154--5158
  5. Brooks FM, Glenn MC, Hernandez V, Saez J, Mehrens H, Pollard-Larkin JM, Howell RM, Peterson CB, et al. A radiotherapy community data‐driven approach to determine which complexity metrics best predict the impact of atypical TPS beam modeling on clinical dose calculation accuracy. Journal of Applied Clinical Medical Physics. 25(5): e14318.
  6. Court LE, Aggarwal A, Jhingran A, Naidoo K, Netherton T, Olanrewaju A, Peterson CB, Parkes J, et al. (2024) Artificial intelligence–based radiotherapy contouring and planning to improve global access to cancer care. JCO Global Oncology. 10: e2300376.
  7. He Y, Cazoulat G, Wu C, Svensson S, Almodovar-Abreu L, Rigaud B, McCollum E, Peterson CB, Wooten ZT, et al. (2024) Quantifying the effect of 4-dimensional computed tomography–based deformable dose accumulation on representing radiation damage for patients with locally advanced non-small cell lung cancer treated with standard-fractionated intensity-modulated radiation therapy. International Journal of Radiation Oncology*Biology*Physics. 118(1): 231--241.
  8. Mehrens H, Molineu A, Hernandez N, Court L, Howell R, Jaffray D, Peterson CB, Pollard-Larkin J, Kry SF. (2023) Characterizing the interplay of treatment parameters and complexity and their impact on performance on an IROC IMRT phantom using machine learning. Radiotherapy and Oncology. 182: 109577.
  9. Ryosuke T, Cortes AC, Zaske AM, Williams M, Dupuis C, Tanaka T, Nishiofuku H, Chintalapani G, Peterson CB, Avritscher R. (2023) Liver cancer vascularity driven by extracellular matrix stiffness: implications for imaging research. Investigative Radiology. 58(12): 894--902.
  10. Ahmad M, Sun P, Peterson CB, Anderson MR, Liu X, Morani AC, Jensen CT. (2023) Low pitch significantly reduces helical artifacts in abdominal CT. European Journal of Radiology. 166: 110977.
  11. Gronberg MP, Jhingran A, Netherton TJ, Gay SS, Cardenas CE, …, Peterson CB, Vazquez I, Whitaker TJ, Wooten ZT, Yang M, Court LE. (2023) Deep learning–based dose prediction to improve the plan quality of volumetric modulated arc therapy for gynecologic cancers. Medical Physics. 50(11): 6639--6648.
  12. Glenn MC, Brooks F, Peterson CB, Howell RM, Followill DS, et al. (2022) Photon beam modeling variations predict errors in IMRT dosimetry audits. Radiotherapy and Oncology. 166: 8-14.
  13. McCulloch M, Cazoulat G, Svensson S, Gryshkevych S, Rigaud B, Anderson B, …, Peterson CB, Balter P, Koay EJ, Brock KK. (2022) Leveraging deep learning-based segmentation and contours-driven deformable registration for dose accumulation in abdominal structures. Frontiers in Oncology. 12: 1015608.
  14. Owens CA, Rigaud B, Ludmir EB, Gupta AC, Shrestha S, Paulino AC, Smith SA, Peterson CB, et al. (2022) Development and validation of a population-based anatomical colorectal model for radiation dosimetry in late effects studies of survivors of childhood cancer. Radiotherapy and Oncology. 176: 118-126.
  15. Netherton T, Nguyen C, Cardenas CE, Chung C, Klopp AH, Colbert LE, Rhee DJ, Peterson CB, Howell R, Balter P, Court LE. (2022) An automated treatment planning framework for spinal radiotherapy and vertebral level second check. International Journal of Radiation Oncology*Biology*Physics. 114(3): 516-528.
  16. Hartzell S, Guan F, Taylor P, Peterson CB, Taddei P, Kry S. (2021) Uncertainty in tissue equivalent proportional counter assessments of microdosimetry and RBE estimates in carbon radiotherapy. Physics in Medicine & Biology. 66(15): 155018.
  17. He Y, Cazoulat G, Wu C, Peterson CB, McCulloch M, Anderson B, Pollard‐Larkin J, Balter P, Liao Z, Mohan R, Brock K. (2021) Geometric and dosimetric accuracy of deformable image registration between average-intensity images for 4DCT-based adaptive radiotherapy for non-small cell lung cancer. Journal of Applied Clinical Medical Physics. 22(8): 156-67.
  18. Colen RR, Rolfo C, Ak M, Ayoub M, Ahmed S, Elshafeey N, Mamindla P, Zinn PO, Ng C, Vikram R, Bakas S, Peterson CB, et al. (2021) Radiomics analysis for predicting pembrolizumab response in patients with advanced rare cancers. Journal for Immunotherapy of Cancer. 9(4): e001752.
  19. Olanrewaju A, Court LE, Zhang L, Naidoo K, Burger H, …, Peterson CB, Benson KR, du Toit M, van Reenen R, Beadle BM. (2021) Clinical acceptability of automated radiation treatment planning for head and neck cancer using the radiation planning assistant. Practical Radiation Oncology 11(3): 177-184
  20. Rigaud B, Anderson BM, Yu ZH, Gobeli M, Cazoulat G, …, Peterson CB, Court LE, Svensson S, Löfman F, Klopp AH, Brock KK. (2021) Automatic segmentation using deep learning to enable online dose optimization during adaptive radiation therapy of cervical cancer. International Journal of Radiation Oncology*Biology*Physics 109(4): 1096-1110.
  21. Vassiliev ON, Peterson CB, Chang JY, Mohan R. (2021) Using FFF beams to improve the therapeutic ratio of lung SBRT. Journal of Radiotherapy in Practice. 20(4): 419-425.
  22. Netherton TJ, Rhee DJ, Cardenas CE, Chung C, Klopp AH, Peterson CB, Howell RM, Balter PA, Court LE. (2020) Evaluation of a multiview architecture for automatic vertebral labeling of palliative radiotherapy simulation CT images. Medical Physics. 47(11): 5592-5608.
  23. Branco D, Kry S, Taylor P, Rong J, Zhang X, Peterson CB, Frank S, Followill D. (2020) Development of a stereoscopic CT metal artifact management algorithm using gantry angle tilts for head and neck patients. Journal of Applied Clinical Medical Physics. 21(8): 120-130.
