Giovanni Parmigiani

Giovanni Parmigiani

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Giovanni Parmigiani

Publications by authors named "Giovanni Parmigiani"

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Tree-Weighting for Multi-Study Ensemble Learners.

Pac Symp Biocomput 2020 ;25:451-462

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA,

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January 2020

Frequentist operating characteristics of Bayesian optimal designs via simulation.

Stat Med 2019 Sep 19;38(21):4026-4039. Epub 2019 Jun 19.

Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts.

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http://dx.doi.org/10.1002/sim.8279DOI Listing
September 2019

Performance of breast cancer risk assessment models in a large mammography cohort.

J Natl Cancer Inst 2019 Sep 26. Epub 2019 Sep 26.

Division of Surgical Oncology, Massachusetts General Hospital, Boston, MA.

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http://dx.doi.org/10.1093/jnci/djz177DOI Listing
September 2019

Clinical Factors Associated With Gastric Cancer in Individuals With Lynch Syndrome.

Clin Gastroenterol Hepatol 2019 Jul 15. Epub 2019 Jul 15.

Division of Population Sciences, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts. Electronic address:

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http://dx.doi.org/10.1016/j.cgh.2019.07.012DOI Listing
July 2019

Multi-study factor analysis.

Biometrics 2019 03 8;75(1):337-346. Epub 2019 Mar 8.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.

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http://doi.wiley.com/10.1111/biom.12974
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http://dx.doi.org/10.1111/biom.12974DOI Listing
March 2019

Family History of Breast or Prostate Cancer and Prostate Cancer Risk.

Clin Cancer Res 2018 12 6;24(23):5910-5917. Epub 2018 Aug 6.

Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.

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http://dx.doi.org/10.1158/1078-0432.CCR-18-0370DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6279573PMC
December 2018

Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration.

iScience 2018 Nov 2;9:451-460. Epub 2018 Nov 2.

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.isci.2018.10.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6249353PMC
November 2018

A Clinical Decision Support Tool to Predict Cancer Risk for Commonly Tested Cancer-Related Germline Mutations.

J Genet Couns 2018 09 2;27(5):1187-1199. Epub 2018 Mar 2.

Division of Surgical Oncology, Massachusetts General Hospital, Boston, MA, USA.

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http://link.springer.com/10.1007/s10897-018-0238-4
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http://dx.doi.org/10.1007/s10897-018-0238-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6240422PMC
September 2018

Efficient computation of the joint probability of multiple inherited risk alleles from pedigree data.

Genet Epidemiol 2018 09 25;42(6):528-538. Epub 2018 Jun 25.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.

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http://dx.doi.org/10.1002/gepi.22130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129424PMC
September 2018

The impact of different sources of heterogeneity on loss of accuracy from genomic prediction models.

Biostatistics 2018 Sep 6. Epub 2018 Sep 6.

Graduate School of Public Health and Health Policy, Institute for Implementation Science in Population Health, City University of New York, 55 W 125th St, New York, NY, USA.

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http://dx.doi.org/10.1093/biostatistics/kxy044DOI Listing
September 2018

Adding experimental arms to platform clinical trials: randomization procedures and interim analyses.

Biostatistics 2018 04;19(2):199-215

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Ave., Boston, MA 02115, USA and Department of Biostatistics, Harvard T. H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA.

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http://dx.doi.org/10.1093/biostatistics/kxx030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5862294PMC
April 2018

Integrative factor analysis - An unsupervised method for quantifying cross-study consistency of gene expression data.

Genomics 2018 03 4;110(2):80-88. Epub 2017 Sep 4.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S08887543173007
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http://dx.doi.org/10.1016/j.ygeno.2017.08.009DOI Listing
March 2018

Training replicable predictors in multiple studies.

Proc Natl Acad Sci U S A 2018 03 12;115(11):2578-2583. Epub 2018 Mar 12.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215;

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http://dx.doi.org/10.1073/pnas.1708283115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5856504PMC
March 2018

Propensity scores with misclassified treatment assignment: a likelihood-based adjustment.

