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Improved state change estimation in dynamic functional connectivity using hidden semi-Markov models.

Shappell H, Caffo BS, Pekar JJ, Lindquist MA.

Neuroimage. 2019 May 1;191:243-257. doi: 10.1016/j.neuroimage.2019.02.013. Epub 2019 Feb 10.


Modular preprocessing pipelines can reintroduce artifacts into fMRI data.

Lindquist MA, Geuter S, Wager TD, Caffo BS.

Hum Brain Mapp. 2019 Jun 1;40(8):2358-2376. doi: 10.1002/hbm.24528. Epub 2019 Jan 21.


Mixed effect machine learning: A framework for predicting longitudinal change in hemoglobin A1c.

Ngufor C, Van Houten H, Caffo BS, Shah ND, McCoy RG.

J Biomed Inform. 2019 Jan;89:56-67. doi: 10.1016/j.jbi.2018.09.001. Epub 2018 Sep 4.


An M-estimator for reduced-rank system identification.

Chen S, Liu K, Yang Y, Xu Y, Lee S, Lindquist M, Caffo BS, Vogelstein JT.

Pattern Recognit Lett. 2017 Jan 15;86:76-81. doi: 10.1016/j.patrec.2016.12.012. Epub 2016 Dec 19.


Improved estimation of subject-level functional connectivity using full and partial correlation with empirical Bayes shrinkage.

Mejia AF, Nebel MB, Barber AD, Choe AS, Pekar JJ, Caffo BS, Lindquist MA.

Neuroimage. 2018 May 15;172:478-491. doi: 10.1016/j.neuroimage.2018.01.029. Epub 2018 Feb 14.


Neuroconductor: an R platform for medical imaging analysis.

Muschelli J, Gherman A, Fortin JP, Avants B, Whitcher B, Clayden JD, Caffo BS, Crainiceanu CM.

Biostatistics. 2019 Apr 1;20(2):218-239. doi: 10.1093/biostatistics/kxx068.


High-dimensional multivariate mediation with application to neuroimaging data.

Chén OY, Crainiceanu C, Ogburn EL, Caffo BS, Wager TD, Lindquist MA.

Biostatistics. 2018 Apr 1;19(2):121-136. doi: 10.1093/biostatistics/kxx027.


Parallel group independent component analysis for massive fMRI data sets.

Chen S, Huang L, Qiu H, Nebel MB, Mostofsky SH, Pekar JJ, Lindquist MA, Eloyan A, Caffo BS.

PLoS One. 2017 Mar 9;12(3):e0173496. doi: 10.1371/journal.pone.0173496. eCollection 2017.


Ten Simple Rules for Effective Statistical Practice.

Kass RE, Caffo BS, Davidian M, Meng XL, Yu B, Reid N.

PLoS Comput Biol. 2016 Jun 9;12(6):e1004961. doi: 10.1371/journal.pcbi.1004961. eCollection 2016 Jun. No abstract available.


Decoupling of reaction time-related default mode network activity with cognitive demand.

Barber AD, Caffo BS, Pekar JJ, Mostofsky SH.

Brain Imaging Behav. 2017 Jun;11(3):666-676. doi: 10.1007/s11682-016-9543-4.


Reproducibility and Temporal Structure in Weekly Resting-State fMRI over a Period of 3.5 Years.

Choe AS, Jones CK, Joel SE, Muschelli J, Belegu V, Caffo BS, Lindquist MA, van Zijl PC, Pekar JJ.

PLoS One. 2015 Oct 30;10(10):e0140134. doi: 10.1371/journal.pone.0140134. eCollection 2015.


Neural Correlates of Visuomotor Learning in Autism.

Sharer E, Crocetti D, Muschelli J, Barber AD, Nebel MB, Caffo BS, Pekar JJ, Mostofsky SH.

J Child Neurol. 2015 Dec;30(14):1877-86. doi: 10.1177/0883073815600869. Epub 2015 Sep 8.


A Phase 1 Randomized, Blinded Comparison of the Pharmacokinetics and Colonic Distribution of Three Candidate Rectal Microbicide Formulations of Tenofovir 1% Gel with Simulated Unprotected Sex (CHARM-02).