  24. Glenn MC, Peterson CB, Howell RM, Followill DS, Pollard-Larkin JM, Kry SF. (2020) Sensitivity of IROC phantom performance to radiotherapy treatment planning system beam modeling parameters based on community‐driven data. Medical Physics. 47(10): 5250-5259.
  25. McCulloch MM, Cazoulat G, Ford AC, Elgohari B, Bahig H, …, Peterson CB, et al. (2020) Biomechanical modeling of radiation dose-induced volumetric changes of the parotid glands for deformable image registration. Physics in Medicine and Biology. 65(16): 165017.
  26. Edward SS, Alvarez PE, Taylor PA, Molineu HA, Peterson CB, Followill DS, Kry SF. (2020) Differences in the patterns of failure between IROC lung and spine phantom irradiations. Practical Radiation Oncology. 10(5): 372-381.
  27. Edward SS, Glenn MC, Peterson CB, Balter PA, Pollard-Larkin JM, Howell RM, Followill DS, Kry SF. (2020) Dose calculation errors as a component of failing IROC lung and spine phantom irradiations. Medical Physics.
  28. Vassiliev ON, Peterson CB, Grosshans DR, Mohan R. (2020) A simple model for calculating relative biological effectiveness of X-rays and gamma radiation in cell survival. The British Journal of Radiology. 93: 20190949.
  29. Tinoco M, Waga E, Tran K, Vo H, Baker J, Hunter R, Peterson CB, Taku N, Court L. (2020) RapidPlan development of VMAT plans for cervical cancer patients in low- and middle-income countries. Medical Dosimetry. 45(2): 172-178.
  30. Chen C, Hung G, Shen T, Peterson CB, Pan T. (2020) Comparison of ejection fraction calculation between CT and SPECT at high heart rate - a dynamic cardiac phantom study. Journal of Nuclear Cardiology.
  31. Rigaud B, Cazoulat G, Vedam S, Venkatesan AM, Peterson CB, Taku N, Klopp AH, Brock KK. (2020) Modeling complex deformations of the sigmoid colon between external beam radiotherapy and brachytherapy images of cervical cancer. International Journal of Radiation Oncology * Biology * Physics. 106(5): 1084-1094.
  32. Glenn MC, Peterson CB, Followill DS, Howell RM, Pollard-Larkin JM, Kry SF. (2020) Reference dataset of users' photon beam modeling parameters for the Eclipse, Pinnacle, and RayStation treatment planning systems. Medical Physics. 47(1): 282-288.
  33. Meier JG, Erasmus JJ, Gladish GW, Peterson CB, Diab RH, Mawlawi OR. (2020) Characterization of continuous bed motion effects on patient breathing and respiratory motion correction in PET/CT imaging. Journal of Applied Clinical Medical Physics. 21(1): 158-165.
  34. Vassiliev ON, Peterson CB, Cao W, Grosshans DR, Mohan R. (2019) Systematic microdosimetric data for protons of therapeutic energies calculated with Geant4-DNA. Physics in Medicine & Biology. 64(21): 215018.
  35. Rhee DJ, Cardenas CE, Elhalawani H, McCarroll R, Zhang L, Yang J, Garden AS, Peterson CB, Beadle BM, Court LE. (2019) Automatic detection of contouring errors using convolutional neural networks. Medical Physics. 46(11): 5086-5097
  36. McCulloch M, Anderson B, Cazoulat G, Peterson CB, Mohamed A, Volpe S, et al. (2019) Biomechanical modeling of neck flexion for deformable alignment of the salivary glands in head and neck cancer images. Physics in Medicine and Biology. 64(17): 175018.
  37. Kry S, Glenn M, Peterson CB, Branco D, Mehrens H, Steinmann A, Followill D. (2019) Independent recalculation outperforms traditional measurement-based IMRT QA methods in detecting unacceptable plans. Medical Physics. 46(8): 3700-3708.
  38. McCarroll RE, Beadle BM, Balter PA, Burger H, Cardenas CE, Dalvie S, …, Peterson CB, Vorster K, Wetter J, Zhang L, Court LE, Yang J. (2018) Retrospective validation and clinical implementation of automated contouring of organs at risk in the head and neck: a step toward automated radiation treatment planning for low- and middle-income countries. Journal of Global Oncology.
  39. Rubinstein A, Gay S, Peterson CB, Kingsley CV, Tailor RC, Pollard-Larkin JM, Melancon AD, Followill DS, Court LE. (2018) Radiation-induced lung toxicity in mice irradiated in a strong magnetic field. PLoS ONE. 13(11): e0205803.
  40. Owens CA, Peterson CB, Tang C, Koay EJ, Yu W, Mackin DS, Li J, Salehpour MR, Fuentes DT, Court LE, and Yang J. (2018) Lung tumor segmentation methods: impact on the uncertainty of radiomics features for non-small cell lung cancer. PLoS ONE. 13(10): e0205003.
  41. Kisling KD, Ger RB, Netherton TJ, Cardenas CE, Owens CA, Anderson BM, …, Peterson CB, Court LE, Dube S. (2018) A snapshot of medical physics practice patterns. Journal of Applied Clinical Medical Physics. 19(6): 306-315.
  42. Vassiliev ON, Kry SF, Wang HC, Peterson CB, Chang JY, Mohan R. (2018) Radiotherapy of lung cancers: FFF beams improve dose coverage at tumor periphery compromised by electronic disequilibrium. Physics in Medicine & Biology.
  43. Kry S, Peterson CB, Howell R, Izewska J, Lye J, Clark C, et al. (2018) Remote beam output audits: a global assessment of results out of tolerance. Physics & Imaging in Radiation Oncology. 7: 39-44.
  44. Court LE, Kisling K, McCarroll R, Zhang L, Yang J, Simonds H, …, Peterson CB, Beadle B. (2018) Radiation planning assistant – A streamlined, fully automated radiotherapy treatment planning system. The Journal of Visualized Experiments. 134: e57411.
Statistical applications and collaboration: Immunotherapy