Biostatistics 2017 Oct;18(4):695-710

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Statistics, Tel Aviv University, Tel Aviv, Israel and St. Luke's Radiation Oncology Associates, St. Luke's Regional Cancer Center, and Whiteside Institute for Clinical Research / University of Minnesota Duluth, Duluth, MN, USA.

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http://dx.doi.org/10.1093/biostatistics/kxx014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5862346PMC
October 2017

Bayesian response-adaptive designs for basket trials.

Biometrics 2017 09 17;73(3):905-915. Epub 2017 Feb 17.

Dana-Farber Cancer Institute, Boston, Massachusetts.

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http://dx.doi.org/10.1111/biom.12668DOI Listing
September 2017

Designing Clinical Trials That Accept New Arms: An Example in Metastatic Breast Cancer.

J Clin Oncol 2017 Sep 22;35(27):3160-3168. Epub 2017 May 22.

Steffen Ventz, University of Rhode Island, Kingstown, RI; Brian M. Alexander, Giovanni Parmigiani, Richard D. Gelber, and Lorenzo Trippa, Dana-Farber Cancer Institute; Brian M. Alexander and Richard D. Gelber, Harvard Medical School; Giovanni Parmigiani, Richard D. Gelber, and Lorenzo Trippa, Harvard TH Chan School of Public Health; Richard D. Gelber, Frontier Science Foundation, Boston, MA.

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http://dx.doi.org/10.1200/JCO.2016.70.1169DOI Listing
September 2017

Nonparametric Adjustment for Measurement Error in Time-to-Event Data: Application to Risk Prediction Models.

J Am Stat Assoc 2018 14;113(521):14-25. Epub 2017 Sep 14.

Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02115.

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http://dx.doi.org/10.1080/01621459.2017.1311261DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6077989PMC
September 2017

Role of stem-cell divisions in cancer risk.

Nature 2017 08;548(7666):E13-E14

Ludwig Center &Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, 1650 Orleans Street St, Baltimore, Maryland 21205, USA.

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http://dx.doi.org/10.1038/nature23302DOI Listing
August 2017

Leveraging molecular datasets for biomarker-based clinical trial design in glioblastoma.

Neuro Oncol 2017 Jul;19(7):908-917

Department of Radiation Oncology, Department of Pathology, Center for Neuro-Oncology, Dana-Farber/Brigham & Women's Cancer Center (DF/BWCC), Harvard Medical School, Boston, Massachusetts; Department of Biostatistics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts; Accelerate Brain Cancer Cure (ABC2), Washington, DC; Harvard Program in Therapeutic Science, Harvard Medical School, Boston, Massachusetts.

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http://dx.doi.org/10.1093/neuonc/now312DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570228PMC
July 2017

Model averaged double robust estimation.

Biometrics 2017 06 28;73(2):410-421. Epub 2016 Nov 28.

Harvard T.H. Chan School of Public Health, Boston, MA, USA.

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http://dx.doi.org/10.1111/biom.12622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5466877PMC
June 2017

Combinatorial Mixtures of Multiparameter Distributions: An Application to Bivariate Data.

Int J Biostat 2017 02 16;13(1). Epub 2017 Feb 16.

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http://dx.doi.org/10.1515/ijb-2015-0064DOI Listing
February 2017

The Doppelgänger Effect: Hidden Duplicates in Databases of Transcriptome Profiles.

J Natl Cancer Inst 2016 11 5;108(11). Epub 2016 Jul 5.

Affiliations of authors: City University of New York School of Public Health, New York, NY (LW, MRa); Novartis Institutes for BioMedical Research, Cambridge, MA (MRi); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute/Harvard Medical School, Boston, MA (GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB).

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http://dx.doi.org/10.1093/jnci/djw146DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5241903PMC
November 2016

Adaptive Randomization of Neratinib in Early Breast Cancer.

