@article {803,
	title = {Quantifying the reliability of image replication studies: the image intraclass correlation coefficient (I2C2).},
	journal = {Cogn Affect Behav Neurosci},
	volume = {13},
	year = {2013},
	month = {2013 Dec},
	pages = {714-24},
	abstract = {<p>This article proposes the image intraclass correlation (I2C2) coefficient as a global measure of reliability for imaging studies. The I2C2 generalizes the classic intraclass correlation (ICC) coefficient to the case when the data of interest are images, thereby providing a measure that is both intuitive and convenient. Drawing a connection with classical measurement error models for replication experiments, the I2C2 can be computed quickly, even in high-dimensional imaging studies. A nonparametric bootstrap procedure is introduced to quantify the variability of the I2C2 estimator. Furthermore, a Monte Carlo permutation is utilized to test reproducibility versus a zero I2C2, representing complete lack of reproducibility. Methodologies are applied to three replication studies arising from different brain imaging modalities and settings: regional analysis of volumes in normalized space imaging for characterizing brain morphology, seed-voxel brain activation maps based on resting-state functional magnetic resonance imaging (fMRI), and fractional anisotropy in an area surrounding the corpus callosum via diffusion tensor imaging. Notably, resting-state fMRI brain activation maps are found to have low reliability, ranging from .2 to .4. Software and data are available to provide easy access to the proposed methods.</p>},
	keywords = {Adult, Brain, brain mapping, Computer Simulation, Female, Humans, Male, Models, Biological, Neuroimaging, Reproducibility of Results, Statistics as Topic},
	issn = {1531-135X},
	doi = {10.3758/s13415-013-0196-0},
	author = {Shou, H and Eloyan, A and Lee, S and Zipunnikov, V and Crainiceanu, A N and Nebel, N B and Caffo, B and Lindquist, M A and Crainiceanu, C M}
}
@article {calSimex,
	title = {Assessment of bias in experimentally measured diffusion tensor imaging parameters using SIMEX},
	journal = {Accepted in Magnetic Resonance in Medicine},
	year = {2012},
	author = {Lauzon, C and Crainiceanu, C and Caffo, B and Landman, B}
}
@article {landmanb,
	title = {Biological parametric mapping accounting for random regressors with regression calibration and model II regression},
	journal = {Accepted in Neuroimage},
	year = {2012},
	author = {Yang, X and Lauzon, C and Crainiceanu, C and Caffo, B and Resnick, S and Landman, B}
}
@article {thom,
	title = {Comparison of swab versus sponge methodology for the identification of acinetobacter baumannii from the hospital environment},
	journal = {Accepted in the Journal of Clinical Microbiology},
	year = {2012},
	author = {Thom, K and Howard, T and Sembajwe, S and Harris, A and Strassle, P and Caffo, B and Caroll, K and Johnson, J}
}
@article {ellignton,
	title = {Computerized lung sound analysis to improve the specificity of pediatric pneumonia in resource-poor settings},
	journal = {Accepted in the British Medical Journal Open},
	year = {2012},
	author = {Ellington, L and Gilman, R and Tielsch, J and Steinhoff, M and Figueroa, D and Rodriguez, S and Caffo, B and Tracey, B and West, J and Checkley, W}
}
@article {nicole,
	title = {Distribution of cell-free and cell-associated HIV surrogates in the female genital tract following simulated vaginal intercourse},
	journal = {Appeared online in the Journal of Infectious Diseases},
	year = {2012},
	author = {Louissaint, N and Nimmagadda, S and Bakshi, R and Du, Y and Macura, K and King, K and Wahl, R and Goldsmith, J and Caffo, B and Cao, Y and Anderson, J and Fuchs, E and Hendrix, C}
}
@article {james,
	title = {Genetic risk factors for longitudinal changes in structural MRI in former organolead workers},
	journal = {Accepted in the Journal of Aging Research},
	year = {2012},
	author = {James, B and Caffo, B and Stewart, W and Yousem, D and Davatzikos, C. and Schwartz, B}
}
@article {goldsmith,
	title = {Longitudinal penalized functional regression for cognitive outcomes on neuronal tract measurements},
	journal = {Journal of the Royal Statistical Society Series C},
	number = {61},
	year = {2012},
	pages = {453{\textendash}469},
	author = {Goldsmith, J and Crainiceanu, C and Caffo, B and Reich, D.}
}
@article {pmid22241689,
	title = {Mixed effect Poisson log-linear models for clinical and epidemiological sleep hypnogram data},
	journal = {Stat Med},
	volume = {31},
	number = {9},
	year = {2012},
	month = {Apr},
	pages = {855{\textendash}870},
	author = {Swihart, B and Caffo, B and Crainiceanu, C and Punjabi, N.M.}
}
@article {swihartTransition,
	title = {Models of sleep hypnograms scalable to epidemiological studies},