  1. Manzano JM, Sahar H, Aldrich J, Lu M, Shoukier M, Peterson CB, et al. (2024) Treatment patterns and outcomes of high-grade immune checkpoint inhibitor-related pneumonitis in an oncology hospitalist service. Supportive Care in Cancer. 32(3): 160.
  2. Zhou Y, Medik Y, Patel B, Zamler D, Chen S, Chapman T, …, Khan MA, Peterson CB, et al. (2023) Intestinal toxicity to CTLA-4 blockade driven by IL-6 and myeloid infiltration. Journal of Experimental Medicine. 220(2): e20221333.
  3. Mendoza TR, Hong DS, Peterson CB, Stephen B, Dumbrava E, et al. (2022) Patient-reported symptom burden in patients with rare cancers receiving pembrolizumab in a phase II clinical trial. Scientific Reports. 12(1): 14367
  4. Mendoza T, Sheshadri A, Altan M, Hess K, George G, Stephen B, Castillo L, Rodriguez E, Gong J, Peterson CB, Ahnert JR, et al. (2020) Evaluating the psychometric properties of the Immunotherapy module of the MD Anderson Symptom Inventory. Journal for Immunotherapy of Cancer. 8(2): e000931.
Statistical applications and collaboration: Leukemia

  1. Gordon MJ, Jones JE, George B, Peterson CB, Burger JA, et al. (2023) Long-term outcomes in patients with chronic lymphocytic leukemia treated with ibrutinib: Focus on hypertension and cardiovascular toxicity. Cancer. 129(14): 2192-2200.
  2. Thompson PA, Keating MJ, Ferrajoli A, Jain N, Peterson CB, et al. (2023) Venetoclax consolidation in high-risk CLL treated with ibrutinib for ≥1 year achieves a high rate of undetectable MRD. Leukemia. 37: 1444-1453.
  3. Thompson PA, Bazinet A, Wierda WG, Tam CS, O’Brien SM, Saha S, Peterson CB, Plunkett W, Keating MJ. (2023) Sustained remissions in CLL after frontline FCR treatment with very long-term follow-up. Blood. 142(21): 1784--1788.
  4. Chien KC, Peterson CB, Young E, Chihara D, Manasanch E, Ramdial J, Thompson PA. (2023) Outcomes of breakthrough COVID-19 infections in patients with hematologic malignancies. Blood Advances. bloodadvances.2022008827.
  5. Thompson P, Jiang X, Banerjee P, Basar R, Garg N, Chen K, Kaplain M, Nunez Cortes A, Ferrajoli A, Keating M, Peterson CB, Andreeff M, Rezvani K, Wierda W. (2022) A phase two study of high-dose blinatumomab in Richter’s syndrome. Leukemia. 36: 2228-2232.
  6. Thompson PA, Srivastava J, Peterson CB, Strati P, Jorgensen JL, Hether T, et al. (2019) Minimal residual disease undetectable by next-generation sequencing predicts improved outcome in CLL after chemoimmunotherapy. Blood. 134(22): 1951-1959.
  7. Strati P, Takahashi K, Peterson CB, Keating MJ, Thompson PA, Daver NG, et al. (2019) Efficacy and predictors of response of lenalidomide and rituximab in patients with treatment-naive and relapsed CLL. Blood Advances. 3(9): 1533-1539.
  8. Thompson PA, Peterson CB, Strati P, Jorgensen J, Keating MJ, O’Brien SM, et al. (2018) Serial minimal residual disease (MRD) monitoring during first-line FCR treatment for CLL may direct individualized therapeutic strategies. Leukemia. 32(11):2388-2398.
Statistical applications and collaboration: Ovarian cancer