N Engl J Med 2016 10;375(16):1593-4

Dana–Farber Cancer Institute, Boston, MA

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http://dx.doi.org/10.1056/NEJMc1609993DOI Listing
October 2016

Penetrance of ATM Gene Mutations in Breast Cancer: A Meta-Analysis of Different Measures of Risk.

Genet Epidemiol 2016 07 25;40(5):425-31. Epub 2016 Apr 25.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1002/gepi.21971DOI Listing
July 2016

I-SPY 2--A Glimpse of the Future of Phase 2 Drug Development?

N Engl J Med 2016 Jul;375(1):7-9

From the Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and the Department of Biostatistics, Harvard T.H. Chan School of Public Health - both in Boston.

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http://dx.doi.org/10.1056/NEJMp1602256DOI Listing
July 2016

Optimal Bayesian adaptive trials when treatment efficacy depends on biomarkers.

Biometrics 2016 06 17;72(2):414-21. Epub 2015 Nov 17.

Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, U.S.A.

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http://dx.doi.org/10.1111/biom.12437DOI Listing
June 2016

A two-stage approach to genetic risk assessment in primary care.

Breast Cancer Res Treat 2016 Jan 19;155(2):375-83. Epub 2016 Jan 19.

Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, USA.

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http://dx.doi.org/10.1007/s10549-016-3686-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4742331PMC
January 2016

Accounting for uncertainty in confounder and effect modifier selection when estimating average causal effects in generalized linear models.

Biometrics 2015 Sep 20;71(3):654-65. Epub 2015 Apr 20.

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, U.S.A.

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http://dx.doi.org/10.1111/biom.12315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4575246PMC
September 2015

Combining progression-free survival and overall survival as a novel composite endpoint for glioblastoma trials.

Neuro Oncol 2015 Aug 7;17(8):1106-13. Epub 2015 Jan 7.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts (L.T., G.P.); Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts (L.T., G.P.); Center for Neuro-Oncology Dana-Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, Massachusetts, (P.Y.W., B.M.A.); Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, Massachusetts (B.M.A.); Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (D.A.B.).

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http://dx.doi.org/10.1093/neuonc/nou345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4490868PMC
August 2015

Recent Enhancements to the Genetic Risk Prediction Model BRCAPRO.

Cancer Inform 2015 10;14(Suppl 2):147-57. Epub 2015 May 10.

Department of Mathematical Sciences, University of Texas at Dallas, Richardson, TX, USA.

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http://dx.doi.org/10.4137/CIN.S17292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4428390PMC
May 2015

BRCA1 recruitment to transcriptional pause sites is required for R-loop-driven DNA damage repair.

Mol Cell 2015 Feb;57(4):636-647

Department of Genetics, Harvard Medical School, Boston, MA 02215, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2015.01.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351672PMC
February 2015

Only three driver gene mutations are required for the development of lung and colorectal cancers.

Proc Natl Acad Sci U S A 2015 Jan 22;112(1):118-23. Epub 2014 Dec 22.

Ludwig Center for Cancer Genetics and Therapeutics and Howard Hughes Medical Institute, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205

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http://dx.doi.org/10.1073/pnas.1421839112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4291633PMC
January 2015

Completing the results of the 2013 Boston marathon.

PLoS One 2014 11;9(4):e93800. Epub 2014 Apr 11.

Statistical and Applied Mathematical Sciences Institute, Research Triangle Park, North Carolina, United States of America; Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0093800PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3984103PMC
December 2014

Más-o-menos: a simple sign averaging method for discrimination in genomic data analysis.

Bioinformatics 2014 Nov 23;30(21):3062-9. Epub 2014 Jul 23.

Department of Statistics, University of Illinois at Urbana-Champaign, Champaign, IL 61820, Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, City University of New York School of Public Health, Hunter College, New York, NY 10035, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu488DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201155PMC
November 2014

Misreported family histories and underestimation of risk.

J Clin Oncol 2014 Nov 8;32(32):3682-3. Epub 2014 Sep 8.