	journal = {Tentatively accepted in Statistics in Medicine},
	year = {2012},
	author = {Swihart, B and Caffo, B and Crainiceanu, C and Punjabi, N}
}
@article {barber,
	title = {Motor "dexterity"?: evidence that left hemisphere lateralization of motor circuit connectivity is associated with better motor performance in children},
	journal = {Cerebral Cortex},
	year = {2012},
	author = {Barber, A and Srinivasan, P and Joel, S. and Caffo, B and Pekar, J and Mostofsky, S}
}
@article {BaGoCaGlCr2012,
	title = {Movelets: A dictionary of movement},
	journal = {Electronic Journal of Statistics},
	volume = {6},
	year = {2012},
	pages = {559-578},
	issn = {1935-7524},
	doi = {10.1214/12-EJS684},
	author = {Bai, J and Goldsmith, J and Caffo, B and Glass, T and Crainiceanu, C}
}
@article {goldsmithNI,
	title = {Penalized functional regression analysis of white-matter tract profiles in multiple sclerosis},
	journal = {Accepted in Neuroimage, PMCID: PMC3114268},
	year = {2012},
	author = {Goldsmith, J and Crainiceanu, C and Caffo, B and Reich, D.}
}
@article {rectalab,
	title = {Quantification of the spatial distribution of rectally-applied surrogates for microbicide and semen in colon with SPECT imaging},
	journal = {Accepted in the British Journal of Clinical Pharmacology},
	year = {2012},
	author = {Cao, Y and Caffo, B and Fuchs, E and Lee, L and Du, Y and Li, L and Bakshi, R and Khan, W and Wahl, R and Grohskopf, L and Hendrix, C}
}
@article {shee,
	title = {Revisiting Brain Atrophy and Its Relationship to Disability in Multiple Sclerosis},
	journal = {PLoS ONE},
	volume = {7},
	number = {5},
	year = {2012},
	month = {05},
	pages = {e37049},
	publisher = {Public Library of Science},
	doi = {10.1371/journal.pone.0037049},
	url = {http://dx.doi.org/10.1371\%2Fjournal.pone.0037049},
	author = {Shiee, N and Bazin, P and Zackowski, K and Farrell, S and Harrison, D and Newsome, S and Ratchford, J and Caffo, B and Calabresi, P and Pham, D and Reich, D.}
}
@article {nareshCaffeine,
	title = {Sleep-Disordered breathing and caffeine consumption: results of a community-based study},
	journal = {Accepted in Chest},
	year = {2012},
	author = {Aurora, RN and Crainiceanu, C and Caffo, B and Punjabi, N}
}
@article {ANA:ANA22452,
	title = {Assessing bioequivalence of generic antiepilepsy drugs},
	journal = {Annals of Neurology, NIHMSID: 286919},
	volume = {70},
	number = {2},
	year = {2011},
	pages = {221{\textendash}228},
	publisher = {Wiley Subscription Services, Inc., A Wiley Company},
	issn = {1531-8249},
	doi = {10.1002/ana.22452},
	url = {http://dx.doi.org/10.1002/ana.22452},
	author = {Krauss, G and Caffo, B and Chang, Y and Hendrix, C and Chuang, K}
}
@article {pmid21995019,
	title = {Assessment of bias for MRI diffusion tensor imaging using SIMEX},
	journal = {Med Image Comput Comput Assist Interv},
	volume = {14},
	number = {Pt 2},
	year = {2011},
	pages = {107{\textendash}115},
	author = {Lauzon, C and Asman, A. J. and Crainiceanu, C and Caffo, B and Landman, B}
}
@article {springerlink:10.1007/s10928-011-9211-7,
	title = {A Bayesian hierarchical nonlinear mixture model in the presence of artifactual outliers in a population pharmacokinetic study},
	journal = {Journal of Pharmacokinetics and Pharmacodynamics},
	volume = {38},
	year = {2011},
	note = {10.1007/s10928-011-9211-7},
	pages = {613-636},
	publisher = {Springer Netherlands},
	issn = {1567-567X},
	url = {http://dx.doi.org/10.1007/s10928-011-9211-7},
	author = {Choi, L and Caffo, B and Kohli, U and Pandharipande, P and Kurnik, D and Ely, E and Stein, C}
}
@article {PACE:PACE2905,
	title = {Clinical predictors of conduction disease progression in type I myotonic muscular dystrophy},
	journal = {Pacing and Clinical Electrophysiology, PMCID: PMC3035751},
	volume = {34},
	number = {2},
	year = {2011},
	pages = {171{\textendash}176},
	publisher = {Blackwell Publishing Inc},
	keywords = {cardiomyopathy, conduction disease, electrocardiography, myotonic muscular dystrophy, sudden death},
	issn = {1540-8159},
	doi = {10.1111/j.1540-8159.2010.02905.x},
	url = {http://dx.doi.org/10.1111/j.1540-8159.2010.02905.x},
	author = {Nazarian, S and Wagner, K and Caffo, B and Tomaselli, G}
}
@article {li3,
	title = {Comparison of proportions for composite endpoints with missing components},
	journal = {Journal of Biopharmaceutical Statistics, NIHMSID: 316386},
	volume = {21},
	year = {2011},
	pages = {271{\textendash}281},
	author = {Li, X and Caffo, B}
}
@article {aurora2011correlating,
	title = {Correlating subjective and objective sleepiness: revisiting the association using survival analysis.},
	journal = {Sleep},
	volume = {34},
	number = {12},
	year = {2011},
	pages = {1707},
	author = {Aurora, RN and Caffo, B and Crainiceanu, C and Punjabi, N}
}
@article {nicole2,