  1. Steenbeek MP, van Bommel MH, intHout J, Peterson CB, Simons M, et al. (2023) TUBectomy with delayed oophorectomy as an alternative to risk-reducing salpingo-oophorectomy in high-risk women to assess the safety of prevention: the TUBA-WISP II study protocol. International Journal of Gynecologic Cancer. 33(6): 982--987.
  2. Swisher EM, Rayes N, Bowen D, Peterson CB, Norquist BM, et al. (2023) Remotely delivered cancer genetic testing in the Making Genetic Testing Accessible (MAGENTA) trial. JAMA Oncology. 9(11): 1547-1555.
  3. Coffin T, Bowen D, Swisher E, Lu K, Rayes N, …, Peterson CB, et al. (2022) An accessible communication system for population-based genetic testing: development and usability study. JMIR Formative Research. 6(10): e34055.
  4. Coffin T, Bowen D, Lu K, Swisher E, Rayes N, …, Peterson CB, et al. (2022) Using social media to facilitate communication about women’s testing: tool validation study. JMIR Formative Research. 6(9): e35035.
  5. Rayes N, Bowen DJ, Coffin T, Nebgen D, Peterson CB, Munsell MF, et al. (2019) MAGENTA (Making Genetic testing accessible): a prospective randomized controlled trial comparing online genetic education and telephone genetic counseling for hereditary cancer genetic testing. BMC Cancer. 19:648.
Statistical applications and collaboration: Kidney cancer

  1. Liu XD, Zhang YT, McGrail DJ, Zhang X, Lam T, Hoang A, Hasanov E, Manyam G, Peterson CB, et al. (2023) SETD2 loss and ATR inhibition synergize to promote cGAS signaling and immunotherapy response in renal cell carcinoma. Clinical Cancer Research. 29(19): 4002-4015.
  2. Liu X, Kong W, Peterson CB, McGrail DJ, Hoang, et al. (2020) PBRM1 loss defines a nonimmunogenic tumor phenotype associated with checkpoint inhibitor resistance in renal carcinoma. Nature Communications. 11(1): 1-14.
Statistical applications and collaboration: Head and neck cancer