Harvard School of Public Health; Dana-Farber Cancer Institute, Boston, MA.

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http://dx.doi.org/10.1200/JCO.2014.57.4848DOI Listing
November 2014

Differential and limited expression of mutant alleles in multiple myeloma.

Blood 2014 Nov 18;124(20):3110-7. Epub 2014 Sep 18.

Jerome Lipper Multiple Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA; Department of Hematology/Oncology, Boston Veterans Administration Healthcare System, West Roxbury, MA;

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http://dx.doi.org/10.1182/blood-2014-04-569327DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4231420PMC
November 2014

Recent BRCAPRO upgrades significantly improve calibration.

Cancer Epidemiol Biomarkers Prev 2014 Aug 2;23(8):1689-95. Epub 2014 Jun 2.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.

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http://dx.doi.org/10.1158/1055-9965.EPI-13-1364DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4119541PMC
August 2014

Statistical tools and R software for cancer driver probabilities.

Methods Mol Biol 2014 ;1101:113-34

Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA.

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http://dx.doi.org/10.1007/978-1-62703-721-1_7DOI Listing
June 2014

Cross-study validation for the assessment of prediction algorithms.

Bioinformatics 2014 Jun;30(12):i105-12

Leibniz Supercomputing Center, Garching, Department for Medical Informatics, Biometry and Epidemiology, Munich, Germany, Cambridge, MA, Dana-Farber Cancer Institute, Boston, Harvard School of Public Health, Boston, USA and City University of New York School of Public Health, Hunter College, New York, USALeibniz Supercomputing Center, Garching, Department for Medical Informatics, Biometry and Epidemiology, Munich, Germany, Cambridge, MA, Dana-Farber Cancer Institute, Boston, Harvard School of Public Health, Boston, USA and City University of New York School of Public Health, Hunter College, New York, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058929PMC
June 2014

Reclassification of predictions for uncovering subgroup specific improvement.

Stat Med 2014 May 18;33(11):1914-27. Epub 2013 Dec 18.

Department of Mathematical Sciences, University of Texas at Dallas, Richardson, TX 75080-3021, U.S.A.

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http://dx.doi.org/10.1002/sim.6077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4008681PMC
May 2014

Calibrated predictions for multivariate competing risks models.

Lifetime Data Anal 2014 Apr 31;20(2):234-51. Epub 2013 May 31.

Faculty of Industrial Engineering and Management, Technion-Israel Institute of Technology, Technion City, 32000 , Haifa, Israel,

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http://dx.doi.org/10.1007/s10985-013-9260-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3884047PMC
April 2014

Comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer.

J Natl Cancer Inst 2014 Apr 3;106(5). Epub 2014 Apr 3.

Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB).

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http://dx.doi.org/10.1093/jnci/dju049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580554PMC
April 2014

Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples.

J Natl Cancer Inst 2014 Apr 3;106(5). Epub 2014 Apr 3.

Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK).

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http://dx.doi.org/10.1093/jnci/dju048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580556PMC
April 2014

Modular network construction using eQTL data: an analysis of computational costs and benefits.

Front Genet 2014 26;5:40. Epub 2014 Feb 26.

Dana-Farber Cancer Institute and Harvard School of Public Health Boston, MA, USA.

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http://dx.doi.org/10.3389/fgene.2014.00040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3935177PMC
March 2014

Why tyrosine kinase inhibitor resistance is common in advanced gastrointestinal stromal tumors.

F1000Res 2013 9;2:152. Epub 2013 Jul 9.

Department of Biostatistics, Harvard School of Public Health, Boston MA, 02215, USA ; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston MA, 02215, USA.

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http://dx.doi.org/10.12688/f1000research.2-152.v1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892920PMC
February 2014

Integrative correlation: Properties and relation to canonical correlations.

J Multivar Anal 2014 Jan;123:270-280

Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, United States ; Department of Biostatistics, Harvard School of Public Health, United States.