	title = {Distribution of Cell-free and Cell-associated HIV surrogates in the Colon Following Simulated Receptive Anal Intercourse in Healthy Men},
	journal = {Journal of Acquired Immune Defficiency Syndromes, Basic and Translational Science},
	volume = {59},
	number = {1},
	year = {2011},
	pages = {10{\textendash}17},
	author = {Louissaint, N and Nimmagadda, S and Fuchs, E and Bashki, R and Cao, Y and Lee, L and Goldsmith, J and Caffo, B and Du, Y and King, K and Menendez, F and Torbenson, M and Hendrix, C}
}
@article {vadimNI,
	title = {Functional principal components model for high-dimensional brain imaging},
	journal = {Neuroimage, NIHSMID: 316403},
	volume = {58},
	number = {3},
	year = {2011},
	pages = {772 {\textendash} 784},
	author = {Zipunnikov, V. and Caffo, B and Yousem, D and Davatziko, C and Schwartz, B and Crainiceanu, C}
}
@article {shinohara2011longitudinal,
	title = {Longitudinal Analysis of Spatiotemporal Processes: A Case Study of Dynamic Contrast-Enhanced Magnetic Resonance in Multiple Sclerosis},
	journal = {Johns Hopkins University, Dept. of Biostatistics Working Papers},
	year = {2011},
	pages = {231},
	publisher = {bepress},
	author = {Shinohara, R and Crainiceanu, C and Caffo, B and Reich, D S}
}
@article {harrison,
	title = {Longitudinal changes in diffusion-tensor-based quantitative MRI in multiple sclerosis},
	journal = {Neurology, PMCID: PMC3030233},
	volume = {76},
	year = {2011},
	pages = {179{\textendash}186},
	author = {Harrison, D and Caffo, B and Shiee, N and Farrell, J Bazin, P and Farrell, S and Ratchford, J and Calabresi, P and Reich, D.}
}
@article {AJT:AJT3735,
	title = {MELD Exceptions and Rates of Waiting List Outcomes},
	journal = {American Journal of Transplantation},
	volume = {11},
	number = {11},
	year = {2011},
	pages = {2362{\textendash}2371},
	publisher = {Blackwell Publishing Inc},
	keywords = {Liver transplantation, MELD score, organ allocation},
	issn = {1600-6143},
	doi = {10.1111/j.1600-6143.2011.03735.x},
	url = {http://dx.doi.org/10.1111/j.1600-6143.2011.03735.x},
	author = {Massie, A and Caffo, B and Gentry, S and Hall, E and Axelrod, D and Lentine, K and Schnitzler, M and Gheorghian, A and Salvalaggio, P and Segev, D}
}
@article {Mondul2011e6,
	title = {Minimal detection bias in the inverse association between statin drug use and advanced prostate cancer risk: A simulation study},
	journal = {Cancer Epidemiology, PMCID: PMC3142317},
	volume = {35},
	number = {4},
	year = {2011},
	pages = {e6 - e11},
	keywords = {Prostate-specific antigen},
	issn = {1877-7821},
	doi = {DOI: 10.1016/j.canep.2010.11.005},
	url = {http://www.sciencedirect.com/science/article/pii/S1877782110002055},
	author = {Alison M. Mondul and Caffo, B and Elizabeth A. Platz}
}
@article {vadimHDMFPCA,
	title = {Multilevel functional principal component analysis for high-dimensional data},
	journal = {Journal of Computational and Graphical Statistics, NIMHID: 306063},
	volume = {20},
	number = {4},
	year = {2011},
	pages = {852{\textendash}873},
	author = {Zipunnikov, V. and Caffo, B and Crainiceanu, C and Yousem, D and Davatzikos, C. and Schwartz, B}
}
@article {goldsmithAAS,
	title = {Nonlinear tube-fitting for the analysis of anatomical and functional structures},
	journal = {Annals of Applied Statistics, PMCID: PMC3119905},
	volume = {5},
	number = {1},
	year = {2011},
	pages = {337-363},
	issn = {1932-6157},
	doi = {10.1214/10-AOAS384},
	author = {Goldsmith, J and Caffo, B and Crainiceanu, C and Reich, D. and Du, Y and Hendrix, C}
}
@article {caffoSleep,
	title = {A novel approach to prediction of mild sleep disorders in a population-based sample: the Sleep Heart Health Study},
	journal = {Sleep, PMCID: PMC2982734},
	volume = {33},
	number = {12},
	year = {2011},
	pages = {1641{\textendash}1648},
	author = {Caffo, B and Diener-West, M and Punjabi, N and Samet, J}
}
@article {doi:10.1198/jcgs.2010.10007,
	title = {Penalized Functional Regression},
	journal = {Journal of Computational and Graphical Statistics},
	volume = {20},
	number = {4},
	year = {2011},
	pages = {830-851},
	doi = {10.1198/jcgs.2010.10007},
	url = {http://pubs.amstat.org/doi/abs/10.1198/jcgs.2010.10007},
	author = {Goldsmith, J and Bobb, J. and Crainiceanu, C and Caffo, B and Reich, D.}
}
@article {pmid21554962,
	title = {Penalized functional regression analysis of white-matter tract profiles in multiple sclerosis},
	journal = {Neuroimage},
	volume = {57},
	number = {2},
	year = {2011},
	month = {Jul},
	pages = {431{\textendash}439},
	author = {Goldsmith, J and Crainiceanu, C and Caffo, B and Reich, D S}
}
@article {doi:10.1198/jasa.2011.ap10089,
	title = {Population value decomposition, a framework for the analysis of image populations},
	journal = {Journal of the American Statistical Association, with discussion and rejoinder},