Hiruy H, Fuchs EJ, Marzinke MA, Bakshi RP, Breakey JC, Aung WS, Manohar M, Yue C, Caffo BS, Du Y, Abebe KZ, Spiegel HM, Rohan LC, McGowan I, Hendrix CW.

AIDS Res Hum Retroviruses. 2015 Nov;31(11):1098-108. doi: 10.1089/AID.2015.0098. Epub 2015 Aug 24.


Estimating a graphical intra-class correlation coefficient (GICC) using multivariate probit-linear mixed models.

Yue C, Chen S, Sair HI, Airan R, Caffo BS.

Comput Stat Data Anal. 2015 Sep;89:126-133.


Resting brain activity in disorders of consciousness: a systematic review and meta-analysis.

Hannawi Y, Lindquist MA, Caffo BS, Sair HI, Stevens RD.

Neurology. 2015 Mar 24;84(12):1272-80. doi: 10.1212/WNL.0000000000001404. Epub 2015 Feb 20. Review. Erratum in: Neurology. 2016 Jan 12;86(2):202.


Evaluating Model Misspecification in Independent Component Analysis.

Lee S, Caffo BS, Lakshmanan B, Pham DL.

J Stat Comput Simul. 2015 Apr;85(6):1151-1164.


Connectivity supporting attention in children with attention deficit hyperactivity disorder.

Barber AD, Jacobson LA, Wexler JL, Nebel MB, Caffo BS, Pekar JJ, Mostofsky SH.

Neuroimage Clin. 2014 Nov 20;7:68-81. doi: 10.1016/j.nicl.2014.11.011. eCollection 2015.


A unifying framework for marginalized random intercept models of correlated binary outcomes.

Swihart BJ, Caffo BS, Crainiceanu CM.

Int Stat Rev. 2014 Aug;82(2):275-295.


Evaluating dynamic bivariate correlations in resting-state fMRI: a comparison study and a new approach.

Lindquist MA, Xu Y, Nebel MB, Caffo BS.

Neuroimage. 2014 Nov 1;101:531-46. doi: 10.1016/j.neuroimage.2014.06.052. Epub 2014 Jun 30.


Variations in EEG discharges predict ADHD severity within individual Smith-Lemli-Opitz patients.

Schreiber JM, Lanham DC, Trescher WH, Sparks SE, Wassif CA, Caffo BS, Porter FD, Tierney E, Gropman AL, Ewen JB.

Neurology. 2014 Jul 8;83(2):151-9. doi: 10.1212/WNL.0000000000000565. Epub 2014 Jun 11.


Reduction of motion-related artifacts in resting state fMRI using aCompCor.

Muschelli J, Nebel MB, Caffo BS, Barber AD, Pekar JJ, Mostofsky SH.

Neuroimage. 2014 Aug 1;96:22-35. doi: 10.1016/j.neuroimage.2014.03.028. Epub 2014 Mar 18.


Analytic programming with FMRI data: a quick-start guide for statisticians using R.

Eloyan A, Li S, Muschelli J, Pekar JJ, Mostofsky SH, Caffo BS.

PLoS One. 2014 Feb 28;9(2):e89470. doi: 10.1371/journal.pone.0089470. eCollection 2014.


Successful implementation of a unit-based quality nurse to reduce central line-associated bloodstream infections.

Thom KA, Li S, Custer M, Preas MA, Rew CD, Cafeo C, Leekha S, Caffo BS, Scalea TM, Lissauer ME.

Am J Infect Control. 2014 Feb;42(2):139-43. doi: 10.1016/j.ajic.2013.08.006. Epub 2013 Dec 17.


Practical Marginalized Multilevel Models.

Griswold ME, Swihart BJ, Caffo BS, Zeger SL.

Stat. 2013;2(1). doi: 10.1002/sta4.22.


An evaluation of independent component analyses with an application to resting-state fMRI.

Risk BB, Matteson DS, Ruppert D, Eloyan A, Caffo BS.

Biometrics. 2014 Mar;70(1):224-36. doi: 10.1111/biom.12111. Epub 2013 Dec 18.


Practical recommendations for population PK studies with sampling time errors.

Choi L, Crainiceanu CM, Caffo BS.

Eur J Clin Pharmacol. 2013 Dec;69(12):2055-64. doi: 10.1007/s00228-013-1576-7. Epub 2013 Aug 24.


Comparison of total hospital-acquired bloodstream infections to central line-associated bloodstream infections and implications for outcome measures in infection control.