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http://dx.doi.org/10.1016/j.jmva.2013.09.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4447241PMC
January 2014

Frailty Models for Familial Risk with Application to Breast Cancer.

J Am Stat Assoc 2013 Dec;108(504):1205-1215

Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, U.S.A.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3963469PMC
http://dx.doi.org/10.1080/01621459.2013.818001DOI Listing
December 2013

A decision-theory approach to interpretable set analysis for high-dimensional data.

Biometrics 2013 Sep 2;69(3):614-23. Epub 2013 Aug 2.

Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, U.S.A.

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http://dx.doi.org/10.1111/biom.12060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3927844PMC
September 2013

DeMix: deconvolution for mixed cancer transcriptomes using raw measured data.

Bioinformatics 2013 Aug 27;29(15):1865-71. Epub 2013 May 27.

Department of Bioinformatics and Computational Biology and Department of Biostatistics, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt301DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3841439PMC
August 2013

Biomarker-based adaptive trials for patients with glioblastoma--lessons from I-SPY 2.

Neuro Oncol 2013 Aug 14;15(8):972-8. Epub 2013 Jul 14.

Department of Radiation Oncology, Dana-Farber/Brigham and Women’s Cancer Center, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1093/neuonc/not088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3714161PMC
August 2013

Providing access to risk prediction tools via the HL7 XML-formatted risk web service.

Breast Cancer Res Treat 2013 Jul 23;140(1):187-93. Epub 2013 Jun 23.

Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02115, USA.

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http://dx.doi.org/10.1007/s10549-013-2605-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760685PMC
July 2013

Simplifying clinical use of the genetic risk prediction model BRCAPRO.

Breast Cancer Res Treat 2013 Jun 21;139(2):571-9. Epub 2013 May 21.

Department of Mathematical Sciences, FO 35, University of Texas at Dallas, Richardson, TX 75080-3021, USA.

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http://dx.doi.org/10.1007/s10549-013-2564-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3699331PMC
June 2013

Half or more of the somatic mutations in cancers of self-renewing tissues originate prior to tumor initiation.

Proc Natl Acad Sci U S A 2013 Feb 23;110(6):1999-2004. Epub 2013 Jan 23.

Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.

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http://dx.doi.org/10.1073/pnas.1221068110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3568331PMC
February 2013

The penetrance of ductal carcinoma in situ among BRCA1 and BRCA2 mutation carriers.

Breast Cancer Res Treat 2013 Jan 27;137(1):315-8. Epub 2012 Nov 27.

Department of Biostatistics, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215-5450, USA.

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http://dx.doi.org/10.1007/s10549-012-2345-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836600PMC
January 2013

Integrated genomic analyses identify ARID1A and ARID1B alterations in the childhood cancer neuroblastoma.

Nat Genet 2013 Jan 2;45(1):12-7. Epub 2012 Dec 2.

Ludwig Center for Cancer Genetics and Therapeutics, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1038/ng.2493DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3557959PMC
January 2013

Bayesian effect estimation accounting for adjustment uncertainty.

Biometrics 2012 Sep 24;68(3):661-71. Epub 2012 Feb 24.

Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA.

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http://dx.doi.org/10.1111/j.1541-0420.2011.01731.xDOI Listing
September 2012

Bayesian adaptive randomized trial design for patients with recurrent glioblastoma.

J Clin Oncol 2012 Sep 29;30(26):3258-63. Epub 2012 May 29.

Dana-Farber Cancer Institute, Harvard School of Public Health and Dana-Farber/ Brigham and Women's Cancer Center, Boston, MA 02215, USA.

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http://jco.ascopubs.org/content/early/2012/05/29/JCO.2011.39
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http://jco.ascopubs.org/cgi/doi/10.1200/JCO.2011.39.8420
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http://dx.doi.org/10.1200/JCO.2011.39.8420DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3434985PMC
September 2012

Estimation of sequencing error rates in short reads.