	volume = {106},
	number = {495},
	year = {2011},
	pages = {775-790},
	doi = {10.1198/jasa.2011.ap10089},
	url = {http://pubs.amstat.org/doi/abs/10.1198/jasa.2011.ap10089},
	author = {Crainiceanu, C and Caffo, B and Luo, S and Zipunnikov, V. and Punjabi, N}
}
@article {takiPCA,
	title = {Population-wide principal component-based quantification of blood-brain-barrier dynamics in multiple sclerosis},
	journal = {Neuroimage, PMCID: PMC3138825},
	volume = {57},
	number = {4},
	year = {2011},
	pages = {1430 {\textendash} 1446},
	author = {Shinohara, R and Crainiceanu, C and Caffo, B and Gaitan, M and Reich, D.}
}
@article {nazarian2011AI,
	title = {Prospective study to assess the safety of a protocol for magnetic resonance imaging of patients with implanted cardiac devices},
	journal = {Annals of Interal Medicine},
	volume = {155},
	number = {7},
	year = {2011},
	pages = {415{\textendash}424},
	publisher = {American College of Physicians},
	author = {Nazarian, S and Hansford, R and Roguin, A and Goldsher, D and Zviman, M and Lardo, A and Caffo, B and Frick, K and Kraut, M and Kamel, I and Ihab, R and Calkins, H and Berger, R and Bluemke, D and Halperin, H}
}
@article {MRM:MRM22818,
	title = {On the relationship between seed-based and ICA-based measures of functional connectivity},
	journal = {Magnetic Resonance in Medicine},
	volume = {66},
	number = {3},
	year = {2011},
	pages = {644{\textendash}657},
	publisher = {Wiley Subscription Services, Inc., A Wiley Company},
	keywords = {between network connectivity, blood oxygenation level dependent fMRI, functional connectivity, ICA, seed-based connectivity, within network connectivity},
	issn = {1522-2594},
	doi = {10.1002/mrm.22818},
	url = {http://dx.doi.org/10.1002/mrm.22818},
	author = {Joel, S. and Caffo, B and van Zijl, P and Pekar, J}
}
@article {hedlin2009covariate,
	title = {Covariate-adjusted nonparametric analysis of magnetic resonance images using Markov chain Monte Carlo},
	journal = {Statistics and its Interface, NIHMSID: 210823},
	volume = {3},
	number = {1},
	year = {2010},
	pages = {113-123},
	author = {Hedlin, H and Caffo, B and Mahfoud, Z and Bassett, S}
}
@article {schwartz2010evaluation,
	title = {Evaluation of Cumulative Lead Dose and Longitudinal Changes in Structural Magnetic Resonance Imaging in Former Organolead Workers},
	journal = {Journal of Occupational and Environmental Medicine, PMCID: PMC2869464},
	volume = {52},
	number = {4},
	year = {2010},
	pages = {407{\textendash}414},
	author = {Schwartz, B and Caffo, B and Stewart, W and Hedlin, H and James, B and Yousem, D and Davatzikos, C.}
}
@article {swihart2009lasagna,
	title = {Lasagna plots: A Saucy alternative to spaghetti plots},
	journal = {Epidemiology},
	volume = {21},
	number = {5},
	year = {2010},
	pages = {621{\textendash}625},
	author = {Swihart, B and Caffo, B and James, B and Strand, M. and Schwartz, B and Punjabi, N}
}
@article {greven,
	title = {Longitudinal functional principal components analysis},
	journal = {Electronic Journal of Statistics, PMCID: PMC3131008},
	volume = {4},
	year = {2010},
	pages = {1022-1054},
	author = {Greven, S. and Crainiceanu, C and Caffo, B and Reich, D.}
}
@article {reich2,
	title = {MRI of the Corpus Callosum in Multiple Sclerosis: Association with Disability},
	journal = {Multiple Sclerosis, PMCID: PMC2820126},
	volume = {16},
	number = {2},
	year = {2010},
	pages = {166{\textendash}177},
	author = {Ozturk, A and Smith, S and Gordon-Lipkin, E and Harrison, D and Shiee, N and Pham, D and Caffo, B and Calabresi, P and Reich, D.}
}
@article {segev2010perioperative,
	title = {Perioperative Mortality and Long-term Survival Following Live Kidney Donation},
	journal = {Journal of the American Medical Association, NIHMSID: 316358},
	volume = {303},
	number = {10},
	year = {2010},
	pages = {959{\textendash}966},
	publisher = {Am Med Assoc},
	author = {Segev, D and Muzaale, A and Caffo, B and Mehta, S and Singer, A and Taranto, S and McBride, M and Montgomery, R}
}
@article {nazarian:qrs,
	title = {QRS Prolongation in Myotonic Muscular Dystrophy and Diffuse Fibrosis on Cardiac Magnetic Resonance},
	journal = {Magnetic Resonance in Medicine, PMCID: PMC3034129},
	volume = {64},
	number = {1},
	year = {2010},
	pages = {107{\textendash}114},
	author = {Nazarian, S and Bluemke, D and Wagner, K and Zviman, M and Turkbey, E and Caffo, B and Shehata, M and Edwards,D and Butcher, B and Calkins, H and Berger, R and Halperin, H and Tomaselli, G}
}
@article {boatman,
	title = {Quantifying Auditory Event-Related Responses in Multichannel Human Intracranial Recordings},
	journal = {Invited submission to Frontiers in Computational Neuroscience, PMCID: PMC2859880},
	volume = {4},
	number = {4},
	year = {2010},