Leekha S, Li S, Thom KA, Preas MA, Caffo BS, Morgan DJ, Harris AD.

Infect Control Hosp Epidemiol. 2013 Sep;34(9):984-6. doi: 10.1086/671730. Epub 2013 Jul 25.


Isoosmolar enemas demonstrate preferential gastrointestinal distribution, safety, and acceptability compared with hyperosmolar and hypoosmolar enemas as a potential delivery vehicle for rectal microbicides.

Leyva FJ, Bakshi RP, Fuchs EJ, Li L, Caffo BS, Goldsmith AJ, Ventuneac A, Carballo-Diéguez A, Du Y, Leal JP, Lee LA, Torbenson MS, Hendrix CW.

AIDS Res Hum Retroviruses. 2013 Nov;29(11):1487-95. doi: 10.1089/AID.2013.0189. Epub 2013 Aug 24.


Effects of working memory demand on neural mechanisms of motor response selection and control.

Barber AD, Caffo BS, Pekar JJ, Mostofsky SH.

J Cogn Neurosci. 2013 Aug;25(8):1235-48. doi: 10.1162/jocn_a_00394. Epub 2013 Mar 26.


Combining hidden Markov models for comparing the dynamics of multiple sleep electroencephalograms.

Langrock R, Swihart BJ, Caffo BS, Punjabi NM, Crainiceanu CM.

Stat Med. 2013 Aug 30;32(19):3342-56. doi: 10.1002/sim.5747. Epub 2013 Jan 24.


Likelihood-based population independent component analysis.

Eloyan A, Crainiceanu CM, Caffo BS.

Biostatistics. 2013 Jul;14(3):514-27. doi: 10.1093/biostatistics/kxs055. Epub 2013 Jan 10.


Developmental changes in within- and between-network connectivity between late childhood and adulthood.

Barber AD, Caffo BS, Pekar JJ, Mostofsky SH.

Neuropsychologia. 2013 Jan;51(1):156-67. doi: 10.1016/j.neuropsychologia.2012.11.011. Epub 2012 Nov 19.


Myocardial structural associations with local electrograms: a study of postinfarct ventricular tachycardia pathophysiology and magnetic resonance-based noninvasive mapping.

Sasaki T, Miller CF, Hansford R, Yang J, Caffo BS, Zviman MM, Henrikson CA, Marine JE, Spragg D, Cheng A, Tandri H, Sinha S, Kolandaivelu A, Zimmerman SL, Bluemke DA, Tomaselli GF, Berger RD, Calkins H, Halperin HR, Nazarian S.

Circ Arrhythm Electrophysiol. 2012 Dec;5(6):1081-90. doi: 10.1161/CIRCEP.112.970699. Epub 2012 Nov 13.


Disruption of functional organization within the primary motor cortex in children with autism.

Nebel MB, Joel SE, Muschelli J, Barber AD, Caffo BS, Pekar JJ, Mostofsky SH.

Hum Brain Mapp. 2014 Feb;35(2):567-80. doi: 10.1002/hbm.22188. Epub 2012 Nov 1.


Reliability of early cortical auditory gamma-band responses.

Cervenka MC, Franaszczuk PJ, Crone NE, Hong B, Caffo BS, Bhatt P, Lenz FA, Boatman-Reich D.

Clin Neurophysiol. 2013 Jan;124(1):70-82. doi: 10.1016/j.clinph.2012.06.003. Epub 2012 Jul 6.


Revisiting brain atrophy and its relationship to disability in multiple sclerosis.

Shiee N, Bazin PL, Zackowski KM, Farrell SK, Harrison DM, Newsome SD, Ratchford JN, Caffo BS, Calabresi PA, Pham DL, Reich DS.

PLoS One. 2012;7(5):e37049. doi: 10.1371/journal.pone.0037049. Epub 2012 May 15.


Comparison of swab and sponge methodologies for identification of Acinetobacter baumannii from the hospital environment.

Thom KA, Howard T, Sembajwe S, Harris AD, Strassle P, Caffo BS, Carroll KC, Johnson JK.

J Clin Microbiol. 2012 Jun;50(6):2140-1. doi: 10.1128/JCM.00448-12. Epub 2012 Mar 29.