  1. Barbon CE, Peterson CB, Moreno AC, Lai SY, Reddy JP, Sahli A, Martino R, Johnson FM, Fuller CD, Hutcheson KA. (2022) Adhering to eat and exercise status during radiotherapy for oropharyngeal cancer for prevention and mitigation of radiotherapy-associated dysphagia. JAMA Otolaryngology–Head & Neck Surgery. 148(10): 956-964.
  2. Barbon CE, Yao CM, Peterson CB, Moreno AC, Goepfert RP, Johnson FM, Chronowski GM, Fuller CD, Gross ND, Hutcheson KA. (2022) Swallowing after primary TORS and unilateral or bilateral radiation for low-to intermediate-risk tonsil cancer. Otolaryngology–Head and Neck Surgery. 167(3): 484-493
Statistical applications and collaboration: Lung cancer

  1. Francisco-Cruz A, Rocha P, Reuben A, Krishnan SN, Das P, …, Wistuba II, Peterson CB, Zhang J. (2023) Analysis of immune intratumor heterogeneity highlights immunoregulatory and coinhibitory lymphocytes as hallmarks of recurrence in stage I non–small cell lung cancer. Modern Pathology. 36(1): 100028.
  2. de Miguel-Perez D, Russo A, Arrieta O, Ak M, Barron F, Gunasekaran M, Mamindla P, Lara-Mejia L, Peterson CB, et al. (2022) Extracellular vesicle PD-L1 dynamics predict durable response to immune-checkpoint inhibitors and survival in patients with non-small cell lung cancer. Journal of Experimental & Clinical Cancer Research. 41(1): 1--14.
Other statistical applications and collaboration in cancer

  1. Jin Y, Miyama T, Brown A, Hayase T, Song X, …, Peterson CB, …, Jenq RR. (2024) Tsyn-seq: a T cell synapse-based antigen identification platform. Cancer Immunology Research. 12(5): 530-543.
  2. Murphy BR, Dailey Garnes NJ, Hwang H, Peterson CB, Garey KW, Okhuysen P. Increased prevalence of Clostridioides difficile infection among pediatric oncology patients: risk factors for infection and complications. The Pediatric Infectious Disease Journal. 43(2): 136-141.
  3. Fahrmann JF, Wasylishen AR, Pieterman CR, Irajizad E, Vykoukal J, Wu R, Dennison JB, Peterson CB, et al. (2023) Blood-based proteomic signatures associated with MEN1-related duodenopancreatic neuroendocrine tumor progression. The Journal of Clinical Endocrinology & Metabolism. 108(12): 3260-3271.
  4. Lim B, Peterson CB, Davis A, Cho E, Pearson T, Liu H, Hwang M, Ueno NT, Lee J. (2021) ONC201 and an MEK inhibitor trametinib synergistically inhibit the growth of triple-negative breast cancer cells. Biomedicines. 9(10):1410.
  5. McGrail DJ, Pilié PG, Dai H, Lam TN, Liang Y, Voorwerk L, Kok M, Zhang XH, Rosen JM, Heimberger AB, Peterson CB, Jonasch E, Lin S. (2021) Replication stress response defects are associated with response to immune checkpoint blockade in nonhypermutated cancers. Science Translational Medicine. 13(617): eabe6201.
  6. Fahrmann JF, Wasylishen AR, Pieterman CR, Irajizad E, Vykoukal J, Murage E, Wu R, Dennison JB, Krishna H, Peterson CB, Lozano G, et al. (2021) A blood-based polyamine signature associated with MEN1 duodenopancreatic neuroendocrine tumor progression. The Journal of Clinical Endocrinology & Metabolism. 106(12): e4969-80.
  7. Bradley SD, Talukder AH, Lai I, Davis R, Alvarez H, …, Peterson CB, et al. (2020) Vestigial-like 1 is a shared targetable cancer-placenta antigen expressed by pancreatic and basal-like breast cancers. Nature Communications. 11(1): 1-12.
  8. Vykoukal J, Fahrmann JF, Gregg JR, Tang Z, Basourakos S, …, Peterson CB, Davis JW, Kim J, Hanash S, Thompson TC. (2020) Caveolin-1-mediated sphingolipid oncometabolism underlies a metabolic vulnerability of prostate cancer. Nature Communications. 11(1): 1-6.
  9. Wu X, Park M, Sarbassova DA, Ying H, Lee MG, Bhattacharya R, Ellis L, Peterson CB, Hung MC, Lin HK, Bersimbaev RI, Song MS, Sarbassov, DD. (2020) A chirality-dependent action of vitamin C in suppressing KRAS mutant tumor growth by the oxidative combination: rationale for cancer therapeutics. International Journal of Cancer. 146(10): 2822-2828.
  10. Chari NS, Ivan C, Le X, Li J, Mijiti A, Patel AA, Osman AA, Peterson CB, et al. (2020) Disruption of TP63-miR-27a* feedback loop by mutant TP53 in head and neck cancer. Journal of the National Cancer Institute. 112(3): 266-277.
  11. Fahrmann JF, Vykoukal J, Fleury A, Tripathi S, Dennison JB, Murage E, …, Peterson CB, Katayama H, Disis ML, Arun B, Hanash S. (2020) Association between plasma diacetylspermine and tumor spermine synthase with outcome in triple negative breast cancer. Journal of the National Cancer Institute. 112(6): 607-616.
Statistical applications and collaborations: Genetics, genomics, and proteomics