	pages = {1{\textendash}17},
	author = {Boatman-Reich, D and Franaszczuk, Piotr J. and Korzeniewska, A. and Caffo, B and Ritzl, E and Colwell, S and Crone, N}
}
@article {hao,
	title = {Redefining CpG Islands Using a Hidden Markov Models},
	journal = {Biostatistics, PMCID: PMC2883304},
	volume = {11},
	number = {3},
	year = {2010},
	pages = {499{\textendash}514},
	author = {Wu, H and Caffo, B and Jaffee, H and Feinberg, A and Irizarry, R}
}
@article {pmid20227508,
	title = {Two-stage decompositions for the analysis of functional connectivity for fMRI with application to Alzheimer{\textquoteright}s disease risk},
	journal = {Neuroimage},
	volume = {51},
	number = {3},
	year = {2010},
	month = {Jul},
	pages = {1140{\textendash}1149},
	author = {Caffo, B and Crainiceanu, C and Verduzco, G. and Joel, S. and Mostofsky, S and Bassett, S and Pekar, J}
}
@article {laffan2010utility,
	title = {Utility of sleep stage transitions in assessing sleep continuity},
	journal = {Sleep, PMCID: PMC2982738},
	volume = {33},
	number = {12},
	year = {2010},
	pages = {1681},
	issn = {0161-8105},
	author = {Laffan, A and Caffo, B and Swihart, B and Punjabi, N}
}
@article {chen2009adaptive,
	title = {Adaptive control of the false discovery rate in voxel-based morphometry},
	journal = {Human Brain Mapping, NIHMSID: 316414},
	volume = {30},
	number = {7},
	year = {2009},
	pages = {2304{\textendash}2311},
	publisher = {Wiley Subscription Services, Inc., A Wiley Company Hoboken},
	author = {Chen, S and Wang, C. and Eberly, L and Caffo, B and Schwartz, B}
}
@article {reich2009damage,
	title = {Damage to the Optic Radiation in Multiple Sclerosis Is Associated With Retinal Injury and Visual Disability},
	journal = {Archives of Neurology, PMCID: PMC2784485},
	volume = {66},
	number = {8},
	year = {2009},
	pages = {998{\textendash}1006},
	publisher = {Am Med Assoc},
	author = {Reich, D. and Smith, S and Gordon-Lipkin, E and Ozturk, A and Caffo, B and Balcer, L and Calabresi, P}
}
@article {mostofsky2009decreased,
	title = {Decreased connectivity and cerebellar activity in autism during motor task performance},
	journal = {Brain, PMCID: PMC2732264},
	volume = {132},
	number = {9},
	year = {2009},
	pages = {2413{\textendash}2425},
	publisher = {Oxford Univ Press},
	author = {Mostofsky, S and Powell, S and Simmonds, D and Goldberg, M and Caffo, B and Pekar, J}
}
@article {lauzon2009easy,
	title = {Easy Multiplicity Control in Equivalence Testing Using Two One-Sided Tests},
	journal = {The American Statistician, PMCID: PMC2800314},
	volume = {63},
	number = {2},
	year = {2009},
	pages = {147{\textendash}154},
	publisher = {ASA},
	author = {Lauzon, C and Caffo, B}
}
@article {yousem2009intelligence,
	title = {Intelligence and Medial Temporal Lobe Function in Older Adults: A Functional MR Imaging-Based Investigation},
	journal = {American Journal of Neuroradiology, PMCID: PMC2843089},
	volume = {30},
	number = {8},
	year = {2009},
	pages = {1477{\textendash}1481},
	publisher = {Am Soc Neuroradiology},
	author = {Yousem, D and Yassa, M and Cristinzio, C and Kusevic, I and Mohamed, M and Caffo, B and Bassett, S}
}
@article {su2009modified,
	title = {Modified test statistics by inter-voxel variance shrinkage with an application to fMRI},
	journal = {Biostatistics, NIHMSID: 316409},
	volume = {10},
	number = {2},
	year = {2009},
	pages = {219-227},
	author = {Su, S and Caffo, B and Garrett-Mayer, E and Bassett, S}
}
@article {di2009multilevel,
	title = {Multilevel functional principal component analysis},
	journal = {Annals of Applied Statistics, PMCID: PMC2835171},
	volume = {3},
	number = {1},
	year = {2009},
	pages = {458-488},
	author = {Di, C and Crainiceanu, C and Caffo, B and Punjabi, N}
}
@article {Crai:Caff:Di:Punj:nonp:2009,
	title = {Nonparametric Signal Extraction and Measurement Error in the Analysis of Electroencephalographic Activity During Sleep},
	journal = {Journal of the American Statistical Association},
	volume = {104},
	number = {486},
	year = {2009},
	pages = {541{\textendash}555},
	keywords = {Hierarchical smoothing, Measurement error, penalized splines, Sleep},
	author = {Crainiceanu, C and Caffo, B and Di, Chong-Zhi and Punjabi, Naresh M}
}
@article {crainiceanu2009nonparametric,
	title = {Nonparametric signal extraction and measurement error in the analysis of electroencephalographic activity during sleep},
	journal = {Journal of the American Statistical Association, PMCID: PMC2802498},
	volume = {104},
	number = {486},
	year = {2009},
	pages = {541{\textendash}555},
	publisher = {ASA},
	author = {Crainiceanu, C and Caffo, B and Di, C and Punjabi, N}
}
@article {caffo2009overview,
	title = {An overview of observational sleep research with application to sleep stage transitioning},
	journal = {Chance, PMCID: PMC2800358},