BMC Bioinformatics 2012 Jul 30;13:185. Epub 2012 Jul 30.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.

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http://dx.doi.org/10.1186/1471-2105-13-185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495688PMC
July 2012

MODELING DEPENDENT GENE EXPRESSION.

Ann Stat 2012 11;6(2):542-560. Epub 2012 Jun 11.

University of Texas, M.D. Anderson Cancer Center, Department of Gynecologic Oncology, Houston, Texas 7030, USA.

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http://dx.doi.org/10.1214/11-AOAS525DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5412732PMC
June 2012

Assessing the added value of breast tumor markers in genetic risk prediction model BRCAPRO.

Breast Cancer Res Treat 2012 May 21;133(1):347-55. Epub 2012 Jan 21.

Department of Biostatistics, School of Public Health, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107-2699, USA.

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http://dx.doi.org/10.1007/s10549-012-1958-zDOI Listing
May 2012

The predictive capacity of personal genome sequencing.

Sci Transl Med 2012 May 2;4(133):133ra58. Epub 2012 Apr 2.

Ludwig Center for Cancer Genetics and Therapeutics and The Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.

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http://dx.doi.org/10.1126/scitranslmed.3003380DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3741669PMC
May 2012

Report on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues.

BMC Cancer 2012 Mar 29;12:124. Epub 2012 Mar 29.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.

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http://dx.doi.org/10.1186/1471-2407-12-124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342119PMC
March 2012

Opportunities for the primary prevention of colorectal cancer in the United States.

Cancer Prev Res (Phila) 2012 Jan 28;5(1):138-45. Epub 2011 Sep 28.

Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1158/1940-6207.CAPR-11-0322DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3252472PMC
January 2012

OnionTree XML: a format to exchange gene-related probabilities.

J Biomol Struct Dyn 2011 Oct;29(2):417-23

Oncology Biostatistics and Bioinformatics, The Sidney Kimmel Comprehensive Cancer Center 550 North Broadway, Suite 1103, Baltimore, Maryland 21205, USA.

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http://dx.doi.org/10.1080/073911011010524994DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4856015PMC
October 2011

Integrating diverse genomic data using gene sets.

Genome Biol 2011 Oct 21;12(10):R105. Epub 2011 Oct 21.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02115, USA.

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http://dx.doi.org/10.1186/gb-2011-12-10-r105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3333775PMC
October 2011

Patient-oriented gene set analysis for cancer mutation data.

Genome Biol 2010 23;11(11):R112. Epub 2010 Nov 23.

Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N, Wolfe Street, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1186/gb-2010-11-11-r112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3156951PMC
June 2011

Modeling liquid association.

Biometrics 2011 Mar;67(1):133-41

McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA.

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http://dx.doi.org/10.1111/j.1541-0420.2010.01440.xDOI Listing
March 2011

CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data.

Bioinformatics 2010 Nov 1;26(21):2792-3. Epub 2010 Sep 1.

Department of Oncology and Division of Oncology, Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3025742PMC
November 2010

Estimating CDKN2A carrier probability and personalizing cancer risk assessments in hereditary melanoma using MelaPRO.

Cancer Res 2010 Jan 12;70(2):552-9. Epub 2010 Jan 12.

Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Stanford, California, USA.

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http://dx.doi.org/10.1158/0008-5472.CAN-09-2653DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2947347PMC
January 2010

Rejoinder.

J Am Stat Assoc 2009 12;104(488):1318-1323

Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205.

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http://dx.doi.org/10.1198/jasa.2009.ap09575DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3167382PMC
December 2009

The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations.

BMC Bioinformatics 2009 Aug 20;10:256. Epub 2009 Aug 20.

Department of Applied Mathematics and Statistics, The Johns Hopkins University, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1186/1471-2105-10-256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745389PMC
August 2009

Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays.

Ann Appl Stat 2008 Jun;2(2):687-713

Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205.

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http://dx.doi.org/10.1214/07-AOAS155DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2710854PMC
June 2008