Publications


Google Scholar citations


Under review

  1. Osborne N, Peterson CB, Vannucci M. (2020+) Latent network estimation and variable selection for compositional data via variational EM. Revised.
  2. Shi Y, Zhang L, Do K, Jenq RR, Peterson CB. (2020+) Bayesian approaches for flexible and informative clustering of microbiome data. Submitted.
  3. Zhang L, Shi Y, Do K, Peterson CB, Jenq RR. (2020+) ProgPermute: Progressive permutation for a dynamic representation of the robustness of microbiome discoveries. Revised.

Peer reviewed

Underlining denotes trainees supervised or co-supervised

Statistical methodology

  1. Ha MJ, Kim J, Galloway-Pena J, Do KA, Peterson CB. (2020) Compositional zero-inflated network estimation for microbiome data. BMC Bioinformatics. 21(21):1--20.
  2. Bogomolov M*, Peterson CB*, Benjamini Y, Sabatti C. (2020) Hypotheses on a tree: new error rates and testing strategies. Biometrika. *Authors contributed equally.
  3. Zhang L, Shi Y, Jenq RR, Do K, Peterson CB. (2020) Bayesian compositional regression with structured priors for microbiome feature selection. Biometrics.
  4. Shi Y, Zhang L, Do K, Peterson CB, Jenq RR. (2020) aPCoA: covariate adjusted principal coordinates analysis. Bioinformatics. 36(13): 4099-4101. Co-corresponding authors.
  5. 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.
  6. 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.
  7. 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.
  8. Kim J, Do K, Ha MJ, Peterson CB. (2019) Bayesian inference of hub nodes across multiple networks. Biometrics. 75(1): 172-182.
  9. 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.
  10. 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.
  11. 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.
  12. Peterson CB, Bogomolov M, Benjamini Y, Sabatti C. (2016) TreeQTL: hierarchical error control for eQTL findings. Bioinformatics. 32(16): 2556-2558.
  13. 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.
    See here for more information, including online supplement and implementation details.
  14. 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.
  15. Peterson CB, Stingo FC, Vannucci M. (2015) Bayesian inference of multiple Gaussian graphical models. Journal of the American Statistical Association. 110(509): 159—174.
  16. 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.
  17. 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.
Statistical applications and collaborations: Microbiome research

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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. 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: 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.
Statistical applications and collaborations: Medical physics

  1. Vassiliev ON, Peterson CB, Chang JY, Mohan R. (2020) Using FFF beams to improve the therapeutic ratio of lung SBRT. Journal of Radiotherapy in Practice. 1--7.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. Meier JG, Erasmus JJ, Gladish GW, Peterson CB, Diab RH, Mawlawi OR. (2019) Characterization of continuous bed motion effects on patient breathing and respiratory motion correction in PET/CT imaging. Journal of Applied Clinical Medical Physics.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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: Leukemia

  1. 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.
  2. 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.
  3. 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. 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 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: Cancer biomarkers and drug discovery

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.

Book chapters

  1. 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.