	volume = {22},
	number = {1},
	year = {2009},
	pages = {10{\textendash}15},
	publisher = {Springer},
	author = {Caffo, B and Swihart, B and Crainiceanu, C and Laffan, A and Punjabi, N}
}
@article {Caff:Swih:Crai:Laff:Punj:an:2009,
	title = {An Overview of Observational Sleep Research with Application to Sleep State Transitioning},
	journal = {Chance},
	volume = {22},
	number = {1},
	year = {2009},
	pages = {10{\textendash}15},
	author = {Caffo, B and Swihart, B and Crainiceanu, C and Laffan, A and Punjabi, Naresh}
}
@article {o2009prospective,
	title = {Prospective Study of Sleep-disordered Breathing and Hypertension: The Sleep Heart Health Study},
	journal = {American Journal of Respiratory and Critical Care Medicine, PMCID: PMC2695498},
	volume = {179},
	number = {12},
	year = {2009},
	pages = {1159{\textendash}1164},
	publisher = {Am Thoracic Soc},
	author = {O{\textquoteright}Connor, G and Caffo, B and Newman, A and Quan, S and Rapoport, D and Redline, S and Resnick, H and Samet, J and Shahar, E}
}
@article {punjabi,
	title = {Sleep-disordered Breathing and Mortality: a Prospective Cohort Study},
	journal = {PLOS Medicine, PMCID: PMC2722083},
	volume = {6},
	year = {2009},
	author = {Punjabi, N and Caffo, B and Goodwin, J and Gottlieb, D and Newman, A and O{\textquoteright}Connor, G and Rapoport, D and Redline, S and Resnick, H and Robbins, J and Samet, J and Shahar, E and Unruh, M}
}
@article {scharfstein2008accounting,
	title = {Accounting for within-patient correlation in assessing relative sensitivity of an adjunctive diagnostic test: Application to lung cancer},
	journal = {Statistics in Medicine},
	volume = {27},
	number = {12},
	year = {2008},
	pages = {2110{\textendash}2126},
	publisher = {John Wiley \& Sons, Ltd Chichester, UK},
	author = {Scharfstein, D and Ryea, J and Caffo, B}
}
@article {bowman2008bayesian,
	title = {A Bayesian hierarchical framework for spatial modeling of fMRI data},
	journal = {NeuroImage, PMCID: PMC2134321},
	volume = {39},
	number = {1},
	year = {2008},
	pages = {146{\textendash}156},
	publisher = {Elsevier},
	author = {Bowman, F and Caffo, B and Bassett, S and Kilts, C}
}
@article {Caff:Crai:Deng:Hend:case:2008,
	title = {A Case Study in Pharmacologic Colon Imaging Using Principal Curves in Single-Photon Emission Computed Tomography},
	journal = {Journal of the American Statistical Association},
	volume = {103},
	number = {484},
	year = {2008},
	pages = {1470{\textendash}1480},
	keywords = {Curve fitting, medical imaging, Pharmacology, Smoothing, SPECT},
	author = {Caffo, B and Crainiceanu, C and Deng, Lijuan and Hendrix, C}
}
@article {swihart2008quantitative,
	title = {Characterizing Sleep Structure Using the Hypnogram},
	journal = {Journal of Clinical Sleep Medicine, PMCID: PMC2542492},
	volume = {4},
	number = {4},
	year = {2008},
	pages = {349{\textendash}355},
	author = {Swihart, B and Caffo, B and Bandeen-Roche, K and Punjabi, N}
}
@article {redgrave2008differential,
	title = {Differential brain activation in anorexia nervosa to Fat and Thin words during a Stroop task},
	journal = {NeuroReport, PMCID: PMC2891098},
	volume = {19},
	number = {12},
	year = {2008},
	pages = {1181{\textendash}1185},
	author = {Redgrave, G and Bakker, A and Bello, N and Caffo, B and Coughlin, J and Guarda, A and McEntee, J and Pekar, J and Reinblatt, S and Verduzco, G. and Moran, T}
}
@article {guilarte2008dysregulation,
	title = {Dysregulation of Glutamate Carboxypeptidase II in Psychiatric Disease},
	journal = {Schizophrenia Research, PMCID: PMC2287371},
	volume = {99},
	number = {1-3},
	year = {2008},
	pages = {324{\textendash}332},
	publisher = {NIH Public Access},
	author = {Guilarte, T and Hammoud, D and McGlothan, J and Caffo, B and Foss, C and Kozikowski, A and Pomper, M}
}
@article {stamatakis2008fasting,
	title = {Fasting Glycemia in Sleep Disordered Breathing: Lowering the Threshold on Oxyhemoglobin Desaturation},
	journal = {Sleep, PMCID: PMC2491502},
	volume = {31},
	number = {7},
	year = {2008},
	pages = {1018{\textendash}1024},
	publisher = {American Academy of Sleep Medicine},
	author = {Stamatakis, K and Sanders, M and Caffo, B and Resnick, H and Gottlieb, D and Mehra, R and Punjabi, N}
}
@article {suskauer2008fmri,
	title = {fMRI of Intrasubject Variability in ADHD: Anomalous Premotor Activity With Prefrontal Compensation},
	journal = {Journal of American Academy of Child \& Adolescent Psychiatry, NIHMSID: 71813},
	volume = {47},
	number = {10},
	year = {2008},
	pages = {1141{\textendash}1150},
	author = {Suskauer, S and Simmonds, D and Caffo, B and Denckla, M and Pekar, J and Mostofsky, S}
}
@article {caffo2008likelihood,
	title = {Likelihood Estimation of Conjugacy Relationships in Linear Models with Applications to High-Throughput Genomics},