  1. Jasinska AJ, Zelaya I, Service SK, Peterson CB, Cantor RM, Choi, O., et al. (2017) Genetic variation and gene expression across multiple tissues and developmental stages in a non-human primate. Nature Genetics. 49: 1714-1721.
  2. GTEx Consortium [including Peterson CB]. (2017) Genetic effects on gene expression across human tissues. Nature. 550: 204—213.
  3. Peterson CB, Service S, Jasinska A, Gao F, Zelaya I, Teshiba T, Bearden C, Reus V, Macaya G, López-Jaramillo C, Bogomolov M, Benjamini Y, Eskin E, Coppola G, Freimer N, Sabatti C. (2016) Characterization of expression quantitative trait loci in pedigrees from Colombia and Costa Rica ascertained for bipolar disorder. PLOS Genetics. 12(5): e1006046.
  4. Rembach A, Stingo FC, Peterson CB, Vannucci M, Do K, Wilson WJ, Macaulay SL, Ryan TM, Martins RN, Ames D, Masters CL, Doecke JD, AIBL Research Group. (2015) Bayesian graphical network analyses reveal complex biological interactions specific to Alzheimer’s Disease. Journal of Alzheimer's Disease. 10(4): P796—P797.
  5. Cowley AW, Moreno C, Jacob HJ, Peterson CB, Stingo FC, Ahn KW, Liu P, Vannucci M, Laud PW, Reddy P, Lazar J, Evans L, Yang C, Kurth T, Liang M. (2014) Characterization of biological pathways associated with a 1.37 Mbp genomic region protective of hypertension in Dahl S rats<. Physiological Genomics. 46(11): 398—410.
  6. Swartz MD, Peterson CB, Lupo PJ, Wu X, Forman MR, Spitz MR, Hernandez LM, Vannucci M, Shete S. (2013) Investigating multiple candidate genes and nutrients in the folate metabolism pathway to detect genetic and nutritional risk factors for lung cancer. PLoS ONE. 8(1): e53475.

Book chapters

  1. Peterson CB, Stingo F. (2021) Bayesian estimation of single and multiple graphs. In Handbook of Bayesian Variable Selection, MG Tadesse and M Vannucci (Eds). Chapman and Hall/CRC. 327-348.
  2. Peterson CB, Swartz MD, Shete S, Vannucci M. (2013) Bayesian model averaging for genetic association studies. In Advances in Statistical Bioinformatics: Models and Integrative Inference for High-Throughput Data, K Do, Z Qin, and M Vannucci (Eds). Cambridge University Press, 208—223.

Other papers and discussions

  1. Osborne N, Peterson CB, Vannucci M. (2020) Network estimation of compositional data. In Book of Short Papers - Italian Statistical Society 2020, Pollice A, Salvati N, Schirripa Spagnolo F (Eds). Pearson, 28-33.
  2. Peterson CB, Stingo FC. (2013) Invited discussion of “On the prior and posterior distributions used in graphical modelling” by Marco Scutari. Bayesian Analysis. 8(3): 539—542.

Dissertation

  1. Peterson CB. (2013) Bayesian graphical models for biological network inference. Doctoral thesis, Rice University.