Quantification of the spatial distribution of rectally applied surrogates for microbicide and semen in colon with SPECT and magnetic resonance imaging.

Cao YJ, Caffo BS, Fuchs EJ, Lee LA, Du Y, Li L, Bakshi RP, Macura K, Khan WA, Wahl RL, Grohskopf LA, Hendrix CW.

Br J Clin Pharmacol. 2012 Dec;74(6):1013-22. doi: 10.1111/j.1365-2125.2012.04267.x.


Mixed effect Poisson log-linear models for clinical and epidemiological sleep hypnogram data.

Swihart BJ, Caffo BS, Crainiceanu CM, Punjabi NM.

Stat Med. 2012 Apr 30;31(9):855-70. doi: 10.1002/sim.4457. Epub 2012 Jan 13.


A prospective evaluation of a protocol for magnetic resonance imaging of patients with implanted cardiac devices.

Nazarian S, Hansford R, Roguin A, Goldsher D, Zviman MM, Lardo AC, Caffo BS, Frick KD, Kraut MA, Kamel IR, Calkins H, Berger RD, Bluemke DA, Halperin HR.

Ann Intern Med. 2011 Oct 4;155(7):415-24. doi: 10.7326/0003-4819-155-7-201110040-00004.


Distribution of cell-free and cell-associated HIV surrogates in the colon after simulated receptive anal intercourse in men who have sex with men.

Louissaint NA, Nimmagadda S, Fuchs EJ, Bakshi RP, Cao YJ, Lee LA, Goldsmith J, Caffo BS, Du Y, King KE, Menendez FA, Torbenson MS, Hendrix CW.

J Acquir Immune Defic Syndr. 2012 Jan 1;59(1):10-7. doi: 10.1097/QAI.0b013e3182373b5e.


A Bayesian hierarchical nonlinear mixture model in the presence of artifactual outliers in a population pharmacokinetic study.

Choi L, Caffo BS, Kohli U, Pandharipande P, Kurnik D, Ely EW, Stein CM.

J Pharmacokinet Pharmacodyn. 2011 Oct;38(5):613-36. doi: 10.1007/s10928-011-9211-7. Epub 2011 Aug 17.


Population-wide principal component-based quantification of blood-brain-barrier dynamics in multiple sclerosis.

Shinohara RT, Crainiceanu CM, Caffo BS, Gaitán MI, Reich DS.

Neuroimage. 2011 Aug 15;57(4):1430-46. doi: 10.1016/j.neuroimage.2011.05.038. Epub 2011 May 23.


Motor "dexterity"?: Evidence that left hemisphere lateralization of motor circuit connectivity is associated with better motor performance in children.

Barber AD, Srinivasan P, Joel SE, Caffo BS, Pekar JJ, Mostofsky SH.

Cereb Cortex. 2012 Jan;22(1):51-9. doi: 10.1093/cercor/bhr062. Epub 2011 May 25.


Penalized functional regression analysis of white-matter tract profiles in multiple sclerosis.

Goldsmith J, Crainiceanu CM, Caffo BS, Reich DS.

Neuroimage. 2011 Jul 15;57(2):431-9. doi: 10.1016/j.neuroimage.2011.04.044. Epub 2011 Apr 30.


On the relationship between seed-based and ICA-based measures of functional connectivity.

Joel SE, Caffo BS, van Zijl PC, Pekar JJ.

Magn Reson Med. 2011 Sep;66(3):644-57. doi: 10.1002/mrm.22818. Epub 2011 Mar 10.


Comparison of proportions for composite endpoints with missing components.

Li X, Caffo BS.

J Biopharm Stat. 2011 Mar;21(2):271-81. doi: 10.1080/10543406.2011.550109.


Longitudinal changes in diffusion tensor-based quantitative MRI in multiple sclerosis.

Harrison DM, Caffo BS, Shiee N, Farrell JA, Bazin PL, Farrell SK, Ratchford JN, Calabresi PA, Reich DS.

Neurology. 2011 Jan 11;76(2):179-86. doi: 10.1212/WNL.0b013e318206ca61.


Population Value Decomposition, a Framework for the Analysis of Image Populations.

Crainiceanu CM, Caffo BS, Luo S, Zipunnikov VM, Punjabi NM.

J Am Stat Assoc. 2011;106(495). doi: 10.1198/jasa.2011.ap10089.

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