	journal = {International Journal of Biostatistics, PMCID: PMC2827886},
	volume = {5},
	year = {2008},
	note = {Issue 18},
	publisher = {bepress},
	author = {Caffo, B and Dongmei, L and Scharpf, R and Parmigiani, G.}
}
@article {choi2008mechanistic,
	title = {A mechanistic latent variable model for estimating drug concentrations in the male genital tract: A case study in drug kinetics},
	journal = {Statistics in Medicine, PMCID: PMC2763330},
	volume = {27},
	number = {14},
	year = {2008},
	pages = {2697{\textendash}2714},
	publisher = {John Wiley \& Sons, Ltd Chichester, UK},
	author = {Choi, L and Caffo, B and Rohde, C and Ndovi, T and Hendrix, C}
}
@article {cao2008noninvasive,
	title = {Noninvasive Quantitation of Drug Concentration in Prostate and Seminal Vesicles: Improvement and Validation With Desipramine and Aspirin},
	journal = {The Journal of Clinical Pharmacology},
	volume = {48},
	number = {2},
	year = {2008},
	pages = {176-183},
	publisher = {Am Coll Clin Pharm},
	author = {Cao, Y and Caffo, B and Choi, L and Radebaugh, C and Fuchs, E and Hendrix, C}
}
@article {zhang2008power,
	title = {Power Spectral Analysis of EEG Activity During Sleep in Cigarette Smokers},
	journal = {Chest},
	volume = {133},
	number = {2},
	year = {2008},
	pages = {427{\textendash}432},
	publisher = {Am Coll Chest Phys},
	author = {Zhang, L and Samet, J and Caffo, B and Bankman, I and Punjabi, N}
}
@article {choi2008survey,
	title = {A survey of the likelihood approach to bioequivalence trials},
	journal = {Statistics in Medicine, PMCID: PMC2778077},
	volume = {27},
	number = {24},
	year = {2008},
	pages = {4874{\textendash}4894},
	publisher = {John Wiley \& Sons, Ltd Chichester, UK},
	author = {Choi, L and Caffo, B and Rohde, C}
}
@article {he2008toward,
	title = {Toward Realistic and Practical Ideal Observer (IO) Estimation for the Optimization of Medical Imaging Systems},
	journal = {IEEE Transactions on Medical Imaging, PMCID: PMC2739397},
	volume = {27},
	number = {10},
	year = {2008},
	pages = {1535{\textendash}1543},
	author = {He, X and Caffo, B and Frey, E}
}
@article {caffo2007brain,
	title = {Are Brain Volumes based on Magnetic Resonance Imaging Mediators of the Associations of Cumulative Lead Dose with Cognitive Function?},
	journal = {American Journal of Epidemiology},
	volume = {167},
	number = {4},
	year = {2007},
	pages = {429{\textendash}437},
	publisher = {Oxford Univ Press},
	author = {Caffo, B and Chen, S and Stewart, W and Bolla, K and Yousem, D and Davatzikos, C. and Schwartz, B}
}
@article {cao2007effect,
	title = {Effect of semen sampling frequency on seminal antiretroviral drug concentration},
	journal = {Clinical Pharmacology \& Therapeutics},
	volume = {83},
	number = {6},
	year = {2007},
	pages = {848{\textendash}856},
	publisher = {Nature Publishing Group},
	author = {Cao, Y and Ndovi, T and Parsons, T and Guidos, A and Caffo, B and Hendrix, C}
}
@article {caffo2007flexible,
	title = {Flexible random intercept models for binary outcomes using mixtures of normals},
	journal = {Computational Statistics and Data Analysis, PMCID: PMC2031853},
	volume = {51},
	number = {11},
	year = {2007},
	pages = {5220{\textendash}5235},
	publisher = {Elsevier},
	author = {Caffo, B and An, M and Rohde, C}
}
@article {ndovi2007new,
	title = {A new method to estimate quantitatively seminal vesicle and prostate gland contributions to ejaculate},
	journal = {British Journal of Clinical Pharmacology, PMCID: PMC2203235},
	volume = {63},
	number = {4},
	year = {2007},
	pages = {404-420},
	publisher = {Blackwell Publishing},
	author = {Ndovi, T and Parsons, T and Choi, L and Caffo, B and Rohde, C and Hendrix, C}
}
@article {choi2007optimal,
	title = {Optimal sampling times in bioequivalence studies using a simulated annealing algorithm},
	journal = {Statistics and Computing},
	volume = {17},
	number = {4},
	year = {2007},
	pages = {337{\textendash}347},
	publisher = {Springer},
	author = {Choi, L and Caffo, B and Rohde, C}
}
@article {li2007potential,
	title = {On the potential for ill logic with logically defined outcomes},
	journal = {Biostatistics},
	volume = {8},
	number = {4},
	year = {2007},
	pages = {800},
	author = {Li, X and Caffo, B and Scharfstein, D}
}
@article {schwartz2007relations,
	title = {Relations of brain volumes with cognitive function in males 45 years and older with past lead exposure},
	journal = {Neuroimage, PMCID: PMC2038986},
	volume = {37},
	number = {2},
	year = {2007},
	pages = {633{\textendash}641},
	publisher = {Elsevier},
	author = {Schwartz, B and Chen, S and Caffo, B and Stewart, W and Bolla, K and Yousem, D and Davatzikos, C.}
}
@article {zhang2006cigarette,
	title = {Cigarette smoking and nocturnal sleep architecture},
	journal = {American Journal of Epidemiology},
	volume = {164},
	number = {6},
	year = {2006},
	pages = {529},
	publisher = {Oxford Univ Press},
	author = {Zhang, L and Samet, J and Caffo, B and Punjabi, N}
}
@article {caffo2006exact,
	title = {Exact Hypothesis Tests for Log-linear Models with exactLoglinTest},
	journal = {Journal of Statistical Software},
	volume = {17},
	number = {7},
	year = {2006},
	pages = {1{\textendash}17},
	author = {Caffo, B}
}
@article {bassett2006familial,
	title = {Familial risk for Alzheimer{\textquoteright}s disease alters fMRI activation patterns},
	journal = {Brain, PMCID: PMC2744898},
	volume = {129},
	number = {5},
	year = {2006},
	pages = {1229{\textendash}1239},
	publisher = {Oxford Univ Press},
	author = {Bassett, S and Yousem, D and Cristinzio, C and Kusevic, I and Yassa, M and Caffo, B and Zeger, S}
}
@article {jones2006fixed,
	title = {Fixed-width output analysis for Markov chain Monte Carlo},
	journal = {Journal of the American Statistical Association},
	volume = {101},
	number = {476},
	year = {2006},
	pages = {1537{\textendash}1547},
	publisher = {ASA},
	author = {Jones, G and Haran, M and Caffo, B and Neath, R}
}
@article {ndovi2006quantitative,
	title = {Quantitative assessment of seminal vesicle and prostate drug concentrations by use of a noninvasive method},
	journal = {Clinical Pharmacology \& Therapeutics},
	volume = {80},
	number = {2},
	year = {2006},
	pages = {146{\textendash}158},
	publisher = {Nature Publishing Group},
	author = {Ndovi, T and Choi, L and Caffo, B and Parsons, T and Baker, S and Zhao, M and Rohde, C and Hendrix, C}
}
@article {caffo2006user,
	title = {A user-friendly tutorial on link-probit-normal models},
	journal = {The American Statistician},
	volume = {60},
	year = {2006},
	pages = {139{\textendash}145},
	author = {Caffo, B and Griswold, M}
}
@article {caffo2005ascent,
	title = {Ascent-Based Monte Carlo EM},
	journal = {Journal of the Royal Statistical Society, Series B},
	volume = {67},
	year = {2005},
	pages = {235{\textendash}252},
	author = {Caffo, B and Jank, W and Jones, G}
}
@article {agresti2004examples,
	title = {Examples in which misspecification of a random effects distribution reduces efficiency, and possible remedies},
	journal = {Computational Statistics and Data Analysis},
	volume = {47},
	number = {3},
	year = {2004},
	pages = {639{\textendash}653},
	publisher = {Elsevier},
	author = {Agresti, A and Caffo, B and Ohman-Strickland, P}
}
@article {caffo2003monte,
	title = {Monte Carlo conditional inference for log-linear and logistic models: a survey of current methodology},
	journal = {Statistical Methods in Medical Research},
	volume = {12},
	number = {2},
	year = {2003},
	pages = {109},
	author = {Caffo, B and Booth, J}
}
@article {caffo2002empirical,
	title = {Empirical supremum rejection sampling},
	journal = {Biometrika},
	volume = {89},
	number = {4},
	year = {2002},
	pages = {745{\textendash}754},
	publisher = {Biometrika Trust},
	author = {Caffo, B and Booth, J and Davison, A}
}
@article {agresti2002measures,
	title = {Measures of relative model fit},
	journal = {Computational Statistics and Data Analysis},
	volume = {39},
	number = {2},
	year = {2002},
	pages = {127{\textendash}136},
	publisher = {Elsevier},
	author = {Agresti, A and Caffo, B}
}
@article {booth2002unequal,
	title = {Unequal sampling for Monte Carlo EM algorithms},
	journal = {Computational Statistics and Data Analysis},
	volume = {39},
	number = {3},
	year = {2002},
	pages = {261{\textendash}270},
	publisher = {Elsevier},
	author = {Booth, J and Caffo, B}
}
@article {caffo2001markov,
	title = {A Markov chain Monte Carlo algorithm for approximating exact conditional probabilities},
	journal = {Journal of Computational and Graphical Statistics},
	volume = {10},
	number = {4},
	year = {2001},
	pages = {730{\textendash}745},
	publisher = {ASA},
	author = {Caffo, B and Booth, J}
}
@article {hartzel2001multinomial,
	title = {Multinomial logit random effects models},
	journal = {Statistical Modelling},
	volume = {1},
	number = {2},
	year = {2001},
	pages = {81},
	author = {Hartzel, J and Agresti, A and Caffo, B}
}
@article {agresti2000random,
	title = {Random-effects modeling of categorical response data},
	journal = {Sociological Methodology},
	volume = {30},
	year = {2000},
	pages = {27{\textendash}80},
	publisher = {Blackwell Publishers},
	author = {Agresti, A and Booth, J and Hobert, J and Caffo, B}
}
@article {agresti2000simple,
	title = {Simple and effective confidence intervals for proportions and differences of proportions result from adding two successes and two failures},
	journal = {The American Statistician},
	volume = {54},
	number = {4},
	year = {2000},
	pages = {280{\textendash}288},
	publisher = {American Statistical Association},
	author = {Agresti, A and Caffo, B}
}
